[ITK] [slicer-devel] BigTIFF
Matt McCormick
matt.mccormick at kitware.com
Wed Sep 17 13:05:56 EDT 2014
Great to hear!
On Wed, Sep 17, 2014 at 12:04 PM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:
> I forgot to mention that ITK builds correctly, and my test program that uses it to create big tiffs now works fine.
> ________________________________________
> From: Matt McCormick [matt.mccormick at kitware.com]
> Sent: Thursday, 18 September 2014 3:55 a.m.
> To: Gib Bogle
> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org
> Subject: Re: [slicer-devel] BigTIFF
>
> Hi Gib,
>
> Getting the builds states to propagate and follow how the get set can
> be tricky. A few pointers on where to look for the status:
>
> 1) CMakeCache.txt (this file contains the build settings that CMake
> recognized from your input when you run CMake)
> 2) ITKConfig.cmake (this file will exist in the build tree or the
> install tree, and it contains CMake varables that may be used by other
> projects building against ITK)
> 3) itkConfigure.h (this is a header that has configured preprocessor
> definitions used when building)
>
> HTH,
> Matt
>
>
>
> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:
>> Hi Bradley, Matt and Steve,
>>
>> Now for the embarrassing confession. In External_ITK4.cmake I turned
>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I
>> finally checked what the code that is being built was using (with #if
>> defined ...) I discovered that both ITKV3_COMPATIBILITY and
>> ITK_USE_64BITS_IDS were off. How can this be?
>>
>> It's easy, all it takes is a typo:
>> -DITK_USE_64_BITS_IDS:BOOL=ON
>> That typo has cost me a couple of days, and caused annoyance to a few
>> people, I suspect.
>>
>> Unfortunately... now Slicer's vtkITK does not build. There are very many
>> errors like this:
>>
>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------
>> 3>Build started 17/09/2014 7:25:52 p.m..
>> 3>InitializeBuildStatus:
>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild".
>> 3>CustomBuild:
>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt
>> 3> CMake does not need to re-run because
>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date.
>> 3>ClCompile:
>> 3> vtkITKNumericTraits.cxx
>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx
>> 3> vtkITKArchetypeImageSeriesReader.cxx
>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx
>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx
>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx
>> 3> vtkITKImageWriter.cxx
>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx
>> 3> vtkITKDistanceTransform.cxx
>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179):
>> error C2679: binary '=' : no operator found which takes a right-hand operand
>> of type 'itk::ImportImageContainer<TElementIdentifier,TElement> *' (or there
>> is no acceptable conversion)
>> 3> with
>> 3> [
>> 3> TElementIdentifier=unsigned __int64,
>> 3> TElement=double
>> 3> ]
>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124):
>> could be 'itk::SmartPointer<TObjectType>
>> &itk::SmartPointer<TObjectType>::operator =(const
>> itk::SmartPointer<TObjectType> &)'
>> 3> with
>> 3> [
>> 3> TObjectType=itk::ImportImageContainer<unsigned long,double>
>> 3> ]
>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128):
>> or 'itk::SmartPointer<TObjectType>
>> &itk::SmartPointer<TObjectType>::operator
>> =(itk::ImportImageContainer<TElementIdentifier,TElement> *)'
>> 3> with
>> 3> [
>> 3> TObjectType=itk::ImportImageContainer<unsigned long,double>,
>> 3> TElementIdentifier=unsigned long,
>> 3> TElement=double
>> 3> ]
>> 3> while trying to match the argument list
>> '(itk::SmartPointer<TObjectType>,
>> itk::ImportImageContainer<TElementIdentifier,TElement> *)'
>> 3> with
>> 3> [
>> 3> TObjectType=itk::ImportImageContainer<unsigned long,double>
>> 3> ]
>> 3> and
>> 3> [
>> 3> TElementIdentifier=unsigned __int64,
>> 3> TElement=double
>> 3> ]
>>
>> I presume these are related to the use of 64-bit integers.
>>
>> Over to you guys :)
>>
>> Gib
>> ________________________________
>> From: Bradley Lowekamp [blowekamp at mail.nih.gov]
>> Sent: Tuesday, 16 September 2014 12:45 a.m.
>> To: Steve Pieper
>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu
>> Subject: Re: [slicer-devel] BigTIFF
>>
>> Hello,
>>
>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here:
>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48
>>
>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7
>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to
>> read and write files like these there. More information about getting
>> started is here[1].
>>
>> You should be a able to generate a image with:
>>
>> import SimpleITK as sitk
>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8)
>> img += 10
>> stats = sitk.StatisticsImageFilter()
>> stats.Execute(img)
>> print stats
>>
>> This should give you basic access to ITK in python to interactively
>> experiment with options with these large images. I have been able to load
>> large images with the binaries of SimpleITK on windows 64-bits. I don't know
>> if I have tried big tiff though.
>>
>> A simular test could be done with C++ and ITK directly, but I think
>> SimpleITK in python may be quicker for experimentation.
>>
>> Brad
>>
>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted
>> [2]
>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee
>>
>> On Sep 15, 2014, at 7:37 AM, Steve Pieper <pieper at isomics.com> wrote:
>>
>> Hi Gib -
>>
>> Are you testing only on windows? What we would often try to do for this
>> kind of debugging is to create a small example that other people can test on
>> their configurations. Slicer has a mechanism called a Self Test [1] to
>> allow easy replication and debugging across multiple platforms. It's ideal
>> if we can hone it down to something like what is described as a 'sscce' [2].
>> The self tests will typically download some data from a public web site, run
>> some operations, and then print something out saying if it passed or failed
>> (or it may crash). Since it's possible to make a small data file that
>> expands into a giant tiff image it should be pretty tractable to pose this
>> issue in the form of a self test.
>>
>> Best,
>> Steve
>>
>>
>> [1]
>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule
>>
>> [2] http://sscce.org/
>>
>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:
>>>
>>> Hi J-C,
>>>
>>> Some more info about Slicer with big tiff files.
>>>
>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly
>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything
>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page
>>> 72)
>>>
>>> All suggestions will be gratefully received.
>>>
>>> Cheers
>>> Gib
>>> ________________________________
>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com]
>>> Sent: Sunