From andx_roo at live.com Tue Aug 1 00:50:06 2017 From: andx_roo at live.com (Andaharoo) Date: Mon, 31 Jul 2017 21:50:06 -0700 (MST) Subject: [ITK-users] Downcasting GPU Filters Message-ID: <1501563006868-7590096.post@n2.nabble.com> Hi, I'm trying to store GPU filters in an array of ImageToImageFilters but they don't seem to be connecting right. However, the GPUGradientAnisotropicImageFilter works fine. I did notice it's one of the only gpu filters that keeps the TParentImageFilter template parameter at default. Another thing I noticed, Applying the gpu anisotropic and then successively applying another gpu filter works. These filters failed: GPUBinaryThresholdImageFilter GPUDiscreteGaussianImageFilter GPUMeanImageFilter I'm using vtk and itk and have created a class to let me store vtk image filters, itk filters, and itk gpu filters in a single array adding conversion filters when needed. So I call addFilter and it adds the filter connecting it to the last filter in the array or input image and adding conversion filters if need be. It works fine with cpu itk filters and vtk filters but not with all the gpu filters. One of the problems I faced was that I couldn't SetInput with a GPU filter downcasted to ImageToImageFilter. It had to be a GPUImageToImageFilter for the SetInput to work. So I overloaded addFilter with a GPUImageToImageFilter parameter to set the input and then downcast to ImageToImageFilter. I'd create and add a filter like so (psuedo): GPUGradientAnisotropicFilter filter Set filter parameters filterSeries->addFilter(filter as GPUImageToImageFilter) Then addFilter would essentially just set the input to the output of the last filter then downcast to ImageToImageFilter to store it. As for the error. GPUImageDataManager never gets allocated and thus it breaks. It throws a read access violation on line 97 of itkSmartPointer.h Here's part of the stack frame: itk::SmartPointer > >::GetPointer() Line 97 itk::GPUImage::GetGPUDataManager() Line 170 itk::GPUMeanImageFilter,itk::GPUImage >::GPUGenerateData() Line 105 itk::GPUImageToImageFilter,itk::GPUImage,itk::MeanImageFilter,itk::GPUImage > >::GenerateData() Line 61 ... I'm not sure where GPUImageDataManager gets allocated, the source is confusing, and I only ever found a single sentence and ppt slide on it. When it has to convert from CPU to GPU does it create GPUImage on the fly? What would be reasons for it not to get allocated? -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Downcasting-GPU-Filters-tp7590096.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From swetha.bsharma at gmail.com Tue Aug 1 05:11:24 2017 From: swetha.bsharma at gmail.com (Swetha Sharma) Date: Tue, 1 Aug 2017 14:41:24 +0530 Subject: [ITK-users] saving 3D mesh as stl Message-ID: Hi All, I want to save a 3d mesh as stl. I followed the following article https://stackoverflow.com/questions/42281881/get-stl-format-3d-mesh-from-binary-mask-segmentation/42296376#42296376, which explains how to build the itk to include the "itkstlmeshiofactory " header in the project. When I configured in CMAKE the below is the error which I got: Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) CMake Error at CMake/ITKModuleRemote.cmake:12 (message): Failed to clone repository: 'git://github.com/InsightSoftwareConsortium/ITKSTLMeshIO.git' Call Stack (most recent call first): CMake/ITKModuleRemote.cmake:107 (_git_clone) CMake/ITKModuleRemote.cmake:151 (_fetch_with_git) Modules/Remote/IOSTL.remote.cmake:2 (itk_fetch_module) Modules/Remote/CMakeLists.txt:6 (include) What could be the problem? Is there any other way to clone the repository? -swetha -------------- next part -------------- An HTML attachment was scrubbed... URL: From rc1515 at ic.ac.uk Tue Aug 1 08:21:44 2017 From: rc1515 at ic.ac.uk (Ramana C) Date: Tue, 1 Aug 2017 05:21:44 -0700 (MST) Subject: [ITK-users] Extracting image coordinate transform matrix Message-ID: <1501590104563-38537.post@n7.nabble.com> Hi All, I am using SimpleITK in Python (but help for any ITK/SimpleITK version would be appreciated too!). I am looking for a way to extract (or construct) the 4 by 4 transformation matrix from an image that lets me transform physical space coordinates to voxel coordinates of the image grid, and vice-versa. I know that the image class has methods such as image.TransformIndexToPhysicalPoint, but I was hoping that it would be possible to extract the transformation matrix itself. Any help with this would be greatly appreciated. -Ramana -- View this message in context: http://itk-users.7.n7.nabble.com/Extracting-image-coordinate-transform-matrix-tp38537.html Sent from the ITK - Users mailing list archive at Nabble.com. From dzenanz at gmail.com Tue Aug 1 09:59:35 2017 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 1 Aug 2017 09:59:35 -0400 Subject: [ITK-users] saving 3D mesh as stl In-Reply-To: References: Message-ID: Hi Swetha, you could manually clone the repository into ...\ITK-git\Modules\Remote\ Regards, D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.) On Tue, Aug 1, 2017 at 5:11 AM, Swetha Sharma wrote: > Hi All, > > > I want to save a 3d mesh as stl. I followed the following article > https://stackoverflow.com/questions/42281881/get-stl- > format-3d-mesh-from-binary-mask-segmentation/42296376#42296376, which > explains how to build the itk to include the "itkstlmeshiofactory " header > in the project. When I configured in CMAKE the below is the error which I > got: > > > Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) > > Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) > > CMake Error at CMake/ITKModuleRemote.cmake:12 (message): > Failed to clone repository: > 'git://github.com/InsightSoftwareConsortium/ITKSTLMeshIO.git' > Call Stack (most recent call first): > CMake/ITKModuleRemote.cmake:107 (_git_clone) > CMake/ITKModuleRemote.cmake:151 (_fetch_with_git) > Modules/Remote/IOSTL.remote.cmake:2 (itk_fetch_module) > Modules/Remote/CMakeLists.txt:6 (include) > > > What could be the problem? Is there any other way to clone the repository? > > -swetha > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cory.quammen at kitware.com Tue Aug 1 10:27:45 2017 From: cory.quammen at kitware.com (Cory Quammen) Date: Tue, 1 Aug 2017 10:27:45 -0400 Subject: [ITK-users] [ITK] [ITK-dev] Migration to GitHub In-Reply-To: References: Message-ID: I don't have much of an opinion on moving ITK to GitHub, but I'd like to address some things Andras mentioned about GitLab and VTK. > About GitHub/Kitware GitLab: > > I heard that VTK is going to move to GitHub, too. Maybe I misunderstood, > but make sure to talk to VTK folks before considering moving to GitLab. I am not aware of any plans to move VTK to GitLab or even any discussion of doing so. > Anyway, as a very active user but only occasional contributor of VTK, I > find VTK GitLab quite frustrating due to that: > 1. It is slow. I heard that it's fast when accessed from inside Kitware > network, but most community members are outside. > The first few versions were indeed a bit slow, but new updates come out regularly, and the speed is quite snappy. I use it both from within the Kitware network and outside the network and haven't noticed a difference. > 2. I need to re-learn each time I use it: I review code, submit PR or bug > report once in every few months - and each time I need to spend 20-30 > minutes extra, just to find out how things work. > Andras > > -----Original Message----- > From: Community [mailto:community-bounces at itk.org] On Behalf Of Matt > McCormick > Sent: Monday, July 31, 2017 7:00 PM > To: Bill Lorensen > Cc: Insight-Users ; Hans Johnson < > hans-johnson at uiowa.edu>; Insight Developers List < > insight-developers at public.kitware.com> > Subject: Re: [ITK] [ITK-dev] [ITK-users] Migration to GitHub > > I have followed VTK's migration to GitLab, and Kitware has done an > excellent job with it. That said, I still think GitHub is the better choice > for ITK. Also, the technical and social situation has changed in the time > since VTK moved to GitLab. > > I think the key factor is "community", and GitHub has the open source > community. > > On Mon, Jul 31, 2017 at 6:42 PM, Bill Lorensen > wrote: > > Vtk moved to GitLab. Have you checked with the Kitware folks to see > > why they didn't use gitlab? For me, either github or gitlab is great. > > > > On Jul 31, 2017 6:03 PM, "Johnson, Hans J" > wrote: > >> > >> 1000 x +1 > >> > >> I enthusiastically support this proposal. > >> > >> Hans > >> > >> > >> On 7/31/17, 4:57 PM, "Insight-users on behalf of Jim Miller" > >> wrote: > >> > >> +1 > >> > >> Jim > >> > >> > On Jul 31, 2017, at 5:07 PM, Matt McCormick > >> wrote: > >> > > >> > Hi folks, > >> > > >> > We are considering migration of ITK's software process to > >> GitHub, and > >> > we would like your feedback. > >> > > >> > As an open-source, community-driven project, mechanisms to > >> communicate > >> > and interact with the community are a high priority for ITK. > >> > Contributing should be as easy as possible. Increasingly over > >> the past > >> > many years, GitHub has become the de facto place to interact > >> for open > >> > source development. It is now a hub for: > >> > > >> > Microsoft > >> > Facebook > >> > Google > >> > The Scientific Python Community > >> > The 3D Slicer Community > >> > > >> > Our InsightSoftwareConsortium GitHub organization [1] already has > 67 > >> > people in it and 74 repositories. There are hundreds of > >> projects that > >> > depend on ITK on GitHub. Many ITK developers are familiar with the > >> > development process on GitHub (i.e the pull request process) and > >> > already have an account on this platform. There are also > >> advantages to > >> > linking issues and commits with other projects and repositories. > >> Since > >> > ITK thrives on the open-source development idea, everyone who > >> wants to > >> > help the project should be able to contribute, and therefore it > >> should > >> > be as easy as possible to start participating in the community. > >> > > >> > Recently, GitHub's code review capabilities have greatly improved, > >> > which make it more feasible to coordinate contributions for a > large > >> > project like ITK. And, there are many existing GitHub-integrated > >> > services that we can leverage. > >> > > >> > Thanks to resources from the National Library of Medicine and > >> > technological advances, it is now feasible to migrate the > project's > >> > software process to GitHub. There are many infrastructural > >> aspects to > >> > the migration, and it would take multiple months to complete. > Please > >> > let us know your thoughts before we embark on the journey. > >> > > >> > > >> > [1] https://na01.safelinks.protection.outlook.com/?url= > https%3A%2F%2Fgithub.com%2FInsightSoftwareConsortium&data=02%7C01%7Classo% > 40queensu.ca%7C96f312d049d7448d6db208d4d867f888% > 7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata= > onq3vW0pCjrT8pDNShHXc4JkohBMBoHv1lxOD6Nkg4o%3D&reserved=0 > >> > _____________________________________ > >> > Powered by https://na01.safelinks.protection.outlook.com/?url= > www.kitware.com&data=02%7C01%7Classo%40queensu.ca% > 7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b > 925c%7C1%7C0%7C636371388439104668&sdata=TbmgQahvMJx3Czk56R8% > 2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 > >> > > >> > Visit other Kitware open-source projects at > >> > https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fwww.kitware.com%2Fopensource%2Fopensource. > html&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888% > 7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata= > BQ97jxO1o0jxL0Nk0n1styLRKu5P9Xb8JPOsASbPMNc%3D&reserved=0 > >> > > >> > Kitware offers ITK Training Courses, for more information visit: > >> > https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fwww.kitware.com%2Fproducts%2Fprotraining.php& > data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888% > 7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata= > iR5J0Yx6p31iobZibGN4nJbHsd2mYmeNshJVj12Azgw%3D&reserved=0 > >> > > >> > Please keep messages on-topic and check the ITK FAQ at: > >> > https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fwww.itk.org%2FWiki%2FITK_FAQ&data=02%7C01% > 7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888% > 7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata= > lnYum27haYjI7jbzMagLEL0eg13MhwdARYTPZivjDe0%3D&reserved=0 > >> > > >> > Follow this link to subscribe/unsubscribe: > >> > https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo% > 2Finsight-users&data=02%7C01%7Classo%40queensu.ca% > 7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b > 925c%7C1%7C0%7C636371388439104668&sdata=3rk3ntG% > 2Fvv1h8UgHGKvxd8FcajlDjZqK6BHweskvql8%3D&reserved=0 > >> _____________________________________ > >> Powered by > >> https://na01.safelinks.protection.outlook.com/?url=www.kitware.com&da > >> ta=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7C > >> d61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=T > >> bmgQahvMJx3Czk56R8%2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 > >> > >> Visit other Kitware open-source projects at > >> > >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.k > >> itware.com%2Fopensource%2Fopensource.html&data=02%7C01%7Classo%40quee > >> nsu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb28 > >> 38b925c%7C1%7C0%7C636371388439104668&sdata=BQ97jxO1o0jxL0Nk0n1styLRKu > >> 5P9Xb8JPOsASbPMNc%3D&reserved=0 > >> > >> Kitware offers ITK Training Courses, for more information visit: > >> > >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.k > >> itware.com%2Fproducts%2Fprotraining.php&data=02%7C01%7Classo%40queens > >> u.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838 > >> b925c%7C1%7C0%7C636371388439104668&sdata=iR5J0Yx6p31iobZibGN4nJbHsd2m > >> YmeNshJVj12Azgw%3D&reserved=0 > >> > >> Please keep messages on-topic and check the ITK FAQ at: > >> > >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.i > >> tk.org%2FWiki%2FITK_FAQ&data=02%7C01%7Classo%40queensu.ca%7C96f312d04 > >> 9d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C > >> 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itware.com%2Fopensource%2Fopensource.html&data=02%7C01%7Classo%40quee > >> nsu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb28 > >> 38b925c%7C1%7C0%7C636371388439104668&sdata=BQ97jxO1o0jxL0Nk0n1styLRKu > >> 5P9Xb8JPOsASbPMNc%3D&reserved=0 > >> > >> Kitware offers ITK Training Courses, for more information visit: > >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.k > >> itware.com%2Fproducts%2Fprotraining.php&data=02%7C01%7Classo%40queens > >> u.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838 > >> b925c%7C1%7C0%7C636371388439104668&sdata=iR5J0Yx6p31iobZibGN4nJbHsd2m > >> YmeNshJVj12Azgw%3D&reserved=0 > >> > >> Please keep messages on-topic and check the ITK FAQ at: > >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.i > >> tk.org%2FWiki%2FITK_FAQ&data=02%7C01%7Classo%40queensu.ca%7C96f312d04 > >> 9d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C > >> 636371388439104668&sdata=lnYum27haYjI7jbzMagLEL0eg13MhwdARYTPZivjDe0% > >> 3D&reserved=0 > >> > >> Follow this link to subscribe/unsubscribe: > >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpubli > >> c.kitware.com%2Fmailman%2Flistinfo%2Finsight-users&data=02%7C01%7Clas > >> so%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d5 > >> 82c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=3rk3ntG%2Fvv1h8Ug > >> HGKvxd8FcajlDjZqK6BHweskvql8%3D&reserved=0 > _______________________________________________ > Powered by https://na01.safelinks.protection.outlook.com/?url= > www.kitware.com&data=02%7C01%7Classo%40queensu.ca% > 7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b > 925c%7C1%7C0%7C636371388439104668&sdata=TbmgQahvMJx3Czk56R8% > 2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 > > Visit other Kitware open-source projects at > https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fwww.kitware.com%2Fopensource%2Fopensource. > html&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888% > 7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata= > BQ97jxO1o0jxL0Nk0n1styLRKu5P9Xb8JPOsASbPMNc%3D&reserved=0 > > Kitware offers ITK Training Courses, for more information visit: > https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fkitware.com%2Fproducts%2Fprotraining.php& > data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888% > 7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=4W% > 2B%2B3MiNoGmr%2FKnI9Kmyl4BPOJ0%2BDu9Mcdgk5A%2Foi3c%3D&reserved=0 > > Please keep messages on-topic and check the ITK FAQ at: > https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fwww.itk.org%2FWiki%2FITK_FAQ&data=02%7C01% > 7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888% > 7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata= > lnYum27haYjI7jbzMagLEL0eg13MhwdARYTPZivjDe0%3D&reserved=0 > > Follow this link to subscribe/unsubscribe: > https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo% > 2Finsight-developers&data=02%7C01%7Classo%40queensu.ca% > 7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b > 925c%7C1%7C0%7C636371388439104668&sdata=aJgjy9V6YWhdNpqDtQSNkBEfKEW6dN > cKVW3C1fT%2FH9Q%3D&reserved=0 > _______________________________________________ > Community mailing list > Community at itk.org > https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo% > 2Fcommunity&data=02%7C01%7Classo%40queensu.ca% > 7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b > 925c%7C1%7C0%7C636371388439104668&sdata=7%2FDK5kxboSdWy9zTD2f% > 2FP8CqdebW%2B82BJZQXMFQfCOQ%3D&reserved=0 > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -- Cory Quammen Staff R&D Engineer Kitware, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jhlegarreta at vicomtech.org Tue Aug 1 10:45:55 2017 From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta) Date: Tue, 1 Aug 2017 16:45:55 +0200 Subject: [ITK-users] [ITK] [ITK-dev] Migration to GitHub In-Reply-To: References: Message-ID: +1 for the transition. I'm pretty sure the ITK core devs and maintainers have carefully considered all choices over time. So beyond my personal likings, I guess github beats the rest of the possibilities in terms of the needs and future plans of ITK. JON HAITZ -- On 1 August 2017 at 16:27, Cory Quammen wrote: > I don't have much of an opinion on moving ITK to GitHub, but I'd like to > address some things Andras mentioned about GitLab and VTK. > > >> About GitHub/Kitware GitLab: >> >> I heard that VTK is going to move to GitHub, too. Maybe I misunderstood, >> but make sure to talk to VTK folks before considering moving to GitLab. > > > I am not aware of any plans to move VTK to GitLab or even any discussion > of doing so. > > >> Anyway, as a very active user but only occasional contributor of VTK, I >> find VTK GitLab quite frustrating due to that: >> 1. It is slow. I heard that it's fast when accessed from inside Kitware >> network, but most community members are outside. >> > > The first few versions were indeed a bit slow, but new updates come out > regularly, and the speed is quite snappy. I use it both from within the > Kitware network and outside the network and haven't noticed a difference. > > >> 2. I need to re-learn each time I use it: I review code, submit PR or bug >> report once in every few months - and each time I need to spend 20-30 >> minutes extra, just to find out how things work. > > >> Andras >> >> -----Original Message----- >> From: Community [mailto:community-bounces at itk.org] On Behalf Of Matt >> McCormick >> Sent: Monday, July 31, 2017 7:00 PM >> To: Bill Lorensen >> Cc: Insight-Users ; Hans Johnson < >> hans-johnson at uiowa.edu>; Insight Developers List < >> insight-developers at public.kitware.com> >> Subject: Re: [ITK] [ITK-dev] [ITK-users] Migration to GitHub >> >> I have followed VTK's migration to GitLab, and Kitware has done an >> excellent job with it. That said, I still think GitHub is the better choice >> for ITK. Also, the technical and social situation has changed in the time >> since VTK moved to GitLab. >> >> I think the key factor is "community", and GitHub has the open source >> community. >> >> On Mon, Jul 31, 2017 at 6:42 PM, Bill Lorensen >> wrote: >> > Vtk moved to GitLab. Have you checked with the Kitware folks to see >> > why they didn't use gitlab? For me, either github or gitlab is great. >> > >> > On Jul 31, 2017 6:03 PM, "Johnson, Hans J" >> wrote: >> >> >> >> 1000 x +1 >> >> >> >> I enthusiastically support this proposal. >> >> >> >> Hans >> >> >> >> >> >> On 7/31/17, 4:57 PM, "Insight-users on behalf of Jim Miller" >> >> wrote: >> >> >> >> +1 >> >> >> >> Jim >> >> >> >> > On Jul 31, 2017, at 5:07 PM, Matt McCormick >> >> wrote: >> >> > >> >> > Hi folks, >> >> > >> >> > We are considering migration of ITK's software process to >> >> GitHub, and >> >> > we would like your feedback. >> >> > >> >> > As an open-source, community-driven project, mechanisms to >> >> communicate >> >> > and interact with the community are a high priority for ITK. >> >> > Contributing should be as easy as possible. Increasingly over >> >> the past >> >> > many years, GitHub has become the de facto place to interact >> >> for open >> >> > source development. It is now a hub for: >> >> > >> >> > Microsoft >> >> > Facebook >> >> > Google >> >> > The Scientific Python Community >> >> > The 3D Slicer Community >> >> > >> >> > Our InsightSoftwareConsortium GitHub organization [1] already >> has 67 >> >> > people in it and 74 repositories. There are hundreds of >> >> projects that >> >> > depend on ITK on GitHub. Many ITK developers are familiar with >> the >> >> > development process on GitHub (i.e the pull request process) and >> >> > already have an account on this platform. There are also >> >> advantages to >> >> > linking issues and commits with other projects and repositories. >> >> Since >> >> > ITK thrives on the open-source development idea, everyone who >> >> wants to >> >> > help the project should be able to contribute, and therefore it >> >> should >> >> > be as easy as possible to start participating in the community. >> >> > >> >> > Recently, GitHub's code review capabilities have greatly >> improved, >> >> > which make it more feasible to coordinate contributions for a >> large >> >> > project like ITK. And, there are many existing GitHub-integrated >> >> > services that we can leverage. >> >> > >> >> > Thanks to resources from the National Library of Medicine and >> >> > technological advances, it is now feasible to migrate the >> project's >> >> > software process to GitHub. There are many infrastructural >> >> aspects to >> >> > the migration, and it would take multiple months to complete. >> Please >> >> > let us know your thoughts before we embark on the journey. >> >> > >> >> > >> >> > [1] https://na01.safelinks.protection.outlook.com/?url=https%3A% >> 2F%2Fgithub.com%2FInsightSoftwareConsortium&data=02%7C01% >> 7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd6 >> 1ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668& >> sdata=onq3vW0pCjrT8pDNShHXc4JkohBMBoHv1lxOD6Nkg4o%3D&reserved=0 >> >> > _____________________________________ >> >> > Powered by https://na01.safelinks.protect >> ion.outlook.com/?url=www.kitware.com&data=02%7C01%7Clas >> so%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3 >> b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668& >> sdata=TbmgQahvMJx3Czk56R8%2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 >> >> > >> >> > Visit other Kitware open-source projects at >> >> > https://na01.safelinks.protection.outlook.com/?url=http%3A% >> 2F%2Fwww.kitware.com%2Fopensource%2Fopensource.html&data=02% >> 7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888 >> %7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C63637138843910 >> 4668&sdata=BQ97jxO1o0jxL0Nk0n1styLRKu5P9Xb8JPOsASbPMNc%3D&reserved=0 >> >> > >> >> > Kitware offers ITK Training Courses, for more information visit: >> >> > https://na01.safelinks.protection.outlook.com/?url=http%3A% >> 2F%2Fwww.kitware.com%2Fproducts%2Fprotraining.php&data=02% >> 7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888 >> %7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C63637138843910 >> 4668&sdata=iR5J0Yx6p31iobZibGN4nJbHsd2mYmeNshJVj12Azgw%3D&reserved=0 >> >> > >> >> > Please keep messages on-topic and check the ITK FAQ at: >> >> > https://na01.safelinks.protection.outlook.com/?url=http%3A% >> 2F%2Fwww.itk.org%2FWiki%2FITK_FAQ&data=02%7C01%7Classo% >> 40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38 >> 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https://na01.safelinks.protection.outlook.com/?url=http%3A% >> 2F%2Fwww.kitware.com%2Fopensource%2Fopensource.html&data=02% >> 7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888 >> %7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C63637138843910 >> 4668&sdata=BQ97jxO1o0jxL0Nk0n1styLRKu5P9Xb8JPOsASbPMNc%3D&reserved=0 >> >> Kitware offers ITK Training Courses, for more information visit: >> https://na01.safelinks.protection.outlook.com/?url=http%3A% >> 2F%2Fkitware.com%2Fproducts%2Fprotraining.php&data=02% >> 7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888 >> %7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C63637138843910 >> 4668&sdata=4W%2B%2B3MiNoGmr%2FKnI9Kmyl4BPOJ0%2BDu9Mcdgk5A%2F >> oi3c%3D&reserved=0 >> >> Please keep messages on-topic and check the ITK FAQ at: >> https://na01.safelinks.protection.outlook.com/?url=http%3A% >> 2F%2Fwww.itk.org%2FWiki%2FITK_FAQ&data=02%7C01%7Classo% >> 40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38 >> 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>> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> > > > > -- > Cory Quammen > Staff R&D Engineer > Kitware, Inc. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mike.jackson at bluequartz.net Tue Aug 1 10:53:40 2017 From: mike.jackson at bluequartz.net (Michael Jackson) Date: Tue, 01 Aug 2017 10:53:40 -0400 Subject: [ITK-users] [ITK] [ITK-dev] Migration to GitHub In-Reply-To: References: Message-ID: <598095F4.9040000@bluequartz.net> I would like to see the Kitware sponsored projects (Itk, Vtk, ParaView.. ) ALL use the same mechanisms and host providers. Just lessens the confusion on outside developers. But +1 for moving to GitHub. -- Michael A. Jackson BlueQuartz Software, LLC [e]: mike.jackson at bluequartz.net Jon Haitz Legarreta wrote: > +1 for the transition. > > I'm pretty sure the ITK core devs and maintainers have carefully > considered all choices over time. So beyond my personal likings, I guess > github beats the rest of the possibilities in terms of the needs and > future plans of ITK. > > JON HAITZ > > -- > > > On 1 August 2017 at 16:27, Cory Quammen > wrote: > > I don't have much of an opinion on moving ITK to GitHub, but I'd > like to address some things Andras mentioned about GitLab and VTK. > > > About GitHub/Kitware GitLab: > > I heard that VTK is going to move to GitHub, too. Maybe I > misunderstood, but make sure to talk to VTK folks before > considering moving to GitLab. > > > I am not aware of any plans to move VTK to GitLab or even any > discussion of doing so. > > Anyway, as a very active user but only occasional contributor of > VTK, I find VTK GitLab quite frustrating due to that: > 1. It is slow. I heard that it's fast when accessed from inside > Kitware network, but most community members are outside. > > > The first few versions were indeed a bit slow, but new updates come > out regularly, and the speed is quite snappy. I use it both from > within the Kitware network and outside the network and haven't > noticed a difference. > > 2. I need to re-learn each time I use it: I review code, submit > PR or bug report once in every few months - and each time I need > to spend 20-30 minutes extra, just to find out how things work. > > > Andras > > -----Original Message----- > From: Community [mailto:community-bounces at itk.org > ] On Behalf Of Matt McCormick > Sent: Monday, July 31, 2017 7:00 PM > To: Bill Lorensen > > Cc: Insight-Users >; Hans Johnson > >; > Insight Developers List > > Subject: Re: [ITK] [ITK-dev] [ITK-users] Migration to GitHub > > I have followed VTK's migration to GitLab, and Kitware has done > an excellent job with it. That said, I still think GitHub is the > better choice for ITK. Also, the technical and social situation > has changed in the time since VTK moved to GitLab. > > I think the key factor is "community", and GitHub has the open > source community. > > On Mon, Jul 31, 2017 at 6:42 PM, Bill Lorensen > > wrote: > > Vtk moved to GitLab. Have you checked with the Kitware folks > to see > > why they didn't use gitlab? For me, either github or gitlab > is great. > > > > On Jul 31, 2017 6:03 PM, "Johnson, Hans J" > > wrote: > >> > >> 1000 x +1 > >> > >> I enthusiastically support this proposal. > >> > >> Hans > >> > >> > >> On 7/31/17, 4:57 PM, "Insight-users on behalf of Jim Miller" > >> on behalf of > millerjv at gmail.com > wrote: > >> > >> +1 > >> > >> Jim > >> > >> > On Jul 31, 2017, at 5:07 PM, Matt McCormick > >> > wrote: > >> > > >> > Hi folks, > >> > > >> > We are considering migration of ITK's software process to > >> GitHub, and > >> > we would like your feedback. > >> > > >> > As an open-source, community-driven project, mechanisms to > >> communicate > >> > and interact with the community are a high priority for ITK. > >> > Contributing should be as easy as possible. Increasingly over > >> the past > >> > many years, GitHub has become the de facto place to interact > >> for open > >> > source development. It is now a hub for: > >> > > >> > Microsoft > >> > Facebook > >> > Google > >> > The Scientific Python Community > >> > The 3D Slicer Community > >> > > >> > Our InsightSoftwareConsortium GitHub organization [1] > already has 67 > >> > people in it and 74 repositories. There are hundreds of > >> projects that > >> > depend on ITK on GitHub. Many ITK developers are familiar > with the > >> > development process on GitHub (i.e the pull request > process) and > >> > already have an account on this platform. There are also > >> advantages to > >> > linking issues and commits with other projects and > repositories. > >> Since > >> > ITK thrives on the open-source development idea, everyone who > >> wants to > >> > help the project should be able to contribute, and > therefore it > >> should > >> > be as easy as possible to start participating in the > community. > >> > > >> > Recently, GitHub's code review capabilities have greatly > improved, > >> > which make it more feasible to coordinate contributions > for a large > >> > project like ITK. And, there are many existing > GitHub-integrated > >> > services that we can leverage. > >> > > >> > Thanks to resources from the National Library of Medicine and > >> > technological advances, it is now feasible to migrate the > project's > >> > software process to GitHub. There are many infrastructural > >> aspects to > >> > the migration, and it would take multiple months to > complete. Please > >> > let us know your thoughts before we embark on the journey. > >> > > >> > > >> > [1] > > -- > Cory Quammen > Staff R&D Engineer > Kitware, Inc. > From bill.lorensen at gmail.com Tue Aug 1 10:56:37 2017 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 1 Aug 2017 10:56:37 -0400 Subject: [ITK-users] [ITK] [ITK-dev] Migration to GitHub In-Reply-To: <598095F4.9040000@bluequartz.net> References: <598095F4.9040000@bluequartz.net> Message-ID: ++++1 On Tue, Aug 1, 2017 at 10:53 AM, Michael Jackson wrote: > I would like to see the Kitware sponsored projects (Itk, Vtk, ParaView.. ) > ALL use the same mechanisms and host providers. Just lessens the confusion > on outside developers. > > But +1 for moving to GitHub. > -- > Michael A. Jackson > BlueQuartz Software, LLC > [e]: mike.jackson at bluequartz.net > > > Jon Haitz Legarreta wrote: >> >> +1 for the transition. >> >> I'm pretty sure the ITK core devs and maintainers have carefully >> considered all choices over time. So beyond my personal likings, I guess >> github beats the rest of the possibilities in terms of the needs and >> future plans of ITK. >> >> JON HAITZ >> >> -- >> >> >> On 1 August 2017 at 16:27, Cory Quammen > > wrote: >> >> I don't have much of an opinion on moving ITK to GitHub, but I'd >> like to address some things Andras mentioned about GitLab and VTK. >> >> >> About GitHub/Kitware GitLab: >> >> I heard that VTK is going to move to GitHub, too. Maybe I >> misunderstood, but make sure to talk to VTK folks before >> considering moving to GitLab. >> >> >> I am not aware of any plans to move VTK to GitLab or even any >> discussion of doing so. >> >> Anyway, as a very active user but only occasional contributor of >> VTK, I find VTK GitLab quite frustrating due to that: >> 1. It is slow. I heard that it's fast when accessed from inside >> Kitware network, but most community members are outside. >> >> >> The first few versions were indeed a bit slow, but new updates come >> out regularly, and the speed is quite snappy. I use it both from >> within the Kitware network and outside the network and haven't >> noticed a difference. >> >> 2. I need to re-learn each time I use it: I review code, submit >> PR or bug report once in every few months - and each time I need >> to spend 20-30 minutes extra, just to find out how things work. >> >> >> Andras >> >> -----Original Message----- >> From: Community [mailto:community-bounces at itk.org >> ] On Behalf Of Matt McCormick >> Sent: Monday, July 31, 2017 7:00 PM >> To: Bill Lorensen > > >> Cc: Insight-Users > >; Hans Johnson >> >; >> Insight Developers List > > >> Subject: Re: [ITK] [ITK-dev] [ITK-users] Migration to GitHub >> >> I have followed VTK's migration to GitLab, and Kitware has done >> an excellent job with it. That said, I still think GitHub is the >> better choice for ITK. Also, the technical and social situation >> has changed in the time since VTK moved to GitLab. >> >> I think the key factor is "community", and GitHub has the open >> source community. >> >> On Mon, Jul 31, 2017 at 6:42 PM, Bill Lorensen >> > wrote: >> > Vtk moved to GitLab. Have you checked with the Kitware folks >> to see >> > why they didn't use gitlab? For me, either github or gitlab >> is great. >> > >> > On Jul 31, 2017 6:03 PM, "Johnson, Hans J" >> > wrote: >> >> >> >> 1000 x +1 >> >> >> >> I enthusiastically support this proposal. >> >> >> >> Hans >> >> >> >> >> >> On 7/31/17, 4:57 PM, "Insight-users on behalf of Jim Miller" >> >> > on behalf of >> millerjv at gmail.com > wrote: >> >> >> >> +1 >> >> >> >> Jim >> >> >> >> > On Jul 31, 2017, at 5:07 PM, Matt McCormick >> >> > > wrote: >> >> > >> >> > Hi folks, >> >> > >> >> > We are considering migration of ITK's software process to >> >> GitHub, and >> >> > we would like your feedback. >> >> > >> >> > As an open-source, community-driven project, mechanisms to >> >> communicate >> >> > and interact with the community are a high priority for ITK. >> >> > Contributing should be as easy as possible. Increasingly >> over >> >> the past >> >> > many years, GitHub has become the de facto place to interact >> >> for open >> >> > source development. It is now a hub for: >> >> > >> >> > Microsoft >> >> > Facebook >> >> > Google >> >> > The Scientific Python Community >> >> > The 3D Slicer Community >> >> > >> >> > Our InsightSoftwareConsortium GitHub organization [1] >> already has 67 >> >> > people in it and 74 repositories. There are hundreds of >> >> projects that >> >> > depend on ITK on GitHub. Many ITK developers are familiar >> with the >> >> > development process on GitHub (i.e the pull request >> process) and >> >> > already have an account on this platform. There are also >> >> advantages to >> >> > linking issues and commits with other projects and >> repositories. >> >> Since >> >> > ITK thrives on the open-source development idea, everyone >> who >> >> wants to >> >> > help the project should be able to contribute, and >> therefore it >> >> should >> >> > be as easy as possible to start participating in the >> community. >> >> > >> >> > Recently, GitHub's code review capabilities have greatly >> improved, >> >> > which make it more feasible to coordinate contributions >> for a large >> >> > project like ITK. And, there are many existing >> GitHub-integrated >> >> > services that we can leverage. >> >> > >> >> > Thanks to resources from the National Library of Medicine >> and >> >> > technological advances, it is now feasible to migrate the >> project's >> >> > software process to GitHub. There are many infrastructural >> >> aspects to >> >> > the migration, and it would take multiple months to >> complete. Please >> >> > let us know your thoughts before we embark on the journey. >> >> > >> >> > >> >> > [1] >> >> -- >> Cory Quammen >> Staff R&D Engineer >> Kitware, Inc. >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -- Unpaid intern in BillsBasement at noware dot com From davis.vigneault at gmail.com Tue Aug 1 11:05:57 2017 From: davis.vigneault at gmail.com (Davis Vigneault) Date: Tue, 1 Aug 2017 16:05:57 +0100 Subject: [ITK-users] [ITK] [ITK-dev] Migration to GitHub In-Reply-To: References: <598095F4.9040000@bluequartz.net> Message-ID: +1 for the move to github! One small point is that ITK is highly integrated with VNL, the development of which is also coordinated on Github. Frequently, when I start investigating something in ITK, I end up in VNL's codebase. For those of us that flip back and forth between ITK and VNL, this move might help to minimize task switching somewhat. Also, thanks very much to Matt for coordinating this effort! On Tue, Aug 1, 2017 at 3:56 PM, Bill Lorensen wrote: > ++++1 > > > On Tue, Aug 1, 2017 at 10:53 AM, Michael Jackson > wrote: > > I would like to see the Kitware sponsored projects (Itk, Vtk, ParaView.. > ) > > ALL use the same mechanisms and host providers. Just lessens the > confusion > > on outside developers. > > > > But +1 for moving to GitHub. > > -- > > Michael A. Jackson > > BlueQuartz Software, LLC > > [e]: mike.jackson at bluequartz.net > > > > > > Jon Haitz Legarreta wrote: > >> > >> +1 for the transition. > >> > >> I'm pretty sure the ITK core devs and maintainers have carefully > >> considered all choices over time. So beyond my personal likings, I guess > >> github beats the rest of the possibilities in terms of the needs and > >> future plans of ITK. > >> > >> JON HAITZ > >> > >> -- > >> > >> > >> On 1 August 2017 at 16:27, Cory Quammen >> > wrote: > >> > >> I don't have much of an opinion on moving ITK to GitHub, but I'd > >> like to address some things Andras mentioned about GitLab and VTK. > >> > >> > >> About GitHub/Kitware GitLab: > >> > >> I heard that VTK is going to move to GitHub, too. Maybe I > >> misunderstood, but make sure to talk to VTK folks before > >> considering moving to GitLab. > >> > >> > >> I am not aware of any plans to move VTK to GitLab or even any > >> discussion of doing so. > >> > >> Anyway, as a very active user but only occasional contributor of > >> VTK, I find VTK GitLab quite frustrating due to that: > >> 1. It is slow. I heard that it's fast when accessed from inside > >> Kitware network, but most community members are outside. > >> > >> > >> The first few versions were indeed a bit slow, but new updates come > >> out regularly, and the speed is quite snappy. I use it both from > >> within the Kitware network and outside the network and haven't > >> noticed a difference. > >> > >> 2. I need to re-learn each time I use it: I review code, submit > >> PR or bug report once in every few months - and each time I need > >> to spend 20-30 minutes extra, just to find out how things work. > >> > >> > >> Andras > >> > >> -----Original Message----- > >> From: Community [mailto:community-bounces at itk.org > >> ] On Behalf Of Matt McCormick > >> Sent: Monday, July 31, 2017 7:00 PM > >> To: Bill Lorensen >> > > >> Cc: Insight-Users >> >; Hans Johnson > >> >; > >> Insight Developers List >> > > >> Subject: Re: [ITK] [ITK-dev] [ITK-users] Migration to GitHub > >> > >> I have followed VTK's migration to GitLab, and Kitware has done > >> an excellent job with it. That said, I still think GitHub is the > >> better choice for ITK. Also, the technical and social situation > >> has changed in the time since VTK moved to GitLab. > >> > >> I think the key factor is "community", and GitHub has the open > >> source community. > >> > >> On Mon, Jul 31, 2017 at 6:42 PM, Bill Lorensen > >> > > wrote: > >> > Vtk moved to GitLab. Have you checked with the Kitware folks > >> to see > >> > why they didn't use gitlab? For me, either github or gitlab > >> is great. > >> > > >> > On Jul 31, 2017 6:03 PM, "Johnson, Hans J" > >> > wrote: > >> >> > >> >> 1000 x +1 > >> >> > >> >> I enthusiastically support this proposal. > >> >> > >> >> Hans > >> >> > >> >> > >> >> On 7/31/17, 4:57 PM, "Insight-users on behalf of Jim Miller" > >> >> >> on behalf of > >> millerjv at gmail.com > wrote: > >> >> > >> >> +1 > >> >> > >> >> Jim > >> >> > >> >> > On Jul 31, 2017, at 5:07 PM, Matt McCormick > >> >> >> > wrote: > >> >> > > >> >> > Hi folks, > >> >> > > >> >> > We are considering migration of ITK's software process to > >> >> GitHub, and > >> >> > we would like your feedback. > >> >> > > >> >> > As an open-source, community-driven project, mechanisms to > >> >> communicate > >> >> > and interact with the community are a high priority for > ITK. > >> >> > Contributing should be as easy as possible. Increasingly > >> over > >> >> the past > >> >> > many years, GitHub has become the de facto place to > interact > >> >> for open > >> >> > source development. It is now a hub for: > >> >> > > >> >> > Microsoft > >> >> > Facebook > >> >> > Google > >> >> > The Scientific Python Community > >> >> > The 3D Slicer Community > >> >> > > >> >> > Our InsightSoftwareConsortium GitHub organization [1] > >> already has 67 > >> >> > people in it and 74 repositories. There are hundreds of > >> >> projects that > >> >> > depend on ITK on GitHub. Many ITK developers are familiar > >> with the > >> >> > development process on GitHub (i.e the pull request > >> process) and > >> >> > already have an account on this platform. There are also > >> >> advantages to > >> >> > linking issues and commits with other projects and > >> repositories. > >> >> Since > >> >> > ITK thrives on the open-source development idea, everyone > >> who > >> >> wants to > >> >> > help the project should be able to contribute, and > >> therefore it > >> >> should > >> >> > be as easy as possible to start participating in the > >> community. > >> >> > > >> >> > Recently, GitHub's code review capabilities have greatly > >> improved, > >> >> > which make it more feasible to coordinate contributions > >> for a large > >> >> > project like ITK. And, there are many existing > >> GitHub-integrated > >> >> > services that we can leverage. > >> >> > > >> >> > Thanks to resources from the National Library of Medicine > >> and > >> >> > technological advances, it is now feasible to migrate the > >> project's > >> >> > software process to GitHub. There are many infrastructural > >> >> aspects to > >> >> > the migration, and it would take multiple months to > >> complete. Please > >> >> > let us know your thoughts before we embark on the journey. > >> >> > > >> >> > > >> >> > [1] > >> > >> -- > >> Cory Quammen > >> Staff R&D Engineer > >> Kitware, Inc. > >> > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > > -- > Unpaid intern in BillsBasement at noware dot com > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Tue Aug 1 11:13:04 2017 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 1 Aug 2017 11:13:04 -0400 Subject: [ITK-users] [ITK] [ITK-dev] Migration to GitHub In-Reply-To: References: Message-ID: Cory, I think you meant to say VTK has no plans to move to GitHub. On Aug 1, 2017 10:27 AM, "Cory Quammen" wrote: > I don't have much of an opinion on moving ITK to GitHub, but I'd like to > address some things Andras mentioned about GitLab and VTK. > > >> About GitHub/Kitware GitLab: >> >> I heard that VTK is going to move to GitHub, too. Maybe I misunderstood, >> but make sure to talk to VTK folks before considering moving to GitLab. > > > I am not aware of any plans to move VTK to GitLab or even any discussion > of doing so. > > >> Anyway, as a very active user but only occasional contributor of VTK, I >> find VTK GitLab quite frustrating due to that: >> 1. It is slow. I heard that it's fast when accessed from inside Kitware >> network, but most community members are outside. >> > > The first few versions were indeed a bit slow, but new updates come out > regularly, and the speed is quite snappy. I use it both from within the > Kitware network and outside the network and haven't noticed a difference. > > >> 2. I need to re-learn each time I use it: I review code, submit PR or bug >> report once in every few months - and each time I need to spend 20-30 >> minutes extra, just to find out how things work. > > >> Andras >> >> -----Original Message----- >> From: Community [mailto:community-bounces at itk.org] On Behalf Of Matt >> McCormick >> Sent: Monday, July 31, 2017 7:00 PM >> To: Bill Lorensen >> Cc: Insight-Users ; Hans Johnson < >> hans-johnson at uiowa.edu>; Insight Developers List < >> insight-developers at public.kitware.com> >> Subject: Re: [ITK] [ITK-dev] [ITK-users] Migration to GitHub >> >> I have followed VTK's migration to GitLab, and Kitware has done an >> excellent job with it. That said, I still think GitHub is the better choice >> for ITK. Also, the technical and social situation has changed in the time >> since VTK moved to GitLab. >> >> I think the key factor is "community", and GitHub has the open source >> community. >> >> On Mon, Jul 31, 2017 at 6:42 PM, Bill Lorensen >> wrote: >> > Vtk moved to GitLab. Have you checked with the Kitware folks to see >> > why they didn't use gitlab? For me, either github or gitlab is great. >> > >> > On Jul 31, 2017 6:03 PM, "Johnson, Hans J" >> wrote: >> >> >> >> 1000 x +1 >> >> >> >> I enthusiastically support this proposal. >> >> >> >> Hans >> >> >> >> >> >> On 7/31/17, 4:57 PM, "Insight-users on behalf of Jim Miller" >> >> wrote: >> >> >> >> +1 >> >> >> >> Jim >> >> >> >> > On Jul 31, 2017, at 5:07 PM, Matt McCormick >> >> wrote: >> >> > >> >> > Hi folks, >> >> > >> >> > We are considering migration of ITK's software process to >> >> GitHub, and >> >> > we would like your feedback. >> >> > >> >> > As an open-source, community-driven project, mechanisms to >> >> communicate >> >> > and interact with the community are a high priority for ITK. >> >> > Contributing should be as easy as possible. Increasingly over >> >> the past >> >> > many years, GitHub has become the de facto place to interact >> >> for open >> >> > source development. It is now a hub for: >> >> > >> >> > Microsoft >> >> > Facebook >> >> > Google >> >> > The Scientific Python Community >> >> > The 3D Slicer Community >> >> > >> >> > Our InsightSoftwareConsortium GitHub organization [1] already >> has 67 >> >> > people in it and 74 repositories. There are hundreds of >> >> projects that >> >> > depend on ITK on GitHub. Many ITK developers are familiar with >> the >> >> > development process on GitHub (i.e the pull request process) and >> >> > already have an account on this platform. There are also >> >> advantages to >> >> > linking issues and commits with other projects and repositories. >> >> Since >> >> > ITK thrives on the open-source development idea, everyone who >> >> wants to >> >> > help the project should be able to contribute, and therefore it >> >> should >> >> > be as easy as possible to start participating in the community. >> >> > >> >> > Recently, GitHub's code review capabilities have greatly >> improved, >> >> > which make it more feasible to coordinate contributions for a >> large >> >> > project like ITK. And, there are many existing GitHub-integrated >> >> > services that we can leverage. >> >> > >> >> > Thanks to resources from the National Library of Medicine and >> >> > technological advances, it is now feasible to migrate the >> project's >> >> > software process to GitHub. There are many infrastructural >> >> aspects to >> >> > the migration, and it would take multiple months to complete. >> Please >> >> > let us know your thoughts before we embark on the journey. >> >> > >> >> > >> >> > [1] https://na01.safelinks.protection.outlook.com/?url=https%3A% >> 2F%2Fgithub.com%2FInsightSoftwareConsortium&data=02%7C01% >> 7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd6 >> 1ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668& >> sdata=onq3vW0pCjrT8pDNShHXc4JkohBMBoHv1lxOD6Nkg4o%3D&reserved=0 >> >> > _____________________________________ >> >> > Powered by https://na01.safelinks.protect >> ion.outlook.com/?url=www.kitware.com&data=02%7C01%7Clas >> so%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3 >> b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668& >> sdata=TbmgQahvMJx3Czk56R8%2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 >> >> > >> >> > Visit other Kitware open-source projects at >> >> > https://na01.safelinks.protection.outlook.com/?url=http%3A% >> 2F%2Fwww.kitware.com%2Fopensource%2Fopensource.html&data=02% >> 7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888 >> %7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C63637138843910 >> 4668&sdata=BQ97jxO1o0jxL0Nk0n1styLRKu5P9Xb8JPOsASbPMNc%3D&reserved=0 >> >> > >> >> > Kitware offers ITK Training Courses, for more information visit: >> >> > https://na01.safelinks.protection.outlook.com/?url=http%3A% >> 2F%2Fwww.kitware.com%2Fproducts%2Fprotraining.php&data=02% >> 7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888 >> %7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C63637138843910 >> 4668&sdata=iR5J0Yx6p31iobZibGN4nJbHsd2mYmeNshJVj12Azgw%3D&reserved=0 >> >> > >> >> > Please keep messages on-topic and check the ITK FAQ at: >> >> > https://na01.safelinks.protection.outlook.com/?url=http%3A% >> 2F%2Fwww.itk.org%2FWiki%2FITK_FAQ&data=02%7C01%7Classo% >> 40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38 >> 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https://na01.safelinks.protection.outlook.com/?url=http%3A% >> 2F%2Fwww.kitware.com%2Fopensource%2Fopensource.html&data=02% >> 7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888 >> %7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C63637138843910 >> 4668&sdata=BQ97jxO1o0jxL0Nk0n1styLRKu5P9Xb8JPOsASbPMNc%3D&reserved=0 >> >> Kitware offers ITK Training Courses, for more information visit: >> https://na01.safelinks.protection.outlook.com/?url=http%3A% >> 2F%2Fkitware.com%2Fproducts%2Fprotraining.php&data=02% >> 7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888 >> %7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C63637138843910 >> 4668&sdata=4W%2B%2B3MiNoGmr%2FKnI9Kmyl4BPOJ0%2BDu9Mcdgk5A%2F >> oi3c%3D&reserved=0 >> >> Please keep messages on-topic and check the ITK FAQ at: >> https://na01.safelinks.protection.outlook.com/?url=http%3A% >> 2F%2Fwww.itk.org%2FWiki%2FITK_FAQ&data=02%7C01%7Classo% >> 40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38 >> 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>> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> > > > > -- > Cory Quammen > Staff R&D Engineer > Kitware, Inc. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zivrafael.yaniv at nih.gov Tue Aug 1 11:12:53 2017 From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]) Date: Tue, 1 Aug 2017 15:12:53 +0000 Subject: [ITK-users] Extracting image coordinate transform matrix In-Reply-To: <1501590104563-38537.post@n7.nabble.com> References: <1501590104563-38537.post@n7.nabble.com> Message-ID: Hello Ramana, Curious what your use case is, as I can?t think of the reason to do the computation the way you want to. In any case, the code below does what you want: image_direction = image.GetDirection() image_spacing = image.GetSpacing() image_origin = image.GetOrigin() dim = 3 matrix = [m*s for m,s in zip(image_direction, image_spacing*dim)] index_2_physical = sitk.AffineTransform(dim) index_2_physical.SetMatrix(matrix) index_2_physical.SetTranslation(image_origin) physical_2_continous_index = index_2_physical.GetInverse() If you need the indexes as integers you will need to transform the point, round the result (np.rint) and then astype(int): np.rint(physical_2_continous_index.TransformPoint([-82.76, 33.32, 101.5])).astype(int) hope this helps Ziv On 8/1/17, 8:22 AM, "Ramana C" wrote: Hi All, I am using SimpleITK in Python (but help for any ITK/SimpleITK version would be appreciated too!). I am looking for a way to extract (or construct) the 4 by 4 transformation matrix from an image that lets me transform physical space coordinates to voxel coordinates of the image grid, and vice-versa. I know that the image class has methods such as image.TransformIndexToPhysicalPoint, but I was hoping that it would be possible to extract the transformation matrix itself. Any help with this would be greatly appreciated. -Ramana -- View this message in context: http://itk-users.7.n7.nabble.com/Extracting-image-coordinate-transform-matrix-tp38537.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From cory.quammen at kitware.com Tue Aug 1 11:22:38 2017 From: cory.quammen at kitware.com (Cory Quammen) Date: Tue, 1 Aug 2017 11:22:38 -0400 Subject: [ITK-users] [ITK] [ITK-dev] Migration to GitHub In-Reply-To: References: Message-ID: On Tue, Aug 1, 2017 at 11:13 AM, Bill Lorensen wrote: > Cory, > I think you meant to say VTK has no plans to move to GitHub. > Yes indeed, thanks for catching ("Hu" and "La" aren't even that close on the keyboard). VTK is firmly ensconced in GitLab, and not moving to GitHub. > On Aug 1, 2017 10:27 AM, "Cory Quammen" wrote: > >> I don't have much of an opinion on moving ITK to GitHub, but I'd like to >> address some things Andras mentioned about GitLab and VTK. >> >> >>> About GitHub/Kitware GitLab: >>> >>> I heard that VTK is going to move to GitHub, too. Maybe I misunderstood, >>> but make sure to talk to VTK folks before considering moving to GitLab. >> >> >> I am not aware of any plans to move VTK to GitLab or even any discussion >> of doing so. >> >> >>> Anyway, as a very active user but only occasional contributor of VTK, I >>> find VTK GitLab quite frustrating due to that: >>> 1. It is slow. I heard that it's fast when accessed from inside Kitware >>> network, but most community members are outside. >>> >> >> The first few versions were indeed a bit slow, but new updates come out >> regularly, and the speed is quite snappy. I use it both from within the >> Kitware network and outside the network and haven't noticed a difference. >> >> >>> 2. I need to re-learn each time I use it: I review code, submit PR or >>> bug report once in every few months - and each time I need to spend 20-30 >>> minutes extra, just to find out how things work. >> >> >>> Andras >>> >>> -----Original Message----- >>> From: Community [mailto:community-bounces at itk.org] On Behalf Of Matt >>> McCormick >>> Sent: Monday, July 31, 2017 7:00 PM >>> To: Bill Lorensen >>> Cc: Insight-Users ; Hans Johnson < >>> hans-johnson at uiowa.edu>; Insight Developers List < >>> insight-developers at public.kitware.com> >>> Subject: Re: [ITK] [ITK-dev] [ITK-users] Migration to GitHub >>> >>> I have followed VTK's migration to GitLab, and Kitware has done an >>> excellent job with it. That said, I still think GitHub is the better choice >>> for ITK. Also, the technical and social situation has changed in the time >>> since VTK moved to GitLab. >>> >>> I think the key factor is "community", and GitHub has the open source >>> community. >>> >>> On Mon, Jul 31, 2017 at 6:42 PM, Bill Lorensen >>> wrote: >>> > Vtk moved to GitLab. Have you checked with the Kitware folks to see >>> > why they didn't use gitlab? For me, either github or gitlab is great. >>> > >>> > On Jul 31, 2017 6:03 PM, "Johnson, Hans J" >>> wrote: >>> >> >>> >> 1000 x +1 >>> >> >>> >> I enthusiastically support this proposal. >>> >> >>> >> Hans >>> >> >>> >> >>> >> On 7/31/17, 4:57 PM, "Insight-users on behalf of Jim Miller" >>> >> >>> wrote: >>> >> >>> >> +1 >>> >> >>> >> Jim >>> >> >>> >> > On Jul 31, 2017, at 5:07 PM, Matt McCormick >>> >> wrote: >>> >> > >>> >> > Hi folks, >>> >> > >>> >> > We are considering migration of ITK's software process to >>> >> GitHub, and >>> >> > we would like your feedback. >>> >> > >>> >> > As an open-source, community-driven project, mechanisms to >>> >> communicate >>> >> > and interact with the community are a high priority for ITK. >>> >> > Contributing should be as easy as possible. Increasingly over >>> >> the past >>> >> > many years, GitHub has become the de facto place to interact >>> >> for open >>> >> > source development. It is now a hub for: >>> >> > >>> >> > Microsoft >>> >> > Facebook >>> >> > Google >>> >> > The Scientific Python Community >>> >> > The 3D Slicer Community >>> >> > >>> >> > Our InsightSoftwareConsortium GitHub organization [1] already >>> has 67 >>> >> > people in it and 74 repositories. There are hundreds of >>> >> projects that >>> >> > depend on ITK on GitHub. Many ITK developers are familiar with >>> the >>> >> > development process on GitHub (i.e the pull request process) and >>> >> > already have an account on this platform. There are also >>> >> advantages to >>> >> > linking issues and commits with other projects and repositories. >>> >> Since >>> >> > ITK thrives on the open-source development idea, everyone who >>> >> wants to >>> >> > help the project should be able to contribute, and therefore it >>> >> should >>> >> > be as easy as possible to start participating in the community. >>> >> > >>> >> > Recently, GitHub's code review capabilities have greatly >>> improved, >>> >> > which make it more feasible to coordinate contributions for a >>> large >>> >> > project like ITK. And, there are many existing GitHub-integrated >>> >> > services that we can leverage. >>> >> > >>> >> > Thanks to resources from the National Library of Medicine and >>> >> > technological advances, it is now feasible to migrate the >>> project's >>> >> > software process to GitHub. There are many infrastructural >>> >> aspects to >>> >> > the migration, and it would take multiple months to complete. >>> Please >>> >> > let us know your thoughts before we embark on the journey. >>> >> > >>> >> > >>> >> > [1] https://na01.safelinks.protect >>> ion.outlook.com/?url=https%3A%2F%2Fgithub.com%2FInsightSoftw >>> areConsortium&data=02%7C01%7Classo%40queensu.ca%7C96f312d049 >>> d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c% >>> 7C1%7C0%7C636371388439104668&sdata=onq3vW0pCjrT8pDNShHXc4Jko >>> hBMBoHv1lxOD6Nkg4o%3D&reserved=0 >>> >> > _____________________________________ >>> >> > Powered by https://na01.safelinks.protect >>> ion.outlook.com/?url=www.kitware.com&data=02%7C01%7Classo% >>> 40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38 >>> b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata= >>> TbmgQahvMJx3Czk56R8%2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 >>> >> > >>> >> > Visit other Kitware open-source projects at >>> >> > https://na01.safelinks.protection.outlook.com/?url=http%3A%2 >>> F%2Fwww.kitware.com%2Fopensource%2Fopensource.html&data=02%7 >>> C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888% >>> 7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104 >>> 668&sdata=BQ97jxO1o0jxL0Nk0n1styLRKu5P9Xb8JPOsASbPMNc%3D&reserved=0 >>> >> > >>> >> > Kitware offers ITK Training Courses, for more information visit: >>> >> > https://na01.safelinks.protection.outlook.com/?url=http%3A%2 >>> F%2Fwww.kitware.com%2Fproducts%2Fprotraining.php&data=02%7C0 >>> 1%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888% >>> 7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104 >>> 668&sdata=iR5J0Yx6p31iobZibGN4nJbHsd2mYmeNshJVj12Azgw%3D&reserved=0 >>> >> > >>> >> > Please keep messages on-topic and check the ITK FAQ at: >>> >> > https://na01.safelinks.protection.outlook.com/?url=http%3A%2 >>> F%2Fwww.itk.org%2FWiki%2FITK_FAQ&data=02%7C01%7Classo%40quee >>> nsu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d5 >>> 82c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata= >>> lnYum27haYjI7jbzMagLEL0eg13MhwdARYTPZivjDe0%3D&reserved=0 >>> >> > >>> >> > Follow this link to subscribe/unsubscribe: >>> >> > https://na01.safelinks.protection.outlook.com/?url=http%3A%2 >>> F%2Fpublic.kitware.com%2Fmailman%2Flistinfo%2Finsight-users& >>> data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4 >>> d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0% >>> 7C636371388439104668&sdata=3rk3ntG%2Fvv1h8UgHGKvxd8FcajlD >>> jZqK6BHweskvql8%3D&reserved=0 >>> >> _____________________________________ >>> >> Powered by >>> >> https://na01.safelinks.protection.outlook.com/?url=www.kitware.com&da >>> >> ta=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7C >>> >> d61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=T >>> >> bmgQahvMJx3Czk56R8%2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 >>> >> >>> >> Visit other Kitware open-source projects at >>> >> >>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.k >>> >> itware.com%2Fopensource%2Fopensource.html&data=02%7C01%7Classo%40quee >>> >> nsu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb28 >>> >> 38b925c%7C1%7C0%7C636371388439104668&sdata=BQ97jxO1o0jxL0Nk0n1styLRKu >>> >> 5P9Xb8JPOsASbPMNc%3D&reserved=0 >>> >> >>> >> Kitware offers ITK Training Courses, for more information visit: >>> >> >>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.k >>> >> itware.com%2Fproducts%2Fprotraining.php&data=02%7C01%7Classo%40queens >>> >> u.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838 >>> >> b925c%7C1%7C0%7C636371388439104668&sdata=iR5J0Yx6p31iobZibGN4nJbHsd2m >>> >> YmeNshJVj12Azgw%3D&reserved=0 >>> >> >>> >> Please keep messages on-topic and check the ITK FAQ at: >>> >> >>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.i >>> >> 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bmgQahvMJx3Czk56R8%2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 >>> >> >>> >> Visit other Kitware open-source projects at >>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.k >>> >> itware.com%2Fopensource%2Fopensource.html&data=02%7C01%7Classo%40quee >>> >> nsu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb28 >>> >> 38b925c%7C1%7C0%7C636371388439104668&sdata=BQ97jxO1o0jxL0Nk0n1styLRKu >>> >> 5P9Xb8JPOsASbPMNc%3D&reserved=0 >>> >> >>> >> Kitware offers ITK Training Courses, for more information visit: >>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.k >>> >> itware.com%2Fproducts%2Fprotraining.php&data=02%7C01%7Classo%40queens >>> >> u.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838 >>> >> b925c%7C1%7C0%7C636371388439104668&sdata=iR5J0Yx6p31iobZibGN4nJbHsd2m >>> >> YmeNshJVj12Azgw%3D&reserved=0 >>> >> >>> >> Please keep messages on-topic and check the ITK FAQ at: >>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.i >>> >> tk.org%2FWiki%2FITK_FAQ&data=02%7C01%7Classo%40queensu.ca%7C96f312d04 >>> >> 9d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C >>> >> 636371388439104668&sdata=lnYum27haYjI7jbzMagLEL0eg13MhwdARYTPZivjDe0% >>> >> 3D&reserved=0 >>> >> >>> >> Follow this link to subscribe/unsubscribe: >>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpubli >>> >> c.kitware.com%2Fmailman%2Flistinfo%2Finsight-users&data=02%7C01%7Clas >>> >> so%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d5 >>> >> 82c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=3rk3ntG%2Fvv1h8Ug >>> >> HGKvxd8FcajlDjZqK6BHweskvql8%3D&reserved=0 >>> _______________________________________________ >>> Powered by https://na01.safelinks.protection.outlook.com/?url=www.kitwa >>> re.com&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448 >>> d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0 >>> 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data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4 >>> d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0% >>> 7C636371388439104668&sdata=7%2FDK5kxboSdWy9zTD2f%2FP8CqdebW >>> %2B82BJZQXMFQfCOQ%3D&reserved=0 >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >> >> >> >> -- >> Cory Quammen >> Staff R&D Engineer >> Kitware, Inc. >> > -- Cory Quammen Staff R&D Engineer Kitware, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Tue Aug 1 11:29:37 2017 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 1 Aug 2017 11:29:37 -0400 Subject: [ITK-users] [ITK] [ITK-dev] Migration to GitHub In-Reply-To: References: Message-ID: Since Paraview, VTK, VTK-m, KWIVER, and CMake are all hosted on gitlab, I still don't see why ITK is moving to github? On Tue, Aug 1, 2017 at 11:22 AM, Cory Quammen wrote: > On Tue, Aug 1, 2017 at 11:13 AM, Bill Lorensen > wrote: >> >> Cory, >> I think you meant to say VTK has no plans to move to GitHub. > > > Yes indeed, thanks for catching ("Hu" and "La" aren't even that close on the > keyboard). > > VTK is firmly ensconced in GitLab, and not moving to GitHub. > >> >> On Aug 1, 2017 10:27 AM, "Cory Quammen" wrote: >>> >>> I don't have much of an opinion on moving ITK to GitHub, but I'd like to >>> address some things Andras mentioned about GitLab and VTK. >>> >>>> >>>> About GitHub/Kitware GitLab: >>>> >>>> I heard that VTK is going to move to GitHub, too. Maybe I misunderstood, >>>> but make sure to talk to VTK folks before considering moving to GitLab. >>> >>> >>> I am not aware of any plans to move VTK to GitLab or even any discussion >>> of doing so. >>> >>>> >>>> Anyway, as a very active user but only occasional contributor of VTK, I >>>> find VTK GitLab quite frustrating due to that: >>>> 1. It is slow. I heard that it's fast when accessed from inside Kitware >>>> network, but most community members are outside. >>> >>> >>> The first few versions were indeed a bit slow, but new updates come out >>> regularly, and the speed is quite snappy. I use it both from within the >>> Kitware network and outside the network and haven't noticed a difference. >>> >>>> >>>> 2. I need to re-learn each time I use it: I review code, submit PR or >>>> bug report once in every few months - and each time I need to spend 20-30 >>>> minutes extra, just to find out how things work. >>>> >>>> >>>> Andras >>>> >>>> -----Original Message----- >>>> From: Community [mailto:community-bounces at itk.org] On Behalf Of Matt >>>> McCormick >>>> Sent: Monday, July 31, 2017 7:00 PM >>>> To: Bill Lorensen >>>> Cc: Insight-Users ; Hans Johnson >>>> ; Insight Developers List >>>> >>>> Subject: Re: [ITK] [ITK-dev] [ITK-users] Migration to GitHub >>>> >>>> I have followed VTK's migration to GitLab, and Kitware has done an >>>> excellent job with it. That said, I still think GitHub is the better choice >>>> for ITK. Also, the technical and social situation has changed in the time >>>> since VTK moved to GitLab. >>>> >>>> I think the key factor is "community", and GitHub has the open source >>>> community. >>>> >>>> On Mon, Jul 31, 2017 at 6:42 PM, Bill Lorensen >>>> wrote: >>>> > Vtk moved to GitLab. Have you checked with the Kitware folks to see >>>> > why they didn't use gitlab? For me, either github or gitlab is great. >>>> > >>>> > On Jul 31, 2017 6:03 PM, "Johnson, Hans J" >>>> > wrote: >>>> >> >>>> >> 1000 x +1 >>>> >> >>>> >> I enthusiastically support this proposal. >>>> >> >>>> >> Hans >>>> >> >>>> >> >>>> >> On 7/31/17, 4:57 PM, "Insight-users on behalf of Jim Miller" >>>> >> >>>> >> wrote: >>>> >> >>>> >> +1 >>>> >> >>>> >> Jim >>>> >> >>>> >> > On Jul 31, 2017, at 5:07 PM, Matt McCormick >>>> >> wrote: >>>> >> > >>>> >> > Hi folks, >>>> >> > >>>> >> > We are considering migration of ITK's software process to >>>> >> GitHub, and >>>> >> > we would like your feedback. >>>> >> > >>>> >> > As an open-source, community-driven project, mechanisms to >>>> >> communicate >>>> >> > and interact with the community are a high priority for ITK. >>>> >> > Contributing should be as easy as possible. Increasingly over >>>> >> the past >>>> >> > many years, GitHub has become the de facto place to interact >>>> >> for open >>>> >> > source development. It is now a hub for: >>>> >> > >>>> >> > Microsoft >>>> >> > Facebook >>>> >> > Google >>>> >> > The Scientific Python Community >>>> >> > The 3D Slicer Community >>>> >> > >>>> >> > Our InsightSoftwareConsortium GitHub organization [1] already >>>> >> has 67 >>>> >> > people in it and 74 repositories. There are hundreds of >>>> >> projects that >>>> >> > depend on ITK on GitHub. Many ITK developers are familiar with >>>> >> the >>>> >> > development process on GitHub (i.e the pull request process) >>>> >> and >>>> >> > already have an account on this platform. There are also >>>> >> advantages to >>>> >> > linking issues and commits with other projects and >>>> >> repositories. >>>> >> Since >>>> >> > ITK thrives on the open-source development idea, everyone who >>>> >> wants to >>>> >> > help the project should be able to contribute, and therefore it >>>> >> should >>>> >> > be as easy as possible to start participating in the community. >>>> >> > >>>> >> > Recently, GitHub's code review capabilities have greatly >>>> >> improved, >>>> >> > which make it more feasible to coordinate contributions for a >>>> >> large >>>> >> > project like ITK. And, there are many existing >>>> >> GitHub-integrated >>>> >> > services that we can leverage. >>>> >> > >>>> >> > Thanks to resources from the National Library of Medicine and >>>> >> > technological advances, it is now feasible to migrate the >>>> >> project's >>>> >> > software process to GitHub. There are many infrastructural >>>> >> aspects to >>>> >> > the migration, and it would take multiple months to complete. >>>> >> Please >>>> >> > let us know your thoughts before we embark on the journey. >>>> >> > >>>> >> > >>>> >> > [1] >>>> >> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FInsightSoftwareConsortium&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=onq3vW0pCjrT8pDNShHXc4JkohBMBoHv1lxOD6Nkg4o%3D&reserved=0 >>>> >> > _____________________________________ >>>> >> > Powered by >>>> >> https://na01.safelinks.protection.outlook.com/?url=www.kitware.com&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=TbmgQahvMJx3Czk56R8%2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 >>>> >> > >>>> >> > Visit other Kitware open-source projects at >>>> >> > >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.kitware.com%2Fopensource%2Fopensource.html&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=BQ97jxO1o0jxL0Nk0n1styLRKu5P9Xb8JPOsASbPMNc%3D&reserved=0 >>>> >> > >>>> >> > Kitware offers ITK Training Courses, for more information >>>> >> visit: >>>> >> > >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.kitware.com%2Fproducts%2Fprotraining.php&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=iR5J0Yx6p31iobZibGN4nJbHsd2mYmeNshJVj12Azgw%3D&reserved=0 >>>> >> > >>>> >> > Please keep messages on-topic and check the ITK FAQ at: >>>> >> > >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.itk.org%2FWiki%2FITK_FAQ&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=lnYum27haYjI7jbzMagLEL0eg13MhwdARYTPZivjDe0%3D&reserved=0 >>>> >> > >>>> >> > Follow this link to subscribe/unsubscribe: >>>> >> > >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo%2Finsight-users&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=3rk3ntG%2Fvv1h8UgHGKvxd8FcajlDjZqK6BHweskvql8%3D&reserved=0 >>>> >> _____________________________________ >>>> >> Powered by >>>> >> https://na01.safelinks.protection.outlook.com/?url=www.kitware.com&da >>>> >> ta=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7C >>>> >> d61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=T >>>> >> bmgQahvMJx3Czk56R8%2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 >>>> >> >>>> >> Visit other Kitware open-source projects at >>>> >> >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.k >>>> >> itware.com%2Fopensource%2Fopensource.html&data=02%7C01%7Classo%40quee >>>> >> nsu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb28 >>>> >> 38b925c%7C1%7C0%7C636371388439104668&sdata=BQ97jxO1o0jxL0Nk0n1styLRKu >>>> >> 5P9Xb8JPOsASbPMNc%3D&reserved=0 >>>> >> >>>> >> Kitware offers ITK Training Courses, for more information visit: >>>> >> >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.k >>>> >> itware.com%2Fproducts%2Fprotraining.php&data=02%7C01%7Classo%40queens >>>> >> u.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838 >>>> >> b925c%7C1%7C0%7C636371388439104668&sdata=iR5J0Yx6p31iobZibGN4nJbHsd2m >>>> >> YmeNshJVj12Azgw%3D&reserved=0 >>>> >> >>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>> >> >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.i >>>> >> tk.org%2FWiki%2FITK_FAQ&data=02%7C01%7Classo%40queensu.ca%7C96f312d04 >>>> >> 9d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C >>>> >> 636371388439104668&sdata=lnYum27haYjI7jbzMagLEL0eg13MhwdARYTPZivjDe0% >>>> >> 3D&reserved=0 >>>> >> >>>> >> Follow this link to subscribe/unsubscribe: >>>> >> >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpubli >>>> >> c.kitware.com%2Fmailman%2Flistinfo%2Finsight-users&data=02%7C01%7Clas >>>> >> so%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d5 >>>> >> 82c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=3rk3ntG%2Fvv1h8Ug >>>> >> HGKvxd8FcajlDjZqK6BHweskvql8%3D&reserved=0 >>>> >> >>>> >> >>>> >> _____________________________________ >>>> >> Powered by >>>> >> https://na01.safelinks.protection.outlook.com/?url=www.kitware.com&da >>>> >> ta=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7C >>>> >> d61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=T >>>> >> bmgQahvMJx3Czk56R8%2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 >>>> >> >>>> >> Visit other Kitware open-source projects at >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.k >>>> >> itware.com%2Fopensource%2Fopensource.html&data=02%7C01%7Classo%40quee >>>> >> nsu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb28 >>>> >> 38b925c%7C1%7C0%7C636371388439104668&sdata=BQ97jxO1o0jxL0Nk0n1styLRKu >>>> >> 5P9Xb8JPOsASbPMNc%3D&reserved=0 >>>> >> >>>> >> Kitware offers ITK Training Courses, for more information visit: >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.k >>>> >> itware.com%2Fproducts%2Fprotraining.php&data=02%7C01%7Classo%40queens >>>> >> u.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838 >>>> >> b925c%7C1%7C0%7C636371388439104668&sdata=iR5J0Yx6p31iobZibGN4nJbHsd2m >>>> >> YmeNshJVj12Azgw%3D&reserved=0 >>>> >> >>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.i >>>> >> tk.org%2FWiki%2FITK_FAQ&data=02%7C01%7Classo%40queensu.ca%7C96f312d04 >>>> >> 9d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C >>>> >> 636371388439104668&sdata=lnYum27haYjI7jbzMagLEL0eg13MhwdARYTPZivjDe0% >>>> >> 3D&reserved=0 >>>> >> >>>> >> Follow this link to subscribe/unsubscribe: >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpubli >>>> >> c.kitware.com%2Fmailman%2Flistinfo%2Finsight-users&data=02%7C01%7Clas >>>> >> so%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d5 >>>> >> 82c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=3rk3ntG%2Fvv1h8Ug >>>> >> HGKvxd8FcajlDjZqK6BHweskvql8%3D&reserved=0 >>>> _______________________________________________ >>>> Powered by >>>> https://na01.safelinks.protection.outlook.com/?url=www.kitware.com&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=TbmgQahvMJx3Czk56R8%2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 >>>> >>>> Visit other Kitware open-source projects at >>>> >>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.kitware.com%2Fopensource%2Fopensource.html&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=BQ97jxO1o0jxL0Nk0n1styLRKu5P9Xb8JPOsASbPMNc%3D&reserved=0 >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> >>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fkitware.com%2Fproducts%2Fprotraining.php&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=4W%2B%2B3MiNoGmr%2FKnI9Kmyl4BPOJ0%2BDu9Mcdgk5A%2Foi3c%3D&reserved=0 >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> >>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.itk.org%2FWiki%2FITK_FAQ&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=lnYum27haYjI7jbzMagLEL0eg13MhwdARYTPZivjDe0%3D&reserved=0 >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> >>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo%2Finsight-developers&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=aJgjy9V6YWhdNpqDtQSNkBEfKEW6dNcKVW3C1fT%2FH9Q%3D&reserved=0 >>>> _______________________________________________ >>>> Community mailing list >>>> Community at itk.org >>>> >>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo%2Fcommunity&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=7%2FDK5kxboSdWy9zTD2f%2FP8CqdebW%2B82BJZQXMFQfCOQ%3D&reserved=0 >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >>> >>> >>> -- >>> Cory Quammen >>> Staff R&D Engineer >>> Kitware, Inc. > > > > > -- > Cory Quammen > Staff R&D Engineer > Kitware, Inc. -- Unpaid intern in BillsBasement at noware dot com From francois.budin at kitware.com Tue Aug 1 11:40:25 2017 From: francois.budin at kitware.com (Francois Budin) Date: Tue, 1 Aug 2017 11:40:25 -0400 Subject: [ITK-users] [ITK] [ITK-dev] Migration to GitHub In-Reply-To: References: Message-ID: As Matt mentioned, the main reason is because a lot of ITK users already have Github accounts and are familiar with that environment. The idea is really to make is as simple as possible for the community to contribute. Using Gitlab would still require users to have an account on GitLab to push patches. Most ITK users already have a Github account with their own projects, and contributing to ITK just requires cloning the project and creating a pull-request. On Tue, Aug 1, 2017 at 11:29 AM, Bill Lorensen wrote: > Since > Paraview, VTK, VTK-m, KWIVER, and CMake are all hosted on gitlab, I > still don't see why ITK is moving to github? > > > On Tue, Aug 1, 2017 at 11:22 AM, Cory Quammen > wrote: > > On Tue, Aug 1, 2017 at 11:13 AM, Bill Lorensen > > wrote: > >> > >> Cory, > >> I think you meant to say VTK has no plans to move to GitHub. > > > > > > Yes indeed, thanks for catching ("Hu" and "La" aren't even that close on > the > > keyboard). > > > > VTK is firmly ensconced in GitLab, and not moving to GitHub. > > > >> > >> On Aug 1, 2017 10:27 AM, "Cory Quammen" > wrote: > >>> > >>> I don't have much of an opinion on moving ITK to GitHub, but I'd like > to > >>> address some things Andras mentioned about GitLab and VTK. > >>> > >>>> > >>>> About GitHub/Kitware GitLab: > >>>> > >>>> I heard that VTK is going to move to GitHub, too. Maybe I > misunderstood, > >>>> but make sure to talk to VTK folks before considering moving to > GitLab. > >>> > >>> > >>> I am not aware of any plans to move VTK to GitLab or even any > discussion > >>> of doing so. > >>> > >>>> > >>>> Anyway, as a very active user but only occasional contributor of VTK, > I > >>>> find VTK GitLab quite frustrating due to that: > >>>> 1. It is slow. I heard that it's fast when accessed from inside > Kitware > >>>> network, but most community members are outside. > >>> > >>> > >>> The first few versions were indeed a bit slow, but new updates come out > >>> regularly, and the speed is quite snappy. I use it both from within the > >>> Kitware network and outside the network and haven't noticed a > difference. > >>> > >>>> > >>>> 2. I need to re-learn each time I use it: I review code, submit PR or > >>>> bug report once in every few months - and each time I need to spend > 20-30 > >>>> minutes extra, just to find out how things work. > >>>> > >>>> > >>>> Andras > >>>> > >>>> -----Original Message----- > >>>> From: Community [mailto:community-bounces at itk.org] On Behalf Of Matt > >>>> McCormick > >>>> Sent: Monday, July 31, 2017 7:00 PM > >>>> To: Bill Lorensen > >>>> Cc: Insight-Users ; Hans Johnson > >>>> ; Insight Developers List > >>>> > >>>> Subject: Re: [ITK] [ITK-dev] [ITK-users] Migration to GitHub > >>>> > >>>> I have followed VTK's migration to GitLab, and Kitware has done an > >>>> excellent job with it. That said, I still think GitHub is the better > choice > >>>> for ITK. Also, the technical and social situation has changed in the > time > >>>> since VTK moved to GitLab. > >>>> > >>>> I think the key factor is "community", and GitHub has the open source > >>>> community. > >>>> > >>>> On Mon, Jul 31, 2017 at 6:42 PM, Bill Lorensen < > bill.lorensen at gmail.com> > >>>> wrote: > >>>> > Vtk moved to GitLab. Have you checked with the Kitware folks to see > >>>> > why they didn't use gitlab? For me, either github or gitlab is > great. > >>>> > > >>>> > On Jul 31, 2017 6:03 PM, "Johnson, Hans J" > >>>> > wrote: > >>>> >> > >>>> >> 1000 x +1 > >>>> >> > >>>> >> I enthusiastically support this proposal. > >>>> >> > >>>> >> Hans > >>>> >> > >>>> >> > >>>> >> On 7/31/17, 4:57 PM, "Insight-users on behalf of Jim Miller" > >>>> >> > >>>> >> wrote: > >>>> >> > >>>> >> +1 > >>>> >> > >>>> >> Jim > >>>> >> > >>>> >> > On Jul 31, 2017, at 5:07 PM, Matt McCormick > >>>> >> wrote: > >>>> >> > > >>>> >> > Hi folks, > >>>> >> > > >>>> >> > We are considering migration of ITK's software process to > >>>> >> GitHub, and > >>>> >> > we would like your feedback. > >>>> >> > > >>>> >> > As an open-source, community-driven project, mechanisms to > >>>> >> communicate > >>>> >> > and interact with the community are a high priority for ITK. > >>>> >> > Contributing should be as easy as possible. Increasingly over > >>>> >> the past > >>>> >> > many years, GitHub has become the de facto place to interact > >>>> >> for open > >>>> >> > source development. It is now a hub for: > >>>> >> > > >>>> >> > Microsoft > >>>> >> > Facebook > >>>> >> > Google > >>>> >> > The Scientific Python Community > >>>> >> > The 3D Slicer Community > >>>> >> > > >>>> >> > Our InsightSoftwareConsortium GitHub organization [1] already > >>>> >> has 67 > >>>> >> > people in it and 74 repositories. There are hundreds of > >>>> >> projects that > >>>> >> > depend on ITK on GitHub. Many ITK developers are familiar > with > >>>> >> the > >>>> >> > development process on GitHub (i.e the pull request process) > >>>> >> and > >>>> >> > already have an account on this platform. There are also > >>>> >> advantages to > >>>> >> > linking issues and commits with other projects and > >>>> >> repositories. > >>>> >> Since > >>>> >> > ITK thrives on the open-source development idea, everyone who > >>>> >> wants to > >>>> >> > help the project should be able to contribute, and therefore > it > >>>> >> should > >>>> >> > be as easy as possible to start participating in the > community. > >>>> >> > > >>>> >> > Recently, GitHub's code review capabilities have greatly > >>>> >> improved, > >>>> >> > which make it more feasible to coordinate contributions for a > >>>> >> large > >>>> >> > project like ITK. And, there are many existing > >>>> >> GitHub-integrated > >>>> >> > services that we can leverage. > >>>> >> > > >>>> >> > Thanks to resources from the National Library of Medicine and > >>>> >> > technological advances, it is now feasible to migrate the > >>>> >> project's > >>>> >> > software process to GitHub. There are many infrastructural > >>>> >> aspects to > >>>> >> > the migration, and it would take multiple months to complete. > >>>> >> Please > >>>> >> > let us know your thoughts before we embark on the journey. > >>>> >> > > >>>> >> > > >>>> >> > [1] > >>>> >> https://na01.safelinks.protection.outlook.com/?url= > https%3A%2F%2Fgithub.com%2FInsightSoftwareConsortium&data=02%7C01%7Classo% > 40queensu.ca%7C96f312d049d7448d6db208d4d867f888% > 7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata= > onq3vW0pCjrT8pDNShHXc4JkohBMBoHv1lxOD6Nkg4o%3D&reserved=0 > >>>> >> > _____________________________________ > >>>> >> > Powered by > >>>> >> https://na01.safelinks.protection.outlook.com/?url= > www.kitware.com&data=02%7C01%7Classo%40queensu.ca% > 7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b > 925c%7C1%7C0%7C636371388439104668&sdata=TbmgQahvMJx3Czk56R8% > 2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 > >>>> >> > > >>>> >> > Visit other Kitware open-source 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http%3A%2F%2Fwww.itk.org%2FWiki%2FITK_FAQ&data=02%7C01% > 7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888% > 7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata= > lnYum27haYjI7jbzMagLEL0eg13MhwdARYTPZivjDe0%3D&reserved=0 > >>>> >> > > >>>> >> > Follow this link to subscribe/unsubscribe: > >>>> >> > > >>>> >> https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo% > 2Finsight-users&data=02%7C01%7Classo%40queensu.ca% > 7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b > 925c%7C1%7C0%7C636371388439104668&sdata=3rk3ntG% > 2Fvv1h8UgHGKvxd8FcajlDjZqK6BHweskvql8%3D&reserved=0 > >>>> >> _____________________________________ > >>>> >> Powered by > >>>> >> https://na01.safelinks.protection.outlook.com/?url= > www.kitware.com&da > >>>> >> ta=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867 > f888%7C > >>>> >> d61ecb3b38b142d582c4efb2838b925c%7C1%7C0% > 7C636371388439104668&sdata=T > >>>> >> 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https://na01.safelinks.protection.outlook.com/?url= > www.kitware.com&da > >>>> >> ta=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867 > f888%7C > >>>> >> d61ecb3b38b142d582c4efb2838b925c%7C1%7C0% > 7C636371388439104668&sdata=T > >>>> >> bmgQahvMJx3Czk56R8%2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 > >>>> >> > >>>> >> Visit other Kitware open-source projects at > >>>> >> https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fwww.k > >>>> >> itware.com%2Fopensource%2Fopensource.html&data=02% > 7C01%7Classo%40quee > >>>> >> nsu.ca%7C96f312d049d7448d6db208d4d867f888% > 7Cd61ecb3b38b142d582c4efb28 > >>>> >> 38b925c%7C1%7C0%7C636371388439104668&sdata= > BQ97jxO1o0jxL0Nk0n1styLRKu > >>>> >> 5P9Xb8JPOsASbPMNc%3D&reserved=0 > >>>> >> > >>>> >> Kitware offers ITK Training Courses, for more information visit: > >>>> >> https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fwww.k > >>>> >> itware.com%2Fproducts%2Fprotraining.php&data=02% > 7C01%7Classo%40queens > >>>> >> u.ca%7C96f312d049d7448d6db208d4d867f888% > 7Cd61ecb3b38b142d582c4efb2838 > >>>> >> b925c%7C1%7C0%7C636371388439104668&sdata= > iR5J0Yx6p31iobZibGN4nJbHsd2m > >>>> >> YmeNshJVj12Azgw%3D&reserved=0 > >>>> >> > >>>> >> Please keep messages on-topic and check the ITK FAQ at: > >>>> >> https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fwww.i > >>>> >> tk.org%2FWiki%2FITK_FAQ&data=02%7C01%7Classo%40queensu.ca% > 7C96f312d04 > >>>> >> 9d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b > 925c%7C1%7C0%7C > >>>> >> 636371388439104668&sdata=lnYum27haYjI7jbzMagLEL0eg13Mhw > dARYTPZivjDe0% > >>>> >> 3D&reserved=0 > >>>> >> > >>>> >> Follow this link to subscribe/unsubscribe: > >>>> >> https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fpubli > >>>> >> c.kitware.com%2Fmailman%2Flistinfo%2Finsight-users& > data=02%7C01%7Clas > >>>> >> so%40queensu.ca%7C96f312d049d7448d6db208d4d867 > f888%7Cd61ecb3b38b142d5 > >>>> >> 82c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata= > 3rk3ntG%2Fvv1h8Ug > >>>> >> HGKvxd8FcajlDjZqK6BHweskvql8%3D&reserved=0 > >>>> _______________________________________________ > >>>> Powered by > >>>> https://na01.safelinks.protection.outlook.com/?url= > www.kitware.com&data=02%7C01%7Classo%40queensu.ca% > 7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b > 925c%7C1%7C0%7C636371388439104668&sdata=TbmgQahvMJx3Czk56R8% > 2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 > >>>> > >>>> Visit other Kitware open-source projects at > >>>> > >>>> https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fwww.kitware.com%2Fopensource%2Fopensource. > html&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888% > 7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata= > BQ97jxO1o0jxL0Nk0n1styLRKu5P9Xb8JPOsASbPMNc%3D&reserved=0 > >>>> > >>>> Kitware offers ITK Training Courses, for more information visit: > >>>> > >>>> https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fkitware.com%2Fproducts%2Fprotraining.php& > data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888% > 7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=4W% > 2B%2B3MiNoGmr%2FKnI9Kmyl4BPOJ0%2BDu9Mcdgk5A%2Foi3c%3D&reserved=0 > >>>> > >>>> Please keep messages on-topic and check the ITK FAQ at: > >>>> > >>>> https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fwww.itk.org%2FWiki%2FITK_FAQ&data=02%7C01% > 7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888% > 7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata= > lnYum27haYjI7jbzMagLEL0eg13MhwdARYTPZivjDe0%3D&reserved=0 > >>>> > >>>> Follow this link to subscribe/unsubscribe: > >>>> > >>>> https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo% > 2Finsight-developers&data=02%7C01%7Classo%40queensu.ca% > 7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b > 925c%7C1%7C0%7C636371388439104668&sdata=aJgjy9V6YWhdNpqDtQSNkBEfKEW6dN > cKVW3C1fT%2FH9Q%3D&reserved=0 > >>>> _______________________________________________ > >>>> Community mailing list > >>>> Community at itk.org > >>>> > >>>> https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo% > 2Fcommunity&data=02%7C01%7Classo%40queensu.ca% > 7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b > 925c%7C1%7C0%7C636371388439104668&sdata=7%2FDK5kxboSdWy9zTD2f% > 2FP8CqdebW%2B82BJZQXMFQfCOQ%3D&reserved=0 > >>>> _____________________________________ > >>>> Powered by www.kitware.com > >>>> > >>>> Visit other Kitware open-source projects at > >>>> http://www.kitware.com/opensource/opensource.html > >>>> > >>>> Kitware offers ITK Training Courses, for more information visit: > >>>> http://www.kitware.com/products/protraining.php > >>>> > >>>> Please keep messages on-topic and check the ITK FAQ at: > >>>> http://www.itk.org/Wiki/ITK_FAQ > >>>> > >>>> Follow this link to subscribe/unsubscribe: > >>>> http://public.kitware.com/mailman/listinfo/insight-users > >>> > >>> > >>> > >>> > >>> -- > >>> Cory Quammen > >>> Staff R&D Engineer > >>> Kitware, Inc. > > > > > > > > > > -- > > Cory Quammen > > Staff R&D Engineer > > Kitware, Inc. > > > > -- > Unpaid intern in BillsBasement at noware dot com > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From rc1515 at ic.ac.uk Tue Aug 1 11:47:38 2017 From: rc1515 at ic.ac.uk (Ramana C) Date: Tue, 1 Aug 2017 08:47:38 -0700 (MST) Subject: [ITK-users] Extracting image coordinate transform matrix In-Reply-To: References: <1501590104563-38537.post@n7.nabble.com> Message-ID: <1501602458344-38549.post@n7.nabble.com> Hi Ziv, Thanks very much, that's exactly what I needed. I needed the matrix for some code I'm writing to invert a displacement field. The fixed-point deformation field inversion isn't included in the SimpleITK python libraries, so I'm going about implementing it myself. Anyway, thanks very much for the help again! Ramana -- View this message in context: http://itk-users.7.n7.nabble.com/Extracting-image-coordinate-transform-matrix-tp38537p38549.html Sent from the ITK - Users mailing list archive at Nabble.com. From blowekamp at mail.nih.gov Tue Aug 1 12:01:38 2017 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Tue, 1 Aug 2017 16:01:38 +0000 Subject: [ITK-users] [ITK-dev] [ITK] Migration to GitHub In-Reply-To: References: Message-ID: <2C7BD08F-FCCA-4477-8F62-D0935AC2B050@mail.nih.gov> Bill, I believe Matt addressed the reason in the opening post. The goal is not to make things consistent for the current developers, but to improve engagement with the ITK community. With the ITK external modules residing in GitHub, and innumerable number of project which use ITK in GitHub the ITK community is already on GitHub. The ability to link issues and pull request across projects will be quite valuable. Recently, SimpleITK has been using GitHub for issue tracking and pull request. We were quite impressed with the increased interaction with the SimpleITK community including discussion of issues, linking to other projects and pull requests. Brad On 8/1/17, 11:30 AM, "Bill Lorensen" wrote: Since Paraview, VTK, VTK-m, KWIVER, and CMake are all hosted on gitlab, I still don't see why ITK is moving to github? On Tue, Aug 1, 2017 at 11:22 AM, Cory Quammen wrote: > On Tue, Aug 1, 2017 at 11:13 AM, Bill Lorensen > wrote: >> >> Cory, >> I think you meant to say VTK has no plans to move to GitHub. > > > Yes indeed, thanks for catching ("Hu" and "La" aren't even that close on the > keyboard). > > VTK is firmly ensconced in GitLab, and not moving to GitHub. > >> >> On Aug 1, 2017 10:27 AM, "Cory Quammen" wrote: >>> >>> I don't have much of an opinion on moving ITK to GitHub, but I'd like to >>> address some things Andras mentioned about GitLab and VTK. >>> >>>> >>>> About GitHub/Kitware GitLab: >>>> >>>> I heard that VTK is going to move to GitHub, too. Maybe I misunderstood, >>>> but make sure to talk to VTK folks before considering moving to GitLab. >>> >>> >>> I am not aware of any plans to move VTK to GitLab or even any discussion >>> of doing so. >>> >>>> >>>> Anyway, as a very active user but only occasional contributor of VTK, I >>>> find VTK GitLab quite frustrating due to that: >>>> 1. It is slow. I heard that it's fast when accessed from inside Kitware >>>> network, but most community members are outside. >>> >>> >>> The first few versions were indeed a bit slow, but new updates come out >>> regularly, and the speed is quite snappy. I use it both from within the >>> Kitware network and outside the network and haven't noticed a difference. >>> >>>> >>>> 2. I need to re-learn each time I use it: I review code, submit PR or >>>> bug report once in every few months - and each time I need to spend 20-30 >>>> minutes extra, just to find out how things work. >>>> >>>> >>>> Andras >>>> >>>> -----Original Message----- >>>> From: Community [mailto:community-bounces at itk.org] On Behalf Of Matt >>>> McCormick >>>> Sent: Monday, July 31, 2017 7:00 PM >>>> To: Bill Lorensen >>>> Cc: Insight-Users ; Hans Johnson >>>> ; Insight Developers List >>>> >>>> Subject: Re: [ITK] [ITK-dev] [ITK-users] Migration to GitHub >>>> >>>> I have followed VTK's migration to GitLab, and Kitware has done an >>>> excellent job with it. That said, I still think GitHub is the better choice >>>> for ITK. Also, the technical and social situation has changed in the time >>>> since VTK moved to GitLab. >>>> >>>> I think the key factor is "community", and GitHub has the open source >>>> community. >>>> >>>> On Mon, Jul 31, 2017 at 6:42 PM, Bill Lorensen >>>> wrote: >>>> > Vtk moved to GitLab. Have you checked with the Kitware folks to see >>>> > why they didn't use gitlab? For me, either github or gitlab is great. >>>> > >>>> > On Jul 31, 2017 6:03 PM, "Johnson, Hans J" >>>> > wrote: >>>> >> >>>> >> 1000 x +1 >>>> >> >>>> >> I enthusiastically support this proposal. >>>> >> >>>> >> Hans >>>> >> >>>> >> >>>> >> On 7/31/17, 4:57 PM, "Insight-users on behalf of Jim Miller" >>>> >> >>>> >> wrote: >>>> >> >>>> >> +1 >>>> >> >>>> >> Jim >>>> >> >>>> >> > On Jul 31, 2017, at 5:07 PM, Matt McCormick >>>> >> wrote: >>>> >> > >>>> >> > Hi folks, >>>> >> > >>>> >> > We are considering migration of ITK's software process to >>>> >> GitHub, and >>>> >> > we would like your feedback. >>>> >> > >>>> >> > As an open-source, community-driven project, mechanisms to >>>> >> communicate >>>> >> > and interact with the community are a high priority for ITK. >>>> >> > Contributing should be as easy as possible. Increasingly over >>>> >> the past >>>> >> > many years, GitHub has become the de facto place to interact >>>> >> for open >>>> >> > source development. It is now a hub for: >>>> >> > >>>> >> > Microsoft >>>> >> > Facebook >>>> >> > Google >>>> >> > The Scientific Python Community >>>> >> > The 3D Slicer Community >>>> >> > >>>> >> > Our InsightSoftwareConsortium GitHub organization [1] already >>>> >> has 67 >>>> >> > people in it and 74 repositories. There are hundreds of >>>> >> projects that >>>> >> > depend on ITK on GitHub. Many ITK developers are familiar with >>>> >> the >>>> >> > development process on GitHub (i.e the pull request process) >>>> >> and >>>> >> > already have an account on this platform. There are also >>>> >> advantages to >>>> >> > linking issues and commits with other projects and >>>> >> repositories. >>>> >> Since >>>> >> > ITK thrives on the open-source development idea, everyone who >>>> >> wants to >>>> >> > help the project should be able to contribute, and therefore it >>>> >> should >>>> >> > be as easy as possible to start participating in the community. >>>> >> > >>>> >> > Recently, GitHub's code review capabilities have greatly >>>> >> improved, >>>> >> > which make it more feasible to coordinate contributions for a >>>> >> large >>>> >> > project like ITK. And, there are many existing >>>> >> GitHub-integrated >>>> >> > services that we can leverage. >>>> >> > >>>> >> > Thanks to resources from the National Library of Medicine and >>>> >> > technological advances, it is now feasible to migrate the >>>> >> project's >>>> >> > software process to GitHub. There are many infrastructural >>>> >> aspects to >>>> >> > the migration, and it would take multiple months to complete. >>>> >> Please >>>> >> > let us know your thoughts before we embark on the journey. >>>> >> > >>>> >> > >>>> >> > [1] >>>> >> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FInsightSoftwareConsortium&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=onq3vW0pCjrT8pDNShHXc4JkohBMBoHv1lxOD6Nkg4o%3D&reserved=0 >>>> >> > _____________________________________ >>>> >> > Powered by >>>> >> https://na01.safelinks.protection.outlook.com/?url=www.kitware.com&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=TbmgQahvMJx3Czk56R8%2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 >>>> >> > >>>> >> > Visit other Kitware open-source projects at >>>> >> > >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.kitware.com%2Fopensource%2Fopensource.html&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=BQ97jxO1o0jxL0Nk0n1styLRKu5P9Xb8JPOsASbPMNc%3D&reserved=0 >>>> >> > >>>> >> > Kitware offers ITK Training Courses, for more information >>>> >> visit: >>>> >> > >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.kitware.com%2Fproducts%2Fprotraining.php&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=iR5J0Yx6p31iobZibGN4nJbHsd2mYmeNshJVj12Azgw%3D&reserved=0 >>>> >> > >>>> >> > Please keep messages on-topic and check the ITK FAQ at: >>>> >> > >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.itk.org%2FWiki%2FITK_FAQ&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=lnYum27haYjI7jbzMagLEL0eg13MhwdARYTPZivjDe0%3D&reserved=0 >>>> >> > >>>> >> > Follow this link to subscribe/unsubscribe: >>>> >> > >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo%2Finsight-users&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=3rk3ntG%2Fvv1h8UgHGKvxd8FcajlDjZqK6BHweskvql8%3D&reserved=0 >>>> >> _____________________________________ >>>> >> Powered by >>>> >> https://na01.safelinks.protection.outlook.com/?url=www.kitware.com&da >>>> >> ta=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7C >>>> >> d61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=T >>>> >> bmgQahvMJx3Czk56R8%2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 >>>> >> >>>> >> Visit other Kitware open-source projects at >>>> >> >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.k >>>> >> itware.com%2Fopensource%2Fopensource.html&data=02%7C01%7Classo%40quee >>>> >> nsu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb28 >>>> >> 38b925c%7C1%7C0%7C636371388439104668&sdata=BQ97jxO1o0jxL0Nk0n1styLRKu >>>> >> 5P9Xb8JPOsASbPMNc%3D&reserved=0 >>>> >> >>>> >> Kitware offers ITK Training Courses, for more information visit: >>>> >> >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.k >>>> >> itware.com%2Fproducts%2Fprotraining.php&data=02%7C01%7Classo%40queens >>>> >> u.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838 >>>> >> b925c%7C1%7C0%7C636371388439104668&sdata=iR5J0Yx6p31iobZibGN4nJbHsd2m >>>> >> YmeNshJVj12Azgw%3D&reserved=0 >>>> >> >>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>> >> >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.i >>>> >> tk.org%2FWiki%2FITK_FAQ&data=02%7C01%7Classo%40queensu.ca%7C96f312d04 >>>> >> 9d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C >>>> >> 636371388439104668&sdata=lnYum27haYjI7jbzMagLEL0eg13MhwdARYTPZivjDe0% >>>> >> 3D&reserved=0 >>>> >> >>>> >> Follow this link to subscribe/unsubscribe: >>>> >> >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpubli >>>> >> c.kitware.com%2Fmailman%2Flistinfo%2Finsight-users&data=02%7C01%7Clas >>>> >> so%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d5 >>>> >> 82c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=3rk3ntG%2Fvv1h8Ug >>>> >> HGKvxd8FcajlDjZqK6BHweskvql8%3D&reserved=0 >>>> >> >>>> >> >>>> >> _____________________________________ >>>> >> Powered by >>>> >> https://na01.safelinks.protection.outlook.com/?url=www.kitware.com&da >>>> >> ta=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7C >>>> >> d61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=T >>>> >> bmgQahvMJx3Czk56R8%2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 >>>> >> >>>> >> Visit other Kitware open-source projects at >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.k >>>> >> itware.com%2Fopensource%2Fopensource.html&data=02%7C01%7Classo%40quee >>>> >> nsu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb28 >>>> >> 38b925c%7C1%7C0%7C636371388439104668&sdata=BQ97jxO1o0jxL0Nk0n1styLRKu >>>> >> 5P9Xb8JPOsASbPMNc%3D&reserved=0 >>>> >> >>>> >> Kitware offers ITK Training Courses, for more information visit: >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.k >>>> >> itware.com%2Fproducts%2Fprotraining.php&data=02%7C01%7Classo%40queens >>>> >> u.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838 >>>> >> b925c%7C1%7C0%7C636371388439104668&sdata=iR5J0Yx6p31iobZibGN4nJbHsd2m >>>> >> YmeNshJVj12Azgw%3D&reserved=0 >>>> >> >>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.i >>>> >> tk.org%2FWiki%2FITK_FAQ&data=02%7C01%7Classo%40queensu.ca%7C96f312d04 >>>> >> 9d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C >>>> >> 636371388439104668&sdata=lnYum27haYjI7jbzMagLEL0eg13MhwdARYTPZivjDe0% >>>> >> 3D&reserved=0 >>>> >> >>>> >> Follow this link to subscribe/unsubscribe: >>>> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpubli >>>> >> c.kitware.com%2Fmailman%2Flistinfo%2Finsight-users&data=02%7C01%7Clas >>>> >> so%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d5 >>>> >> 82c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=3rk3ntG%2Fvv1h8Ug >>>> >> HGKvxd8FcajlDjZqK6BHweskvql8%3D&reserved=0 >>>> _______________________________________________ >>>> Powered by >>>> https://na01.safelinks.protection.outlook.com/?url=www.kitware.com&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=TbmgQahvMJx3Czk56R8%2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 >>>> >>>> Visit other Kitware open-source projects at >>>> >>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.kitware.com%2Fopensource%2Fopensource.html&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=BQ97jxO1o0jxL0Nk0n1styLRKu5P9Xb8JPOsASbPMNc%3D&reserved=0 >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> >>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fkitware.com%2Fproducts%2Fprotraining.php&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=4W%2B%2B3MiNoGmr%2FKnI9Kmyl4BPOJ0%2BDu9Mcdgk5A%2Foi3c%3D&reserved=0 >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> >>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.itk.org%2FWiki%2FITK_FAQ&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=lnYum27haYjI7jbzMagLEL0eg13MhwdARYTPZivjDe0%3D&reserved=0 >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> >>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo%2Finsight-developers&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=aJgjy9V6YWhdNpqDtQSNkBEfKEW6dNcKVW3C1fT%2FH9Q%3D&reserved=0 >>>> _______________________________________________ >>>> Community mailing list >>>> Community at itk.org >>>> >>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo%2Fcommunity&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=7%2FDK5kxboSdWy9zTD2f%2FP8CqdebW%2B82BJZQXMFQfCOQ%3D&reserved=0 >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >>> >>> >>> -- >>> Cory Quammen >>> Staff R&D Engineer >>> Kitware, Inc. > > > > > -- > Cory Quammen > Staff R&D Engineer > Kitware, Inc. -- Unpaid intern in BillsBasement at noware dot com _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From bill.lorensen at gmail.com Tue Aug 1 12:07:27 2017 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 1 Aug 2017 12:07:27 -0400 Subject: [ITK-users] [ITK-dev] [ITK] Migration to GitHub In-Reply-To: <2C7BD08F-FCCA-4477-8F62-D0935AC2B050@mail.nih.gov> References: <2C7BD08F-FCCA-4477-8F62-D0935AC2B050@mail.nih.gov> Message-ID: It's funny, VTK moved to gitlab to improve engagement with the VTK community. I really don't care which is picked. I picked github for the new VTK Wiki Examples because I thought it would be better for the community. I argued against vtk moving to gitlab but lost... BTW, the new VTK example site is here: https://lorensen.github.io/VTKExamples/site/ The interface uses mkdocs and Google's material look and feel. It performs well on desktops and mobile platforms. On Tue, Aug 1, 2017 at 12:01 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote: > Bill, > > I believe Matt addressed the reason in the opening post. The goal is not to make things consistent for the current developers, but to improve engagement with the ITK community. With the ITK external modules residing in GitHub, and innumerable number of project which use ITK in GitHub the ITK community is already on GitHub. The ability to link issues and pull request across projects will be quite valuable. > > Recently, SimpleITK has been using GitHub for issue tracking and pull request. We were quite impressed with the increased interaction with the SimpleITK community including discussion of issues, linking to other projects and pull requests. > > Brad > > On 8/1/17, 11:30 AM, "Bill Lorensen" wrote: > > Since > Paraview, VTK, VTK-m, KWIVER, and CMake are all hosted on gitlab, I > still don't see why ITK is moving to github? > > > On Tue, Aug 1, 2017 at 11:22 AM, Cory Quammen wrote: > > On Tue, Aug 1, 2017 at 11:13 AM, Bill Lorensen > > wrote: > >> > >> Cory, > >> I think you meant to say VTK has no plans to move to GitHub. > > > > > > Yes indeed, thanks for catching ("Hu" and "La" aren't even that close on the > > keyboard). > > > > VTK is firmly ensconced in GitLab, and not moving to GitHub. > > > >> > >> On Aug 1, 2017 10:27 AM, "Cory Quammen" wrote: > >>> > >>> I don't have much of an opinion on moving ITK to GitHub, but I'd like to > >>> address some things Andras mentioned about GitLab and VTK. > >>> > >>>> > >>>> About GitHub/Kitware GitLab: > >>>> > >>>> I heard that VTK is going to move to GitHub, too. Maybe I misunderstood, > >>>> but make sure to talk to VTK folks before considering moving to GitLab. > >>> > >>> > >>> I am not aware of any plans to move VTK to GitLab or even any discussion > >>> of doing so. > >>> > >>>> > >>>> Anyway, as a very active user but only occasional contributor of VTK, I > >>>> find VTK GitLab quite frustrating due to that: > >>>> 1. It is slow. I heard that it's fast when accessed from inside Kitware > >>>> network, but most community members are outside. > >>> > >>> > >>> The first few versions were indeed a bit slow, but new updates come out > >>> regularly, and the speed is quite snappy. I use it both from within the > >>> Kitware network and outside the network and haven't noticed a difference. > >>> > >>>> > >>>> 2. I need to re-learn each time I use it: I review code, submit PR or > >>>> bug report once in every few months - and each time I need to spend 20-30 > >>>> minutes extra, just to find out how things work. > >>>> > >>>> > >>>> Andras > >>>> > >>>> -----Original Message----- > >>>> From: Community [mailto:community-bounces at itk.org] On Behalf Of Matt > >>>> McCormick > >>>> Sent: Monday, July 31, 2017 7:00 PM > >>>> To: Bill Lorensen > >>>> Cc: Insight-Users ; Hans Johnson > >>>> ; Insight Developers List > >>>> > >>>> Subject: Re: [ITK] [ITK-dev] [ITK-users] Migration to GitHub > >>>> > >>>> I have followed VTK's migration to GitLab, and Kitware has done an > >>>> excellent job with it. That said, I still think GitHub is the better choice > >>>> for ITK. Also, the technical and social situation has changed in the time > >>>> since VTK moved to GitLab. > >>>> > >>>> I think the key factor is "community", and GitHub has the open source > >>>> community. > >>>> > >>>> On Mon, Jul 31, 2017 at 6:42 PM, Bill Lorensen > >>>> wrote: > >>>> > Vtk moved to GitLab. Have you checked with the Kitware folks to see > >>>> > why they didn't use gitlab? For me, either github or gitlab is great. > >>>> > > >>>> > On Jul 31, 2017 6:03 PM, "Johnson, Hans J" > >>>> > wrote: > >>>> >> > >>>> >> 1000 x +1 > >>>> >> > >>>> >> I enthusiastically support this proposal. > >>>> >> > >>>> >> Hans > >>>> >> > >>>> >> > >>>> >> On 7/31/17, 4:57 PM, "Insight-users on behalf of Jim Miller" > >>>> >> > >>>> >> wrote: > >>>> >> > >>>> >> +1 > >>>> >> > >>>> >> Jim > >>>> >> > >>>> >> > On Jul 31, 2017, at 5:07 PM, Matt McCormick > >>>> >> wrote: > >>>> >> > > >>>> >> > Hi folks, > >>>> >> > > >>>> >> > We are considering migration of ITK's software process to > >>>> >> GitHub, and > >>>> >> > we would like your feedback. > >>>> >> > > >>>> >> > As an open-source, community-driven project, mechanisms to > >>>> >> communicate > >>>> >> > and interact with the community are a high priority for ITK. > >>>> >> > Contributing should be as easy as possible. Increasingly over > >>>> >> the past > >>>> >> > many years, GitHub has become the de facto place to interact > >>>> >> for open > >>>> >> > source development. It is now a hub for: > >>>> >> > > >>>> >> > Microsoft > >>>> >> > Facebook > >>>> >> > Google > >>>> >> > The Scientific Python Community > >>>> >> > The 3D Slicer Community > >>>> >> > > >>>> >> > Our InsightSoftwareConsortium GitHub organization [1] already > >>>> >> has 67 > >>>> >> > people in it and 74 repositories. There are hundreds of > >>>> >> projects that > >>>> >> > depend on ITK on GitHub. Many ITK developers are familiar with > >>>> >> the > >>>> >> > development process on GitHub (i.e the pull request process) > >>>> >> and > >>>> >> > already have an account on this platform. There are also > >>>> >> advantages to > >>>> >> > linking issues and commits with other projects and > >>>> >> repositories. > >>>> >> Since > >>>> >> > ITK thrives on the open-source development idea, everyone who > >>>> >> wants to > >>>> >> > help the project should be able to contribute, and therefore it > >>>> >> should > >>>> >> > be as easy as possible to start participating in the community. > >>>> >> > > >>>> >> > Recently, GitHub's code review capabilities have greatly > >>>> >> improved, > >>>> >> > which make it more feasible to coordinate contributions for a > >>>> >> large > >>>> >> > project like ITK. And, there are many existing > >>>> >> GitHub-integrated > >>>> >> > services that we can leverage. > >>>> >> > > >>>> >> > Thanks to resources from the National Library of Medicine and > >>>> >> > technological advances, it is now feasible to migrate the > >>>> >> project's > >>>> >> > software process to GitHub. There are many infrastructural > >>>> >> aspects to > >>>> >> > the migration, and it would take multiple months to complete. > >>>> >> Please > >>>> >> > let us know your thoughts before we embark on the journey. > >>>> >> > > >>>> >> > > >>>> >> > [1] > >>>> >> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FInsightSoftwareConsortium&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=onq3vW0pCjrT8pDNShHXc4JkohBMBoHv1lxOD6Nkg4o%3D&reserved=0 > >>>> >> > _____________________________________ > >>>> >> > Powered by > >>>> >> https://na01.safelinks.protection.outlook.com/?url=www.kitware.com&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=TbmgQahvMJx3Czk56R8%2Bg3WKDWopBJkIpgnqkxx3xj4%3D&reserved=0 > >>>> >> > > >>>> >> > Visit other Kitware open-source projects at > >>>> >> > > >>>> 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https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo%2Finsight-developers&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=aJgjy9V6YWhdNpqDtQSNkBEfKEW6dNcKVW3C1fT%2FH9Q%3D&reserved=0 > >>>> _______________________________________________ > >>>> Community mailing list > >>>> Community at itk.org > >>>> > >>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo%2Fcommunity&data=02%7C01%7Classo%40queensu.ca%7C96f312d049d7448d6db208d4d867f888%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636371388439104668&sdata=7%2FDK5kxboSdWy9zTD2f%2FP8CqdebW%2B82BJZQXMFQfCOQ%3D&reserved=0 > >>>> _____________________________________ > >>>> Powered by www.kitware.com > >>>> > >>>> Visit other Kitware open-source projects at > >>>> http://www.kitware.com/opensource/opensource.html > >>>> > >>>> Kitware offers ITK Training Courses, for more information visit: > >>>> http://www.kitware.com/products/protraining.php > >>>> > >>>> Please keep messages on-topic and check the ITK FAQ at: > >>>> http://www.itk.org/Wiki/ITK_FAQ > >>>> > >>>> Follow this link to subscribe/unsubscribe: > >>>> http://public.kitware.com/mailman/listinfo/insight-users > >>> > >>> > >>> > >>> > >>> -- > >>> Cory Quammen > >>> Staff R&D Engineer > >>> Kitware, Inc. > > > > > > > > > > -- > > Cory Quammen > > Staff R&D Engineer > > Kitware, Inc. > > > > -- > Unpaid intern in BillsBasement at noware dot com > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > -- Unpaid intern in BillsBasement at noware dot com From blowekamp at mail.nih.gov Tue Aug 1 11:59:35 2017 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Tue, 1 Aug 2017 15:59:35 +0000 Subject: [ITK-users] [ITK] Extracting image coordinate transform matrix In-Reply-To: <1501602458344-38549.post@n7.nabble.com> References: <1501590104563-38537.post@n7.nabble.com> <1501602458344-38549.post@n7.nabble.com> Message-ID: <86E5161A-FBC7-4ED6-8A76-94B4DC01B75F@mail.nih.gov> Ramana, Have you looked at the InvertDisplacementFieldImageFilter? https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1InvertDisplacementFieldImageFilter.html It was my understanding that the above is the preferred inversion algorithm. I actually have the wrapping code for FixedPointInverseDisplacementFieldImageFilter sitting around. I can make this available if needed. However, documentation improvements need to be made to these classes to clarify the differences. Please add a feature request on Github if this is something you really need: https://github.com/SimpleITK/SimpleITK/issues Thanks, Brad On 8/1/17, 11:48 AM, "Ramana C" wrote: Hi Ziv, Thanks very much, that's exactly what I needed. I needed the matrix for some code I'm writing to invert a displacement field. The fixed-point deformation field inversion isn't included in the SimpleITK python libraries, so I'm going about implementing it myself. Anyway, thanks very much for the help again! Ramana -- View this message in context: http://itk-users.7.n7.nabble.com/Extracting-image-coordinate-transform-matrix-tp38537p38549.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community From andx_roo at live.com Tue Aug 1 14:15:11 2017 From: andx_roo at live.com (Andaharoo) Date: Tue, 1 Aug 2017 11:15:11 -0700 (MST) Subject: [ITK-users] Problems Using GPU Filters In-Reply-To: References: <1498789176254-7590036.post@n2.nabble.com> <1501002308962-7590057.post@n2.nabble.com> Message-ID: <1501611311517-7590114.post@n2.nabble.com> Yeah I figured this out and it allowed me to use GPUGradientAnisotropicImageFilter. I was using GPUGradientAnisotropicImageFilter and using GPUGradientAnisotropicImageFilter fixed it. But I can't seem to use any other GPU filters unless I apply them after the gradient anisotropic? It's not converting and I'm unable to setup my readers to use itkGPUImage so I can't do GPUGradientAnisotropicImageFilter Pipeline: vtkImage -> vtktoitk filter -> gpu filter -> itktovtkfilter -> Also does GPUGradientAnisotropicImageFilter differ from GPUGradientAnisotropicImageFilter because the output of a gpu filter can go back to a cpu filter? This is what made me initially think I would use GPUGradientAnisotropicImageFilter Thanks -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Problems-Using-GPU-Filters-tp7590036p7590114.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From matt.mccormick at kitware.com Tue Aug 1 17:13:40 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 1 Aug 2017 17:13:40 -0400 Subject: [ITK-users] Problems Using GPU Filters In-Reply-To: <1501611311517-7590114.post@n2.nabble.com> References: <1498789176254-7590036.post@n2.nabble.com> <1501002308962-7590057.post@n2.nabble.com> <1501611311517-7590114.post@n2.nabble.com> Message-ID: Hi Andaharoo, As a rule of thumb, use itk::GPUImage with itk::GPU*ImageFilter. This ensures that the input image can be pass from CPU to GPU memory and the output image can be passed from GPU to CPU memory if required. Hope this helps, Matt On Tue, Aug 1, 2017 at 2:15 PM, Andaharoo wrote: > Yeah I figured this out and it allowed me to use > GPUGradientAnisotropicImageFilter. > I was using GPUGradientAnisotropicImageFilter and using > GPUGradientAnisotropicImageFilter fixed it. > > But I can't seem to use any other GPU filters unless I apply them after the > gradient anisotropic? It's not converting and I'm unable to setup my readers > to use itkGPUImage so I can't do > GPUGradientAnisotropicImageFilter > > Pipeline: > vtkImage -> vtktoitk filter -> gpu filter -> itktovtkfilter -> > > Also does > GPUGradientAnisotropicImageFilter differ from > GPUGradientAnisotropicImageFilter because the output > of a gpu filter can go back to a cpu filter? This is what made me initially > think I would use GPUGradientAnisotropicImageFilter > > Thanks > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Problems-Using-GPU-Filters-tp7590036p7590114.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Aug 1 17:23:59 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 1 Aug 2017 17:23:59 -0400 Subject: [ITK-users] Cardiac Deformation using Segmentation and Registration of Ultrasound Images In-Reply-To: References: Message-ID: Hi Thanos, A few thoughts, - The ultrasound speckle can interfere with the segmentation -- itk::CurvatureAnisotropicDiffusionImageFilter is one approach, but the ITKAnisotropicDiffusionLBR filters can give better results [1]. - Active contour segmentation is also available in ITK. It works in 3D and it is fast. - One approach is to generate signed distance maps from the segmentations, then register the signed distance maps. - Another approach is to generate itk::PointSet's from the segmentation, the register the point sets with [2]. Hope this helps, Matt [1] https://github.com/InsightSoftwareConsortium/ITKAnisotropicDiffusionLBR [2] https://itk.org/Doxygen/html/classitk_1_1PointSetToPointSetMetricv4.html On Thu, Jul 27, 2017 at 8:08 AM, thanos thanos wrote: > Hello everyone, > > The past months I have been working on tasks of Segmentation and > Registration of 4D ultrasound images so I can eventually do a proper Cardiac > Deformation analysis. Unfortunately I am struggling on my own to solve these > problems so I still haven't found a proper workflow and this is why I am > posting here in case someone has a suggestion or a recommendation. > > For the acquisition of my data, a pig heart was placed inside a water tank > with the 4D transducer on the bottom of the tank (the apex of the heart was > about 5 cm from the transducer) and with around 50 volumes per second I > obtained images of 120x90x80, that after masking I ended up with volumes of > 75x70x52 (x,y,z). > > So far, I use Curvature Anisotropic Diffusion using the ITK libraries in > order to perform an automatic segmentation using Active Contours (with > Matlab). I filtered my data, mostly to assist my 2D segmentation algorithm, > which I perform slice by slice on the z axis. I obtain a 3D model using the > isosurfaces. > > Then I tried both the Demons registration and the Bsplines registration on > the 3D volumes. I tried both on the original (unsegmented) data and two > segmented volumes, but I can not say that I am quite satisfied with any of > the results. > > So my questions are the following : > 1) Is it necessary to perform segmentation before the registration since my > heart is placed in a water tank, so there are no other organs around? > 2) Should the registration be done on the filtered or the unfiltered data? > 3) I am not satisfied at all with my segmentation algorithm since active > contours are quite sensitive to noise and because of the nature of the data > I have to use different parameters for every 4-5 slices. Therefore I was > thinking to perform an almost manual segmentation on one volume and then use > registration for the segmentation of the rest (if that is necessary). So I > am now studying and trying to say if something like that is possible (and > especially on ITK). If someone knows something about it, I would be happy to > hear. > 4) What would be a proper number of grid points for my 75x70x52 images, when > using the B-Splines registration? > > I am sorry for the long post but I have been struggling for too long with > this problem and I would really appreciate any kind of help. > > Best regards, > Thanos > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > From matt.mccormick at kitware.com Tue Aug 1 17:29:45 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 1 Aug 2017 17:29:45 -0400 Subject: [ITK-users] Migration to GitHub In-Reply-To: <1190885272.3593749.1501546053079@mail.yahoo.com> References: <1190885272.3593749.1501546053079@mail.yahoo.com> Message-ID: On Mon, Jul 31, 2017 at 8:07 PM, Nick Cullen wrote: > As a new user, I think this is a no brainer. > Thanks for the feedback, Nick. > > Along those lines, I'm not sure if this email-chain users list is the main > way the community asks questions (maybe I'm missing some other forum?) but > if so, that desperately should be updated. See PyTorch Forums > for an example of what some modern > open-source software tools use. It's built with https://github.com/ > discourse/discourse which lets you embed code and has good search > capabilities. > > We are investigating Discourse deployment. > > PyTorch Forums > A place to discuss PyTorch code, issues, install, research > > > > > On Monday, July 31, 2017 7:55 PM, Bill Lorensen > wrote: > > > Here are comments I made 3 years ago on the VTK discussion about > changing VTK's code review process. > ------------- > > Berk, > > I think we need to reach out to potential developers. Especially those > outside of Kitware(and their paying customers) and the long term VTK > developers outside Kitware. Those communities can adapt to anything. > We need to focus on is how can we can attract new developers. In the > past, new processes were adopted and adapted by Kitware, their > customers and hard core VTK developers with very little input from the > broader community of potential developers. > > ITK is going through the same issues but addressing the issues not > through process change. They are looking at outreach and better > documentation of the current process. Matt McCormick at Kitware has > been leading this effort. > > I think there are lots of non-process improvements possible. But I > don't have a silver bullet for attracting new developers. Perhaps VTK > is too old school for today's developers. Stuck with an old > architecture, old graphics architecture, old and complex languages. I > honestly don't know what the root causes are. If we only include the > old-timers in theses discussion then we will not attract a younger set > of devleopers. > > Bill > --------------- > > On Mon, Jul 31, 2017 at 5:07 PM, Matt McCormick > wrote: > > Hi folks, > > > > We are considering migration of ITK's software process to GitHub, and > > we would like your feedback. > > > > As an open-source, community-driven project, mechanisms to communicate > > and interact with the community are a high priority for ITK. > > Contributing should be as easy as possible. Increasingly over the past > > many years, GitHub has become the de facto place to interact for open > > source development. It is now a hub for: > > > > Microsoft > > Facebook > > Google > > The Scientific Python Community > > The 3D Slicer Community > > > > Our InsightSoftwareConsortium GitHub organization [1] already has 67 > > people in it and 74 repositories. There are hundreds of projects that > > depend on ITK on GitHub. Many ITK developers are familiar with the > > development process on GitHub (i.e the pull request process) and > > already have an account on this platform. There are also advantages to > > linking issues and commits with other projects and repositories. Since > > ITK thrives on the open-source development idea, everyone who wants to > > help the project should be able to contribute, and therefore it should > > be as easy as possible to start participating in the community. > > > > Recently, GitHub's code review capabilities have greatly improved, > > which make it more feasible to coordinate contributions for a large > > project like ITK. And, there are many existing GitHub-integrated > > services that we can leverage. > > > > Thanks to resources from the National Library of Medicine and > > technological advances, it is now feasible to migrate the project's > > software process to GitHub. There are many infrastructural aspects to > > the migration, and it would take multiple months to complete. Please > > let us know your thoughts before we embark on the journey. > > > > > > [1] https://github.com/InsightSoftwareConsortium > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > > -- > Unpaid intern in BillsBasement at noware dot com > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Tue Aug 1 17:30:31 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 1 Aug 2017 17:30:31 -0400 Subject: [ITK-users] [ITK-dev] [ITK] Migration to GitHub In-Reply-To: References: <2C7BD08F-FCCA-4477-8F62-D0935AC2B050@mail.nih.gov> Message-ID: On Tue, Aug 1, 2017 at 12:07 PM, Bill Lorensen wrote: > It's funny, VTK moved to gitlab to improve engagement with the VTK community. > > I really don't care which is picked. I picked github for the new VTK > Wiki Examples because I thought it would be better for the community. > I argued against vtk moving to gitlab but lost... > > BTW, the new VTK example site is here: > https://lorensen.github.io/VTKExamples/site/ This is fantastic! From sean at rogue-research.com Tue Aug 1 17:45:14 2017 From: sean at rogue-research.com (Sean McBride) Date: Tue, 1 Aug 2017 17:45:14 -0400 Subject: [ITK-users] [ITK] [ITK-dev] Migration to GitHub In-Reply-To: References: Message-ID: <20170801214514.1391365852@mail.rogue-research.com> On Tue, 1 Aug 2017 11:40:25 -0400, Francois Budin said: >As Matt mentioned, the main reason is because a lot of ITK users already >have Github accounts and are familiar with that environment. The idea is >really to make is as simple as possible for the community to contribute. >Using Gitlab would still require users to have an account on GitLab to push >patches. Most ITK users already have a Github account with their own >projects, and contributing to ITK just requires cloning the project and >creating a pull-request. The fact that many people are familiar with github and its workflow is indeed a good argument. But the "using Gitlab would still require users to have an account on GitLab" I think is no argument at all. Creating a GitLab account is a fast and easy one-time task, the browser can then remember your password, etc. Everyone is used to having a zillion accounts for all the zillion services we all use. Cheers, Sean From matt.mccormick at kitware.com Tue Aug 1 17:54:55 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 1 Aug 2017 17:54:55 -0400 Subject: [ITK-users] [ITK-dev] Migration to GitHub In-Reply-To: <20170731232003.1609494024@mail.rogue-research.com> References: <20170731232003.1609494024@mail.rogue-research.com> Message-ID: On Mon, Jul 31, 2017 at 7:20 PM, Sean McBride wrote: > On Mon, 31 Jul 2017 17:07:44 -0400, Matt McCormick said: > >>We are considering migration of ITK's software process to GitHub, and >>we would like your feedback. > > My 2 cents: > - I'd be happy to see a move away from gerrit. > - I'd prefer a move to a Kitware-hosted GitLab, like VTK did. > - GitHub is nice and all, but not itself open source. GitLab is open source. Better that the infrastructure of an open source project also be open source itself. The fact that GitHub is closed source is compelling. However, like our support for macOS and Windows, we may have to use a closed platform for pragmatic reasons. From matt.mccormick at kitware.com Tue Aug 1 17:59:37 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 1 Aug 2017 17:59:37 -0400 Subject: [ITK-users] [ITK] [ITK-dev] Migration to GitHub In-Reply-To: <20170801214514.1391365852@mail.rogue-research.com> References: <20170801214514.1391365852@mail.rogue-research.com> Message-ID: On Tue, Aug 1, 2017 at 5:45 PM, Sean McBride wrote: > On Tue, 1 Aug 2017 11:40:25 -0400, Francois Budin said: > >>As Matt mentioned, the main reason is because a lot of ITK users already >>have Github accounts and are familiar with that environment. The idea is >>really to make is as simple as possible for the community to contribute. >>Using Gitlab would still require users to have an account on GitLab to push >>patches. Most ITK users already have a Github account with their own >>projects, and contributing to ITK just requires cloning the project and >>creating a pull-request. > > The fact that many people are familiar with github and its workflow is indeed a good argument. > > But the "using Gitlab would still require users to have an account on GitLab" I think is no argument at all. Creating a GitLab account is a fast and easy one-time task, the browser can then remember your password, etc. Everyone is used to having a zillion accounts for all the zillion services we all use. Yes, this is true. We already have OAuth sign-in for Gerrit that uses GitHub credentials. But, the benefits come more from a familiarity with the user interface and deeper integrations like notifications, user and issue references, etc. From andx_roo at live.com Tue Aug 1 18:23:01 2017 From: andx_roo at live.com (Andaharoo) Date: Tue, 1 Aug 2017 15:23:01 -0700 (MST) Subject: [ITK-users] Problems Using GPU Filters In-Reply-To: References: <1498789176254-7590036.post@n2.nabble.com> <1501002308962-7590057.post@n2.nabble.com> <1501611311517-7590114.post@n2.nabble.com> Message-ID: <1501626181039-7590122.post@n2.nabble.com> I can't get the images to go from CPU to GPU on GPUMeanImageFilter, GPUBinaryThresholdImageFilter, and GPUDiscreteGaussianImageFilter. So I can't start my gpu pipeline with these filters. If I apply something like GPUGradientAnisotropicImageFilter (which does work) then I can apply the other filters confirming that it can go GPU to GPU but not CPU to GPU on those 3 filters. Do these 3 filters not support conversion? GPUInputImage::Pointer?inPtr = dynamic_cast(this->ProcessObject::GetInput(0)); inPtr was null when I debugged GPUMeanImageFilter. This line also doesn't make sense in terms of using an Image since it would just return null if you gave it an Image that wasn't allocated as a GPUImage. Unless the cpu image gets converted to a gpu image elsewhere beforehand? It seems as though only GPUInPlaceImageFilters work with CPU - GPU conversion for me? I can't quite understand the GPUInPlaceImageFilters source yet so I'm not so sure why GPUGradientAnisotropicImageFilter works. They are, of course, different in terms of how they manage memory. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Problems-Using-GPU-Filters-tp7590036p7590122.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From lasso at queensu.ca Tue Aug 1 20:50:53 2017 From: lasso at queensu.ca (Andras Lasso) Date: Wed, 2 Aug 2017 00:50:53 +0000 Subject: [ITK-users] [ITK] Migration to GitHub In-Reply-To: References: <1190885272.3593749.1501546053079@mail.yahoo.com>, Message-ID: +1 for Discourse Slicer community switched from mailing list to Discourse about 4 months ago and it's awesome. It can do everything that a mailing list can do and of course much more. What I found particularly important: 1. You can discuss topics in detail, without worrying that it generates too much traffic and makes people leave the list (you can very easily subscribe/unsubscribe to categories, individual topics, etc depending on what you are interested in and how much time you have). 2. It turns a series of random discussions to an organized knowledge base (by allowing splitting, merging, renaming topics, fixing typos, applying nice formatting, etc.) As a large open-source project, ITK can get free hosting from Discourse. Andras From: Matt McCormick Sent: Tuesday, August 1, 2017 17:30 To: Nick Cullen Cc: insight-users at itk.org; Insight Developers List Subject: Re: [ITK] [ITK-users] Migration to GitHub On Mon, Jul 31, 2017 at 8:07 PM, Nick Cullen > wrote: As a new user, I think this is a no brainer. Thanks for the feedback, Nick. Along those lines, I'm not sure if this email-chain users list is the main way the community asks questions (maybe I'm missing some other forum?) but if so, that desperately should be updated. See PyTorch Forums for an example of what some modern open-source software tools use. It's built with https://github.com/discourse/discourse which lets you embed code and has good search capabilities. We are investigating Discourse deployment. PyTorch Forums A place to discuss PyTorch code, issues, install, research On Monday, July 31, 2017 7:55 PM, Bill Lorensen > wrote: Here are comments I made 3 years ago on the VTK discussion about changing VTK's code review process. ------------- Berk, I think we need to reach out to potential developers. Especially those outside of Kitware(and their paying customers) and the long term VTK developers outside Kitware. Those communities can adapt to anything. We need to focus on is how can we can attract new developers. In the past, new processes were adopted and adapted by Kitware, their customers and hard core VTK developers with very little input from the broader community of potential developers. ITK is going through the same issues but addressing the issues not through process change. They are looking at outreach and better documentation of the current process. Matt McCormick at Kitware has been leading this effort. I think there are lots of non-process improvements possible. But I don't have a silver bullet for attracting new developers. Perhaps VTK is too old school for today's developers. Stuck with an old architecture, old graphics architecture, old and complex languages. I honestly don't know what the root causes are. If we only include the old-timers in theses discussion then we will not attract a younger set of devleopers. Bill --------------- On Mon, Jul 31, 2017 at 5:07 PM, Matt McCormick > wrote: > Hi folks, > > We are considering migration of ITK's software process to GitHub, and > we would like your feedback. > > As an open-source, community-driven project, mechanisms to communicate > and interact with the community are a high priority for ITK. > Contributing should be as easy as possible. Increasingly over the past > many years, GitHub has become the de facto place to interact for open > source development. It is now a hub for: > > Microsoft > Facebook > Google > The Scientific Python Community > The 3D Slicer Community > > Our InsightSoftwareConsortium GitHub organization [1] already has 67 > people in it and 74 repositories. There are hundreds of projects that > depend on ITK on GitHub. Many ITK developers are familiar with the > development process on GitHub (i.e the pull request process) and > already have an account on this platform. There are also advantages to > linking issues and commits with other projects and repositories. Since > ITK thrives on the open-source development idea, everyone who wants to > help the project should be able to contribute, and therefore it should > be as easy as possible to start participating in the community. > > Recently, GitHub's code review capabilities have greatly improved, > which make it more feasible to coordinate contributions for a large > project like ITK. And, there are many existing GitHub-integrated > services that we can leverage. > > Thanks to resources from the National Library of Medicine and > technological advances, it is now feasible to migrate the project's > software process to GitHub. There are many infrastructural aspects to > the migration, and it would take multiple months to complete. Please > let us know your thoughts before we embark on the journey. > > > [1] https://github.com/InsightSoftwareConsortium > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From rc1515 at ic.ac.uk Wed Aug 2 06:38:11 2017 From: rc1515 at ic.ac.uk (Ramana C) Date: Wed, 2 Aug 2017 03:38:11 -0700 (MST) Subject: [ITK-users] [ITK] Extracting image coordinate transform matrix In-Reply-To: <86E5161A-FBC7-4ED6-8A76-94B4DC01B75F@mail.nih.gov> References: <1501590104563-38537.post@n7.nabble.com> <1501602458344-38549.post@n7.nabble.com> <86E5161A-FBC7-4ED6-8A76-94B4DC01B75F@mail.nih.gov> Message-ID: <1501670291371-38563.post@n7.nabble.com> Hi Brad, I have actually tried using that, but the results were pretty poor. Making the wrapping available would be very helpful, if at all possible. I'll put in a feature request. Thanks very much for your help. Ramana -- View this message in context: http://itk-users.7.n7.nabble.com/Extracting-image-coordinate-transform-matrix-tp38537p38563.html Sent from the ITK - Users mailing list archive at Nabble.com. From jonasteuwen at gmail.com Wed Aug 2 12:49:28 2017 From: jonasteuwen at gmail.com (Jonas Teuwen) Date: Wed, 2 Aug 2017 18:49:28 +0200 Subject: [ITK-users] Problem with SliceBySliceImageFilter, only applied on the first slice Message-ID: Hi all, Using the SliceBySliceImageFilter as in the Insight Journal http://www.insight-journal.org/browse/publication/133 works. However, when I build a pipeline such as https://itk.org/Doxygen46/html/Filtering_2CompositeFilterExample_8cxx-example.html and plug that in the above example, the output has the right size, but the output is the filter applied to the first slice and copied to all the others. What would be the appropriate way to debug this? Best, Jonas -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Wed Aug 2 13:38:06 2017 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Wed, 2 Aug 2017 17:38:06 +0000 Subject: [ITK-users] Problem with SliceBySliceImageFilter, only applied on the first slice In-Reply-To: References: Message-ID: Hello, Does using the that example filter cause the problem? There are many subtle problems that a composite filter implementation can have. These include not properly grafting the input or output in the GenerateData method. Also issues with the incorrect modified times not being modified or being modified too often are common. The example illustrates having the mini-pipeline filter of the composite filter as member variables. This can make things more problematic when executing a filter multiple times. I prefer to create the individual filters in the GenerateData method, as it generally has been more reliable, and may side step some issues related to the modified times. The ways to debug a complex pipeline include: interactively using a debug to set up break points, add a number of Event call backs to monitor the execution of different filters and using the PipelineMonitorImageFilter to record the steps in a pipeline execution. Your first steps may be to determine if the composite filter is being executed for each slice, and if it is being executed then is the internal mini-pipeline being executed or do the modified time indicate it is up to date?. HTH, Brad From: Jonas Teuwen Date: Wednesday, August 2, 2017 at 12:51 PM To: "insight-users at itk.org" Subject: [ITK-users] Problem with SliceBySliceImageFilter, only applied on the first slice Hi all, Using the SliceBySliceImageFilter as in the Insight Journal http://www.insight-journal.org/browse/publication/133 works. However, when I build a pipeline such as https://itk.org/Doxygen46/html/Filtering_2CompositeFilterExample_8cxx-example.html and plug that in the above example, the output has the right size, but the output is the filter applied to the first slice and copied to all the others. What would be the appropriate way to debug this? Best, Jonas -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonasteuwen at gmail.com Wed Aug 2 14:08:03 2017 From: jonasteuwen at gmail.com (Jonas Teuwen) Date: Wed, 2 Aug 2017 20:08:03 +0200 Subject: [ITK-users] Problem with SliceBySliceImageFilter, only applied on the first slice In-Reply-To: References: Message-ID: Thank Brad, Following your suggestion to move the creation of the invidual filters to the GenerateData method, it works. I assume I will understand why once, I get more experience with ITK. Best, Jonas On Wed, Aug 2, 2017 at 7:38 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] < blowekamp at mail.nih.gov> wrote: > Hello, > > > > Does using the that example filter cause the problem? > > > > There are many subtle problems that a composite filter implementation can > have. These include not properly grafting the input or output in the > GenerateData method. Also issues with the incorrect modified times not > being modified or being modified too often are common. The example > illustrates having the mini-pipeline filter of the composite filter as > member variables. This can make things more problematic when executing a > filter multiple times. I prefer to create the individual filters in the > GenerateData method, as it generally has been more reliable, and may side > step some issues related to the modified times. > > > > The ways to debug a complex pipeline include: interactively using a debug > to set up break points, add a number of Event call backs to monitor the > execution of different filters and using the PipelineMonitorImageFilter to > record the steps in a pipeline execution. > > > > Your first steps may be to determine if the composite filter is being > executed for each slice, and if it is being executed then is the internal > mini-pipeline being executed or do the modified time indicate it is up to > date?. > > > > HTH, > > Brad > > > > > > *From: *Jonas Teuwen > *Date: *Wednesday, August 2, 2017 at 12:51 PM > *To: *"insight-users at itk.org" > *Subject: *[ITK-users] Problem with SliceBySliceImageFilter, only applied > on the first slice > > > > Hi all, > > > > Using the SliceBySliceImageFilter as in the Insight Journal > http://www.insight-journal.org/browse/publication/133 works. > > > > However, when I build a pipeline such as https://itk.org/Doxygen46/ > html/Filtering_2CompositeFilterExample_8cxx-example.html and plug that in > the above example, the output has the right size, but the output is the > filter applied to the first slice and copied to all the others. > > > > What would be the appropriate way to debug this? > > > > Best, > > Jonas > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pedromorais-17 at hotmail.com Wed Aug 2 14:17:00 2017 From: pedromorais-17 at hotmail.com (Pedro Morais) Date: Wed, 2 Aug 2017 11:17:00 -0700 (MST) Subject: [ITK-users] Problem with GPUNeighborhoodOperator Message-ID: <1501697820794-7590128.post@n2.nabble.com> Hi all, I'm testing the gpu version of the neighborhood operator (itkGPUNeighborhoodOperatorImageFilter) to perform a gaussian derivative of a 3D image. I started by running the test example provided in ITK ( itkGPUNeighborhoodOperatorImageFilterTest.cxx) and it worked perfectly for the default parameters. However, I simply changed the SetDirection option from '0' to '1' (line 65, 'oper->SetDirection(1)'), and the result is a blank image (all zeros). I have created a similar pipeline but using the CPU version and it worked. Does anyone has an idea of what error is? Does itk-GPU allows the application of these filters in directions other than zero? Thanks in advance. Best Regards, Pedro -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Problem-with-GPUNeighborhoodOperator-tp7590128.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From pablo.hernandez.cerdan at outlook.com Wed Aug 2 20:29:39 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Thu, 3 Aug 2017 00:29:39 +0000 Subject: [ITK-users] [ITK] Recommended approach for cross-platform deploying ITK+Vtk+Qt5 In-Reply-To: References: Message-ID: Hi Matt, this is super helpful. I created a Dockerfie with all the dependencies, but I used Ubuntu 16.04 as base... so, I should compile with an older glib... I will definitely check AppLauncher. Thanks! Pablo On Tue, Aug 1, 2017 at 2:36 AM, matt.mccormick at kitware.com > wrote: Hi Pablo, Good questions -- C++ ITK/VTK/Qt package development on GitHub CI services is non-trivial. A common issue is timeout's, and a strategy is to use pre-built binaries of ITK/VTK/Qt. Regarding Linux package development, CircleCI is recommended with a custom Docker image that has ITK / VTK / Qt pre-built. Since glibc is forward compatible but not backwards compatible, a base image that uses the oldest version of glibc will generate the most compatible image. For many projects, we use CentOS 5 with a newer GCC, but I think only Qt4 can be built with this and not Qt5. The build can be generated on one Linux Docker image for glibc purposes and tested on another that provides the graphical context. See the CommonTK AppLauncher configuration as an example [1]. This uses the thewtex/opengl Docker image [2] to provide a portable, reproducible, CPU-based graphical testing environment [2]. The CTK AppLauncher is also of interest as an alternative to windowsqtdeploy, etc. It is cross-platform, and provides the setup to use shared libraries and avoid Qt LGPL licensing issues. For Windows builds, the dockcross/windows-x64 (uses MXE/MinGW-x64) image could work nicely. A derived image that builds the MXE packages for ITK / VTK / Qt could be created [3]. Since dockcross also comes with WINE for testing, it may also be possible to use thewtex/opengl for testing on CircleCI (although I have never tried this). For macOS builds, TravisCI has Homebrew installed on their images, and ITK / VTK / Qt can be installed via Homebrew [4]. HTH, Matt [1] https://github.com/commontk/AppLauncher/blob/5b592f1baaa7dd41d68e1cd56a2a82e298196ebe/circle.yml [2] https://github.com/thewtex/docker-opengl [3] http://mxe.cc/ [4] https://blog.kitware.com/kitware-packages-on-os-x-with-homebrew/ On Sun, Jul 30, 2017 at 8:02 AM, Andras Lasso > wrote: > Currently, Slicer does not use AppVeyor for continuous integration on > Windows. Also, the full test suite of Slicer takes several hours to run, so > CircleCI only checks for build errors. > > > > Andras > > > > From: Pablo Hern?ndez > Sent: Sunday, July 30, 2017 6:58 > To: Insight-users > Subject: [ITK] [ITK-users] Recommended approach for cross-platform deploying > ITK+Vtk+Qt5 > > > > Hi, > I wonder what is the recommended approach for deploying a cross-platform > application involving ITK+Vtk+Qt nowadays with all the available tools: > docker containers, travis-ci, appveyor, circle-ci etc. > > Is it still recommended to create a SuperBuild with all your dependencies as > ExternalProjects in CMake? How do you reduce the time it takes to build? > The build time for all my dependencies (Vtk (with qt5), ITK, boost) plus my > small app is surpassing the 60min limit in both, AppVeyor and Travis-CI. To > alleviate this, do you use docker?. > > My main concern is Windows, I have seen that @thewtex and @jcfr have a repo > with closs-platform buildings ( https://github.com/dockcross/dockcross ), > there is a Windows64 there with Mingw that might help. I have no idea if I > can generate windows binaries from AppVeyor using docker, or instead, I > generate them using that docker image with Wine+MinGw in Travis-CI. > > Instead of CPack from CMake I have been thinking to use windowsqtdeploy, > linuxqtdeploy from Qt... > > I have been looking to Slicer source code to see how they are doing it, and > it seems super structured, but not 100% sure how they generate their nightly > packages ( I guess it involves these docker images: > https://github.com/thewtex/SlicerDocker, but also in Windows?) > > Maybe this is the not best forum to ask, but if you have any recommendations > for deploying a small GUI app based on ITK, I will be extremely grateful to > hear them. Thanks! > > Cheers, > Pablo > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pablo.hernandez.cerdan at outlook.com Wed Aug 2 20:29:41 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Thu, 3 Aug 2017 00:29:41 +0000 Subject: [ITK-users] [ITK] Recommended approach for cross-platform deploying ITK+Vtk+Qt5 In-Reply-To: References: Message-ID: Hi Matt, this is super helpful. I created a Dockerfie with all the dependencies, but I used Ubuntu 16.04 as base... so, I should compile with an older glib... I will definitely check AppLauncher. Thanks! Pablo On Tue, Aug 1, 2017 at 2:36 AM, matt.mccormick at kitware.com > wrote: Hi Pablo, Good questions -- C++ ITK/VTK/Qt package development on GitHub CI services is non-trivial. A common issue is timeout's, and a strategy is to use pre-built binaries of ITK/VTK/Qt. Regarding Linux package development, CircleCI is recommended with a custom Docker image that has ITK / VTK / Qt pre-built. Since glibc is forward compatible but not backwards compatible, a base image that uses the oldest version of glibc will generate the most compatible image. For many projects, we use CentOS 5 with a newer GCC, but I think only Qt4 can be built with this and not Qt5. The build can be generated on one Linux Docker image for glibc purposes and tested on another that provides the graphical context. See the CommonTK AppLauncher configuration as an example [1]. This uses the thewtex/opengl Docker image [2] to provide a portable, reproducible, CPU-based graphical testing environment [2]. The CTK AppLauncher is also of interest as an alternative to windowsqtdeploy, etc. It is cross-platform, and provides the setup to use shared libraries and avoid Qt LGPL licensing issues. For Windows builds, the dockcross/windows-x64 (uses MXE/MinGW-x64) image could work nicely. A derived image that builds the MXE packages for ITK / VTK / Qt could be created [3]. Since dockcross also comes with WINE for testing, it may also be possible to use thewtex/opengl for testing on CircleCI (although I have never tried this). For macOS builds, TravisCI has Homebrew installed on their images, and ITK / VTK / Qt can be installed via Homebrew [4]. HTH, Matt [1] https://github.com/commontk/AppLauncher/blob/5b592f1baaa7dd41d68e1cd56a2a82e298196ebe/circle.yml [2] https://github.com/thewtex/docker-opengl [3] http://mxe.cc/ [4] https://blog.kitware.com/kitware-packages-on-os-x-with-homebrew/ On Sun, Jul 30, 2017 at 8:02 AM, Andras Lasso > wrote: > Currently, Slicer does not use AppVeyor for continuous integration on > Windows. Also, the full test suite of Slicer takes several hours to run, so > CircleCI only checks for build errors. > > > > Andras > > > > From: Pablo Hern?ndez > Sent: Sunday, July 30, 2017 6:58 > To: Insight-users > Subject: [ITK] [ITK-users] Recommended approach for cross-platform deploying > ITK+Vtk+Qt5 > > > > Hi, > I wonder what is the recommended approach for deploying a cross-platform > application involving ITK+Vtk+Qt nowadays with all the available tools: > docker containers, travis-ci, appveyor, circle-ci etc. > > Is it still recommended to create a SuperBuild with all your dependencies as > ExternalProjects in CMake? How do you reduce the time it takes to build? > The build time for all my dependencies (Vtk (with qt5), ITK, boost) plus my > small app is surpassing the 60min limit in both, AppVeyor and Travis-CI. To > alleviate this, do you use docker?. > > My main concern is Windows, I have seen that @thewtex and @jcfr have a repo > with closs-platform buildings ( https://github.com/dockcross/dockcross ), > there is a Windows64 there with Mingw that might help. I have no idea if I > can generate windows binaries from AppVeyor using docker, or instead, I > generate them using that docker image with Wine+MinGw in Travis-CI. > > Instead of CPack from CMake I have been thinking to use windowsqtdeploy, > linuxqtdeploy from Qt... > > I have been looking to Slicer source code to see how they are doing it, and > it seems super structured, but not 100% sure how they generate their nightly > packages ( I guess it involves these docker images: > https://github.com/thewtex/SlicerDocker, but also in Windows?) > > Maybe this is the not best forum to ask, but if you have any recommendations > for deploying a small GUI app based on ITK, I will be extremely grateful to > hear them. Thanks! > > Cheers, > Pablo > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pablo.hernandez.cerdan at outlook.com Wed Aug 2 20:29:45 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Thu, 3 Aug 2017 00:29:45 +0000 Subject: [ITK-users] [ITK] Recommended approach for cross-platform deploying ITK+Vtk+Qt5 In-Reply-To: References: Message-ID: Hi Matt, this is super helpful. I created a Dockerfie with all the dependencies, but I used Ubuntu 16.04 as base... so, I should compile with an older glib... I will definitely check AppLauncher. Thanks! Pablo On Tue, Aug 1, 2017 at 2:36 AM, matt.mccormick at kitware.com > wrote: Hi Pablo, Good questions -- C++ ITK/VTK/Qt package development on GitHub CI services is non-trivial. A common issue is timeout's, and a strategy is to use pre-built binaries of ITK/VTK/Qt. Regarding Linux package development, CircleCI is recommended with a custom Docker image that has ITK / VTK / Qt pre-built. Since glibc is forward compatible but not backwards compatible, a base image that uses the oldest version of glibc will generate the most compatible image. For many projects, we use CentOS 5 with a newer GCC, but I think only Qt4 can be built with this and not Qt5. The build can be generated on one Linux Docker image for glibc purposes and tested on another that provides the graphical context. See the CommonTK AppLauncher configuration as an example [1]. This uses the thewtex/opengl Docker image [2] to provide a portable, reproducible, CPU-based graphical testing environment [2]. The CTK AppLauncher is also of interest as an alternative to windowsqtdeploy, etc. It is cross-platform, and provides the setup to use shared libraries and avoid Qt LGPL licensing issues. For Windows builds, the dockcross/windows-x64 (uses MXE/MinGW-x64) image could work nicely. A derived image that builds the MXE packages for ITK / VTK / Qt could be created [3]. Since dockcross also comes with WINE for testing, it may also be possible to use thewtex/opengl for testing on CircleCI (although I have never tried this). For macOS builds, TravisCI has Homebrew installed on their images, and ITK / VTK / Qt can be installed via Homebrew [4]. HTH, Matt [1] https://github.com/commontk/AppLauncher/blob/5b592f1baaa7dd41d68e1cd56a2a82e298196ebe/circle.yml [2] https://github.com/thewtex/docker-opengl [3] http://mxe.cc/ [4] https://blog.kitware.com/kitware-packages-on-os-x-with-homebrew/ On Sun, Jul 30, 2017 at 8:02 AM, Andras Lasso > wrote: > Currently, Slicer does not use AppVeyor for continuous integration on > Windows. Also, the full test suite of Slicer takes several hours to run, so > CircleCI only checks for build errors. > > > > Andras > > > > From: Pablo Hern?ndez > Sent: Sunday, July 30, 2017 6:58 > To: Insight-users > Subject: [ITK] [ITK-users] Recommended approach for cross-platform deploying > ITK+Vtk+Qt5 > > > > Hi, > I wonder what is the recommended approach for deploying a cross-platform > application involving ITK+Vtk+Qt nowadays with all the available tools: > docker containers, travis-ci, appveyor, circle-ci etc. > > Is it still recommended to create a SuperBuild with all your dependencies as > ExternalProjects in CMake? How do you reduce the time it takes to build? > The build time for all my dependencies (Vtk (with qt5), ITK, boost) plus my > small app is surpassing the 60min limit in both, AppVeyor and Travis-CI. To > alleviate this, do you use docker?. > > My main concern is Windows, I have seen that @thewtex and @jcfr have a repo > with closs-platform buildings ( https://github.com/dockcross/dockcross ), > there is a Windows64 there with Mingw that might help. I have no idea if I > can generate windows binaries from AppVeyor using docker, or instead, I > generate them using that docker image with Wine+MinGw in Travis-CI. > > Instead of CPack from CMake I have been thinking to use windowsqtdeploy, > linuxqtdeploy from Qt... > > I have been looking to Slicer source code to see how they are doing it, and > it seems super structured, but not 100% sure how they generate their nightly > packages ( I guess it involves these docker images: > https://github.com/thewtex/SlicerDocker, but also in Windows?) > > Maybe this is the not best forum to ask, but if you have any recommendations > for deploying a small GUI app based on ITK, I will be extremely grateful to > hear them. Thanks! > > Cheers, > Pablo > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pablo.hernandez.cerdan at outlook.com Wed Aug 2 20:29:51 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Thu, 3 Aug 2017 00:29:51 +0000 Subject: [ITK-users] [ITK] Recommended approach for cross-platform deploying ITK+Vtk+Qt5 In-Reply-To: References: Message-ID: Hi Matt, this is super helpful. I created a Dockerfie with all the dependencies, but I used Ubuntu 16.04 as base... so, I should compile with an older glib... I will definitely check AppLauncher. Thanks! Pablo On Tue, Aug 1, 2017 at 2:36 AM, matt.mccormick at kitware.com > wrote: Hi Pablo, Good questions -- C++ ITK/VTK/Qt package development on GitHub CI services is non-trivial. A common issue is timeout's, and a strategy is to use pre-built binaries of ITK/VTK/Qt. Regarding Linux package development, CircleCI is recommended with a custom Docker image that has ITK / VTK / Qt pre-built. Since glibc is forward compatible but not backwards compatible, a base image that uses the oldest version of glibc will generate the most compatible image. For many projects, we use CentOS 5 with a newer GCC, but I think only Qt4 can be built with this and not Qt5. The build can be generated on one Linux Docker image for glibc purposes and tested on another that provides the graphical context. See the CommonTK AppLauncher configuration as an example [1]. This uses the thewtex/opengl Docker image [2] to provide a portable, reproducible, CPU-based graphical testing environment [2]. The CTK AppLauncher is also of interest as an alternative to windowsqtdeploy, etc. It is cross-platform, and provides the setup to use shared libraries and avoid Qt LGPL licensing issues. For Windows builds, the dockcross/windows-x64 (uses MXE/MinGW-x64) image could work nicely. A derived image that builds the MXE packages for ITK / VTK / Qt could be created [3]. Since dockcross also comes with WINE for testing, it may also be possible to use thewtex/opengl for testing on CircleCI (although I have never tried this). For macOS builds, TravisCI has Homebrew installed on their images, and ITK / VTK / Qt can be installed via Homebrew [4]. HTH, Matt [1] https://github.com/commontk/AppLauncher/blob/5b592f1baaa7dd41d68e1cd56a2a82e298196ebe/circle.yml [2] https://github.com/thewtex/docker-opengl [3] http://mxe.cc/ [4] https://blog.kitware.com/kitware-packages-on-os-x-with-homebrew/ On Sun, Jul 30, 2017 at 8:02 AM, Andras Lasso > wrote: > Currently, Slicer does not use AppVeyor for continuous integration on > Windows. Also, the full test suite of Slicer takes several hours to run, so > CircleCI only checks for build errors. > > > > Andras > > > > From: Pablo Hern?ndez > Sent: Sunday, July 30, 2017 6:58 > To: Insight-users > Subject: [ITK] [ITK-users] Recommended approach for cross-platform deploying > ITK+Vtk+Qt5 > > > > Hi, > I wonder what is the recommended approach for deploying a cross-platform > application involving ITK+Vtk+Qt nowadays with all the available tools: > docker containers, travis-ci, appveyor, circle-ci etc. > > Is it still recommended to create a SuperBuild with all your dependencies as > ExternalProjects in CMake? How do you reduce the time it takes to build? > The build time for all my dependencies (Vtk (with qt5), ITK, boost) plus my > small app is surpassing the 60min limit in both, AppVeyor and Travis-CI. To > alleviate this, do you use docker?. > > My main concern is Windows, I have seen that @thewtex and @jcfr have a repo > with closs-platform buildings ( https://github.com/dockcross/dockcross ), > there is a Windows64 there with Mingw that might help. I have no idea if I > can generate windows binaries from AppVeyor using docker, or instead, I > generate them using that docker image with Wine+MinGw in Travis-CI. > > Instead of CPack from CMake I have been thinking to use windowsqtdeploy, > linuxqtdeploy from Qt... > > I have been looking to Slicer source code to see how they are doing it, and > it seems super structured, but not 100% sure how they generate their nightly > packages ( I guess it involves these docker images: > https://github.com/thewtex/SlicerDocker, but also in Windows?) > > Maybe this is the not best forum to ask, but if you have any recommendations > for deploying a small GUI app based on ITK, I will be extremely grateful to > hear them. Thanks! > > Cheers, > Pablo > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pablo.hernandez.cerdan at outlook.com Wed Aug 2 23:07:02 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Thu, 3 Aug 2017 03:07:02 +0000 Subject: [ITK-users] About the distribution of wrapped python for ITK external modules Message-ID: Hi there, It seems that the only way to install an external module is to build the ITK source with the option -DModule_xxx:BOOL=ON, but I was thinking... if the module is optional in the ITK source code and provides python wraps, is it available in the python itk package with `pip install itk`? In other words, do you wrap all the optional external modules when distributing the python itk or only the default modules? If the latter, would it be possible to create optional python packages for External Modules with the same deploying pipeline you use? Cheers, Pablo -------------- next part -------------- An HTML attachment was scrubbed... URL: From pablo.hernandez.cerdan at outlook.com Thu Aug 3 08:27:39 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Thu, 3 Aug 2017 12:27:39 +0000 Subject: [ITK-users] [ITK] About the distribution of wrapped python for ITK external modules In-Reply-To: References: Message-ID: Hi Bea, that's awesome, I will try to copy the configuration from the repo of your publication: https://github.com/InsightSoftwareConsortium/ITKTextureFeatures Thanks, Pablo On Fri, Aug 4, 2017 at 12:00 AM, Beatriz Paniagua > wrote: Hi Pablo, We have created external module specific python wraps for some applications. One example is the work that Matt M and JB Vimort did in the ITKTextureFilters. http://review.source.kitware.com/#/c/22531/ Hope that helps! Best, Bea On Wed, Aug 2, 2017 at 11:07 PM, Pablo Hern?ndez > wrote: Hi there, It seems that the only way to install an external module is to build the ITK source with the option -DModule_xxx:BOOL=ON, but I was thinking... if the module is optional in the ITK source code and provides python wraps, is it available in the python itk package with `pip install itk`? In other words, do you wrap all the optional external modules when distributing the python itk or only the default modules? If the latter, would it be possible to create optional python packages for External Modules with the same deploying pipeline you use? Cheers, Pablo _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -- Beatriz Paniagua, PhD Technical Leader Kitware, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From pablo.hernandez.cerdan at outlook.com Thu Aug 3 08:27:42 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Thu, 3 Aug 2017 12:27:42 +0000 Subject: [ITK-users] [ITK] About the distribution of wrapped python for ITK external modules In-Reply-To: References: Message-ID: Hi Bea, that's awesome, I will try to copy the configuration from the repo of your publication: https://github.com/InsightSoftwareConsortium/ITKTextureFeatures Thanks, Pablo On Fri, Aug 4, 2017 at 12:00 AM, Beatriz Paniagua > wrote: Hi Pablo, We have created external module specific python wraps for some applications. One example is the work that Matt M and JB Vimort did in the ITKTextureFilters. http://review.source.kitware.com/#/c/22531/ Hope that helps! Best, Bea On Wed, Aug 2, 2017 at 11:07 PM, Pablo Hern?ndez > wrote: Hi there, It seems that the only way to install an external module is to build the ITK source with the option -DModule_xxx:BOOL=ON, but I was thinking... if the module is optional in the ITK source code and provides python wraps, is it available in the python itk package with `pip install itk`? In other words, do you wrap all the optional external modules when distributing the python itk or only the default modules? If the latter, would it be possible to create optional python packages for External Modules with the same deploying pipeline you use? Cheers, Pablo _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -- Beatriz Paniagua, PhD Technical Leader Kitware, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Thu Aug 3 08:48:27 2017 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Thu, 3 Aug 2017 12:48:27 +0000 Subject: [ITK-users] [ITK] About the distribution of wrapped python for ITK external modules In-Reply-To: References: Message-ID: <5E37A920-455F-4CDB-BA6F-8E031D860C8D@mail.nih.gov> I would also look at the ITKModuleTemplate repository: https://github.com/InsightSoftwareConsortium/ITKModuleTemplate Brad From: Pablo Hern?ndez Date: Thursday, August 3, 2017 at 8:28 AM To: Beatriz Paniagua Cc: "insight-users at itk.org" Subject: Re: [ITK-users] [ITK] About the distribution of wrapped python for ITK external modules Hi Bea, that's awesome, I will try to copy the configuration from the repo of your publication: https://github.com/InsightSoftwareConsortium/ITKTextureFeatures Thanks, Pablo On Fri, Aug 4, 2017 at 12:00 AM, Beatriz Paniagua > wrote: Hi Pablo, We have created external module specific python wraps for some applications. One example is the work that Matt M and JB Vimort did in the ITKTextureFilters. http://review.source.kitware.com/#/c/22531/ Hope that helps! Best, Bea On Wed, Aug 2, 2017 at 11:07 PM, Pablo Hern?ndez > wrote: Hi there, It seems that the only way to install an external module is to build the ITK source with the option -DModule_xxx:BOOL=ON, but I was thinking... if the module is optional in the ITK source code and provides python wraps, is it available in the python itk package with `pip install itk`? In other words, do you wrap all the optional external modules when distributing the python itk or only the default modules? If the latter, would it be possible to create optional python packages for External Modules with the same deploying pipeline you use? Cheers, Pablo _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -- Beatriz Paniagua, PhD Technical Leader Kitware, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cgo_2113 at hotmail.com Thu Aug 3 09:03:36 2017 From: cgo_2113 at hotmail.com (CocoM) Date: Thu, 3 Aug 2017 06:03:36 -0700 (MST) Subject: [ITK-users] 3D registration with level set motion Message-ID: <1501765416750-7590137.post@n2.nabble.com> Hi everyone, I'm doing image registration with the example DeformableRegistration5, i.e. with level set motion. So far I've processed 2D images and it worked fine, but I am now trying to register 3D images and I get an exception with any 3D file I have. The exception occurs after triggering the registration filter, in the function GenerateOutputInformation of the class itkImageFileReader.hxx. Apparently ITK can't create IO objet for reading the file (m_ImageIO is NULL). I'm not sure of what I had to do to adapt this algorithm for 3D. The only thing I changed is the image dimension defined in the main program. Is there something more to change? I am working with Dicom 3D images, all the slices in the same file. Thanks a lot! Marie -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/3D-registration-with-level-set-motion-tp7590137.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From ibr_ex at yahoo.com Thu Aug 3 09:14:58 2017 From: ibr_ex at yahoo.com (ibraheem aldhamari) Date: Thu, 3 Aug 2017 13:14:58 +0000 (UTC) Subject: [ITK-users] 3D registration with level set motion In-Reply-To: <1501765416750-7590137.post@n2.nabble.com> References: <1501765416750-7590137.post@n2.nabble.com> Message-ID: <698474956.1007987.1501766098633@mail.yahoo.com> check the image type (probably you are using 2d), check if the path correct and it does not contain?special characters or spaces.? On Thursday, August 3, 2017, 3:03:41 PM GMT+2, CocoM wrote: Hi everyone, I'm doing image registration with the example DeformableRegistration5, i.e. with level set motion. So far I've processed 2D images and it worked fine, but I am now trying to register 3D images and I get an exception with any 3D file I have. The exception occurs after triggering the registration filter, in the function GenerateOutputInformation of the class itkImageFileReader.hxx. Apparently ITK can't create IO objet for reading the file (m_ImageIO is NULL). I'm not sure of what I had to do to adapt this algorithm for 3D. The only thing I changed is the image dimension defined in the main program. Is there something more to change? I am working with Dicom 3D images, all the slices in the same file. Thanks a lot! Marie -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/3D-registration-with-level-set-motion-tp7590137.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From cgo_2113 at hotmail.com Thu Aug 3 09:55:03 2017 From: cgo_2113 at hotmail.com (CocoM) Date: Thu, 3 Aug 2017 06:55:03 -0700 (MST) Subject: [ITK-users] 3D registration with level set motion In-Reply-To: <698474956.1007987.1501766098633@mail.yahoo.com> References: <1501765416750-7590137.post@n2.nabble.com> <698474956.1007987.1501766098633@mail.yahoo.com> Message-ID: <1501768503338-7590139.post@n2.nabble.com> It is 3D I checked. Do you know if the two images need to be the same size in every direction to make it work? -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/3D-registration-with-level-set-motion-tp7590137p7590139.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From ibr_ex at yahoo.com Thu Aug 3 10:00:16 2017 From: ibr_ex at yahoo.com (ibraheem aldhamari) Date: Thu, 3 Aug 2017 14:00:16 +0000 (UTC) Subject: [ITK-users] 3D registration with level set motion In-Reply-To: <1501768503338-7590139.post@n2.nabble.com> References: <1501765416750-7590137.post@n2.nabble.com> <698474956.1007987.1501766098633@mail.yahoo.com> <1501768503338-7590139.post@n2.nabble.com> Message-ID: <695707198.1035116.1501768816125@mail.yahoo.com> Don't think so, you can check by registering one of two images to itself. Comment all the registration code and check if you can just read the images without getting an error. ? ? On Thursday, August 3, 2017, 3:55:10 PM GMT+2, CocoM wrote: It is 3D I checked. Do you know if the two images need to be the same size in every direction to make it work? -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/3D-registration-with-level-set-motion-tp7590137p7590139.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From cgo_2113 at hotmail.com Thu Aug 3 10:18:07 2017 From: cgo_2113 at hotmail.com (CocoM) Date: Thu, 3 Aug 2017 07:18:07 -0700 (MST) Subject: [ITK-users] 3D registration with level set motion In-Reply-To: <695707198.1035116.1501768816125@mail.yahoo.com> References: <1501765416750-7590137.post@n2.nabble.com> <698474956.1007987.1501766098633@mail.yahoo.com> <1501768503338-7590139.post@n2.nabble.com> <695707198.1035116.1501768816125@mail.yahoo.com> Message-ID: <1501769887094-7590141.post@n2.nabble.com> I think this works fine now, I had a format problem, thanks. But when registering two images of different size I get the exception "Inputs do not occupy the same physical space!". If I go on anyway the registration process ends normally, but the metric value is huge and never decreases (1e+308). Plus the output is entirely black. One of my images has 42 slices, the other one has 43. Maybe that's why? -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/3D-registration-with-level-set-motion-tp7590137p7590141.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From samuel.gerber at kitware.com Thu Aug 3 10:36:00 2017 From: samuel.gerber at kitware.com (Samuel Gerber) Date: Thu, 3 Aug 2017 10:36:00 -0400 Subject: [ITK-users] Fwd: [ITK] 3D registration with level set motion In-Reply-To: References: <1501765416750-7590137.post@n2.nabble.com> <698474956.1007987.1501766098633@mail.yahoo.com> <1501768503338-7590139.post@n2.nabble.com> <695707198.1035116.1501768816125@mail.yahoo.com> <1501769887094-7590141.post@n2.nabble.com> Message-ID: Hi Marie, The registration is done in physical space not the image domain, a detailed description is in Section 3.3 in the itk sotware guide ( https://itk.org/ ITKSoftwareGuide/html/Book2/ITKSoftwareGuide-Book2ch3.html#x26-990003.1 ). Each image has a mapping from the image domain, i.e your voxel space where you can index individual pixels, to physical space. If those mappings map the images into physical space in a way that results in no overlap between the images you will get the exception you are seeing. The physical space is determined by: "One important consequence of this fact is that having the correct image origin, image pixel size, and image direction is fundamental for the success of the registration process in ITK, since we need this information to compute the exact location of each pixel lattice in the physical space; we must make sure that the correct values for the origin, spacing, and direction of all fixed, moving and virtual images are provided." So you might want to check those values for the images you are registering. -Sam On Thu, Aug 3, 2017 at 10:18 AM, CocoM wrote: > I think this works fine now, I had a format problem, thanks. But when > registering two images of different size I get the exception "Inputs do not > occupy the same physical space!". If I go on anyway the registration > process > ends normally, but the metric value is huge and never decreases (1e+308). > Plus the output is entirely black. One of my images has 42 slices, the > other > one has 43. Maybe that's why? > > > > -- > View this message in context: http://itk-insight-users.22837 > 40.n2.nabble.com/3D-registration-with-level-set-motion- > tp7590137p7590141.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > -- Samuel Gerber R&D Engineer Kitware, Inc. -- Samuel Gerber R&D Engineer Kitware, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cgo_2113 at hotmail.com Thu Aug 3 11:33:41 2017 From: cgo_2113 at hotmail.com (CocoM) Date: Thu, 3 Aug 2017 08:33:41 -0700 (MST) Subject: [ITK-users] Fwd: [ITK] 3D registration with level set motion In-Reply-To: References: <1501765416750-7590137.post@n2.nabble.com> <698474956.1007987.1501766098633@mail.yahoo.com> <1501768503338-7590139.post@n2.nabble.com> <695707198.1035116.1501768816125@mail.yahoo.com> <1501769887094-7590141.post@n2.nabble.com> Message-ID: <1501774421062-7590143.post@n2.nabble.com> Hi Sam, Thanks a lot for your answer. I think I understand what you mean, and I checked the spacing, origin and direction of my images. The only difference is the origin in z. In one case it's -1177, in the other -1188. But the origins don't need to be the same to get an overlap between images physical spaces right? With my data, I don't understand why I wouldn't get one ; the spacings are [0.781 0.781 1], the origins [-200 -200 -1177 or -1188] and the directions are identity matrix. Why wouldn't it work? Thanks, Marie -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/3D-registration-with-level-set-motion-tp7590137p7590143.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From samuel.gerber at kitware.com Thu Aug 3 11:46:43 2017 From: samuel.gerber at kitware.com (Samuel Gerber) Date: Thu, 3 Aug 2017 11:46:43 -0400 Subject: [ITK-users] Fwd: [ITK] 3D registration with level set motion In-Reply-To: <1501774421062-7590143.post@n2.nabble.com> References: <1501765416750-7590137.post@n2.nabble.com> <698474956.1007987.1501766098633@mail.yahoo.com> <1501768503338-7590139.post@n2.nabble.com> <695707198.1035116.1501768816125@mail.yahoo.com> <1501769887094-7590141.post@n2.nabble.com> <1501774421062-7590143.post@n2.nabble.com> Message-ID: That looks like there should be enough overlap. Do you get the exception while the registration is running? In that case it might be that during the registration the transform pushes the images away from each other until there is not enough overlap. What kind of optimizer are you using? You might need to adjust the step size of your optimizer. -Sam On Thu, Aug 3, 2017 at 11:33 AM, CocoM wrote: > Hi Sam, > > Thanks a lot for your answer. I think I understand what you mean, and I > checked the spacing, origin and direction of my images. The only difference > is the origin in z. In one case it's -1177, in the other -1188. But the > origins don't need to be the same to get an overlap between images physical > spaces right? With my data, I don't understand why I wouldn't get one ; the > spacings are [0.781 0.781 1], the origins [-200 -200 -1177 or -1188] and > the > directions are identity matrix. Why wouldn't it work? > > Thanks, > Marie > > > > -- > View this message in context: http://itk-insight-users. > 2283740.n2.nabble.com/3D-registration-with-level-set- > motion-tp7590137p7590143.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -- Samuel Gerber R&D Engineer Kitware, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cgo_2113 at hotmail.com Thu Aug 3 12:57:04 2017 From: cgo_2113 at hotmail.com (CocoM) Date: Thu, 3 Aug 2017 09:57:04 -0700 (MST) Subject: [ITK-users] Fwd: [ITK] 3D registration with level set motion In-Reply-To: References: <1501765416750-7590137.post@n2.nabble.com> <698474956.1007987.1501766098633@mail.yahoo.com> <1501768503338-7590139.post@n2.nabble.com> <695707198.1035116.1501768816125@mail.yahoo.com> <1501769887094-7590141.post@n2.nabble.com> <1501774421062-7590143.post@n2.nabble.com> Message-ID: <1501779424960-7590145.post@n2.nabble.com> No I don't think so, it happens after triggering the registration process (before any iteration) but just once in the beginning and once in the end. But actually the deformation field is never updated because the physical spaces don't match so theoretically it's endless. The exception occurs both times in the function VerifyInputInformation, called by UpdateOutputInformation (ProcessObject). I am not using any optimizer because it's a registration method solving a PDE iteratively : itkLevelSetMotionRegistrationFilter. It works with a finite difference resolution scheme, but I can modify the time step, although I wouldn't really see the point. Any idea? Thanks, Marie -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/3D-registration-with-level-set-motion-tp7590137p7590145.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From samuel.gerber at kitware.com Thu Aug 3 13:40:12 2017 From: samuel.gerber at kitware.com (Samuel Gerber) Date: Thu, 3 Aug 2017 13:40:12 -0400 Subject: [ITK-users] Fwd: [ITK] 3D registration with level set motion In-Reply-To: <1501779424960-7590145.post@n2.nabble.com> References: <1501765416750-7590137.post@n2.nabble.com> <698474956.1007987.1501766098633@mail.yahoo.com> <1501768503338-7590139.post@n2.nabble.com> <695707198.1035116.1501768816125@mail.yahoo.com> <1501769887094-7590141.post@n2.nabble.com> <1501774421062-7590143.post@n2.nabble.com> <1501779424960-7590145.post@n2.nabble.com> Message-ID: I apologize I did not realize you were using a PDE based registration. It is my understanding that for this approach the images need to match in physical space, since the filter operates in way that matches pixel by pixel. There is a few options: 1. You could limit the output region such that they are both fully contained in both images. See: https://itk.org/ITKExamples/src/Core/Common/ApplyAFilterOnlyToASpecifiedRegionOfAnImage/Documentation.html 2. You could pad the smaller image. 3. You could perform an affine registration first and resample the image. -Sam On Thu, Aug 3, 2017 at 12:57 PM, CocoM wrote: > No I don't think so, it happens after triggering the registration process > (before any iteration) but just once in the beginning and once in the end. > But actually the deformation field is never updated because the physical > spaces don't match so theoretically it's endless. The exception occurs both > times in the function VerifyInputInformation, called by > UpdateOutputInformation (ProcessObject). > > I am not using any optimizer because it's a registration method solving a > PDE iteratively : itkLevelSetMotionRegistrationFilter. It works with a > finite difference resolution scheme, but I can modify the time step, > although I wouldn't really see the point. Any idea? > > Thanks, > Marie > > > > > > -- > View this message in context: http://itk-insight-users. > 2283740.n2.nabble.com/3D-registration-with-level-set- > motion-tp7590137p7590145.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -- Samuel Gerber R&D Engineer Kitware, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonasteuwen at gmail.com Thu Aug 3 18:48:01 2017 From: jonasteuwen at gmail.com (Jonas Teuwen) Date: Fri, 4 Aug 2017 00:48:01 +0200 Subject: [ITK-users] Segfault after SliceBySliceImageFilter Message-ID: Hi all, I wish to apply a filter slice by slice, for which I use SliceBySliceImageFilter (after the appropriate definitions): """ typedef itk::LaplacianSharpeningImageFilter LaplacianSharpeningImageFilterType; LaplacianSharpeningImageFilterType::Pointer LaplacianSharpeningImageFilter = LaplacianSharpeningImageFilterType::New(); LaplacianSharpeningImageFilter->SetInput(reader->GetOutput()); LaplacianSharpeningImageFilter->Update(); typedef itk::FlatStructuringElement<2> StructuringElementType; StructuringElementType::RadiusType AnnulusRadius; AnnulusRadius.Fill(10); StructuringElementType StructuringElement = StructuringElementType::Annulus(AnnulusRadius, Thickness, false, false); typedef itk::SliceBySliceImageFilter SliceFilterType; SliceFilterType::Pointer SliceFilter = SliceFilterType::New(); typedef itk::GrayscaleDilateImageFilter GrayscaleDilateImageFilterType; GrayscaleDilateImageFilterType::Pointer GrayscaleDilateImageFilter = GrayscaleDilateImageFilterType::New(); GrayscaleDilateImageFilter->SetKernel(StructuringElement); SliceFilter->SetInput(LaplacianSharpeningImageFilter->GetOutput()); SliceFilter->SetFilter(GrayscaleDilateImageFilter); """ If I write the output of SliceFilter to a file, I get what I expact, but I do want to compute the minimum between the result and the sharpened image: typedef itk::MinimumImageFilter MinimumImageFilterType; typename MinimumImageFilterType::Pointer MinimumImageFilter; MinimumImageFilter->SetInput(0, SliceFilter->GetOutput()); MinimumImageFilter->SetInput(1, LaplacianSharpeningImageFilter->GetOutput()); But that immediately segfaults, even before the output is written to disk. Whichever order, gdb tells me the program crashes at any ->SetInput in the MinimumImageFilter. If I on the other hand input a 2D image, and I do not use the SliceBySliceImageFilter, the program seems to work as expected. Are there any debugging steps which I could try to find the flaw? Best, Jonas -------------- next part -------------- An HTML attachment was scrubbed... URL: From richard.beare at gmail.com Thu Aug 3 20:05:27 2017 From: richard.beare at gmail.com (Richard Beare) Date: Fri, 4 Aug 2017 10:05:27 +1000 Subject: [ITK-users] Segfault after SliceBySliceImageFilter In-Reply-To: References: Message-ID: You haven't created the MinimumImageFilter: typename MinimumImageFilterType::Pointer MinimumImageFilter = MinimumImageFilterType::New() On Fri, Aug 4, 2017 at 8:48 AM, Jonas Teuwen wrote: > Hi all, > > I wish to apply a filter slice by slice, for which I use > SliceBySliceImageFilter (after the appropriate definitions): > > """ > typedef itk::LaplacianSharpeningImageFilter FloatImageType3D> LaplacianSharpeningImageFilterType; > LaplacianSharpeningImageFilterType::Pointer > LaplacianSharpeningImageFilter = LaplacianSharpeningImageFilter > Type::New(); > LaplacianSharpeningImageFilter->SetInput(reader->GetOutput()); > LaplacianSharpeningImageFilter->Update(); > > typedef itk::FlatStructuringElement<2> StructuringElementType; > StructuringElementType::RadiusType AnnulusRadius; > AnnulusRadius.Fill(10); > StructuringElementType StructuringElement = StructuringElementType::Annulus(AnnulusRadius, > Thickness, false, false); > > typedef itk::SliceBySliceImageFilter FloatImageType3D> SliceFilterType; > SliceFilterType::Pointer SliceFilter = SliceFilterType::New(); > > typedef itk::GrayscaleDilateImageFilter InternalInputImageType, > SliceFilterType::InternalOutputImageType, > StructuringElementType> GrayscaleDilateImageFilterType; > GrayscaleDilateImageFilterType::Pointer GrayscaleDilateImageFilter = > GrayscaleDilateImageFilterType::New(); > GrayscaleDilateImageFilter->SetKernel(StructuringElement); > > SliceFilter->SetInput(LaplacianSharpeningImageFilter->GetOutput()); > SliceFilter->SetFilter(GrayscaleDilateImageFilter); > """ > If I write the output of SliceFilter to a file, I get what I expact, but I > do want to compute the minimum between the result and the sharpened image: > > typedef itk::MinimumImageFilter FloatImageType3D> MinimumImageFilterType; > typename MinimumImageFilterType::Pointer MinimumImageFilter; > MinimumImageFilter->SetInput(0, SliceFilter->GetOutput()); > MinimumImageFilter->SetInput(1, LaplacianSharpeningImageFilter > ->GetOutput()); > > But that immediately segfaults, even before the output is written to disk. > Whichever order, gdb tells me the program crashes at any ->SetInput in the > MinimumImageFilter. > If I on the other hand input a 2D image, and I do not use the > SliceBySliceImageFilter, the program seems to work as expected. > > Are there any debugging steps which I could try to find the flaw? > > Best, > Jonas > > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cgo_2113 at hotmail.com Fri Aug 4 02:23:47 2017 From: cgo_2113 at hotmail.com (CocoM) Date: Thu, 3 Aug 2017 23:23:47 -0700 (MST) Subject: [ITK-users] Fwd: [ITK] 3D registration with level set motion In-Reply-To: References: <1501765416750-7590137.post@n2.nabble.com> <698474956.1007987.1501766098633@mail.yahoo.com> <1501768503338-7590139.post@n2.nabble.com> <695707198.1035116.1501768816125@mail.yahoo.com> <1501769887094-7590141.post@n2.nabble.com> <1501774421062-7590143.post@n2.nabble.com> <1501779424960-7590145.post@n2.nabble.com> Message-ID: <1501827827622-7590149.post@n2.nabble.com> Thanks a lot, I'm gonna check that! -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/3D-registration-with-level-set-motion-tp7590137p7590149.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From matt.mccormick at kitware.com Fri Aug 4 09:36:34 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 4 Aug 2017 09:36:34 -0400 Subject: [ITK-users] Cardiac Deformation using Segmentation and Registration of Ultrasound Images In-Reply-To: References: Message-ID: Hi Thanos, On Thu, Aug 3, 2017 at 1:00 PM, thanos thanos wrote: > Hello everyone, > > D?enan, Andras and Matt thank you very much for your answers. > To be honest I've tried already in the past registration with Slicer using > Demons, B-Splines and also Elastix and Plastimach. > > D?enan, I read your last sentence already many times but I can't really > understand what you mean by "initializing registration of time point n+1 by > resulting transform from time point n." > > Matt, thank you for sharing your thoughts. I already looked at the > AnisotropicDiffusionLBR paper and I have also tried the online interactive > figures > (https://insightsoftwareconsortium.github.io/ITKAnisotropicDiffusionLBR/). > Seems to work nicely, but I wasn't sure how to build the project. I already > configured my ITK by setting the Module_AnisotropicDiffusionLBR at the CMake > and then I tried to build the CoherenceEnhancingDiffusion from the > C:\ITK\src\Modules\Remote\AnisotropicDiffusionLBR\examples but I got " > Cannot open include file: 'CoherenceEnhancingDiffusionFilter.h': No such > file or directory " so I guess I am missing something.. Thanks for the note. I will look into this issue and address it next week. > I tried in the past to perform segmentation using the > GeodesicActiveContourImageFilter (first for 2D images) but I miserably > failed to get a descent result. I then tried to extend it to 3D but I think > that even though I built the project I was not getting valid results (it was > some months ago so I don't remember exactly). > > Now, on important question that I have is how important is it to have a > perfect segmentation in order to perform registration? Is it maybe enough to > just get a just descent segmentation that includes the whole heart even if > that means that the active contours stop before the reach the actual > boundary? > I guess I have to first proceed in a good segmentation before going back to > the registration problems.. In general, "it depends," but segmentation and registration problems can be viewed as coupled. In general we need to identify structures before we can register them. Preprocessing filtering step that reduce noise could be viewed in this respect. > Also, I suppose that the registration should not be done to the filtered > images but to the original in order to preserve the speckle noise which > includes some kind of information. Is that correct? Right. The speckle is not actually noise. It is signal that does not change and indicates the location of tissue. Some motion tracking techniques, like ultrasound strain imaging, use the speckle signal exclusively. However, some registration techniques may be confounded by local minima in the cost function caused my high frequency content. And, the speckle can change when motion is large and the ultrasound beam encounters the tissue at a different angles. > I will have a look within the next days to the last two approaches that you > suggested, although, with a first glance, it wasn't quite obvious how the > PointSetToPointSetMetric works, but I will try to study it a bit more. There are some tests in the ITK test suite that demonstrate how to use the new point set registration framework. Hope this helps, Matt From matt.mccormick at kitware.com Fri Aug 4 09:38:16 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 4 Aug 2017 09:38:16 -0400 Subject: [ITK-users] Problems Using GPU Filters In-Reply-To: <1501626181039-7590122.post@n2.nabble.com> References: <1498789176254-7590036.post@n2.nabble.com> <1501002308962-7590057.post@n2.nabble.com> <1501611311517-7590114.post@n2.nabble.com> <1501626181039-7590122.post@n2.nabble.com> Message-ID: Hi Andaharoo, You may have identified a bug. I am also seeing local failures in the regression tests for the referenced classes. I will investigate further next week. Thanks, Matt On Tue, Aug 1, 2017 at 6:23 PM, Andaharoo wrote: > I can't get the images to go from CPU to GPU on GPUMeanImageFilter, > GPUBinaryThresholdImageFilter, and GPUDiscreteGaussianImageFilter. So I > can't start my gpu pipeline with these filters. If I apply something like > GPUGradientAnisotropicImageFilter (which does work) then I can apply the > other filters confirming that it can go GPU to GPU but not CPU to GPU on > those 3 filters. Do these 3 filters not support conversion? > > GPUInputImage::Pointer inPtr = > dynamic_cast(this->ProcessObject::GetInput(0)); > inPtr was null when I debugged GPUMeanImageFilter. This line also doesn't > make sense in terms of using an Image since it would just return null if you > gave it an Image that wasn't allocated as a GPUImage. Unless the cpu image > gets converted to a gpu image elsewhere beforehand? > > It seems as though only GPUInPlaceImageFilters work with CPU - GPU > conversion for me? I can't quite understand the GPUInPlaceImageFilters > source yet so I'm not so sure why GPUGradientAnisotropicImageFilter works. > They are, of course, different in terms of how they manage memory. > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Problems-Using-GPU-Filters-tp7590036p7590122.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users From cgo_2113 at hotmail.com Fri Aug 4 10:19:12 2017 From: cgo_2113 at hotmail.com (CocoM) Date: Fri, 4 Aug 2017 07:19:12 -0700 (MST) Subject: [ITK-users] Fwd: [ITK] 3D registration with level set motion In-Reply-To: <1501827827622-7590149.post@n2.nabble.com> References: <698474956.1007987.1501766098633@mail.yahoo.com> <1501768503338-7590139.post@n2.nabble.com> <695707198.1035116.1501768816125@mail.yahoo.com> <1501769887094-7590141.post@n2.nabble.com> <1501774421062-7590143.post@n2.nabble.com> <1501779424960-7590145.post@n2.nabble.com> <1501827827622-7590149.post@n2.nabble.com> Message-ID: <1501856352985-7590152.post@n2.nabble.com> Finally I managed running the algorithm by changing the origin of the moving image with itkChangeInformationImageFilter. Before that I transformed my Dicom images into NRRD with DicomSeriesReadImageWrite2. But I got a weird output for the registration process : the image seems really noisy and is unsigned int8 instead of int16. Plus the last slices are black. Is there a special way to write 3D images ? I'm just using the code of DeformableRegistration5. Or maybe the problem is in the warping step ? Thanks a lot, Marie -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/3D-registration-with-level-set-motion-tp7590137p7590152.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From dzenanz at gmail.com Fri Aug 4 11:12:47 2017 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 4 Aug 2017 11:12:47 -0400 Subject: [ITK-users] Fwd: [ITK] 3D registration with level set motion In-Reply-To: <1501856352985-7590152.post@n2.nabble.com> References: <698474956.1007987.1501766098633@mail.yahoo.com> <1501768503338-7590139.post@n2.nabble.com> <695707198.1035116.1501768816125@mail.yahoo.com> <1501769887094-7590141.post@n2.nabble.com> <1501774421062-7590143.post@n2.nabble.com> <1501779424960-7590145.post@n2.nabble.com> <1501827827622-7590149.post@n2.nabble.com> <1501856352985-7590152.post@n2.nabble.com> Message-ID: Hi Marie, in DeformableRegistration5 you should change typedef of OutputPixelType from char to short. The "noise" is caused by values over 255 being cast from short to char. Regards, D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.) On Fri, Aug 4, 2017 at 10:19 AM, CocoM wrote: > Finally I managed running the algorithm by changing the origin of the > moving > image with itkChangeInformationImageFilter. Before that I transformed my > Dicom images into NRRD with DicomSeriesReadImageWrite2. But I got a weird > output for the registration process : the image seems really noisy and is > unsigned int8 instead of int16. Plus the last slices are black. Is there a > special way to write 3D images ? I'm just using the code of > DeformableRegistration5. Or maybe the problem is in the warping step ? > > Thanks a lot, > Marie > > > > -- > View this message in context: http://itk-insight-users. > 2283740.n2.nabble.com/3D-registration-with-level-set- > motion-tp7590137p7590152.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bxt161230 at utdallas.edu Fri Aug 4 14:33:16 2017 From: bxt161230 at utdallas.edu (bipul) Date: Fri, 4 Aug 2017 11:33:16 -0700 (MST) Subject: [ITK-users] Understanding the Geodesic Active Contour Message-ID: <1501871596899-7590154.post@n2.nabble.com> Hi, I was going through the implementation for the Geodesic Active Contour filter and have the following questions about it: 1. The propagation term of the general level set is the speed image in case of the geodesic filter, which is also the feature image, and in the given example it is the output of the sigmoid filter. The advection term is the gradient of the same speed image. I wanted to know the reason for using the speed image for propagation(since it is supposed to be a constant) and also for advection. How do these forces cancel each other out when a boundary is detected? I assume, they must be tuned first for best boundary detection. Also, what might be other choices for the speed image? 2. Another input to the filter is an initial level set, which is a zero level set provided by the output of the fast marching filter. I could not find the use of this input in the implementation. Could you point me to the class where I can find the implementation that this level set is modified with each iteration? Also, I guess, when the contour evolves, we only do the calculations at the boundary of the contour and not the entire volume? I tried looking up for these questions on the forum, but didn't find any answers. I would really appreciate it if you could answer these. Bipul Tarafdar -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Understanding-the-Geodesic-Active-Contour-tp7590154.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From cgo_2113 at hotmail.com Sat Aug 5 16:00:47 2017 From: cgo_2113 at hotmail.com (CocoM) Date: Sat, 5 Aug 2017 13:00:47 -0700 (MST) Subject: [ITK-users] Fwd: [ITK] 3D registration with level set motion In-Reply-To: References: <695707198.1035116.1501768816125@mail.yahoo.com> <1501769887094-7590141.post@n2.nabble.com> <1501774421062-7590143.post@n2.nabble.com> <1501779424960-7590145.post@n2.nabble.com> <1501827827622-7590149.post@n2.nabble.com> <1501856352985-7590152.post@n2.nabble.com> Message-ID: <1501963247479-7590155.post@n2.nabble.com> Thanks a lot it's almost working now! I have another question, about the running time. I don't know anything about it but I'm surprised by the time needed for the algorithm to be done. I'm using the example DeformableRegistration5 (level set PDE solving), but I changed it to use B-spline interpolation. The running time is huge for 3D ; for 2D it takes a little less than 3 minutes and for 3D, I need approximately 20 minutes by iteration, so imagine the time needed by the whole process... My test image is 512x512x43, the algorithm is multi threads. I'm working on a six years old Asus laptop (X53S), nothing extraordinary. I couldn't say exactly what my CPU is but it's a Intel core i5. I know it's not great material but still, I feel like it's very slow. So could someone tell me if it's normal? The thing is I didn't change much, so I guess it is, but I wanted to ask anyway. Plus, if anyone has any idea to speed up the process, except buying a better computer, it would be really great! Thanks a lot, Marie -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/3D-registration-with-level-set-motion-tp7590137p7590155.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From pablo.hernandez.cerdan at outlook.com Sun Aug 6 06:07:41 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Sun, 6 Aug 2017 10:07:41 +0000 Subject: [ITK-users] [ITK] About the distribution of wrapped python for ITK external modules In-Reply-To: <5E37A920-455F-4CDB-BA6F-8E031D860C8D@mail.nih.gov> References: <5E37A920-455F-4CDB-BA6F-8E031D860C8D@mail.nih.gov> Message-ID: Thanks Brad, it helped a lot. I copied the CI files (travis, appveyor and circle) and the setup.py from the ITKModuleTemplate, changed just a little bit on setup.py, and it works! I have the .wheel files for all the platforms. Just a few notes, I had to add a 3.6 in the .travis.yml --which generates the wheels for macOS because I was hitting the time limit (~50min). `./macpython-download-cache-and-build-module-wheels.sh 3.6` Also, to upload it into pypi for using `pip install`, I have registered myself in pypi and testpypi, configured a `.pypirc` file with my credentials and downloaded the wheels from every site into a `dist` folder, then: `twine upload ./dist/* -r testpypi` And it works! (python-test-virtual_environment) pip install --extra-index-url https://testpypi.python.org/pypi itk-isotropicwavelets Amazing, thanks a lot, Cheers, Pablo On Fri, Aug 4, 2017 at 12:48 AM, blowekamp at mail.nih.gov > wrote: I would also look at the ITKModuleTemplate repository: https://github.com/InsightSoftwareConsortium/ITKModuleTemplate Brad From: Pablo Hern?ndez > Date: Thursday, August 3, 2017 at 8:28 AM To: Beatriz Paniagua > Cc: "insight-users at itk.org" > Subject: Re: [ITK-users] [ITK] About the distribution of wrapped python for ITK external modules Hi Bea, that's awesome, I will try to copy the configuration from the repo of your publication: https://github.com/InsightSoftwareConsortium/ITKTextureFeatures Thanks, Pablo On Fri, Aug 4, 2017 at 12:00 AM, Beatriz Paniagua > wrote: Hi Pablo, We have created external module specific python wraps for some applications. One example is the work that Matt M and JB Vimort did in the ITKTextureFilters. http://review.source.kitware.com/#/c/22531/ Hope that helps! Best, Bea On Wed, Aug 2, 2017 at 11:07 PM, Pablo Hern?ndez > wrote: Hi there, It seems that the only way to install an external module is to build the ITK source with the option -DModule_xxx:BOOL=ON, but I was thinking... if the module is optional in the ITK source code and provides python wraps, is it available in the python itk package with `pip install itk`? In other words, do you wrap all the optional external modules when distributing the python itk or only the default modules? If the latter, would it be possible to create optional python packages for External Modules with the same deploying pipeline you use? Cheers, Pablo _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -- Beatriz Paniagua, PhD Technical Leader Kitware, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From pablo.hernandez.cerdan at outlook.com Sun Aug 6 06:07:45 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Sun, 6 Aug 2017 10:07:45 +0000 Subject: [ITK-users] [ITK] About the distribution of wrapped python for ITK external modules In-Reply-To: <5E37A920-455F-4CDB-BA6F-8E031D860C8D@mail.nih.gov> References: <5E37A920-455F-4CDB-BA6F-8E031D860C8D@mail.nih.gov> Message-ID: Thanks Brad, it helped a lot. I copied the CI files (travis, appveyor and circle) and the setup.py from the ITKModuleTemplate, changed just a little bit on setup.py, and it works! I have the .wheel files for all the platforms. Just a few notes, I had to add a 3.6 in the .travis.yml --which generates the wheels for macOS because I was hitting the time limit (~50min). `./macpython-download-cache-and-build-module-wheels.sh 3.6` Also, to upload it into pypi for using `pip install`, I have registered myself in pypi and testpypi, configured a `.pypirc` file with my credentials and downloaded the wheels from every site into a `dist` folder, then: `twine upload ./dist/* -r testpypi` And it works! (python-test-virtual_environment) pip install --extra-index-url https://testpypi.python.org/pypi itk-isotropicwavelets Amazing, thanks a lot, Cheers, Pablo On Fri, Aug 4, 2017 at 12:48 AM, blowekamp at mail.nih.gov > wrote: I would also look at the ITKModuleTemplate repository: https://github.com/InsightSoftwareConsortium/ITKModuleTemplate Brad From: Pablo Hern?ndez > Date: Thursday, August 3, 2017 at 8:28 AM To: Beatriz Paniagua > Cc: "insight-users at itk.org" > Subject: Re: [ITK-users] [ITK] About the distribution of wrapped python for ITK external modules Hi Bea, that's awesome, I will try to copy the configuration from the repo of your publication: https://github.com/InsightSoftwareConsortium/ITKTextureFeatures Thanks, Pablo On Fri, Aug 4, 2017 at 12:00 AM, Beatriz Paniagua > wrote: Hi Pablo, We have created external module specific python wraps for some applications. One example is the work that Matt M and JB Vimort did in the ITKTextureFilters. http://review.source.kitware.com/#/c/22531/ Hope that helps! Best, Bea On Wed, Aug 2, 2017 at 11:07 PM, Pablo Hern?ndez > wrote: Hi there, It seems that the only way to install an external module is to build the ITK source with the option -DModule_xxx:BOOL=ON, but I was thinking... if the module is optional in the ITK source code and provides python wraps, is it available in the python itk package with `pip install itk`? In other words, do you wrap all the optional external modules when distributing the python itk or only the default modules? If the latter, would it be possible to create optional python packages for External Modules with the same deploying pipeline you use? Cheers, Pablo _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -- Beatriz Paniagua, PhD Technical Leader Kitware, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Sun Aug 6 22:27:41 2017 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Sun, 6 Aug 2017 22:27:41 -0400 Subject: [ITK-users] Fwd: [ITK] 3D registration with level set motion In-Reply-To: <1501963247479-7590155.post@n2.nabble.com> References: <695707198.1035116.1501768816125@mail.yahoo.com> <1501769887094-7590141.post@n2.nabble.com> <1501774421062-7590143.post@n2.nabble.com> <1501779424960-7590145.post@n2.nabble.com> <1501827827622-7590149.post@n2.nabble.com> <1501856352985-7590152.post@n2.nabble.com> <1501963247479-7590155.post@n2.nabble.com> Message-ID: Hi Marie, an obvious thing to ask: are you running it in debug or release mode? The difference is usually huge. B-spline registration for your image could take a few minutes - 20 minutes for a single iteration sounds too long. A classic trick for speeding up registration is using multi-resolution approach. It usually involves more code and a lot more testing, though. Regards, D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.) On Sat, Aug 5, 2017 at 4:00 PM, CocoM wrote: > Thanks a lot it's almost working now! > > I have another question, about the running time. > I don't know anything about it but I'm surprised by the time needed for the > algorithm to be done. I'm using the example DeformableRegistration5 (level > set PDE solving), but I changed it to use B-spline interpolation. The > running time is huge for 3D ; for 2D it takes a little less than 3 minutes > and for 3D, I need approximately 20 minutes by iteration, so imagine the > time needed by the whole process... My test image is 512x512x43, the > algorithm is multi threads. I'm working on a six years old Asus laptop > (X53S), nothing extraordinary. I couldn't say exactly what my CPU is but > it's a Intel core i5. I know it's not great material but still, I feel like > it's very slow. So could someone tell me if it's normal? > > The thing is I didn't change much, so I guess it is, but I wanted to ask > anyway. > > Plus, if anyone has any idea to speed up the process, except buying a > better > computer, it would be really great! > > Thanks a lot, > Marie > > > > -- > View this message in context: http://itk-insight-users. > 2283740.n2.nabble.com/3D-registration-with-level-set- > motion-tp7590137p7590155.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cgo_2113 at hotmail.com Mon Aug 7 06:47:30 2017 From: cgo_2113 at hotmail.com (CocoM) Date: Mon, 7 Aug 2017 03:47:30 -0700 (MST) Subject: [ITK-users] Fwd: [ITK] 3D registration with level set motion In-Reply-To: References: <1501774421062-7590143.post@n2.nabble.com> <1501779424960-7590145.post@n2.nabble.com> <1501827827622-7590149.post@n2.nabble.com> <1501856352985-7590152.post@n2.nabble.com> <1501963247479-7590155.post@n2.nabble.com> Message-ID: <1502102850575-7590159.post@n2.nabble.com> Hi D?enan, Thanks a lot for your answer! I was indeed using debug mode, release mode is much better : one iteration for 3D takes now 40 seconds. Cheers, Marie -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/3D-registration-with-level-set-motion-tp7590137p7590159.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From francois.budin at kitware.com Mon Aug 7 09:07:41 2017 From: francois.budin at kitware.com (Francois Budin) Date: Mon, 7 Aug 2017 09:07:41 -0400 Subject: [ITK-users] [ITK] About the distribution of wrapped python for ITK external modules In-Reply-To: References: <5E37A920-455F-4CDB-BA6F-8E031D860C8D@mail.nih.gov> Message-ID: Hello Pablo, It's great to hear that you were able to generate the Python wheels for your package. I was able to install it with the following command: pip install itk-isotropicwavelets It's great to have an really easy access to this module. Thanks for generating the pacakge. Francois On Sun, Aug 6, 2017 at 6:07 AM, Pablo Hern?ndez < pablo.hernandez.cerdan at outlook.com> wrote: > Thanks Brad, it helped a lot. > I copied the CI files (travis, appveyor and circle) and the setup.py from > the ITKModuleTemplate, changed just a little bit on setup.py, and it works! > I have the .wheel files for all the platforms. > > Just a few notes, I had to add a 3.6 in the .travis.yml --which generates > the wheels for macOS because I was hitting the time limit (~50min). > > `./macpython-download-cache-and-build-module-wheels.sh 3.6` > > Also, to upload it into pypi for using `pip install`, I have registered > myself in pypi and testpypi, configured a `.pypirc` file with my > credentials and downloaded the wheels from every site into a `dist` folder, > then: > > `twine upload ./dist/* -r testpypi` > > And it works! > > (python-test-virtual_environment) pip install --extra-index-url > https://testpypi.python.org/pypi itk-isotropicwavelets > > Amazing, thanks a lot, > > Cheers, > Pablo > > On Fri, Aug 4, 2017 at 12:48 AM, blowekamp at mail.nih.gov < > blowekamp at mail.nih.gov> wrote: > >> I would also look at the ITKModuleTemplate repository: >> >> https://github.com/InsightSoftwareConsortium/ITKModuleTemplate >> >> >> >> Brad >> >> >> >> *From: *Pablo Hern?ndez >> *Date: *Thursday, August 3, 2017 at 8:28 AM >> *To: *Beatriz Paniagua >> *Cc: *"insight-users at itk.org" >> *Subject: *Re: [ITK-users] [ITK] About the distribution of wrapped >> python for ITK external modules >> >> >> >> Hi Bea, >> >> that's awesome, I will try to copy the configuration from the repo of >> your publication: https://github.com/InsightSoft >> wareConsortium/ITKTextureFeatures >> >> Thanks, >> >> Pablo >> >> >> >> On Fri, Aug 4, 2017 at 12:00 AM, Beatriz Paniagua < >> beatriz.paniagua at kitware.com> wrote: >> >> Hi Pablo, >> >> We have created external module specific python wraps for some >> applications. One example is the work that Matt M and JB Vimort did in the >> ITKTextureFilters. >> http://review.source.kitware.com/#/c/22531/ >> >> Hope that helps! >> >> Best, >> >> Bea >> >> >> >> >> >> On Wed, Aug 2, 2017 at 11:07 PM, Pablo Hern?ndez < >> pablo.hernandez.cerdan at outlook.com> wrote: >> >> Hi there, >> >> It seems that the only way to install an external module is to build the >> ITK source with the option -DModule_xxx:BOOL=ON, but I was thinking... if >> the module is optional in the ITK source code and provides python wraps, is >> it available in the python itk package with `pip install itk`? >> >> >> In other words, do you wrap all the optional external modules when >> distributing the python itk or only the default modules? If the latter, >> would it be possible to create optional python packages for External >> Modules with the same deploying pipeline you use? >> >> Cheers, >> Pablo >> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> >> >> >> >> -- >> >> Beatriz Paniagua, PhD >> Technical Leader >> >> Kitware, Inc. >> >> >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matimontg at gmail.com Mon Aug 7 15:57:38 2017 From: matimontg at gmail.com (matimont) Date: Mon, 7 Aug 2017 12:57:38 -0700 (MST) Subject: [ITK-users] Reader InvalidRequestedRegionError Message-ID: <1502135858865-7590161.post@n2.nabble.com> Hi, I'm reading a serie from a directory and I get this: itk::InvalidRequestedRegionError (0000001D4B9AEDD8) Location: "unknown" File: c:\itk-4.12.0\modules\io\imagebase\include\itkImageFileReader.hxx Line: 350 Description: ImageIO returns IO region that does not fully contain the requested regionRequested region: ImageRegion (0000001D4B9AEDA0) Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 1] StreamableRegion region: ImageRegion (0000001D4B9AEE00) Dimension: 3 Index: [0, 0, 0] Size: [484, 484, 1] I noticed the images I read have ImageOrientationPatient as: (0020,0037) ImageOrientationPatient -0.4181660095794\0.90837062283655\0\0\0\-1 This only patient has failed, all others work Would this cause the reader to fail? This is part of the code I use to read the series: ImageIOType::Pointer gdcmIO = ImageIOType::New(); InputNamesGeneratorType::Pointer inputNames = InputNamesGeneratorType::New(); inputNames->SetInputDirectory( argv[1] ); const ReaderType::FileNamesContainer & filenames = inputNames->GetInputFileNames(); ReaderType::Pointer reader = ReaderType::New(); reader->SetImageIO( gdcmIO ); reader->SetFileNames( filenames ); try { reader->Update(); } catch (itk::ExceptionObject &excp) { std::cerr << "Exception thrown while reading the series" << std::endl; std::cerr << excp << std::endl; return EXIT_FAILURE; } Thanks, Matias. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Reader-InvalidRequestedRegionError-tp7590161.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From pablo.hernandez.cerdan at outlook.com Mon Aug 7 19:06:57 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Mon, 7 Aug 2017 23:06:57 +0000 Subject: [ITK-users] [ITK] About the distribution of wrapped python for ITK external modules In-Reply-To: References: <5E37A920-455F-4CDB-BA6F-8E031D860C8D@mail.nih.gov> Message-ID: Hello Francois, thanks for testing it. In case you miss something, there are still a few classes not wrapped, will try to add them next weekend. Pablo On Tue, Aug 8, 2017 at 1:07 AM, francois.budin at kitware.com > wrote: Hello Pablo, It's great to hear that you were able to generate the Python wheels for your package. I was able to install it with the following command: pip install itk-isotropicwavelets It's great to have an really easy access to this module. Thanks for generating the pacakge. Francois On Sun, Aug 6, 2017 at 6:07 AM, Pablo Hern?ndez > wrote: Thanks Brad, it helped a lot. I copied the CI files (travis, appveyor and circle) and the setup.py from the ITKModuleTemplate, changed just a little bit on setup.py, and it works! I have the .wheel files for all the platforms. Just a few notes, I had to add a 3.6 in the .travis.yml --which generates the wheels for macOS because I was hitting the time limit (~50min). `./macpython-download-cache-and-build-module-wheels.sh 3.6` Also, to upload it into pypi for using `pip install`, I have registered myself in pypi and testpypi, configured a `.pypirc` file with my credentials and downloaded the wheels from every site into a `dist` folder, then: `twine upload ./dist/* -r testpypi` And it works! (python-test-virtual_environment) pip install --extra-index-url https://testpypi.python.org/pypi itk-isotropicwavelets Amazing, thanks a lot, Cheers, Pablo On Fri, Aug 4, 2017 at 12:48 AM, blowekamp at mail.nih.gov > wrote: I would also look at the ITKModuleTemplate repository: https://github.com/InsightSoftwareConsortium/ITKModuleTemplate Brad From: Pablo Hern?ndez > Date: Thursday, August 3, 2017 at 8:28 AM To: Beatriz Paniagua > Cc: "insight-users at itk.org" > Subject: Re: [ITK-users] [ITK] About the distribution of wrapped python for ITK external modules Hi Bea, that's awesome, I will try to copy the configuration from the repo of your publication: https://github.com/InsightSoftwareConsortium/ITKTextureFeatures Thanks, Pablo On Fri, Aug 4, 2017 at 12:00 AM, Beatriz Paniagua > wrote: Hi Pablo, We have created external module specific python wraps for some applications. One example is the work that Matt M and JB Vimort did in the ITKTextureFilters. http://review.source.kitware.com/#/c/22531/ Hope that helps! Best, Bea On Wed, Aug 2, 2017 at 11:07 PM, Pablo Hern?ndez > wrote: Hi there, It seems that the only way to install an external module is to build the ITK source with the option -DModule_xxx:BOOL=ON, but I was thinking... if the module is optional in the ITK source code and provides python wraps, is it available in the python itk package with `pip install itk`? In other words, do you wrap all the optional external modules when distributing the python itk or only the default modules? If the latter, would it be possible to create optional python packages for External Modules with the same deploying pipeline you use? Cheers, Pablo _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -- Beatriz Paniagua, PhD Technical Leader Kitware, Inc. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From pablo.hernandez.cerdan at outlook.com Mon Aug 7 19:06:58 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Mon, 7 Aug 2017 23:06:58 +0000 Subject: [ITK-users] [ITK] About the distribution of wrapped python for ITK external modules In-Reply-To: References: <5E37A920-455F-4CDB-BA6F-8E031D860C8D@mail.nih.gov> Message-ID: Hello Francois, thanks for testing it. In case you miss something, there are still a few classes not wrapped, will try to add them next weekend. Pablo On Tue, Aug 8, 2017 at 1:07 AM, francois.budin at kitware.com > wrote: Hello Pablo, It's great to hear that you were able to generate the Python wheels for your package. I was able to install it with the following command: pip install itk-isotropicwavelets It's great to have an really easy access to this module. Thanks for generating the pacakge. Francois On Sun, Aug 6, 2017 at 6:07 AM, Pablo Hern?ndez > wrote: Thanks Brad, it helped a lot. I copied the CI files (travis, appveyor and circle) and the setup.py from the ITKModuleTemplate, changed just a little bit on setup.py, and it works! I have the .wheel files for all the platforms. Just a few notes, I had to add a 3.6 in the .travis.yml --which generates the wheels for macOS because I was hitting the time limit (~50min). `./macpython-download-cache-and-build-module-wheels.sh 3.6` Also, to upload it into pypi for using `pip install`, I have registered myself in pypi and testpypi, configured a `.pypirc` file with my credentials and downloaded the wheels from every site into a `dist` folder, then: `twine upload ./dist/* -r testpypi` And it works! (python-test-virtual_environment) pip install --extra-index-url https://testpypi.python.org/pypi itk-isotropicwavelets Amazing, thanks a lot, Cheers, Pablo On Fri, Aug 4, 2017 at 12:48 AM, blowekamp at mail.nih.gov > wrote: I would also look at the ITKModuleTemplate repository: https://github.com/InsightSoftwareConsortium/ITKModuleTemplate Brad From: Pablo Hern?ndez > Date: Thursday, August 3, 2017 at 8:28 AM To: Beatriz Paniagua > Cc: "insight-users at itk.org" > Subject: Re: [ITK-users] [ITK] About the distribution of wrapped python for ITK external modules Hi Bea, that's awesome, I will try to copy the configuration from the repo of your publication: https://github.com/InsightSoftwareConsortium/ITKTextureFeatures Thanks, Pablo On Fri, Aug 4, 2017 at 12:00 AM, Beatriz Paniagua > wrote: Hi Pablo, We have created external module specific python wraps for some applications. One example is the work that Matt M and JB Vimort did in the ITKTextureFilters. http://review.source.kitware.com/#/c/22531/ Hope that helps! Best, Bea On Wed, Aug 2, 2017 at 11:07 PM, Pablo Hern?ndez > wrote: Hi there, It seems that the only way to install an external module is to build the ITK source with the option -DModule_xxx:BOOL=ON, but I was thinking... if the module is optional in the ITK source code and provides python wraps, is it available in the python itk package with `pip install itk`? In other words, do you wrap all the optional external modules when distributing the python itk or only the default modules? If the latter, would it be possible to create optional python packages for External Modules with the same deploying pipeline you use? Cheers, Pablo _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -- Beatriz Paniagua, PhD Technical Leader Kitware, Inc. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From pablo.hernandez.cerdan at outlook.com Mon Aug 7 19:07:01 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Mon, 7 Aug 2017 23:07:01 +0000 Subject: [ITK-users] [ITK] About the distribution of wrapped python for ITK external modules In-Reply-To: References: <5E37A920-455F-4CDB-BA6F-8E031D860C8D@mail.nih.gov> Message-ID: Hello Francois, thanks for testing it. In case you miss something, there are still a few classes not wrapped, will try to add them next weekend. Pablo On Tue, Aug 8, 2017 at 1:07 AM, francois.budin at kitware.com > wrote: Hello Pablo, It's great to hear that you were able to generate the Python wheels for your package. I was able to install it with the following command: pip install itk-isotropicwavelets It's great to have an really easy access to this module. Thanks for generating the pacakge. Francois On Sun, Aug 6, 2017 at 6:07 AM, Pablo Hern?ndez > wrote: Thanks Brad, it helped a lot. I copied the CI files (travis, appveyor and circle) and the setup.py from the ITKModuleTemplate, changed just a little bit on setup.py, and it works! I have the .wheel files for all the platforms. Just a few notes, I had to add a 3.6 in the .travis.yml --which generates the wheels for macOS because I was hitting the time limit (~50min). `./macpython-download-cache-and-build-module-wheels.sh 3.6` Also, to upload it into pypi for using `pip install`, I have registered myself in pypi and testpypi, configured a `.pypirc` file with my credentials and downloaded the wheels from every site into a `dist` folder, then: `twine upload ./dist/* -r testpypi` And it works! (python-test-virtual_environment) pip install --extra-index-url https://testpypi.python.org/pypi itk-isotropicwavelets Amazing, thanks a lot, Cheers, Pablo On Fri, Aug 4, 2017 at 12:48 AM, blowekamp at mail.nih.gov > wrote: I would also look at the ITKModuleTemplate repository: https://github.com/InsightSoftwareConsortium/ITKModuleTemplate Brad From: Pablo Hern?ndez > Date: Thursday, August 3, 2017 at 8:28 AM To: Beatriz Paniagua > Cc: "insight-users at itk.org" > Subject: Re: [ITK-users] [ITK] About the distribution of wrapped python for ITK external modules Hi Bea, that's awesome, I will try to copy the configuration from the repo of your publication: https://github.com/InsightSoftwareConsortium/ITKTextureFeatures Thanks, Pablo On Fri, Aug 4, 2017 at 12:00 AM, Beatriz Paniagua > wrote: Hi Pablo, We have created external module specific python wraps for some applications. One example is the work that Matt M and JB Vimort did in the ITKTextureFilters. http://review.source.kitware.com/#/c/22531/ Hope that helps! Best, Bea On Wed, Aug 2, 2017 at 11:07 PM, Pablo Hern?ndez > wrote: Hi there, It seems that the only way to install an external module is to build the ITK source with the option -DModule_xxx:BOOL=ON, but I was thinking... if the module is optional in the ITK source code and provides python wraps, is it available in the python itk package with `pip install itk`? In other words, do you wrap all the optional external modules when distributing the python itk or only the default modules? If the latter, would it be possible to create optional python packages for External Modules with the same deploying pipeline you use? Cheers, Pablo _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -- Beatriz Paniagua, PhD Technical Leader Kitware, Inc. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nickmarch31 at yahoo.com Mon Aug 7 22:27:52 2017 From: nickmarch31 at yahoo.com (Nick Cullen) Date: Tue, 8 Aug 2017 02:27:52 +0000 (UTC) Subject: [ITK-users] vnl matrix to numpy array gives random numbers References: <2035726053.1574361.1502159272821.ref@mail.yahoo.com> Message-ID: <2035726053.1574361.1502159272821@mail.yahoo.com> Hi Friends !! I'm trying to use itkPyVnl directly in ITK, but I must be getting something wrong with pointers... The following just gives me random numbers: ```? ? typedef typename ImageType::DirectionType ImageDirectionType; ? ?? ? ImageDirectionType * direction = const_cast( &image->GetDirection() ); ? ? typedef typename ImageDirectionType::InternalMatrixType DirectionInternalMatrixType;? ? DirectionInternalMatrixType * fixed_matrix = const_cast( &direction->GetVnlMatrix() ); ? ? const vnl_matrix vnlmat1 = fixed_matrix->as_matrix();? ? vnl_matrix * vnlmat2 = const_cast *>( &vnlmat1 ); ? ? typedef itk::PyVnl PyVnlType;? ? PyObject * mymatrix = PyVnlType::_GetArrayViewFromVnlMatrix( vnlmat2 );``` I've tried a million different things and have problems either 1) due to the constness of ->as_matrix() and others or 2) due to "taking the address of a temporary object" with ->as_matrix() ... -__- I know that this works: ```? ? vnl_matrix * vnlmat = new vnl_matrix;? ? vnlmat->set_size(2,3);? ? vnlmat->fill(0);? ? vnlmat->put(1,2,1.3);? ? vnlmat->put(1,0,2);? ? std::cout << vnlmat << std::endl; ? ? typedef itk::PyVnl PyVnlType;? ? PyObject * mymatrix = PyVnlType::_GetArrayViewFromVnlMatrix( vnlmat );``` Any help above is MUCH appreciated !!!! -------------- next part -------------- An HTML attachment was scrubbed... URL: From nickmarch31 at yahoo.com Mon Aug 7 22:32:24 2017 From: nickmarch31 at yahoo.com (Nick Cullen) Date: Tue, 8 Aug 2017 02:32:24 +0000 (UTC) Subject: [ITK-users] vnl matrix to numpy array gives random numbers In-Reply-To: <2035726053.1574361.1502159272821@mail.yahoo.com> References: <2035726053.1574361.1502159272821.ref@mail.yahoo.com> <2035726053.1574361.1502159272821@mail.yahoo.com> Message-ID: <12053585.1593555.1502159544989@mail.yahoo.com> Oh and to be clear, it gives me random numbers after I hit the numpy view and such (i.e.g?ndarrview ?= numpy.asarray(memview).view(dtype = numpydatatype).reshape(shape).view(numpy.ndarray)) On Monday, August 7, 2017 10:27 PM, Nick Cullen wrote: Hi Friends !! I'm trying to use itkPyVnl directly in ITK, but I must be getting something wrong with pointers... The following just gives me random numbers: ```? ? typedef typename ImageType::DirectionType ImageDirectionType; ? ?? ? ImageDirectionType * direction = const_cast( &image->GetDirection() ); ? ? typedef typename ImageDirectionType::InternalMatrixType DirectionInternalMatrixType;? ? DirectionInternalMatrixType * fixed_matrix = const_cast( &direction->GetVnlMatrix() ); ? ? const vnl_matrix vnlmat1 = fixed_matrix->as_matrix();? ? vnl_matrix * vnlmat2 = const_cast *>( &vnlmat1 ); ? ? typedef itk::PyVnl PyVnlType;? ? PyObject * mymatrix = PyVnlType::_GetArrayViewFromVnlMatrix( vnlmat2 );``` I've tried a million different things and have problems either 1) due to the constness of ->as_matrix() and others or 2) due to "taking the address of a temporary object" with ->as_matrix() ... -__- I know that this works: ```? ? vnl_matrix * vnlmat = new vnl_matrix;? ? vnlmat->set_size(2,3);? ? vnlmat->fill(0);? ? vnlmat->put(1,2,1.3);? ? vnlmat->put(1,0,2);? ? std::cout << vnlmat << std::endl; ? ? typedef itk::PyVnl PyVnlType;? ? PyObject * mymatrix = PyVnlType::_GetArrayViewFromVnlMatrix( vnlmat );``` Any help above is MUCH appreciated !!!! -------------- next part -------------- An HTML attachment was scrubbed... URL: From samuel.gerber at kitware.com Tue Aug 8 07:56:14 2017 From: samuel.gerber at kitware.com (Samuel Gerber) Date: Tue, 8 Aug 2017 07:56:14 -0400 Subject: [ITK-users] vnl matrix to numpy array gives random numbers In-Reply-To: <2035726053.1574361.1502159272821@mail.yahoo.com> References: <2035726053.1574361.1502159272821.ref@mail.yahoo.com> <2035726053.1574361.1502159272821@mail.yahoo.com> Message-ID: I'd guess there is something funky going with vnl_matrix_fixed. From the docs ( https://github.com/vxl/vxl/blob/master/core/vnl/vnl_matrix_fixed.h ) it says that the data resides on the stack. From your code snippet it is not exactly clear to me who owns the data in fixed_matrix, probably image. Might it be that image gets removed before you use the array view? On Mon, Aug 7, 2017 at 10:27 PM, Nick Cullen via Insight-users < insight-users at itk.org> wrote: > Hi Friends !! > > I'm trying to use itkPyVnl directly in ITK, but I must be getting > something wrong with pointers... The following just gives me random numbers: > > ``` > typedef typename ImageType::DirectionType ImageDirectionType; > ImageDirectionType * direction = const_cast( > &image->GetDirection() ); > > typedef typename ImageDirectionType::InternalMatrixType > DirectionInternalMatrixType; > DirectionInternalMatrixType * fixed_matrix = const_cast *>( &direction->GetVnlMatrix() ); > > const vnl_matrix vnlmat1 = fixed_matrix->as_matrix(); > vnl_matrix * vnlmat2 = const_cast *>( > &vnlmat1 ); > > typedef itk::PyVnl PyVnlType; > PyObject * mymatrix = PyVnlType::_GetArrayViewFromVnlMatrix( vnlmat2 > ); > ``` > > I've tried a million different things and have problems either 1) due to > the constness of ->as_matrix() and others or 2) due to "taking the address > of a temporary object" with ->as_matrix() ... -__- > > > I know that this works: > > ``` > vnl_matrix * vnlmat = new vnl_matrix; > vnlmat->set_size(2,3); > vnlmat->fill(0); > vnlmat->put(1,2,1.3); > vnlmat->put(1,0,2); > std::cout << vnlmat << std::endl; > > typedef itk::PyVnl PyVnlType; > PyObject * mymatrix = PyVnlType::_GetArrayViewFromVnlMatrix( vnlmat ); > ``` > > Any help above is MUCH appreciated !!!! > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -- Samuel Gerber R&D Engineer Kitware, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Tue Aug 8 08:51:35 2017 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Tue, 8 Aug 2017 12:51:35 +0000 Subject: [ITK-users] [ITK] vnl matrix to numpy array gives random numbers In-Reply-To: References: <2035726053.1574361.1502159272821.ref@mail.yahoo.com> <2035726053.1574361.1502159272821@mail.yahoo.com> Message-ID: <43846F33-7B8E-4819-B7AA-BF5DB9CB4D1D@mail.nih.gov> Hello, Is there a method named something like ?_GetArrayFromVnlMatrix?? This should perform a copy of the data, as opposed to just a ?view?. Brad From: Samuel Gerber Date: Tuesday, August 8, 2017 at 7:57 AM To: Nick Cullen Cc: "insight-users at itk.org" Subject: Re: [ITK] [ITK-users] vnl matrix to numpy array gives random numbers I'd guess there is something funky going with vnl_matrix_fixed. From the docs ( https://github.com/vxl/vxl/blob/master/core/vnl/vnl_matrix_fixed.h ) it says that the data resides on the stack. From your code snippet it is not exactly clear to me who owns the data in fixed_matrix, probably image. Might it be that image gets removed before you use the array view? On Mon, Aug 7, 2017 at 10:27 PM, Nick Cullen via Insight-users > wrote: Hi Friends !! I'm trying to use itkPyVnl directly in ITK, but I must be getting something wrong with pointers... The following just gives me random numbers: ``` typedef typename ImageType::DirectionType ImageDirectionType; ImageDirectionType * direction = const_cast( &image->GetDirection() ); typedef typename ImageDirectionType::InternalMatrixType DirectionInternalMatrixType; DirectionInternalMatrixType * fixed_matrix = const_cast( &direction->GetVnlMatrix() ); const vnl_matrix vnlmat1 = fixed_matrix->as_matrix(); vnl_matrix * vnlmat2 = const_cast *>( &vnlmat1 ); typedef itk::PyVnl PyVnlType; PyObject * mymatrix = PyVnlType::_GetArrayViewFromVnlMatrix( vnlmat2 ); ``` I've tried a million different things and have problems either 1) due to the constness of ->as_matrix() and others or 2) due to "taking the address of a temporary object" with ->as_matrix() ... -__- I know that this works: ``` vnl_matrix * vnlmat = new vnl_matrix; vnlmat->set_size(2,3); vnlmat->fill(0); vnlmat->put(1,2,1.3); vnlmat->put(1,0,2); std::cout << vnlmat << std::endl; typedef itk::PyVnl PyVnlType; PyObject * mymatrix = PyVnlType::_GetArrayViewFromVnlMatrix( vnlmat ); ``` Any help above is MUCH appreciated !!!! _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users -- Samuel Gerber R&D Engineer Kitware, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Tue Aug 8 09:41:33 2017 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 8 Aug 2017 09:41:33 -0400 Subject: [ITK-users] Reader InvalidRequestedRegionError In-Reply-To: <1502135858865-7590161.post@n2.nabble.com> References: <1502135858865-7590161.post@n2.nabble.com> Message-ID: Hi Matias, can you check that all images in that series have size 512x512? A possible cause is if one of the images has size 484x484. Orientation and region are not connected too much, I doubt that a funky orientation would cause problems for region. Regards, D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.) On Mon, Aug 7, 2017 at 3:57 PM, matimont wrote: > Hi, > > I'm reading a serie from a directory and I get this: > > itk::InvalidRequestedRegionError (0000001D4B9AEDD8) > Location: "unknown" > File: c:\itk-4.12.0\modules\io\imagebase\include\itkImageFileReader.hxx > Line: 350 > Description: ImageIO returns IO region that does not fully contain the > requested regionRequested region: ImageRegion (0000001D4B9AEDA0) > Dimension: 3 > Index: [0, 0, 0] > Size: [512, 512, 1] > StreamableRegion region: ImageRegion (0000001D4B9AEE00) > Dimension: 3 > Index: [0, 0, 0] > Size: [484, 484, 1] > > I noticed the images I read have ImageOrientationPatient as: > (0020,0037) ImageOrientationPatient > -0.4181660095794\0.90837062283655\0\0\0\-1 > > This only patient has failed, all others work > > Would this cause the reader to fail? > > This is part of the code I use to read the series: > > ImageIOType::Pointer gdcmIO = ImageIOType::New(); > InputNamesGeneratorType::Pointer inputNames = > InputNamesGeneratorType::New(); > inputNames->SetInputDirectory( argv[1] ); > > const ReaderType::FileNamesContainer & filenames = > inputNames->GetInputFileNames(); > > ReaderType::Pointer reader = ReaderType::New(); > > reader->SetImageIO( gdcmIO ); > reader->SetFileNames( filenames ); > try > { > reader->Update(); > } > catch (itk::ExceptionObject &excp) > { > std::cerr << "Exception thrown while reading the series" << std::endl; > std::cerr << excp << std::endl; > return EXIT_FAILURE; > } > > Thanks, > > Matias. > > > > -- > View this message in context: http://itk-insight-users. > 2283740.n2.nabble.com/Reader-InvalidRequestedRegionError-tp7590161.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nickmarch31 at yahoo.com Tue Aug 8 09:46:11 2017 From: nickmarch31 at yahoo.com (Nick Cullen) Date: Tue, 8 Aug 2017 13:46:11 +0000 (UTC) Subject: [ITK-users] [ITK] vnl matrix to numpy array gives random numbers In-Reply-To: <43846F33-7B8E-4819-B7AA-BF5DB9CB4D1D@mail.nih.gov> References: <2035726053.1574361.1502159272821.ref@mail.yahoo.com> <2035726053.1574361.1502159272821@mail.yahoo.com> <43846F33-7B8E-4819-B7AA-BF5DB9CB4D1D@mail.nih.gov> Message-ID: <308480851.1839365.1502199971993@mail.yahoo.com> Re: Brad No unfortunately there's only GetArrayView.. the copy happens at the python level in the wrapping.? Re: Samuel, i think you're probably right.? I dont think it's a direct issue with the function though, as shown by the second example. Here is something that works: vnl_matrix * vnlmat = new vnl_matrix;vnlmat->set_size(2,3);vnlmat->fill(0);vnlmat->put(1,2,1.3);vnlmat->put(1,0,2); typedef itk::PyVnl PyVnlType;PyObject * mymatrix = PyVnlType::_GetArrayViewFromVnlMatrix( vnlmat ); Here is something that returns random initialization values (e.g. 1.0232e-307) vnl_matrix vnlmat;vnlmat.set_size(2,3);vnlmat.fill(0);vnlmat.put(1,2,1.3);vnlmat.put(1,0,2); typedef itk::PyVnl PyVnlType;PyObject * mymatrix = PyVnlType::_GetArrayViewFromVnlMatrix( vnlmat ); that's why i say it's a pointer issue . I guess i could just copy the matrix into a new one and use that . i will figure it out. thanks for the help :) On Tuesday, August 8, 2017 8:51 AM, "Lowekamp, Bradley (NIH/NLM/LHC) [C]" wrote: #yiv5516187396 #yiv5516187396 -- _filtered #yiv5516187396 {panose-1:2 4 5 3 5 4 6 3 2 4;} _filtered #yiv5516187396 {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;} _filtered #yiv5516187396 {panose-1:2 0 5 3 0 0 0 2 0 4;}#yiv5516187396 #yiv5516187396 p.yiv5516187396MsoNormal, #yiv5516187396 li.yiv5516187396MsoNormal, #yiv5516187396 div.yiv5516187396MsoNormal {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;}#yiv5516187396 a:link, #yiv5516187396 span.yiv5516187396MsoHyperlink {color:blue;text-decoration:underline;}#yiv5516187396 a:visited, #yiv5516187396 span.yiv5516187396MsoHyperlinkFollowed {color:purple;text-decoration:underline;}#yiv5516187396 span.yiv5516187396EmailStyle17 {color:windowtext;}#yiv5516187396 span.yiv5516187396msoIns {text-decoration:underline;color:teal;}#yiv5516187396 .yiv5516187396MsoChpDefault {font-size:10.0pt;} _filtered #yiv5516187396 {margin:1.0in 1.0in 1.0in 1.0in;}#yiv5516187396 div.yiv5516187396WordSection1 {}#yiv5516187396 Hello, ? Is there a method named something like ?_GetArrayFromVnlMatrix?? This should perform a copy of the data, as opposed to just a ?view?. ? Brad ? ? From:Samuel Gerber Date: Tuesday, August 8, 2017 at 7:57 AM To: Nick Cullen Cc: "insight-users at itk.org" Subject: Re: [ITK] [ITK-users] vnl matrix to numpy array gives random numbers ? I'd guess there is something funky going with vnl_matrix_fixed. >From the docs (https://github.com/vxl/vxl/blob/master/core/vnl/vnl_matrix_fixed.h ) it says that the data resides on the stack. From your code snippet it is not exactly clear to me who owns the data in fixed_matrix, probably image. Might it be that image gets removed before you use the array view? ? On Mon, Aug 7, 2017 at 10:27 PM, Nick Cullen via Insight-users wrote: Hi Friends !! ? I'm trying to use itkPyVnl directly in ITK, but I must be getting something wrong with pointers... The following just gives me random numbers: ? ``` ? ? typedef typename ImageType::DirectionType ImageDirectionType; ? ? ? ? ImageDirectionType * direction = const_cast( &image->GetDirection() ); ? ? ? typedef typename ImageDirectionType::InternalMatrixType DirectionInternalMatrixType; ? ? DirectionInternalMatrixType * fixed_matrix = const_cast( &direction->GetVnlMatrix() ); ? ? ? const vnl_matrix vnlmat1 = fixed_matrix->as_matrix(); ? ? vnl_matrix * vnlmat2 = const_cast *>( &vnlmat1 ); ? ? ? typedef itk::PyVnl PyVnlType; ? ? PyObject * mymatrix = PyVnlType::_GetArrayViewFromVnlMatrix( vnlmat2 ); ``` ? I've tried a million different things and have problems either 1) due to the constness of ->as_matrix() and others or 2) due to "taking the address of a temporary object" with ->as_matrix() ... -__- ? ? I know that this works: ? ``` ? ? vnl_matrix * vnlmat = new vnl_matrix; ? ? vnlmat->set_size(2,3); ? ? vnlmat->fill(0); ? ? vnlmat->put(1,2,1.3); ? ? vnlmat->put(1,0,2); ? ? std::cout << vnlmat << std::endl; ? ? ? typedef itk::PyVnl PyVnlType; ? ? PyObject * mymatrix = PyVnlType::_GetArrayViewFromVnlMatrix( vnlmat ); ``` ? Any help above is MUCH appreciated !!!! _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users ? -- Samuel Gerber R&D Engineer Kitware, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From matimontg at gmail.com Tue Aug 8 09:55:15 2017 From: matimontg at gmail.com (matimont) Date: Tue, 8 Aug 2017 06:55:15 -0700 (MST) Subject: [ITK-users] Reader InvalidRequestedRegionError In-Reply-To: References: <1502135858865-7590161.post@n2.nabble.com> Message-ID: <1502200515875-7590171.post@n2.nabble.com> That was actually the issue, there was an image in the series that was not supposed to be there, thank you for your suggestions, it saved me time! Matias. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Reader-InvalidRequestedRegionError-tp7590161p7590171.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From blowekamp at mail.nih.gov Tue Aug 8 15:03:17 2017 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Tue, 8 Aug 2017 19:03:17 +0000 Subject: [ITK-users] [ANN] SimpleITK 1.0.1 Release Message-ID: The SimpleITK Development Team and on behalf of the Insight Software Consortium, we announce the release of version 1.0.1 of SimpleITK. SimpleITK is available for the following programing languages: Python, R, Java, C#, C++, Lua, Ruby, and TCL. Binary versions of the toolkit are available for the GNU Linux, Apple OS X, and Microsoft Windows operating systems. All of the source code is freely available on Github under an Apache-2.0 license. We are in the process of migrating the old SimpleITK Wiki (https://itk.org/Wiki/SimpleITK), to Read The Docs (http://simpleitk.readthedocs.io/en/latest/). Downloading SimpleITK Complete instructions on getting started with SimpleITK including downloading binaries can be found on Read The Docs (http://simpleitk.readthedocs.io/en/latest/Documentation/docs/source/installation.html). Python Binary Downloads - Python binary wheels are available for download. It is important to have the latest version of pip to ensure correct wheel compatibility and installation. To install the latest SimpleITK package form PyPI: ``` python -m install --upgrade pip python -m install SimpleITK ``` - Many Conda package have been upload to Anaconda Cloud on the `SimpleITK`. These can be installed with: ``` conda install -c simpleitk simpleitk ``` - A complete available set of compiled binaries, including select CSharp and Java distributions, along with source and data tar-balls are available on Source Forge (https://sourceforge.net/projects/simpleitk/files/SimpleITK/1.0.0/). - SimpleITK has a robust Superbuild CMake system which minimized the dependencies needed to build SimpleITK from scratch. Complete compilation instructions can be found on Read the Docs (http://simpleitk.readthedocs.io/en/latest/Documentation/docs/source/building.html). Release Notes - Improvements - Uses ITK 4.11.1, tested for compatibility with ITK 4.12 - Improved error reporting for sitk.Show - Improved search paths for sitk.Show - Updated documentation from ITK and corrected spelling mistakes - Bug Fixes - Numerous compilation issues related to R and mingw - Fix CMake searching for Lua and Python - Fix enabling SITK_4D_IMAGE - Fix SimpleITKConfig.cmake.in compatibility for installed ITK - Fix Superbuild issues with the Example directory as a project - Fix out of bound array access in Image4D.ExtractImageFilter test - Fixes to Python's setup.py for build_ext -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Thu Aug 10 13:32:41 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 10 Aug 2017 13:32:41 -0400 Subject: [ITK-users] [ITK] [ITK-dev] Migration to GitHub In-Reply-To: References: <20170801214514.1391365852@mail.rogue-research.com> <575179844.18333096.1501666754328.JavaMail.zimbra@enst.fr> Message-ID: Thanks to all for participating in the discussion. To conclude, there is a desire to work on an open source platform and stay in sync with CMake, VTK, and ParaView. However, there is overwhelming support to migrate to GitHub for the open source community there and developer familiarity. We will migrate the various infrastructure pieces to GitHub over the coming months. Thanks, Matt On Wed, Aug 2, 2017 at 11:47 AM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] wrote: > My vote is for GitHub for the same reasons D?enan gave, familiarity and that > is where most open source developers interact. > > > > Supporting this with some facts from the git 2016 survey > (https://survs.com/report/nz2odu1spl): > > > > Which git hosting site(s) do you use for your project(s)? > > GitHub, 84%, 7636 > > Bitbucket , 42%, 3840 > > GitLab, 32%, 2917 > > > > my 2 cents > > Ziv > > > > > > > > > > > > > > From: D?enan Zuki? > Date: Wednesday, August 2, 2017 at 11:20 AM > Cc: "community at itk.org" > Subject: Re: [ITK] [ITK-users] [ITK-dev] Migration to GitHub > > > > More projects in general use GitHub, and more people are familiar with it, > myself included. Familiarity alone is enough for my vote! > > > > On Wed, Aug 2, 2017 at 5:39 AM, Timothee Evain > wrote: > > Hello everyone, > > My 2 cents on this brainstorming, if that could help: > Is there any estimation on how well the VTK and ITK communities overlap? I > mean, as a mostly ITK user, I came naturally to VTK for all the > visualization and 3D modelling tasks given the similarities between both > libraries, so even if I can mostly contribute to ITK, there is still chances > that I could help on VTK. It may be a biais since I'm working on 3D volumes > and not 2D images that can be easily displayed elsewhere, but as far as I'm > concerned, I would favor a united framework for ITK, VTK, 3D Slicer, etc. So > if the communities are more or less the same people, I would advocate for > GitLab (plus, that's open sourced). Since you could authentify people from > GitHub credentials, that don't seems a big side-lining. > > However, if there is a clear distinction between communities, I think that > going for GitHub is the best choice to get access to more people, that are > used to GitHub facilities. That would increase chances of involving people > into the project. > (Note that I'm not well aware of the implications of using a close-source > forge.) > > HTH, > > Tim > > ----- Mail original ----- > De: "Matt McCormick" > ?: "Sean McBride" > Cc: "Insight-Users" , "Hans Johnson" > , "Insight Developers List" > > Envoy?: Mardi 1 Ao?t 2017 23:59:37 > Objet: Re: [ITK] [ITK-users] [ITK-dev] Migration to GitHub > > > On Tue, Aug 1, 2017 at 5:45 PM, Sean McBride > wrote: >> On Tue, 1 Aug 2017 11:40:25 -0400, Francois Budin said: >> >>>As Matt mentioned, the main reason is because a lot of ITK users already >>>have Github accounts and are familiar with that environment. The idea is >>>really to make is as simple as possible for the community to contribute. >>>Using Gitlab would still require users to have an account on GitLab to >>> push >>>patches. Most ITK users already have a Github account with their own >>>projects, and contributing to ITK just requires cloning the project and >>>creating a pull-request. >> >> The fact that many people are familiar with github and its workflow is >> indeed a good argument. >> >> But the "using Gitlab would still require users to have an account on >> GitLab" I think is no argument at all. Creating a GitLab account is a fast >> and easy one-time task, the browser can then remember your password, etc. >> Everyone is used to having a zillion accounts for all the zillion services >> we all use. > > Yes, this is true. > > We already have OAuth sign-in for Gerrit that uses GitHub credentials. > But, the benefits come more from a familiarity with the user interface > and deeper integrations like notifications, user and issue references, > etc. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From mihail.isakov at googlemail.com Thu Aug 10 18:50:09 2017 From: mihail.isakov at googlemail.com (Mihail Isakov) Date: Fri, 11 Aug 2017 00:50:09 +0200 Subject: [ITK-users] Segmentation fault in itkBinaryMask3DMeshSource Message-ID: Hello, i wonder how i could avoid crash in itkBinaryMask3DMeshSource (actual version). In most cases the filter works excellent, but some files bring it to segmentation fault. r at deb:~/Desktop/test1/build$ ./test1 ../t.mha Segmentation fault Debug: Modules/Core/Mesh/include/itkBinaryMask3DMeshSource.hxx 2343 if ( currentframetmp[i][0] != 0 ) 2344 { 2345 m_CurrentFrame[m_CurrentFrameIndex][1] = currentframetmp[i][1]; <------------- 2346 m_CurrentFrame[m_CurrentFrameIndex++][0] = currentframetmp[i][0]; the value of 'm_CurrentFrameIndex' in debugger is 65000, 'i' is 1 Minimal project with test file is here https://drive.google.com/file/d/0ByBLJ2-U1t9xUm51d2Mtdzg1ZjQ/view?usp=sharing Thanks. Regards, Mihail From pablo.hernandez.cerdan at outlook.com Thu Aug 10 23:51:42 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Fri, 11 Aug 2017 03:51:42 +0000 Subject: [ITK-users] [ITK] Recommended approach for cross-platform deploying ITK+Vtk+Qt5 In-Reply-To: References: Message-ID: Hi Andreas, now that you mention, do you know how Slicer deals with Windows for continuous integration? concretely in terms of: - deploy - build - test Particularly interested in the deploying part right now. Do they use their own servers for deployment? Pablo On Thu, Aug 3, 2017 at 12:29 PM, Pablo Hern?ndez > wrote: Hi Matt, this is super helpful. I created a Dockerfie with all the dependencies, but I used Ubuntu 16.04 as base... so, I should compile with an older glib... I will definitely check AppLauncher. Thanks! Pablo On Tue, Aug 1, 2017 at 2:36 AM, matt.mccormick at kitware.com > wrote: Hi Pablo, Good questions -- C++ ITK/VTK/Qt package development on GitHub CI services is non-trivial. A common issue is timeout's, and a strategy is to use pre-built binaries of ITK/VTK/Qt. Regarding Linux package development, CircleCI is recommended with a custom Docker image that has ITK / VTK / Qt pre-built. Since glibc is forward compatible but not backwards compatible, a base image that uses the oldest version of glibc will generate the most compatible image. For many projects, we use CentOS 5 with a newer GCC, but I think only Qt4 can be built with this and not Qt5. The build can be generated on one Linux Docker image for glibc purposes and tested on another that provides the graphical context. See the CommonTK AppLauncher configuration as an example [1]. This uses the thewtex/opengl Docker image [2] to provide a portable, reproducible, CPU-based graphical testing environment [2]. The CTK AppLauncher is also of interest as an alternative to windowsqtdeploy, etc. It is cross-platform, and provides the setup to use shared libraries and avoid Qt LGPL licensing issues. For Windows builds, the dockcross/windows-x64 (uses MXE/MinGW-x64) image could work nicely. A derived image that builds the MXE packages for ITK / VTK / Qt could be created [3]. Since dockcross also comes with WINE for testing, it may also be possible to use thewtex/opengl for testing on CircleCI (although I have never tried this). For macOS builds, TravisCI has Homebrew installed on their images, and ITK / VTK / Qt can be installed via Homebrew [4]. HTH, Matt [1] https://github.com/commontk/AppLauncher/blob/5b592f1baaa7dd41d68e1cd56a2a82e298196ebe/circle.yml [2] https://github.com/thewtex/docker-opengl [3] http://mxe.cc/ [4] https://blog.kitware.com/kitware-packages-on-os-x-with-homebrew/ On Sun, Jul 30, 2017 at 8:02 AM, Andras Lasso > wrote: > Currently, Slicer does not use AppVeyor for continuous integration on > Windows. Also, the full test suite of Slicer takes several hours to run, so > CircleCI only checks for build errors. > > > > Andras > > > > From: Pablo Hern?ndez > Sent: Sunday, July 30, 2017 6:58 > To: Insight-users > Subject: [ITK] [ITK-users] Recommended approach for cross-platform deploying > ITK+Vtk+Qt5 > > > > Hi, > I wonder what is the recommended approach for deploying a cross-platform > application involving ITK+Vtk+Qt nowadays with all the available tools: > docker containers, travis-ci, appveyor, circle-ci etc. > > Is it still recommended to create a SuperBuild with all your dependencies as > ExternalProjects in CMake? How do you reduce the time it takes to build? > The build time for all my dependencies (Vtk (with qt5), ITK, boost) plus my > small app is surpassing the 60min limit in both, AppVeyor and Travis-CI. To > alleviate this, do you use docker?. > > My main concern is Windows, I have seen that @thewtex and @jcfr have a repo > with closs-platform buildings ( https://github.com/dockcross/dockcross ), > there is a Windows64 there with Mingw that might help. I have no idea if I > can generate windows binaries from AppVeyor using docker, or instead, I > generate them using that docker image with Wine+MinGw in Travis-CI. > > Instead of CPack from CMake I have been thinking to use windowsqtdeploy, > linuxqtdeploy from Qt... > > I have been looking to Slicer source code to see how they are doing it, and > it seems super structured, but not 100% sure how they generate their nightly > packages ( I guess it involves these docker images: > https://github.com/thewtex/SlicerDocker, but also in Windows?) > > Maybe this is the not best forum to ask, but if you have any recommendations > for deploying a small GUI app based on ITK, I will be extremely grateful to > hear them. Thanks! > > Cheers, > Pablo > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pablo.hernandez.cerdan at outlook.com Thu Aug 10 23:51:45 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Fri, 11 Aug 2017 03:51:45 +0000 Subject: [ITK-users] [ITK] Recommended approach for cross-platform deploying ITK+Vtk+Qt5 In-Reply-To: References: Message-ID: Hi Andreas, now that you mention, do you know how Slicer deals with Windows for continuous integration? concretely in terms of: - deploy - build - test Particularly interested in the deploying part right now. Do they use their own servers for deployment? Pablo On Thu, Aug 3, 2017 at 12:29 PM, Pablo Hern?ndez > wrote: Hi Matt, this is super helpful. I created a Dockerfie with all the dependencies, but I used Ubuntu 16.04 as base... so, I should compile with an older glib... I will definitely check AppLauncher. Thanks! Pablo On Tue, Aug 1, 2017 at 2:36 AM, matt.mccormick at kitware.com > wrote: Hi Pablo, Good questions -- C++ ITK/VTK/Qt package development on GitHub CI services is non-trivial. A common issue is timeout's, and a strategy is to use pre-built binaries of ITK/VTK/Qt. Regarding Linux package development, CircleCI is recommended with a custom Docker image that has ITK / VTK / Qt pre-built. Since glibc is forward compatible but not backwards compatible, a base image that uses the oldest version of glibc will generate the most compatible image. For many projects, we use CentOS 5 with a newer GCC, but I think only Qt4 can be built with this and not Qt5. The build can be generated on one Linux Docker image for glibc purposes and tested on another that provides the graphical context. See the CommonTK AppLauncher configuration as an example [1]. This uses the thewtex/opengl Docker image [2] to provide a portable, reproducible, CPU-based graphical testing environment [2]. The CTK AppLauncher is also of interest as an alternative to windowsqtdeploy, etc. It is cross-platform, and provides the setup to use shared libraries and avoid Qt LGPL licensing issues. For Windows builds, the dockcross/windows-x64 (uses MXE/MinGW-x64) image could work nicely. A derived image that builds the MXE packages for ITK / VTK / Qt could be created [3]. Since dockcross also comes with WINE for testing, it may also be possible to use thewtex/opengl for testing on CircleCI (although I have never tried this). For macOS builds, TravisCI has Homebrew installed on their images, and ITK / VTK / Qt can be installed via Homebrew [4]. HTH, Matt [1] https://github.com/commontk/AppLauncher/blob/5b592f1baaa7dd41d68e1cd56a2a82e298196ebe/circle.yml [2] https://github.com/thewtex/docker-opengl [3] http://mxe.cc/ [4] https://blog.kitware.com/kitware-packages-on-os-x-with-homebrew/ On Sun, Jul 30, 2017 at 8:02 AM, Andras Lasso > wrote: > Currently, Slicer does not use AppVeyor for continuous integration on > Windows. Also, the full test suite of Slicer takes several hours to run, so > CircleCI only checks for build errors. > > > > Andras > > > > From: Pablo Hern?ndez > Sent: Sunday, July 30, 2017 6:58 > To: Insight-users > Subject: [ITK] [ITK-users] Recommended approach for cross-platform deploying > ITK+Vtk+Qt5 > > > > Hi, > I wonder what is the recommended approach for deploying a cross-platform > application involving ITK+Vtk+Qt nowadays with all the available tools: > docker containers, travis-ci, appveyor, circle-ci etc. > > Is it still recommended to create a SuperBuild with all your dependencies as > ExternalProjects in CMake? How do you reduce the time it takes to build? > The build time for all my dependencies (Vtk (with qt5), ITK, boost) plus my > small app is surpassing the 60min limit in both, AppVeyor and Travis-CI. To > alleviate this, do you use docker?. > > My main concern is Windows, I have seen that @thewtex and @jcfr have a repo > with closs-platform buildings ( https://github.com/dockcross/dockcross ), > there is a Windows64 there with Mingw that might help. I have no idea if I > can generate windows binaries from AppVeyor using docker, or instead, I > generate them using that docker image with Wine+MinGw in Travis-CI. > > Instead of CPack from CMake I have been thinking to use windowsqtdeploy, > linuxqtdeploy from Qt... > > I have been looking to Slicer source code to see how they are doing it, and > it seems super structured, but not 100% sure how they generate their nightly > packages ( I guess it involves these docker images: > https://github.com/thewtex/SlicerDocker, but also in Windows?) > > Maybe this is the not best forum to ask, but if you have any recommendations > for deploying a small GUI app based on ITK, I will be extremely grateful to > hear them. Thanks! > > Cheers, > Pablo > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pablo.hernandez.cerdan at outlook.com Thu Aug 10 23:51:48 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Fri, 11 Aug 2017 03:51:48 +0000 Subject: [ITK-users] [ITK] Recommended approach for cross-platform deploying ITK+Vtk+Qt5 In-Reply-To: References: Message-ID: Hi Andreas, now that you mention, do you know how Slicer deals with Windows for continuous integration? concretely in terms of: - deploy - build - test Particularly interested in the deploying part right now. Do they use their own servers for deployment? Pablo On Thu, Aug 3, 2017 at 12:29 PM, Pablo Hern?ndez > wrote: Hi Matt, this is super helpful. I created a Dockerfie with all the dependencies, but I used Ubuntu 16.04 as base... so, I should compile with an older glib... I will definitely check AppLauncher. Thanks! Pablo On Tue, Aug 1, 2017 at 2:36 AM, matt.mccormick at kitware.com > wrote: Hi Pablo, Good questions -- C++ ITK/VTK/Qt package development on GitHub CI services is non-trivial. A common issue is timeout's, and a strategy is to use pre-built binaries of ITK/VTK/Qt. Regarding Linux package development, CircleCI is recommended with a custom Docker image that has ITK / VTK / Qt pre-built. Since glibc is forward compatible but not backwards compatible, a base image that uses the oldest version of glibc will generate the most compatible image. For many projects, we use CentOS 5 with a newer GCC, but I think only Qt4 can be built with this and not Qt5. The build can be generated on one Linux Docker image for glibc purposes and tested on another that provides the graphical context. See the CommonTK AppLauncher configuration as an example [1]. This uses the thewtex/opengl Docker image [2] to provide a portable, reproducible, CPU-based graphical testing environment [2]. The CTK AppLauncher is also of interest as an alternative to windowsqtdeploy, etc. It is cross-platform, and provides the setup to use shared libraries and avoid Qt LGPL licensing issues. For Windows builds, the dockcross/windows-x64 (uses MXE/MinGW-x64) image could work nicely. A derived image that builds the MXE packages for ITK / VTK / Qt could be created [3]. Since dockcross also comes with WINE for testing, it may also be possible to use thewtex/opengl for testing on CircleCI (although I have never tried this). For macOS builds, TravisCI has Homebrew installed on their images, and ITK / VTK / Qt can be installed via Homebrew [4]. HTH, Matt [1] https://github.com/commontk/AppLauncher/blob/5b592f1baaa7dd41d68e1cd56a2a82e298196ebe/circle.yml [2] https://github.com/thewtex/docker-opengl [3] http://mxe.cc/ [4] https://blog.kitware.com/kitware-packages-on-os-x-with-homebrew/ On Sun, Jul 30, 2017 at 8:02 AM, Andras Lasso > wrote: > Currently, Slicer does not use AppVeyor for continuous integration on > Windows. Also, the full test suite of Slicer takes several hours to run, so > CircleCI only checks for build errors. > > > > Andras > > > > From: Pablo Hern?ndez > Sent: Sunday, July 30, 2017 6:58 > To: Insight-users > Subject: [ITK] [ITK-users] Recommended approach for cross-platform deploying > ITK+Vtk+Qt5 > > > > Hi, > I wonder what is the recommended approach for deploying a cross-platform > application involving ITK+Vtk+Qt nowadays with all the available tools: > docker containers, travis-ci, appveyor, circle-ci etc. > > Is it still recommended to create a SuperBuild with all your dependencies as > ExternalProjects in CMake? How do you reduce the time it takes to build? > The build time for all my dependencies (Vtk (with qt5), ITK, boost) plus my > small app is surpassing the 60min limit in both, AppVeyor and Travis-CI. To > alleviate this, do you use docker?. > > My main concern is Windows, I have seen that @thewtex and @jcfr have a repo > with closs-platform buildings ( https://github.com/dockcross/dockcross ), > there is a Windows64 there with Mingw that might help. I have no idea if I > can generate windows binaries from AppVeyor using docker, or instead, I > generate them using that docker image with Wine+MinGw in Travis-CI. > > Instead of CPack from CMake I have been thinking to use windowsqtdeploy, > linuxqtdeploy from Qt... > > I have been looking to Slicer source code to see how they are doing it, and > it seems super structured, but not 100% sure how they generate their nightly > packages ( I guess it involves these docker images: > https://github.com/thewtex/SlicerDocker, but also in Windows?) > > Maybe this is the not best forum to ask, but if you have any recommendations > for deploying a small GUI app based on ITK, I will be extremely grateful to > hear them. Thanks! > > Cheers, > Pablo > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lasso at queensu.ca Fri Aug 11 09:08:55 2017 From: lasso at queensu.ca (Andras Lasso) Date: Fri, 11 Aug 2017 13:08:55 +0000 Subject: [ITK-users] [ITK] Recommended approach for cross-platform deploying ITK+Vtk+Qt5 In-Reply-To: References: Message-ID: Yes, we dedicate a few regular desktop PCs to run nightly and continuous builds. On Windows we just test the master branch after integration, but pull requests are checked before on other platforms. Andras From: Pablo Hern?ndez [mailto:pablo.hernandez.cerdan at outlook.com] Sent: Thursday, August 10, 2017 11:52 PM To: matt.mccormick at kitware.com Cc: Insight-users ; Andras Lasso Subject: Re: [ITK-users] [ITK] Recommended approach for cross-platform deploying ITK+Vtk+Qt5 Hi Andreas, now that you mention, do you know how Slicer deals with Windows for continuous integration? concretely in terms of: - deploy - build - test Particularly interested in the deploying part right now. Do they use their own servers for deployment? Pablo On Thu, Aug 3, 2017 at 12:29 PM, Pablo Hern?ndez > wrote: Hi Matt, this is super helpful. I created a Dockerfie with all the dependencies, but I used Ubuntu 16.04 as base... so, I should compile with an older glib... I will definitely check AppLauncher. Thanks! Pablo On Tue, Aug 1, 2017 at 2:36 AM, matt.mccormick at kitware.com > wrote: Hi Pablo, Good questions -- C++ ITK/VTK/Qt package development on GitHub CI services is non-trivial. A common issue is timeout's, and a strategy is to use pre-built binaries of ITK/VTK/Qt. Regarding Linux package development, CircleCI is recommended with a custom Docker image that has ITK / VTK / Qt pre-built. Since glibc is forward compatible but not backwards compatible, a base image that uses the oldest version of glibc will generate the most compatible image. For many projects, we use CentOS 5 with a newer GCC, but I think only Qt4 can be built with this and not Qt5. The build can be generated on one Linux Docker image for glibc purposes and tested on another that provides the graphical context. See the CommonTK AppLauncher configuration as an example [1]. This uses the thewtex/opengl Docker image [2] to provide a portable, reproducible, CPU-based graphical testing environment [2]. The CTK AppLauncher is also of interest as an alternative to windowsqtdeploy, etc. It is cross-platform, and provides the setup to use shared libraries and avoid Qt LGPL licensing issues. For Windows builds, the dockcross/windows-x64 (uses MXE/MinGW-x64) image could work nicely. A derived image that builds the MXE packages for ITK / VTK / Qt could be created [3]. Since dockcross also comes with WINE for testing, it may also be possible to use thewtex/opengl for testing on CircleCI (although I have never tried this). For macOS builds, TravisCI has Homebrew installed on their images, and ITK / VTK / Qt can be installed via Homebrew [4]. HTH, Matt [1] https://github.com/commontk/AppLauncher/blob/5b592f1baaa7dd41d68e1cd56a2a82e298196ebe/circle.yml [2] https://github.com/thewtex/docker-opengl [3] http://mxe.cc/ [4] https://blog.kitware.com/kitware-packages-on-os-x-with-homebrew/ On Sun, Jul 30, 2017 at 8:02 AM, Andras Lasso > wrote: > Currently, Slicer does not use AppVeyor for continuous integration on > Windows. Also, the full test suite of Slicer takes several hours to run, so > CircleCI only checks for build errors. > > > > Andras > > > > From: Pablo Hern?ndez > Sent: Sunday, July 30, 2017 6:58 > To: Insight-users > Subject: [ITK] [ITK-users] Recommended approach for cross-platform deploying > ITK+Vtk+Qt5 > > > > Hi, > I wonder what is the recommended approach for deploying a cross-platform > application involving ITK+Vtk+Qt nowadays with all the available tools: > docker containers, travis-ci, appveyor, circle-ci etc. > > Is it still recommended to create a SuperBuild with all your dependencies as > ExternalProjects in CMake? How do you reduce the time it takes to build? > The build time for all my dependencies (Vtk (with qt5), ITK, boost) plus my > small app is surpassing the 60min limit in both, AppVeyor and Travis-CI. To > alleviate this, do you use docker?. > > My main concern is Windows, I have seen that @thewtex and @jcfr have a repo > with closs-platform buildings ( https://github.com/dockcross/dockcross ), > there is a Windows64 there with Mingw that might help. I have no idea if I > can generate windows binaries from AppVeyor using docker, or instead, I > generate them using that docker image with Wine+MinGw in Travis-CI. > > Instead of CPack from CMake I have been thinking to use windowsqtdeploy, > linuxqtdeploy from Qt... > > I have been looking to Slicer source code to see how they are doing it, and > it seems super structured, but not 100% sure how they generate their nightly > packages ( I guess it involves these docker images: > https://github.com/thewtex/SlicerDocker, but also in Windows?) > > Maybe this is the not best forum to ask, but if you have any recommendations > for deploying a small GUI app based on ITK, I will be extremely grateful to > hear them. Thanks! > > Cheers, > Pablo > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From francois.budin at kitware.com Fri Aug 11 10:44:46 2017 From: francois.budin at kitware.com (Francois Budin) Date: Fri, 11 Aug 2017 10:44:46 -0400 Subject: [ITK-users] Segmentation fault in itkBinaryMask3DMeshSource In-Reply-To: References: Message-ID: Hello Mihail, Thank you for the bug report. I found that there was a limitation in the current implementation due to the fact that it uses "unsigned short" variables. I will submit a patch and share it with you for your review. It should correct your problem. Is it ok to add your data you shared in this email to the ITK tests? Thanks, Francois On Thu, Aug 10, 2017 at 6:50 PM, Mihail Isakov via Insight-users < insight-users at itk.org> wrote: > Hello, > > i wonder how i could avoid crash in itkBinaryMask3DMeshSource (actual > version). In most cases the filter works excellent, but some files > bring it to segmentation fault. > > r at deb:~/Desktop/test1/build$ ./test1 ../t.mha > Segmentation fault > > Debug: > > Modules/Core/Mesh/include/itkBinaryMask3DMeshSource.hxx > > 2343 if ( currentframetmp[i][0] != 0 ) > 2344 { > 2345 m_CurrentFrame[m_CurrentFrameIndex][1] = > currentframetmp[i][1]; <------------- > 2346 m_CurrentFrame[m_CurrentFrameIndex++][0] = > currentframetmp[i][0]; > > the value of 'm_CurrentFrameIndex' in debugger is 65000, 'i' is 1 > > Minimal project with test file is here > > https://drive.google.com/file/d/0ByBLJ2-U1t9xUm51d2Mtdzg1ZjQ/view?usp= > sharing > > Thanks. > Regards, > Mihail > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Fri Aug 11 12:22:34 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 11 Aug 2017 12:22:34 -0400 Subject: [ITK-users] Problems Using GPU Filters In-Reply-To: References: <1498789176254-7590036.post@n2.nabble.com> <1501002308962-7590057.post@n2.nabble.com> <1501611311517-7590114.post@n2.nabble.com> <1501626181039-7590122.post@n2.nabble.com> Message-ID: Following up, I did not have a chance to fully address this. Progress is started here: http://review.source.kitware.com/#/q/topic:gpu-mean-filters The GPUMeanImageFilter tests are failing: itkGPUMeanImageFilterTest2D itkGPUMeanImageFilterTest3D I will take another look in a few weeks. Thanks, Matt On Fri, Aug 4, 2017 at 9:38 AM, Matt McCormick wrote: > Hi Andaharoo, > > You may have identified a bug. I am also seeing local failures in the > regression tests for the referenced classes. I will investigate > further next week. > > Thanks, > Matt > > On Tue, Aug 1, 2017 at 6:23 PM, Andaharoo wrote: >> I can't get the images to go from CPU to GPU on GPUMeanImageFilter, >> GPUBinaryThresholdImageFilter, and GPUDiscreteGaussianImageFilter. So I >> can't start my gpu pipeline with these filters. If I apply something like >> GPUGradientAnisotropicImageFilter (which does work) then I can apply the >> other filters confirming that it can go GPU to GPU but not CPU to GPU on >> those 3 filters. Do these 3 filters not support conversion? >> >> GPUInputImage::Pointer inPtr = >> dynamic_cast(this->ProcessObject::GetInput(0)); >> inPtr was null when I debugged GPUMeanImageFilter. This line also doesn't >> make sense in terms of using an Image since it would just return null if you >> gave it an Image that wasn't allocated as a GPUImage. Unless the cpu image >> gets converted to a gpu image elsewhere beforehand? >> >> It seems as though only GPUInPlaceImageFilters work with CPU - GPU >> conversion for me? I can't quite understand the GPUInPlaceImageFilters >> source yet so I'm not so sure why GPUGradientAnisotropicImageFilter works. >> They are, of course, different in terms of how they manage memory. >> >> >> >> -- >> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Problems-Using-GPU-Filters-tp7590036p7590122.html >> Sent from the ITK Insight Users mailing list archive at Nabble.com. >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Fri Aug 11 12:55:39 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 11 Aug 2017 12:55:39 -0400 Subject: [ITK-users] Cardiac Deformation using Segmentation and Registration of Ultrasound Images In-Reply-To: References: Message-ID: On Fri, Aug 4, 2017 at 9:36 AM, Matt McCormick wrote: > Hi Thanos, > > On Thu, Aug 3, 2017 at 1:00 PM, thanos thanos wrote: >> Hello everyone, >> >> D?enan, Andras and Matt thank you very much for your answers. >> To be honest I've tried already in the past registration with Slicer using >> Demons, B-Splines and also Elastix and Plastimach. >> >> D?enan, I read your last sentence already many times but I can't really >> understand what you mean by "initializing registration of time point n+1 by >> resulting transform from time point n." >> >> Matt, thank you for sharing your thoughts. I already looked at the >> AnisotropicDiffusionLBR paper and I have also tried the online interactive >> figures >> (https://insightsoftwareconsortium.github.io/ITKAnisotropicDiffusionLBR/). >> Seems to work nicely, but I wasn't sure how to build the project. I already >> configured my ITK by setting the Module_AnisotropicDiffusionLBR at the CMake >> and then I tried to build the CoherenceEnhancingDiffusion from the >> C:\ITK\src\Modules\Remote\AnisotropicDiffusionLBR\examples but I got " >> Cannot open include file: 'CoherenceEnhancingDiffusionFilter.h': No such >> file or directory " so I guess I am missing something.. > > Thanks for the note. I will look into this issue and address it next week. This is addressed here: http://review.source.kitware.com/#/c/22567/ https://github.com/InsightSoftwareConsortium/ITKAnisotropicDiffusionLBR/commit/3d9880d5f52c4c37e3b658abc607a13f3c3d9545 I will also create a Python package for the module. Thanks, Matt From siming.bayer at gmail.com Fri Aug 11 16:08:50 2017 From: siming.bayer at gmail.com (Siming Bayer) Date: Fri, 11 Aug 2017 22:08:50 +0200 Subject: [ITK-users] Integrate new .h and .txx file as a part of ITK Framework Message-ID: Dear all, I am quite new with ITK. I would like to add some new .h file and .txx files, which are not a part of the original ITK framework, into the original ITK Framework and use them together as library. How can I do it? I will be very happy to get any Information/hint/guide about it. best, Siming From siming.bayer at gmail.com Fri Aug 11 16:11:47 2017 From: siming.bayer at gmail.com (Sisi) Date: Fri, 11 Aug 2017 13:11:47 -0700 (MST) Subject: [ITK-users] Integrate new .h and .txx file as a part of ITK Framework Message-ID: <1502482307961-7590184.post@n2.nabble.com> Dear all, I am quite new with ITK. I would like to add some new .h file and .txx files, which are not a part of the original ITK framework, into the original ITK Framework and use them together as library. How can I do it? I will be very happy to get any Information/hint/guide about it. best, Siming -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Integrate-new-h-and-txx-file-as-a-part-of-ITK-Framework-tp7590184.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From francois.budin at kitware.com Fri Aug 11 16:59:18 2017 From: francois.budin at kitware.com (Francois Budin) Date: Fri, 11 Aug 2017 16:59:18 -0400 Subject: [ITK-users] Integrate new .h and .txx file as a part of ITK Framework In-Reply-To: <1502482307961-7590184.post@n2.nabble.com> References: <1502482307961-7590184.post@n2.nabble.com> Message-ID: Hello Siming, Welcome to ITK! I am not sure if you have had a chance to look at the ITKSoftwareGuide [1], but it is a great place to find a lot of information. The chapters that are the most relevant for you are probably Chapter 8 (How to write a filter) and Chapter 9 (How to create a module). To answer your question more specifically, the easiest way to integrate a new filter or new files to ITK is to develop an ITK module. This module can then either be compiled outside of ITK, or if you think it would be useful to the whole ITK community, it can be integrated to ITK as a remote module [2]. I hope this helps. Feel free to ask more questions. Francois [1] https://www.itk.org/ItkSoftwareGuide.pdf [2] https://itk.org/Wiki/ITK/Policy_and_Procedures_for_Adding_Remote_Modules On Fri, Aug 11, 2017 at 4:11 PM, Sisi wrote: > Dear all, > > I am quite new with ITK. I would like to add some new .h file and .txx > files, which are not a part of the original ITK framework, into the > original ITK Framework and use them together as library. How can I do it? > > I will be very happy to get any Information/hint/guide about it. > > best, > Siming > > > > > -- > View this message in context: http://itk-insight-users. > 2283740.n2.nabble.com/Integrate-new-h-and-txx-file- > as-a-part-of-ITK-Framework-tp7590184.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From siming.bayer at gmail.com Fri Aug 11 17:15:58 2017 From: siming.bayer at gmail.com (Sisi) Date: Fri, 11 Aug 2017 14:15:58 -0700 (MST) Subject: [ITK-users] Integrate new .h and .txx file as a part of ITK Framework In-Reply-To: References: <1502482307961-7590184.post@n2.nabble.com> Message-ID: <39A6BCD0-FE1B-4FD8-9B88-F06493D5149E@gmail.com> Dear Francois, Thank you for your answer. In my case, I didn?t?t wrote any filter or module by myself. I just want to try a improved version of its::KernelTransform, developed by Brooks. The source code can be downloaded here (http://www.insight-journal.org/browse/publication/145 ). So my question is really really too simple: How can I integrate those header files and .txx file into the ITK Framework? If this is a remote module, where can I find it and how can I build it? Sorry for this stupid question? Thanks for your help! best, Siming > Am 11.08.2017 um 22:59 schrieb Francois Budin-3 [via ITK Insight Users] : > > Hello Siming, > > Welcome to ITK! I am not sure if you have had a chance to look at the ITKSoftwareGuide [1], but it is a great place to find a lot of information. The chapters that are the most relevant for you are probably Chapter 8 (How to write a filter) and Chapter 9 (How to create a module). To answer your question more specifically, the easiest way to integrate a new filter or new files to ITK is to develop an ITK module. This module can then either be compiled outside of ITK, or if you think it would be useful to the whole ITK community, it can be integrated to ITK as a remote module [2]. > > I hope this helps. Feel free to ask more questions. > > Francois > > [1] https://www.itk.org/ItkSoftwareGuide.pdf > [2] https://itk.org/Wiki/ITK/Policy_and_Procedures_for_Adding_Remote_Modules > > On Fri, Aug 11, 2017 at 4:11 PM, Sisi <[hidden email] > wrote: > Dear all, > > I am quite new with ITK. I would like to add some new .h file and .txx > files, which are not a part of the original ITK framework, into the > original ITK Framework and use them together as library. How can I do it? > > I will be very happy to get any Information/hint/guide about it. > > best, > Siming > > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Integrate-new-h-and-txx-file-as-a-part-of-ITK-Framework-tp7590184.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > If you reply to this email, your message will be added to the discussion below: > http://itk-insight-users.2283740.n2.nabble.com/Integrate-new-h-and-txx-file-as-a-part-of-ITK-Framework-tp7590184p7590185.html > To unsubscribe from Integrate new .h and .txx file as a part of ITK Framework, click here . > NAML -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Integrate-new-h-and-txx-file-as-a-part-of-ITK-Framework-tp7590184p7590186.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From francois.budin at kitware.com Fri Aug 11 17:38:08 2017 From: francois.budin at kitware.com (Francois Budin) Date: Fri, 11 Aug 2017 17:38:08 -0400 Subject: [ITK-users] Integrate new .h and .txx file as a part of ITK Framework In-Reply-To: <39A6BCD0-FE1B-4FD8-9B88-F06493D5149E@gmail.com> References: <1502482307961-7590184.post@n2.nabble.com> <39A6BCD0-FE1B-4FD8-9B88-F06493D5149E@gmail.com> Message-ID: Hello Siming, It looks like this publication is a little old (2007). A lot has changed in ITK since this article has been written. The registration and transformation framework has been greatly improved, and the ThinPlateSpline can now be used in the registration framework (see [1]). If it is what you were looking for, you may not need to integrate the code of the article you mention in ITK. As for using the code that is available in the Insighe Journal article, one would need to first adapt the CMakeLists.txt file to be able to compile the code (see the quick adaptation of the CMakeLists.txt I wrote below). And then one would need to update the code to compile this project with a recent version of ITK. Francois cmake_minimum_required(VERSION 2.8.12) # This is based on the Insight Journal CMake Template #Change PROJECT_NAME to the name of your project PROJECT(KERNEL_TRANSFORM) ENABLE_TESTING() find_package(ITK REQUIRED) include(${ITK_USE_FILE}) #the following block of code is an example of how to build an executable in #cmake. Unmodified, it will add an executable called "MyExe" to the project. #MyExe will be built using the files MyClass.h and MyClass.cxx, and it will #be linked to all the libraries you specified above. #You can build more than one executable per project ADD_EXECUTABLE(itkSplineKernelTransform2Test itkSplineKernelTransform2Test.cxx) TARGET_LINK_LIBRARIES(itkSplineKernelTransform2Test ${ITK_LIBRARIES}) ADD_EXECUTABLE(TPSDeformableRegistration TPSDeformableRegistration.cxx) TARGET_LINK_LIBRARIES(TPSDeformableRegistration ${ITK_LIBRARIES}) #the following line is an example of how to add a test to your project. #Testname is the title for this particular test. ExecutableToRun is the #program which will be running this test. It can either be a part of this #project or an external executable. After that list any args that are needed #for this test. Include as many tests as you like. If your project doesn't have #any tests you can comment out or delete the following line. ADD_TEST(SplineKernelTransform2Test itkSplineKernelTransform2Test) ADD_TEST(TPSDeformableRegistration TPSDeformableRegistration ${CMAKE_SOURCE_DIR}/data/transformpoints.txt ${CMAKE_SOURCE_DIR}/data/BrainProtonDensitySliceWarped.png ${CMAKE_SOURCE_DIR}/data/BrainProtonDensitySliceBorder20.png output.png diffafter.png diffbefore.png) [1] https://itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ThinPlateSplineWarp_8cxx-example.html On Fri, Aug 11, 2017 at 5:15 PM, Sisi wrote: > Dear Francois, > > Thank you for your answer. In my case, I didn?t?t wrote any filter or > module by myself. I just want to try a improved version of > its::KernelTransform, developed by Brooks. The source code can be > downloaded here (http://www.insight-journal.org/browse/publication/145 < > http://www.insight-journal.org/browse/publication/145>). So my question > is really really too simple: How can I integrate those header files and > .txx file into the ITK Framework? If this is a remote module, where can I > find it and how can I build it? > > Sorry for this stupid question? > > Thanks for your help! > best, > Siming > > Am 11.08.2017 um 22:59 schrieb Francois Budin-3 [via ITK Insight Users] < > ml+s2283740n7590185h17 at n2.nabble.com>: > > > > Hello Siming, > > > > Welcome to ITK! I am not sure if you have had a chance to look at the > ITKSoftwareGuide [1], but it is a great place to find a lot of information. > The chapters that are the most relevant for you are probably Chapter 8 (How > to write a filter) and Chapter 9 (How to create a module). To answer your > question more specifically, the easiest way to integrate a new filter or > new files to ITK is to develop an ITK module. This module can then either > be compiled outside of ITK, or if you think it would be useful to the whole > ITK community, it can be integrated to ITK as a remote module [2]. > > > > I hope this helps. Feel free to ask more questions. > > > > Francois > > > > [1] https://www.itk.org/ItkSoftwareGuide.pdf ItkSoftwareGuide.pdf> > > [2] https://itk.org/Wiki/ITK/Policy_and_Procedures_for_ > Adding_Remote_Modules Adding_Remote_Modules> > > > > On Fri, Aug 11, 2017 at 4:11 PM, Sisi <[hidden email] > > wrote: > > Dear all, > > > > I am quite new with ITK. I would like to add some new .h file and .txx > > files, which are not a part of the original ITK framework, into the > > original ITK Framework and use them together as library. How can I do it? > > > > I will be very happy to get any Information/hint/guide about it. > > > > best, > > Siming > > > > > > > > > > -- > > View this message in context: http://itk-insight-users. > 2283740.n2.nabble.com/Integrate-new-h-and-txx-file- > as-a-part-of-ITK-Framework-tp7590184.html 2283740.n2.nabble.com/Integrate-new-h-and-txx-file- > as-a-part-of-ITK-Framework-tp7590184.html> > > Sent from the ITK Insight Users mailing list archive at Nabble.com. > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html < > http://www.kitware.com/opensource/opensource.html> > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php products/protraining.php> > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users < > http://public.kitware.com/mailman/listinfo/insight-users> > > > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html < > http://www.kitware.com/opensource/opensource.html> > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php products/protraining.php> > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users < > http://public.kitware.com/mailman/listinfo/insight-users> > > > > > > If you reply to this email, your message will be added to the discussion > below: > > http://itk-insight-users.2283740.n2.nabble.com/ > Integrate-new-h-and-txx-file-as-a-part-of-ITK-Framework- > tp7590184p7590185.html Integrate-new-h-and-txx-file-as-a-part-of-ITK-Framework- > tp7590184p7590185.html> > > To unsubscribe from Integrate new .h and .txx file as a part of ITK > Framework, click here template/NamlServlet.jtp?macro=unsubscribe_by_code&node=7590184&code= > c2ltaW5nLmJheWVyQGdtYWlsLmNvbXw3NTkwMTg0fC0xNTI5Nzc4MTM3>. > > NAML template/NamlServlet.jtp?macro=macro_viewer&id=instant_ > html%21nabble%3Aemail.naml&base=nabble.naml.namespaces. > BasicNamespace-nabble.view.web.template.NabbleNamespace- > nabble.naml.namespaces.BasicNamespace-nabble.view. > web.template.NabbleNamespace-nabble.naml.namespaces. > BasicNamespace-nabble.view.web.template.NabbleNamespace- > nabble.naml.namespaces.BasicNamespace-nabble.view. > web.template.NabbleNamespace-nabble.naml.namespaces. > BasicNamespace-nabble.view.web.template.NabbleNamespace- > nabble.view.web.template.NodeNamespace&breadcrumbs= > notify_subscribers%21nabble%3Aemail.naml-instant_emails% > 21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> > > > > > -- > View this message in context: http://itk-insight-users. > 2283740.n2.nabble.com/Integrate-new-h-and-txx-file- > as-a-part-of-ITK-Framework-tp7590184p7590186.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From siming.bayer at gmail.com Fri Aug 11 18:00:14 2017 From: siming.bayer at gmail.com (Siming Bayer) Date: Sat, 12 Aug 2017 00:00:14 +0200 Subject: [ITK-users] Integrate new .h and .txx file as a part of ITK Framework In-Reply-To: References: <1502482307961-7590184.post@n2.nabble.com> <39A6BCD0-FE1B-4FD8-9B88-F06493D5149E@gmail.com> Message-ID: <5AF74E58-6D20-4748-83FE-AEB489918A82@gmail.com> Dear Francois, Well, yes, this publication is quite old. But currently, the implementation of itk:ThinPlatSplineKernelTransform still could not handle the registration problem. The reason is, that the jacobian calculation is not implemented. I have tried to use TPS to do non-rigid image registration ( but not warping) and got this the exception ("jacobian must implemented in subclasses of kernel transform"). I hope this publication from 2007 could help me, because it address this problem directly. Or maybe you know another reason for this exception? Thank you for your Cmake file!! This helps me a lot! best, Siming > Am 11.08.2017 um 23:38 schrieb Francois Budin : > > Hello Siming, > > It looks like this publication is a little old (2007). A lot has changed in ITK since this article has been written. The registration and transformation framework has been greatly improved, and the ThinPlateSpline can now be used in the registration framework (see [1]). If it is what you were looking for, you may not need to integrate the code of the article you mention in ITK. > As for using the code that is available in the Insighe Journal article, one would need to first adapt the CMakeLists.txt file to be able to compile the code (see the quick adaptation of the CMakeLists.txt I wrote below). And then one would need to update the code to compile this project with a recent version of ITK. > > Francois > > cmake_minimum_required(VERSION 2.8.12) > # This is based on the Insight Journal CMake Template > > #Change PROJECT_NAME to the name of your project > PROJECT(KERNEL_TRANSFORM) > > ENABLE_TESTING() > > find_package(ITK REQUIRED) > include(${ITK_USE_FILE}) > > > #the following block of code is an example of how to build an executable in > #cmake. Unmodified, it will add an executable called "MyExe" to the project. > #MyExe will be built using the files MyClass.h and MyClass.cxx, and it will > #be linked to all the libraries you specified above. > #You can build more than one executable per project > ADD_EXECUTABLE(itkSplineKernelTransform2Test itkSplineKernelTransform2Test.cxx) > TARGET_LINK_LIBRARIES(itkSplineKernelTransform2Test ${ITK_LIBRARIES}) > > ADD_EXECUTABLE(TPSDeformableRegistration TPSDeformableRegistration.cxx) > TARGET_LINK_LIBRARIES(TPSDeformableRegistration ${ITK_LIBRARIES}) > > #the following line is an example of how to add a test to your project. > #Testname is the title for this particular test. ExecutableToRun is the > #program which will be running this test. It can either be a part of this > #project or an external executable. After that list any args that are needed > #for this test. Include as many tests as you like. If your project doesn't have > #any tests you can comment out or delete the following line. > ADD_TEST(SplineKernelTransform2Test itkSplineKernelTransform2Test) > > ADD_TEST(TPSDeformableRegistration TPSDeformableRegistration ${CMAKE_SOURCE_DIR}/data/transformpoints.txt ${CMAKE_SOURCE_DIR}/data/BrainProtonDensitySliceWarped.png ${CMAKE_SOURCE_DIR}/data/BrainProtonDensitySliceBorder20.png output.png diffafter.png diffbefore.png) > > > > [1] https://itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ThinPlateSplineWarp_8cxx-example.html > > On Fri, Aug 11, 2017 at 5:15 PM, Sisi > wrote: > Dear Francois, > > Thank you for your answer. In my case, I didn?t?t wrote any filter or module by myself. I just want to try a improved version of its::KernelTransform, developed by Brooks. The source code can be downloaded here (http://www.insight-journal.org/browse/publication/145 >). So my question is really really too simple: How can I integrate those header files and .txx file into the ITK Framework? If this is a remote module, where can I find it and how can I build it? > > Sorry for this stupid question? > > Thanks for your help! > best, > Siming > > Am 11.08.2017 um 22:59 schrieb Francois Budin-3 [via ITK Insight Users] >: > > > > Hello Siming, > > > > Welcome to ITK! I am not sure if you have had a chance to look at the ITKSoftwareGuide [1], but it is a great place to find a lot of information. The chapters that are the most relevant for you are probably Chapter 8 (How to write a filter) and Chapter 9 (How to create a module). To answer your question more specifically, the easiest way to integrate a new filter or new files to ITK is to develop an ITK module. This module can then either be compiled outside of ITK, or if you think it would be useful to the whole ITK community, it can be integrated to ITK as a remote module [2]. > > > > I hope this helps. Feel free to ask more questions. > > > > Francois > > > > [1] https://www.itk.org/ItkSoftwareGuide.pdf > > > [2] https://itk.org/Wiki/ITK/Policy_and_Procedures_for_Adding_Remote_Modules > > > > > On Fri, Aug 11, 2017 at 4:11 PM, Sisi <[hidden email] > wrote: > > Dear all, > > > > I am quite new with ITK. I would like to add some new .h file and .txx > > files, which are not a part of the original ITK framework, into the > > original ITK Framework and use them together as library. How can I do it? > > > > I will be very happy to get any Information/hint/guide about it. > > > > best, > > Siming > > > > > > > > > > -- > > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Integrate-new-h-and-txx-file-as-a-part-of-ITK-Framework-tp7590184.html > > > Sent from the ITK Insight Users mailing list archive at Nabble.com. > > _____________________________________ > > Powered by www.kitware.com > > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > > > > > If you reply to this email, your message will be added to the discussion below: > > http://itk-insight-users.2283740.n2.nabble.com/Integrate-new-h-and-txx-file-as-a-part-of-ITK-Framework-tp7590184p7590185.html > > > To unsubscribe from Integrate new .h and .txx file as a part of ITK Framework, click here >. > > NAML > > > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Integrate-new-h-and-txx-file-as-a-part-of-ITK-Framework-tp7590184p7590186.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Darren.Thompson at csiro.au Mon Aug 14 01:26:13 2017 From: Darren.Thompson at csiro.au (Darren.Thompson at csiro.au) Date: Mon, 14 Aug 2017 05:26:13 +0000 Subject: [ITK-users] FW: External modules In-Reply-To: <94f32ffc245646b2a74fe8f0f3cb90d3@exch3-mel.nexus.csiro.au> References: <94f32ffc245646b2a74fe8f0f3cb90d3@exch3-mel.nexus.csiro.au> Message-ID: <3f98ee173f98425bb3e2128f296338bd@exch3-mel.nexus.csiro.au> Hi, I'm currently using ITK 4.12 under linux and am trying to configure/build ITK so I can create external modules. After some Googling I see that I need to make use of the "ITKModuleExternal" module however I can't seem to configure/build ITK (via CMake) such that the corresponding "ITKModuleExternal.cmake" file is installed. I am currently building ITK with a custom range of options and modules turned on but can't seem to locate any relevant option in CMake that directly related to ITKModueExternal (even in Advanced mode). Can someone enlighten me as to how to get this particular module configured and deployed? Regards, Darren Thompson -------------- next part -------------- An HTML attachment was scrubbed... URL: From mihail.isakov at googlemail.com Mon Aug 14 01:53:40 2017 From: mihail.isakov at googlemail.com (Mihail Isakov) Date: Mon, 14 Aug 2017 07:53:40 +0200 Subject: [ITK-users] Segmentation fault in itkBinaryMask3DMeshSource In-Reply-To: References: Message-ID: On Fri, Aug 11, 2017 at 4:44 PM, Francois Budin wrote: > I found that there was a limitation in the > current implementation due to the fact that it uses "unsigned short" > variables. Thank you very much. Fantastic! I changed in itkBinaryMask3DMeshSource.h unsigned short m_CurrentRowIndex; unsigned short m_CurrentFrameIndex; unsigned short m_LastRowNum; unsigned short m_LastFrameNum; unsigned short m_CurrentRowNum; unsigned short m_CurrentFrameNum; to 'int' and it works, no crashes. BTW, IMHO, it looks like variables m_NodeLimit(2000) and int m_CellLimit(4000) and allocations in constructor this->GetOutput()->GetPoints()->Reserve(m_NodeLimit); this->GetOutput()->GetCells()->Reserve(m_CellLimit); don't have any effect and can be deleted... I generated huge meshes without problems very fast (with or without those limits and allocations). Also i have seen that 3D binary images with dimension 1 cause segmentation fault of filter too, eg. this one https://drive.google.com/file/d/0ByBLJ2-U1t9xS2VCa0RnVVdBYjg/view?usp=sharing It not relevant to unsigned short issue above. Of course such images should not be used at all to generate mesh, the same for the first noisy image, but anyway for filter robustness some precondition check might be done. The filter is very good, very fast. > Is it ok to add your data you shared in this I am sorry, i asked the owner of the original data set i derived the image from. Unfortunately he don't want to add it permanently to tests due to some kind of policy. Sorry Regards, Mihail From francois.budin at kitware.com Mon Aug 14 08:56:32 2017 From: francois.budin at kitware.com (Francois Budin) Date: Mon, 14 Aug 2017 08:56:32 -0400 Subject: [ITK-users] Integrate new .h and .txx file as a part of ITK Framework In-Reply-To: <5AF74E58-6D20-4748-83FE-AEB489918A82@gmail.com> References: <1502482307961-7590184.post@n2.nabble.com> <39A6BCD0-FE1B-4FD8-9B88-F06493D5149E@gmail.com> <5AF74E58-6D20-4748-83FE-AEB489918A82@gmail.com> Message-ID: Hello Siming, Indeed, in the example that I shared with you previously, the TPS transform is computed independently. If you want to use this class in the registration framework, you will most likely have to update the old code available in the Insight Journal article to make it compile with the newest versions of ITK. Best, Fran?ois On Fri, Aug 11, 2017 at 6:00 PM, Siming Bayer wrote: > Dear Francois, > > > Well, yes, this publication is quite old. But currently, the > implementation of itk:ThinPlatSplineKernelTransform still could not > handle the registration problem. The reason is, that the jacobian > calculation is not implemented. I have tried to use TPS to do non-rigid > image registration ( but not warping) and got this the exception ("jacobian > must implemented in subclasses of kernel transform"). I hope this > publication from 2007 could help me, because it address this problem > directly. > > Or maybe you know another reason for this exception? > > Thank you for your Cmake file!! This helps me a lot! > > best, > Siming > > Am 11.08.2017 um 23:38 schrieb Francois Budin >: > > Hello Siming, > > It looks like this publication is a little old (2007). A lot has changed > in ITK since this article has been written. The registration and > transformation framework has been greatly improved, and the ThinPlateSpline > can now be used in the registration framework (see [1]). If it is what you > were looking for, you may not need to integrate the code of the article you > mention in ITK. > As for using the code that is available in the Insighe Journal article, > one would need to first adapt the CMakeLists.txt file to be able to compile > the code (see the quick adaptation of the CMakeLists.txt I wrote below). > And then one would need to update the code to compile this project with a > recent version of ITK. > > Francois > > cmake_minimum_required(VERSION 2.8.12) > # This is based on the Insight Journal CMake Template > > #Change PROJECT_NAME to the name of your project > PROJECT(KERNEL_TRANSFORM) > > ENABLE_TESTING() > > find_package(ITK REQUIRED) > include(${ITK_USE_FILE}) > > > #the following block of code is an example of how to build an executable in > #cmake. Unmodified, it will add an executable called "MyExe" to the > project. > #MyExe will be built using the files MyClass.h and MyClass.cxx, and it will > #be linked to all the libraries you specified above. > #You can build more than one executable per project > ADD_EXECUTABLE(itkSplineKernelTransform2Test > itkSplineKernelTransform2Test.cxx) > TARGET_LINK_LIBRARIES(itkSplineKernelTransform2Test ${ITK_LIBRARIES}) > > ADD_EXECUTABLE(TPSDeformableRegistration TPSDeformableRegistration.cxx) > TARGET_LINK_LIBRARIES(TPSDeformableRegistration ${ITK_LIBRARIES}) > > #the following line is an example of how to add a test to your project. > #Testname is the title for this particular test. ExecutableToRun is the > #program which will be running this test. It can either be a part of this > #project or an external executable. After that list any args that are > needed > #for this test. Include as many tests as you like. If your project > doesn't have > #any tests you can comment out or delete the following line. > ADD_TEST(SplineKernelTransform2Test itkSplineKernelTransform2Test) > > ADD_TEST(TPSDeformableRegistration TPSDeformableRegistration > ${CMAKE_SOURCE_DIR}/data/transformpoints.txt ${CMAKE_SOURCE_DIR}/data/ > BrainProtonDensitySliceWarped.png ${CMAKE_SOURCE_DIR}/data/ > BrainProtonDensitySliceBorder20.png output.png diffafter.png > diffbefore.png) > > > > [1] https://itk.org/Doxygen/html/Examples_2RegistrationITKv4_ > 2ThinPlateSplineWarp_8cxx-example.html > > On Fri, Aug 11, 2017 at 5:15 PM, Sisi wrote: > >> Dear Francois, >> >> Thank you for your answer. In my case, I didn?t?t wrote any filter or >> module by myself. I just want to try a improved version of >> its::KernelTransform, developed by Brooks. The source code can be >> downloaded here (http://www.insight-journal.org/browse/publication/145 < >> http://www.insight-journal.org/browse/publication/145>). So my question >> is really really too simple: How can I integrate those header files and >> .txx file into the ITK Framework? If this is a remote module, where can I >> find it and how can I build it? >> >> Sorry for this stupid question? >> >> Thanks for your help! >> best, >> Siming >> > Am 11.08.2017 um 22:59 schrieb Francois Budin-3 [via ITK Insight Users] >> : >> > >> > Hello Siming, >> > >> > Welcome to ITK! I am not sure if you have had a chance to look at the >> ITKSoftwareGuide [1], but it is a great place to find a lot of information. >> The chapters that are the most relevant for you are probably Chapter 8 (How >> to write a filter) and Chapter 9 (How to create a module). To answer your >> question more specifically, the easiest way to integrate a new filter or >> new files to ITK is to develop an ITK module. This module can then either >> be compiled outside of ITK, or if you think it would be useful to the whole >> ITK community, it can be integrated to ITK as a remote module [2]. >> > >> > I hope this helps. Feel free to ask more questions. >> > >> > Francois >> > >> > [1] https://www.itk.org/ItkSoftwareGuide.pdf < >> https://www.itk.org/ItkSoftwareGuide.pdf> >> > [2] https://itk.org/Wiki/ITK/Policy_and_Procedures_for_Adding_ >> Remote_Modules > cy_and_Procedures_for_Adding_Remote_Modules> >> > >> > On Fri, Aug 11, 2017 at 4:11 PM, Sisi <[hidden email] < >> x-msg://27/user/SendEmail.jtp?type=node&node=7590185&i=0>> wrote: >> > Dear all, >> > >> > I am quite new with ITK. I would like to add some new .h file and .txx >> > files, which are not a part of the original ITK framework, into the >> > original ITK Framework and use them together as library. How can I do >> it? >> > >> > I will be very happy to get any Information/hint/guide about it. >> > >> > best, >> > Siming >> > >> > >> > >> > >> > -- >> > View this message in context: http://itk-insight-users.22837 >> 40.n2.nabble.com/Integrate-new-h-and-txx-file-as-a-part- >> of-ITK-Framework-tp7590184.html > 740.n2.nabble.com/Integrate-new-h-and-txx-file-as-a-part- >> of-ITK-Framework-tp7590184.html> >> > Sent from the ITK Insight Users mailing list archive at Nabble.com. >> > _____________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html < >> http://www.kitware.com/opensource/opensource.html> >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://www.kitware.com/products/protraining.php < >> http://www.kitware.com/products/protraining.php> >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-users < >> http://public.kitware.com/mailman/listinfo/insight-users> >> > >> > >> > _____________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html < >> http://www.kitware.com/opensource/opensource.html> >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://www.kitware.com/products/protraining.php < >> http://www.kitware.com/products/protraining.php> >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-users < >> http://public.kitware.com/mailman/listinfo/insight-users> >> > >> > >> > If you reply to this email, your message will be added to the >> discussion below: >> > http://itk-insight-users.2283740.n2.nabble.com/Integrate- >> new-h-and-txx-file-as-a-part-of-ITK-Framework-tp7590184p7590185.html < >> http://itk-insight-users.2283740.n2.nabble.com/Integrate- >> new-h-and-txx-file-as-a-part-of-ITK-Framework-tp7590184p7590185.html> >> > To unsubscribe from Integrate new .h and .txx file as a part of ITK >> Framework, click here > 740.n2.nabble.com/template/NamlServlet.jtp?macro= >> unsubscribe_by_code&node=7590184&code=c2ltaW5nLmJheWVyQ >> GdtYWlsLmNvbXw3NTkwMTg0fC0xNTI5Nzc4MTM3>. >> > NAML > NamlServlet.jtp?macro=macro_viewer&id=instant_html% >> 21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNa >> mespace-nabble.view.web.template.NabbleNamespace-nabbl >> e.naml.namespaces.BasicNamespace-nabble.view.web.template. >> NabbleNamespace-nabble.naml.namespaces.BasicNamespace- >> nabble.view.web.template.NabbleNamespace-nabble.naml. >> namespaces.BasicNamespace-nabble.view.web.template. >> NabbleNamespace-nabble.naml.namespaces.BasicNamespace- >> nabble.view.web.template.NabbleNamespace-nabble.view. >> web.template.NodeNamespace&breadcrumbs=notify_ >> subscribers%21nabble%3Aemail.naml-instant_emails%21nabble% >> 3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> >> >> >> >> >> -- >> View this message in context: http://itk-insight-users.22837 >> 40.n2.nabble.com/Integrate-new-h-and-txx-file-as-a-part- >> of-ITK-Framework-tp7590184p7590186.html >> Sent from the ITK Insight Users mailing list archive at Nabble.com. >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From francois.budin at kitware.com Mon Aug 14 09:00:55 2017 From: francois.budin at kitware.com (Francois Budin) Date: Mon, 14 Aug 2017 09:00:55 -0400 Subject: [ITK-users] Segmentation fault in itkBinaryMask3DMeshSource In-Reply-To: References: Message-ID: Thank you for checking if we could use the data to add tests. I will try to generate an image that is large enough to create the same problem. Replacing the unsigned short with ints is very similar to what I have done on my local branch (I used long), so I am glad to see that this solution also works for you. I'll look into the allocations in the constructor to see if things can be improved. This might be for a second patch. Best, Fran?ois On Mon, Aug 14, 2017 at 1:53 AM, Mihail Isakov via Insight-users < insight-users at itk.org> wrote: > On Fri, Aug 11, 2017 at 4:44 PM, Francois Budin > wrote: > > > I found that there was a limitation in the > > current implementation due to the fact that it uses "unsigned short" > > variables. > > Thank you very much. Fantastic! I changed in itkBinaryMask3DMeshSource.h > > unsigned short m_CurrentRowIndex; > unsigned short m_CurrentFrameIndex; > unsigned short m_LastRowNum; > unsigned short m_LastFrameNum; > unsigned short m_CurrentRowNum; > unsigned short m_CurrentFrameNum; > > to 'int' and it works, no crashes. > > BTW, IMHO, it looks like variables m_NodeLimit(2000) and int > m_CellLimit(4000) > and allocations in constructor > this->GetOutput()->GetPoints()->Reserve(m_NodeLimit); > this->GetOutput()->GetCells()->Reserve(m_CellLimit); > don't have any effect and can be deleted... I generated huge meshes > without problems > very fast (with or without those limits and allocations). > > Also i have seen that 3D binary images with dimension 1 cause > segmentation fault of filter too, > eg. this one > https://drive.google.com/file/d/0ByBLJ2-U1t9xS2VCa0RnVVdBYjg/view?usp= > sharing > It not relevant to unsigned short issue above. > Of course such images should not be used at all to generate mesh, > the same for the first noisy image, but anyway for filter robustness > some precondition check might be > done. The filter is very good, very fast. > > > Is it ok to add your data you shared in this > > I am sorry, i asked the owner of the original data set i derived the > image from. Unfortunately he don't want to add it permanently to tests > due to some kind of policy. Sorry > > > Regards, > Mihail > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From francois.budin at kitware.com Mon Aug 14 09:07:13 2017 From: francois.budin at kitware.com (Francois Budin) Date: Mon, 14 Aug 2017 09:07:13 -0400 Subject: [ITK-users] FW: External modules In-Reply-To: <3f98ee173f98425bb3e2128f296338bd@exch3-mel.nexus.csiro.au> References: <94f32ffc245646b2a74fe8f0f3cb90d3@exch3-mel.nexus.csiro.au> <3f98ee173f98425bb3e2128f296338bd@exch3-mel.nexus.csiro.au> Message-ID: Hello Darren, Are you trying to create a new external module? In this case there is nothing that needs to be changed in your configuration inside ITK. You can create a new folder for an independent project outside of your ITK source tree and create your new external (remote) module in this new folder. Good reference to see how things are done are this example [1] and the ITK Software Guide [2] (Chapter 9). You can then configure and compile your remote module (you will need to specify ITK_DIR (ITK build directory or directory containing ITKConfig.cmake) as a separate project. Hope this helps, Fran?ois [1] https://github.com/InsightSoftwareConsortium/ITKModuleTemplate [2] https://www.itk.org/ItkSoftwareGuide.pdf On Mon, Aug 14, 2017 at 1:26 AM, wrote: > Hi, > > > > I?m currently using ITK 4.12 under linux and am trying to configure/build > ITK so I can create external modules. After some Googling I see that I need > to make use of the ?ITKModuleExternal? module however I can?t seem to > configure/build ITK (via CMake) such that the corresponding > ?ITKModuleExternal.cmake? file is installed. > > > > I am currently building ITK with a custom range of options and modules > turned on but can?t seem to locate any relevant option in CMake that > directly related to ITKModueExternal (even in Advanced mode). > > > > Can someone enlighten me as to how to get this particular module > configured and deployed? > > > > Regards, > > > > Darren Thompson > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From thanosxania at gmail.com Mon Aug 14 12:42:19 2017 From: thanosxania at gmail.com (thanos thanos) Date: Mon, 14 Aug 2017 18:42:19 +0200 Subject: [ITK-users] Cardiac Deformation using Segmentation and Registration of Ultrasound Images In-Reply-To: References: Message-ID: Hello again, Matt, thank you for solving the example issue. I tried to use the filter and although it worked great for a 2D png image, it failed for a 2D jpg and dicom images as well as for a 3D nrrd volume. I got the error "Could not create ImageIO" so maybe that has to do with the ImageIOFactory. I liked the suggested and accepted values when I run the .exe but maybe to avoid confusion you could replace the "Weickert diffusion type. Accepted values: Edge, Coherence. Default: Edge." with Weickert diffusion type. Accepted values: EED cEED CED cCED Isotropic" Best regards, Thanos On Fri, Aug 11, 2017 at 6:55 PM, Matt McCormick wrote: > On Fri, Aug 4, 2017 at 9:36 AM, Matt McCormick > wrote: > > Hi Thanos, > > > > On Thu, Aug 3, 2017 at 1:00 PM, thanos thanos > wrote: > >> Hello everyone, > >> > >> D?enan, Andras and Matt thank you very much for your answers. > >> To be honest I've tried already in the past registration with Slicer > using > >> Demons, B-Splines and also Elastix and Plastimach. > >> > >> D?enan, I read your last sentence already many times but I can't really > >> understand what you mean by "initializing registration of time point > n+1 by > >> resulting transform from time point n." > >> > >> Matt, thank you for sharing your thoughts. I already looked at the > >> AnisotropicDiffusionLBR paper and I have also tried the online > interactive > >> figures > >> (https://insightsoftwareconsortium.github.io/ > ITKAnisotropicDiffusionLBR/). > >> Seems to work nicely, but I wasn't sure how to build the project. I > already > >> configured my ITK by setting the Module_AnisotropicDiffusionLBR at the > CMake > >> and then I tried to build the CoherenceEnhancingDiffusion from the > >> C:\ITK\src\Modules\Remote\AnisotropicDiffusionLBR\examples but I got " > >> Cannot open include file: 'CoherenceEnhancingDiffusionFilter.h': No > such > >> file or directory " so I guess I am missing something.. > > > > Thanks for the note. I will look into this issue and address it next > week. > > This is addressed here: > > http://review.source.kitware.com/#/c/22567/ > https://github.com/InsightSoftwareConsortium/ITKAnisotropicDiffusionLBR/ > commit/3d9880d5f52c4c37e3b658abc607a13f3c3d9545 > > I will also create a Python package for the module. > > Thanks, > Matt > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wagner.h.fabien at gmail.com Fri Aug 18 12:47:37 2017 From: wagner.h.fabien at gmail.com (FWagner) Date: Fri, 18 Aug 2017 09:47:37 -0700 (MST) Subject: [ITK-users] SimpleITK and R demons_registration problem Message-ID: <1503074857606-38641.post@n7.nabble.com> Hi, I have some trouble using the demons_registration from https://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/R_html/66_Registration_Demons.html I have tested the example and it work well. however when i used the function demons_registration with two image .png that i have generated i have some strange errors. See the R code and the error below # generate two image of a square slighty differents library(raster) library(imager) r=raster(ncol=600,nrow=600) r=setValues(r,1) im1=as.cimg(r) im1[200:300,200:300]=0 plot(im1) im2=as.cimg(r) im2[210:320,210:320]=0 plot(im2) save.image(im1,"square1.png") save.image(im2,"square2.png") library(SimpleITK) cntrl <- ReadImage("square1.png") img1 = Cast(cntrl,"sitkFloat32") img1 cntrl <- ReadImage("square2.png") img2 = Cast(cntrl,"sitkFloat32") img2 # the demons_registration function can be downloaded here : https://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/R_html/66_Registration_Demons.html tx <- demons_registration(fixed_image = img1, moving_image = img2) Show Traceback Rerun with Debug Error in f(...) : Exception in SITK - check warning messages In addition: Warning message: In f(...) : Exception thrown in SimpleITK TransformToDisplacementFieldFilter_Execute: /tmp/RtmpE4PobR/devtools25774a9d4940/SimpleITK-SimpleITKRInstaller-5f821a0/SITK/Build/SimpleITK-build/Code/BasicFilters/src/sitkTransformToDisplacementFieldFilter.cxx:178: sitk::ERROR: Unexpected error converting transform! Possible miss matching dimensions! Does anyone have an idea of the problem ? Thank you very much, Fabien -- View this message in context: http://itk-users.7.n7.nabble.com/SimpleITK-and-R-demons-registration-problem-tp38641.html Sent from the ITK - Users mailing list archive at Nabble.com. From kris.vorren at duke.edu Fri Aug 18 13:55:11 2017 From: kris.vorren at duke.edu (Kris Vorren) Date: Fri, 18 Aug 2017 17:55:11 +0000 Subject: [ITK-users] ITK GDCM python wrapping Message-ID: <71050FBA-A449-40B4-8B83-E53F52035C0F@win.duke.edu> Hello, I am trying to load DICOMRT structure data into a tbd ITK class via a python script. I found some useful C++ code by Jason Dowling that extracts contours from DICOMRT and draws them on the corresponding image data. I?ve managed to get this code to work on my own DICOM data. While trying to port sections of this code to python, I realized that Jason was directly instantiating GDCM classes to access the structure data. This is where I got stuck. My install of ITK used the built-in GDCM library, and it does?t appear that Python wrappings for GDCM were built. Is there a way to build GDCM python wrappers in ITK? I couldn?t find a CMAKE flag for it. Would it be simpler to just build GDCM separately, rebuild ITK setting the system GDCM flag, and then import GDCM into Python? Thanks, -Kris -------------- next part -------------- An HTML attachment was scrubbed... URL: From francois.budin at kitware.com Fri Aug 18 15:48:10 2017 From: francois.budin at kitware.com (Francois Budin) Date: Fri, 18 Aug 2017 15:48:10 -0400 Subject: [ITK-users] ITK GDCM python wrapping In-Reply-To: <71050FBA-A449-40B4-8B83-E53F52035C0F@win.duke.edu> References: <71050FBA-A449-40B4-8B83-E53F52035C0F@win.duke.edu> Message-ID: Hello Kris, ITK does not expose the third party libraries it uses in its Python wrapping. If you are trying to reimplement this nice insight journal paper in Python, you may want to install GDCMPython and use both ITK and gdcm, however you may have to duplicate the memory (load your DICOM once with each library). If you are trying to write some Python code that uses this C++ implementation, you could convert this filter into an ITK remote module [1][2] and wrap that module in Python. Hope this helps, Fran?ois [1] https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch9.html#x48-1460009 [2] https://github.com/InsightSoftwareConsortium/ITKModuleTemplate On Fri, Aug 18, 2017 at 1:55 PM, Kris Vorren wrote: > Hello, > > I am trying to load DICOMRT structure data into a tbd ITK class via a > python script. I found some useful C++ code > by Jason Dowling > that extracts contours from DICOMRT and draws them on the corresponding > image data. I?ve managed to get this code to work on my own DICOM data. > While trying to port sections of this code to python, I realized that Jason > was directly instantiating GDCM classes to access the structure data. This > is where I got stuck. > > My install of ITK used the built-in GDCM library, and it does?t appear > that Python wrappings for GDCM were built. Is there a way to build GDCM > python wrappers in ITK? I couldn?t find a CMAKE flag for it. Would it be > simpler to just build GDCM separately, rebuild ITK setting the system GDCM > flag, and then import GDCM into Python? > > Thanks, > -Kris > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Fri Aug 18 18:05:32 2017 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Fri, 18 Aug 2017 22:05:32 +0000 Subject: [ITK-users] [ITK] SimpleITK and R demons_registration problem In-Reply-To: <1503074857606-38641.post@n7.nabble.com> References: <1503074857606-38641.post@n7.nabble.com> Message-ID: Have you tried casting to sitkFloat64? > On Aug 18, 2017, at 12:49 PM, FWagner wrote: > > Hi, > I have some trouble using the demons_registration from > https://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/R_html/66_Registration_Demons.html > I have tested the example and it work well. however when i used the function > demons_registration with two image .png that i have generated i have some > strange errors. See the R code and the error below > > # generate two image of a square slighty differents > library(raster) > library(imager) > r=raster(ncol=600,nrow=600) > r=setValues(r,1) > im1=as.cimg(r) > im1[200:300,200:300]=0 > plot(im1) > > im2=as.cimg(r) > im2[210:320,210:320]=0 > plot(im2) > > save.image(im1,"square1.png") > save.image(im2,"square2.png") > > library(SimpleITK) > > cntrl <- ReadImage("square1.png") > img1 = Cast(cntrl,"sitkFloat32") > img1 > > cntrl <- ReadImage("square2.png") > img2 = Cast(cntrl,"sitkFloat32") > img2 > > # the demons_registration function can be downloaded here : > https://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/R_html/66_Registration_Demons.html > > tx <- demons_registration(fixed_image = img1, moving_image = img2) > Show Traceback > > Rerun with Debug > Error in f(...) : Exception in SITK - check warning messages In addition: > Warning message: > In f(...) : > Exception thrown in SimpleITK TransformToDisplacementFieldFilter_Execute: > /tmp/RtmpE4PobR/devtools25774a9d4940/SimpleITK-SimpleITKRInstaller-5f821a0/SITK/Build/SimpleITK-build/Code/BasicFilters/src/sitkTransformToDisplacementFieldFilter.cxx:178: > sitk::ERROR: Unexpected error converting transform! Possible miss matching > dimensions! > > > Does anyone have an idea of the problem ? > > Thank you very much, > > > Fabien > > > > > -- > View this message in context: http://itk-users.7.n7.nabble.com/SimpleITK-and-R-demons-registration-problem-tp38641.html > Sent from the ITK - Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From wagner.h.fabien at gmail.com Mon Aug 21 13:10:40 2017 From: wagner.h.fabien at gmail.com (FWagner) Date: Mon, 21 Aug 2017 10:10:40 -0700 (MST) Subject: [ITK-users] [ITK] SimpleITK and R demons_registration problem In-Reply-To: References: <1503074857606-38641.post@n7.nabble.com> Message-ID: Hi Bradley, I have tried casting to sitkFloat64, but the same error message : Error in f(...) : Exception in SITK - check warning messages In addition: Warning message: In f(...) : Exception thrown in SimpleITK TransformToDisplacementFieldFilter_Execute: /tmp/RtmpE4PobR/devtools25774a9d4940/SimpleITK-SimpleITKRInstaller-5f821a0/SITK/Build/SimpleITK-build/Code/BasicFilters/src/sitkTransformToDisplacementFieldFilter.cxx:178: sitk::ERROR: Unexpected error converting transform! Possible miss matching dimensions! do you have a code example of 2D registration involving two png in simpleITK ? it could help me to test where the problem comes from Cheers, Fabien 2017-08-18 19:05 GMT-03:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] [via ITK - Users] : > Have you tried casting to sitkFloat64? > > > On Aug 18, 2017, at 12:49 PM, FWagner <[hidden email] > > wrote: > > > > Hi, > > I have some trouble using the demons_registration from > > https://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/ > R_html/66_Registration_Demons.html > > I have tested the example and it work well. however when i used the > function > > demons_registration with two image .png that i have generated i have > some > > strange errors. See the R code and the error below > > > > # generate two image of a square slighty differents > > library(raster) > > library(imager) > > r=raster(ncol=600,nrow=600) > > r=setValues(r,1) > > im1=as.cimg(r) > > im1[200:300,200:300]=0 > > plot(im1) > > > > im2=as.cimg(r) > > im2[210:320,210:320]=0 > > plot(im2) > > > > save.image(im1,"square1.png") > > save.image(im2,"square2.png") > > > > library(SimpleITK) > > > > cntrl <- ReadImage("square1.png") > > img1 = Cast(cntrl,"sitkFloat32") > > img1 > > > > cntrl <- ReadImage("square2.png") > > img2 = Cast(cntrl,"sitkFloat32") > > img2 > > > > # the demons_registration function can be downloaded here : > > https://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/ > R_html/66_Registration_Demons.html > > > > tx <- demons_registration(fixed_image = img1, moving_image = img2) > > Show Traceback > > > > Rerun with Debug > > Error in f(...) : Exception in SITK - check warning messages In > addition: > > Warning message: > > In f(...) : > > Exception thrown in SimpleITK TransformToDisplacementFieldFilter_Execute: > > > /tmp/RtmpE4PobR/devtools25774a9d4940/SimpleITK-SimpleITKRInstaller- > 5f821a0/SITK/Build/SimpleITK-build/Code/BasicFilters/src/ > sitkTransformToDisplacementFieldFilter.cxx:178: > > sitk::ERROR: Unexpected error converting transform! Possible miss > matching > > dimensions! > > > > > > Does anyone have an idea of the problem ? > > > > Thank you very much, > > > > > > Fabien > > > > > > > > > > -- > > View this message in context: http://itk-users.7.n7.nabble. > com/SimpleITK-and-R-demons-registration-problem-tp38641.html > > Sent from the ITK - Users mailing list archive at Nabble.com. > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > _______________________________________________ > > Community mailing list > > [hidden email] > > http://public.kitware.com/mailman/listinfo/community > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > http://itk-users.7.n7.nabble.com/SimpleITK-and-R-demons- > registration-problem-tp38641p38644.html > To unsubscribe from SimpleITK and R demons_registration problem, click > here > > . > NAML > > -- View this message in context: http://itk-users.7.n7.nabble.com/SimpleITK-and-R-demons-registration-problem-tp38641p38645.html Sent from the ITK - Users mailing list archive at Nabble.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Tue Aug 22 00:02:14 2017 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 22 Aug 2017 04:02:14 +0000 Subject: [ITK-users] VS input library files Message-ID: <1503374512314.42554@auckland.ac.nz> I am building applications using ITK on Windows 7, with cmake and Visual Studio 2010. The CMakeLists.txt file is very simple: PROJECT(compress) FIND_PACKAGE(ITK) IF(ITK_FOUND) INCLUDE(${ITK_USE_FILE}) ELSE(ITK_FOUND) MESSAGE(FATAL_ERROR "ITK not found. Please set ITK_DIR.") ENDIF(ITK_FOUND) set(PROJECTNAME "compress") ADD_EXECUTABLE(${PROJECTNAME} compress.cpp) TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) and the cmake command is: cmake -G "Visual Studio 10 Win64" The .vcproj file created has, in the Linker > Input > Additional Dependencies list not only what looks like all the ITK libraries (about 78) but also a whole lot of VTK libraries (about 35) and 3 Qt libraries. This is for a program that uses neither VTK nor Qt. I don't understand why all these libraries are included. I guess it doesn't really matter, since they don't finish up in the .exe, but it is a nuisance because for some reason the Qt libraries that it expects are a different version from those on the computer, which means I have to either delete those libraries from the list or change the version number. If I was having to do this just a couple of times it wouldn't be worth worrying about, but I am rebuilding on a new machine a large number of programs that all have this issue. It would help to have a better understanding of the system that generates this list. Maybe there is a simple way to prevent unwanted libraries from getting into the list. -------------- next part -------------- An HTML attachment was scrubbed... URL: From francois.budin at kitware.com Tue Aug 22 09:32:39 2017 From: francois.budin at kitware.com (Francois Budin) Date: Tue, 22 Aug 2017 09:32:39 -0400 Subject: [ITK-users] VS input library files In-Reply-To: <1503374512314.42554@auckland.ac.nz> References: <1503374512314.42554@auckland.ac.nz> Message-ID: Hello Gib, It seems that you built ITK with the VTK bridge (CMake option Module_ITKVtkGlue), and you probably built VTK with Qt support. It is surprising that the Qt libraries do not match the Qt version on your computer. Did you build VTK on a different computer? To be able to compile any project that you link against ITK, CMake needs to know of all the dependencies of ITK. Because ITK is still using the CMake 2 paradigm (project based dependencies, vs CMake 3 that is target based), if you do not specify which module needs to be loaded, all the dependencies will be added to all your targets. If you want to limit the number of dependencies, you can specify the ITK components that are loaded by CMake: find_package(ITK COMPONENTS {add required components here} ) Another solution is to rebuild ITK without VTK support. Hope this helps, Francois On Tue, Aug 22, 2017 at 12:02 AM, Gib Bogle wrote: > I am building applications using ITK on Windows 7, with cmake and Visual > Studio 2010. The CMakeLists.txt file is very simple: > > > PROJECT(compress) > FIND_PACKAGE(ITK) > IF(ITK_FOUND) > INCLUDE(${ITK_USE_FILE}) > ELSE(ITK_FOUND) > MESSAGE(FATAL_ERROR > "ITK not found. Please set ITK_DIR.") > ENDIF(ITK_FOUND) > > set(PROJECTNAME "compress") > ADD_EXECUTABLE(${PROJECTNAME} compress.cpp) > TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) > > > and the cmake command is: > > > cmake -G "Visual Studio 10 Win64" > > > The .vcproj file created has, in the Linker > Input > Additional > Dependencies list not only what looks like all the ITK libraries (about 78) > but also a whole lot of VTK libraries (about 35) and 3 Qt libraries. This > is for a program that uses neither VTK nor Qt. I don't understand why all > these libraries are included. I guess it doesn't really matter, since they > don't finish up in the .exe, but it is a nuisance because for some reason > the Qt libraries that it expects are a different version from those on the > computer, which means I have to either delete those libraries from the list > or change the version number. If I was having to do this just a couple of > times it wouldn't be worth worrying about, but I am rebuilding on a new > machine a large number of programs that all have this issue. > > > It would help to have a better understanding of the system that generates > this list. Maybe there is a simple way to prevent unwanted libraries from > getting into the list. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Tue Aug 22 15:08:36 2017 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 22 Aug 2017 19:08:36 +0000 Subject: [ITK-users] VS input library files In-Reply-To: References: <1503374512314.42554@auckland.ac.nz>, Message-ID: <1503428917526.26309@auckland.ac.nz> Thanks Francois, that makes it all clear. Yes, I did build VTK on a different computer, and have upgraded Qt. Since it is simpler to just delete the unwanted Qt libraries in VS than to customise all the cmake files, I'll just stick to what I'm doing. Cheers, Gib ________________________________ From: Francois Budin Sent: Wednesday, 23 August 2017 1:32 a.m. To: Gib Bogle Cc: insight-users at itk.org Subject: Re: [ITK-users] VS input library files Hello Gib, It seems that you built ITK with the VTK bridge (CMake option Module_ITKVtkGlue), and you probably built VTK with Qt support. It is surprising that the Qt libraries do not match the Qt version on your computer. Did you build VTK on a different computer? To be able to compile any project that you link against ITK, CMake needs to know of all the dependencies of ITK. Because ITK is still using the CMake 2 paradigm (project based dependencies, vs CMake 3 that is target based), if you do not specify which module needs to be loaded, all the dependencies will be added to all your targets. If you want to limit the number of dependencies, you can specify the ITK components that are loaded by CMake: find_package(ITK COMPONENTS {add required components here} ) Another solution is to rebuild ITK without VTK support. Hope this helps, Francois On Tue, Aug 22, 2017 at 12:02 AM, Gib Bogle > wrote: I am building applications using ITK on Windows 7, with cmake and Visual Studio 2010. The CMakeLists.txt file is very simple: PROJECT(compress) FIND_PACKAGE(ITK) IF(ITK_FOUND) INCLUDE(${ITK_USE_FILE}) ELSE(ITK_FOUND) MESSAGE(FATAL_ERROR "ITK not found. Please set ITK_DIR.") ENDIF(ITK_FOUND) set(PROJECTNAME "compress") ADD_EXECUTABLE(${PROJECTNAME} compress.cpp) TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) and the cmake command is: cmake -G "Visual Studio 10 Win64" The .vcproj file created has, in the Linker > Input > Additional Dependencies list not only what looks like all the ITK libraries (about 78) but also a whole lot of VTK libraries (about 35) and 3 Qt libraries. This is for a program that uses neither VTK nor Qt. I don't understand why all these libraries are included. I guess it doesn't really matter, since they don't finish up in the .exe, but it is a nuisance because for some reason the Qt libraries that it expects are a different version from those on the computer, which means I have to either delete those libraries from the list or change the version number. If I was having to do this just a couple of times it wouldn't be worth worrying about, but I am rebuilding on a new machine a large number of programs that all have this issue. It would help to have a better understanding of the system that generates this list. Maybe there is a simple way to prevent unwanted libraries from getting into the list. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Wed Aug 23 16:49:54 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 23 Aug 2017 16:49:54 -0400 Subject: [ITK-users] [ANN] ITK 4.12.1 has been released! Message-ID: On behalf of the Insight Segmentation and Registration Toolkit (ITK) Community, we are happy to announce the release of ITK 4.12.1! Release files can be downloaded from https://itk.org/ITK/resources/software.html This is a patch release that fixes critical issues, regressions, documentation, and compiler support. Of the numerous issues addressed in this release, most notable are fixes to enable compilation of ITK on Linux platforms that use the musl C standard library (such as Alpine Linux). Other important fixes include computation of the oriented bounding box, computation of the Jacobian local vector, and support by the MetaIO library for files larger than 4 GB. The next feature release, 4.13.0, is scheduled for mid-December. Enjoy ITK! Changes from v4.12.0 to v4.12.1: Bradley Lowekamp (8): BUG: Manually set seed for ParticleSwarmOptimzerTest BUG: Fix computation for Jacobian local vector BUG: Error only when unknown module is enabled. BUG: Fix computation of central moments for shape label map BUG: shape label object elongation incorrectly zero BUG: Fix computation of oriented bounding box BUG: Add missing OrientedBoundingBox option ENH: Update FixedPointInverseDisplacementField remote module Francois Budin (1): BUG: Used ITK_HAVE_FEENABLEEXCEPT instead of ITK_HAS_FEENABLEEXCEPT Matthew McCormick (4): COMP: IsNull() capitalization in LevelSetEquationAdvectionTerm COMP: Detect the presence of mallinfo COMP: Detect the presence of feenableexcept COMP: Use GDCM_HAVE_BYTESWAP_H MetaIO Maintainers (2): MetaIO 2017-07-20 (92caf34d) MetaIO 2017-08-17 (3e1cb552) From niels-xtk at xs4all.nl Fri Aug 25 11:28:02 2017 From: niels-xtk at xs4all.nl (Niels Dekker) Date: Fri, 25 Aug 2017 17:28:02 +0200 Subject: [ITK-users] [ITK] [ANN] ITK 4.12.1 has been released! In-Reply-To: References: Message-ID: First of all, thank you very much for the new release. Unfortunately I see it does not include the fix that I submitted two months ago: "COMP: Fixed leak into user code", http://review.source.kitware.com/#/c/22461/ The fix is still at the master: https://github.com/Kitware/ITK/commit/f37853fa4f2bbbc60d2fa00f01aaedd8be158767 Is there a specific reason why this fix didn't make it into version 4.12.1? Kind regards, Niels On 2017-08-23 22:49, Matt McCormick wrote: > On behalf of the Insight Segmentation and Registration Toolkit (ITK) > Community, we are happy to announce the release of ITK 4.12.1! > > > Release files can be downloaded from > > https://itk.org/ITK/resources/software.html > > > This is a patch release that fixes critical issues, regressions, > documentation, and compiler support. Of the numerous issues addressed > in this release, most notable are fixes to enable compilation of ITK > on Linux platforms that use the musl C standard library (such as > Alpine Linux). Other important fixes include computation of the > oriented bounding box, computation of the Jacobian local vector, and > support by the MetaIO library for files larger than 4 GB. -- Niels Dekker Scientific programmer LKEB, Leiden University Medical Center, Netherlands From matt.mccormick at kitware.com Fri Aug 25 13:54:28 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 25 Aug 2017 13:54:28 -0400 Subject: [ITK-users] [ITK] [ANN] ITK 4.12.1 has been released! In-Reply-To: References: Message-ID: Hi Niels, Thanks for pointing out the omission. The patch has now been merged to the "release" branch, and it will be in the next release. Thanks, Matt On Fri, Aug 25, 2017 at 11:28 AM, Niels Dekker wrote: > First of all, thank you very much for the new release. > > Unfortunately I see it does not include the fix that I submitted two months > ago: "COMP: Fixed leak into user code", > http://review.source.kitware.com/#/c/22461/ > > The fix is still at the master: > https://github.com/Kitware/ITK/commit/f37853fa4f2bbbc60d2fa00f01aaedd8be158767 > > Is there a specific reason why this fix didn't make it into version 4.12.1? > > Kind regards, Niels > > > > On 2017-08-23 22:49, Matt McCormick wrote: >> >> On behalf of the Insight Segmentation and Registration Toolkit (ITK) >> Community, we are happy to announce the release of ITK 4.12.1! >> >> >> Release files can be downloaded from >> >> https://itk.org/ITK/resources/software.html >> >> >> This is a patch release that fixes critical issues, regressions, >> documentation, and compiler support. Of the numerous issues addressed >> in this release, most notable are fixes to enable compilation of ITK >> on Linux platforms that use the musl C standard library (such as >> Alpine Linux). Other important fixes include computation of the >> oriented bounding box, computation of the Jacobian local vector, and >> support by the MetaIO library for files larger than 4 GB. > > > -- > Niels Dekker > Scientific programmer > LKEB, Leiden University Medical Center, Netherlands > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From niels-xtk at xs4all.nl Mon Aug 28 05:29:09 2017 From: niels-xtk at xs4all.nl (Niels Dekker) Date: Mon, 28 Aug 2017 11:29:09 +0200 Subject: [ITK-users] [ITK] [ANN] ITK 4.12.1 has been released! In-Reply-To: References: Message-ID: <124dd4b5ebaa05ae932b0e586ec8a22f@xs4all.nl> Thank you, Matt! I'm glad to see, you did the merge: https://github.com/Kitware/ITK/commit/35a7420f72ecfd92c4c605cf127008ab9e08e1cc Kind regards, Niels On 2017-08-25 19:54, Matt McCormick wrote: > Hi Niels, > > Thanks for pointing out the omission. > > The patch has now been merged to the "release" branch, and it will be > in the next release. > > Thanks, > Matt > > On Fri, Aug 25, 2017 at 11:28 AM, Niels Dekker > wrote: >> First of all, thank you very much for the new release. >> >> Unfortunately I see it does not include the fix that I submitted two >> months >> ago: "COMP: Fixed leak into user code", >> http://review.source.kitware.com/#/c/22461/ >> >> The fix is still at the master: >> https://github.com/Kitware/ITK/commit/f37853fa4f2bbbc60d2fa00f01aaedd8be158767 >> >> Is there a specific reason why this fix didn't make it into version >> 4.12.1? >> >> Kind regards, Niels >> >> >> >> On 2017-08-23 22:49, Matt McCormick wrote: >>> >>> On behalf of the Insight Segmentation and Registration Toolkit (ITK) >>> Community, we are happy to announce the release of ITK 4.12.1! >>> >>> >>> Release files can be downloaded from >>> >>> https://itk.org/ITK/resources/software.html >>> >>> >>> This is a patch release that fixes critical issues, regressions, >>> documentation, and compiler support. Of the numerous issues addressed >>> in this release, most notable are fixes to enable compilation of ITK >>> on Linux platforms that use the musl C standard library (such as >>> Alpine Linux). Other important fixes include computation of the >>> oriented bounding box, computation of the Jacobian local vector, and >>> support by the MetaIO library for files larger than 4 GB. >> >> >> -- >> Niels Dekker >> Scientific programmer >> LKEB, Leiden University Medical Center, Netherlands -- Niels Dekker Scientific programmer LKEB, Leiden University Medical Center, Netherlands From mbrunet at insa-rennes.fr Tue Aug 29 06:56:01 2017 From: mbrunet at insa-rennes.fr (avazuila) Date: Tue, 29 Aug 2017 03:56:01 -0700 (MST) Subject: [ITK-users] Error encountered when padding: boundary condition is ITK_NULLPTR Message-ID: <1504004161094-38654.post@n7.nabble.com> Hi all, I just performed the segmentation of a vessel from a CT scan and I would like to use it to mask the abovementioned vessel on the image. In order to do so I would like to pad the segmentation image which is smaller than the image from which it has been extracted. I get the following error: "PadImageFilter: Boundary condition is ITK_NULLPTR so no request region can be generated." My code is the following: double* voi_bounds = l_import_preprocess.getBounds(); double* seg_bounds = l_import_seg.getBounds(); double x_min = abs(voi_bounds[0] - seg_bounds[0]); double x_max = abs(voi_bounds[1] - seg_bounds[1]); double y_min = abs(voi_bounds[2] - seg_bounds[2]); double y_max = abs(voi_bounds[3] - seg_bounds[3]); double z_min = abs(voi_bounds[4] - seg_bounds[4]); double z_max = abs(voi_bounds[5] - seg_bounds[5]); const int Dimension = 3; typedef uchar PixelType; typedef itk::Image< PixelType, Dimension > ImageType; ImageType::SizeType upper; ImageType::SizeType lower; lower[0] = x_min; lower[1] = y_min; lower[2] = z_min; upper[0] = x_max; upper[1] = y_max; upper[2] = z_max; typedef itk::PadImageFilter< ImageType, ImageType > PadFilterType; PadFilterType::Pointer l_pad = PadFilterType::New(); l_pad->SetInput(l_import_seg.getOutput()); l_pad->SetPadUpperBound(upper); l_pad->SetPadLowerBound(lower); typedef itk::ImageFileWriter< ImageType > WriterFilterType; WriterFilterType::Pointer l_writer = WriterFilterType::New(); l_writer->SetInput(l_pad->GetOutput()); l_writer->SetFileName(logDir.toStdString() + "voi.mhd"); try{ l_writer->Update(); } catch (itk::ExceptionObject& err) { M_Error(String(err.what())); } I also tried to crop the original image to make it fit the segmentation dimensions but it always is a few pixels smaller than the segmentation image and I have no idea why. Moreover, this gap is never the same and seems to be proportional to the segmentation image size. Why can't I perform the padding of my segmentation image? Plus, does anybody know why I can't crop the original image without having a few pixels less than needed? Thanks in advance, Marie -- View this message in context: http://itk-users.7.n7.nabble.com/Error-encountered-when-padding-boundary-condition-is-ITK-NULLPTR-tp38654.html Sent from the ITK - Users mailing list archive at Nabble.com. From matt.mccormick at kitware.com Tue Aug 29 08:24:49 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 29 Aug 2017 08:24:49 -0400 Subject: [ITK-users] Error encountered when padding: boundary condition is ITK_NULLPTR In-Reply-To: <1504004161094-38654.post@n7.nabble.com> References: <1504004161094-38654.post@n7.nabble.com> Message-ID: Hi Marie, Is getBounds() returning physical coordinates or index coordinates? PadImageFilter uses index coordinates. Here is an example: https://itk.org/ITKExamples/src/Filtering/ImageGrid/PadAnImageWithAConstant/Documentation.html Hope this helps, Matt On Tue, Aug 29, 2017 at 6:56 AM, avazuila wrote: > Hi all, > > I just performed the segmentation of a vessel from a CT scan and I would > like to use it to mask the abovementioned vessel on the image. In order to > do so I would like to pad the segmentation image which is smaller than the > image from which it has been extracted. > > I get the following error: "PadImageFilter: Boundary condition is > ITK_NULLPTR so no request region can be generated." > > My code is the following: > > double* voi_bounds = l_import_preprocess.getBounds(); > double* seg_bounds = l_import_seg.getBounds(); > > double x_min = abs(voi_bounds[0] - seg_bounds[0]); > double x_max = abs(voi_bounds[1] - seg_bounds[1]); > double y_min = abs(voi_bounds[2] - seg_bounds[2]); > double y_max = abs(voi_bounds[3] - seg_bounds[3]); > double z_min = abs(voi_bounds[4] - seg_bounds[4]); > double z_max = abs(voi_bounds[5] - seg_bounds[5]); > > const int Dimension = 3; > typedef uchar PixelType; > typedef itk::Image< PixelType, Dimension > ImageType; > > ImageType::SizeType upper; > ImageType::SizeType lower; > > lower[0] = x_min; > lower[1] = y_min; > lower[2] = z_min; > > upper[0] = x_max; > upper[1] = y_max; > upper[2] = z_max; > > typedef itk::PadImageFilter< ImageType, ImageType > PadFilterType; > PadFilterType::Pointer l_pad = PadFilterType::New(); > l_pad->SetInput(l_import_seg.getOutput()); > l_pad->SetPadUpperBound(upper); > l_pad->SetPadLowerBound(lower); > > typedef itk::ImageFileWriter< ImageType > WriterFilterType; > WriterFilterType::Pointer l_writer = WriterFilterType::New(); > l_writer->SetInput(l_pad->GetOutput()); > l_writer->SetFileName(logDir.toStdString() + "voi.mhd"); > try{ > l_writer->Update(); > } > catch (itk::ExceptionObject& err) { > M_Error(String(err.what())); > } > > I also tried to crop the original image to make it fit the segmentation > dimensions but it always is a few pixels smaller than the segmentation image > and I have no idea why. Moreover, this gap is never the same and seems to be > proportional to the segmentation image size. > > Why can't I perform the padding of my segmentation image? > Plus, does anybody know why I can't crop the original image without having a > few pixels less than needed? > > Thanks in advance, > > Marie > > > > -- > View this message in context: http://itk-users.7.n7.nabble.com/Error-encountered-when-padding-boundary-condition-is-ITK-NULLPTR-tp38654.html > Sent from the ITK - Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users From mbrunet at insa-rennes.fr Tue Aug 29 08:41:03 2017 From: mbrunet at insa-rennes.fr (avazuila) Date: Tue, 29 Aug 2017 05:41:03 -0700 (MST) Subject: [ITK-users] Error encountered when padding: boundary condition is ITK_NULLPTR In-Reply-To: References: <1504004161094-38654.post@n7.nabble.com> Message-ID: <1504010463045-38656.post@n7.nabble.com> Hi Matt, getBounds() returns physical coordinates. Do you know how I could get the index coordinates? I am having a hard time managing to understand what indexes are for and I can't see a getIndex() method in my code (I'm not the author of these methods). Thanks and regards, Marie -- View this message in context: http://itk-users.7.n7.nabble.com/Error-encountered-when-padding-boundary-condition-is-ITK-NULLPTR-tp38654p38656.html Sent from the ITK - Users mailing list archive at Nabble.com. From matt.mccormick at kitware.com Tue Aug 29 10:14:33 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 29 Aug 2017 10:14:33 -0400 Subject: [ITK-users] Error encountered when padding: boundary condition is ITK_NULLPTR In-Reply-To: <1504010463045-38656.post@n7.nabble.com> References: <1504004161094-38654.post@n7.nabble.com> <1504010463045-38656.post@n7.nabble.com> Message-ID: Hi Marie, The relationship between pixel / index coordinates and physical space is described in the ITK Software Guide: https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch4.html#x38-470004.1 There are methods on itk::Image to go between the two, TransformIndexToPhysicalPoint and TransformPhysicalPointToIndex, https://itk.org/Doxygen/html/classitk_1_1ImageBase.html#ab003313ba1a078d89a832dc0a35d2efa https://itk.org/Doxygen/html/classitk_1_1ImageBase.html#af4a7c9c3787e9fdafbaaade2e02efa25 Hope this helps, Matt On Tue, Aug 29, 2017 at 8:41 AM, avazuila wrote: > Hi Matt, > > getBounds() returns physical coordinates. Do you know how I could get the > index coordinates? I am having a hard time managing to understand what > indexes are for and I can't see a getIndex() method in my code (I'm not the > author of these methods). > > Thanks and regards, > > Marie > > > > -- > View this message in context: http://itk-users.7.n7.nabble.com/Error-encountered-when-padding-boundary-condition-is-ITK-NULLPTR-tp38654p38656.html > Sent from the ITK - Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users From siming.bayer at gmail.com Tue Aug 29 12:09:08 2017 From: siming.bayer at gmail.com (Siming Bayer) Date: Tue, 29 Aug 2017 18:09:08 +0200 Subject: [ITK-users] Question about LandmarkDisplacementFieldSource Message-ID: Dear all, I am trying to use LandmarkDisplacementFieldSource to compute a displacement field from 2 point sets. Although the 2 point sets are aligned almost perfectly with thin plate spline - Robust point matching algorithm (TPS-RPM), the resulting displacement field looks simply wrong. For example, the displacement field has a high value where I don?t expect any deformation/displacement. Does anybody knows the mathematical background of the itk implementation of LandmarkDisplacementFieldSource? Could anybody tell me the paper? Does any body knows how many landmarks is meaningful? best, Siming -------------- next part -------------- An HTML attachment was scrubbed... URL: From adrien.bailly at gmail.com Tue Aug 29 12:44:34 2017 From: adrien.bailly at gmail.com (Adrien BAILLY) Date: Tue, 29 Aug 2017 18:44:34 +0200 Subject: [ITK-users] MultiResolutionIterationEvent missing in python [ITK 4.12] Message-ID: Dear all, I am trying to perform a multi-resolution image registration using itk's python module (pip install itk) and following the example from Example/RegistrationITKv4/MultiResImageRegistration1.cxx. Unfortunately the class itk.MultiResolutionIterationEvent does not exists in the python module. After looking around in ITK source code it seems that it is missing from the python wrapper because it is not added in the file Modules/Core/Common/wrapping/ITKCommonBase.wrap line 5-14. Is there another way than using MultiResolutionIterationEvent for changing the optimizer parameters between levels ? Or should I add the wrapping command to ITKCommonBase.wrap and generate the python module manualy? Best regards, Adrien -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Tue Aug 29 15:26:12 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 29 Aug 2017 15:26:12 -0400 Subject: [ITK-users] Question about LandmarkDisplacementFieldSource In-Reply-To: References: Message-ID: Hi Siming, To find the references, see the documentation for the KernelSplines: https://itk.org/Doxygen/html/classitk_1_1KernelTransform.html The Inheritance Diagram has links to specific splines and they also have references. If dealing with two point sets, you may also be interested in the LandmarkBasedTransformInitializer: https://itk.org/Doxygen/html/classitk_1_1LandmarkBasedTransformInitializer.html Hope this helps, Matt On Tue, Aug 29, 2017 at 12:09 PM, Siming Bayer wrote: > Dear all, > > I am trying to use LandmarkDisplacementFieldSource to compute a displacement > field from 2 point sets. Although the 2 point sets are aligned almost > perfectly with thin plate spline - Robust point matching algorithm > (TPS-RPM), the resulting displacement field looks simply wrong. For example, > the displacement field has a high value where I don?t expect any > deformation/displacement. > > Does anybody knows the mathematical background of the itk implementation of > LandmarkDisplacementFieldSource? Could anybody tell me the paper? Does any > body knows how many landmarks is meaningful? > > best, > Siming > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > From matt.mccormick at kitware.com Tue Aug 29 15:28:01 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 29 Aug 2017 15:28:01 -0400 Subject: [ITK-users] MultiResolutionIterationEvent missing in python [ITK 4.12] In-Reply-To: References: Message-ID: Hi Adrien, Thanks for pointing out the omission. Could you please submit a patch to add wrapping for the class? [1] Once integrated, nightly binary builds of the Python packages will be available. Thanks, Matt [1] https://itk.org/Wiki/ITK/Git/Develop On Tue, Aug 29, 2017 at 12:44 PM, Adrien BAILLY wrote: > Dear all, > > I am trying to perform a multi-resolution image registration using itk's > python module (pip install itk) and following the example from > Example/RegistrationITKv4/MultiResImageRegistration1.cxx. > > Unfortunately the class itk.MultiResolutionIterationEvent does not exists in > the python module. After looking around in ITK source code it seems that it > is missing from the python wrapper because it is not added in the file > Modules/Core/Common/wrapping/ITKCommonBase.wrap line 5-14. > > Is there another way than using MultiResolutionIterationEvent for changing > the optimizer parameters between levels ? Or should I add the wrapping > command to ITKCommonBase.wrap and generate the python module manualy? > > Best regards, > > Adrien > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > From siming.bayer at gmail.com Tue Aug 29 15:53:54 2017 From: siming.bayer at gmail.com (Siming Bayer) Date: Tue, 29 Aug 2017 21:53:54 +0200 Subject: [ITK-users] Question about LandmarkDisplacementFieldSource In-Reply-To: References: Message-ID: Hi Matt, Thank you for the information. Since I would like to perform non-rigid image registration, I would like to first compute a displacement field using 2 point set and then deform the image with the displacement field. So LandmarkBasedTransformInitializer is not suitable in my case. Basically, I extract two point sets from images of vessels (one before non-rigid deformation, one after deformation). Those two point sets are then aligned by using TPS-RPM Algorithm by Chui. For my understanding, the output displacement field from LandmarkDisplacementFieldSource should be the perfect deformation field, with which I can warp the input vessel image with WarpImageFilter. According to the documentation and the code of LandmarkDisplacementFieldSource, it also use Kernel Based Spline (TPS as default) to compute the deformation field from two point sets. But now, the resulting displacement field is quite strange, although the point matching algorithm works fine. I simple have no idea why my implementation produce wrong output displacement field. So I think, I need to deepen into the details of the KernelTransform implementation. best, Siming > Am 29.08.2017 um 21:26 schrieb Matt McCormick : > > Hi Siming, > > To find the references, see the documentation for the KernelSplines: > > https://itk.org/Doxygen/html/classitk_1_1KernelTransform.html > > The Inheritance Diagram has links to specific splines and they also > have references. > > > If dealing with two point sets, you may also be interested in the > LandmarkBasedTransformInitializer: > > https://itk.org/Doxygen/html/classitk_1_1LandmarkBasedTransformInitializer.html > > > Hope this helps, > Matt > > > > On Tue, Aug 29, 2017 at 12:09 PM, Siming Bayer wrote: >> Dear all, >> >> I am trying to use LandmarkDisplacementFieldSource to compute a displacement >> field from 2 point sets. Although the 2 point sets are aligned almost >> perfectly with thin plate spline - Robust point matching algorithm >> (TPS-RPM), the resulting displacement field looks simply wrong. For example, >> the displacement field has a high value where I don?t expect any >> deformation/displacement. >> >> Does anybody knows the mathematical background of the itk implementation of >> LandmarkDisplacementFieldSource? Could anybody tell me the paper? Does any >> body knows how many landmarks is meaningful? >> >> best, >> Siming >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> From matt.mccormick at kitware.com Tue Aug 29 16:13:56 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 29 Aug 2017 16:13:56 -0400 Subject: [ITK-users] Question about LandmarkDisplacementFieldSource In-Reply-To: References: Message-ID: Hi Siming, That sounds like a good plan. Other kernel transform may be of interest. The LandmarkBasedTransformInitializer can also be used for non-rigid image registration by generating a b-spline transformation. Hope this helps, Matt. On Tue, Aug 29, 2017 at 3:53 PM, Siming Bayer wrote: > Hi Matt, > > Thank you for the information. > > Since I would like to perform non-rigid image registration, I would like to first compute a displacement field using 2 point set and then deform the image with the displacement field. So LandmarkBasedTransformInitializer is not suitable in my case. > > > Basically, I extract two point sets from images of vessels (one before non-rigid deformation, one after deformation). Those two point sets are then aligned by using TPS-RPM Algorithm by Chui. For my understanding, the output displacement field from LandmarkDisplacementFieldSource should be the perfect deformation field, with which I can warp the input vessel image with WarpImageFilter. According to the documentation and the code of LandmarkDisplacementFieldSource, it also use Kernel Based Spline (TPS as default) to compute the deformation field from two point sets. But now, the resulting displacement field is quite strange, although the point matching algorithm works fine. I simple have no idea why my implementation produce wrong output displacement field. > > So I think, I need to deepen into the details of the KernelTransform implementation. > > best, > Siming > >> Am 29.08.2017 um 21:26 schrieb Matt McCormick : >> >> Hi Siming, >> >> To find the references, see the documentation for the KernelSplines: >> >> https://itk.org/Doxygen/html/classitk_1_1KernelTransform.html >> >> The Inheritance Diagram has links to specific splines and they also >> have references. >> >> >> If dealing with two point sets, you may also be interested in the >> LandmarkBasedTransformInitializer: >> >> https://itk.org/Doxygen/html/classitk_1_1LandmarkBasedTransformInitializer.html >> >> >> Hope this helps, >> Matt >> >> >> >> On Tue, Aug 29, 2017 at 12:09 PM, Siming Bayer wrote: >>> Dear all, >>> >>> I am trying to use LandmarkDisplacementFieldSource to compute a displacement >>> field from 2 point sets. Although the 2 point sets are aligned almost >>> perfectly with thin plate spline - Robust point matching algorithm >>> (TPS-RPM), the resulting displacement field looks simply wrong. For example, >>> the displacement field has a high value where I don?t expect any >>> deformation/displacement. >>> >>> Does anybody knows the mathematical background of the itk implementation of >>> LandmarkDisplacementFieldSource? Could anybody tell me the paper? Does any >>> body knows how many landmarks is meaningful? >>> >>> best, >>> Siming >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> > From siming.bayer at gmail.com Tue Aug 29 16:17:09 2017 From: siming.bayer at gmail.com (Siming Bayer) Date: Tue, 29 Aug 2017 22:17:09 +0200 Subject: [ITK-users] Question about LandmarkDisplacementFieldSource In-Reply-To: References: Message-ID: Thank you Matt ! best, Siming > Am 29.08.2017 um 22:13 schrieb Matt McCormick : > > LandmarkBasedTransformInitializer -------------- next part -------------- An HTML attachment was scrubbed... URL: From fabian.trobles at gmail.com Wed Aug 30 12:24:27 2017 From: fabian.trobles at gmail.com (Fabian Torres) Date: Wed, 30 Aug 2017 11:24:27 -0500 Subject: [ITK-users] Variable Matrix Access Violiotation Message-ID: Hi evryone. I?m using itk VariableMatrix to do some image processing. But I have some problems initializing my matrices. When I use small sizes like this I do not have any problem //matrix A regionSize[0] = 15; regionSze[1] = 15; VariableSizeMatrix matA; matA.SetSize(2*regionSize[0]*regionSize[1],2*regionSize[0]*regionSize[1]); matA.Fill(0.0); But when I use bigger sizes like: regionSize[0] = 100; regionSze[1] = 100; I get an Acces Violation exception Access violation reading location 0xcdcdcdc1. I'm using Visualstudio 2008 and ITK 4.4 Does this has something to do with memory allocation? Is there a way a could verify if I have enough memory to allocate my matrix? Thanks. -- Fabi?n Torres Robles Maestr?a en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos Tel. 58081280, 0445534661338 E-mail fabian.trobles at gmail.com, dae.wong at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From dae.wong at gmail.com Wed Aug 30 18:03:17 2017 From: dae.wong at gmail.com (Fabian Torres) Date: Wed, 30 Aug 2017 17:03:17 -0500 Subject: [ITK-users] Variable Matrix Access Violation Message-ID: Hi everyone. I?m using itk VariableMatrix to do some image processing. But I have some problems initializing my matrices. When I use small sizes like this I do not have any problem //matrix A regionSize[0] = 15; regionSze[1] = 15; VariableSizeMatrix matA; matA.SetSize(2*regionSize[0]*regionSize[1],2*regionSize[0]*regionSize[1]); matA.Fill(0.0); But when I use bigger sizes like: regionSize[0] = 100; regionSze[1] = 100; I get an Acces Violation exception Access violation reading location 0xcdcdcdc1. I'm using Visualstudio 2008 and ITK 4.4 Does this has something to do with memory allocation? Is there a way a could verify if I have enough memory to allocate my matrix? Thanks. -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: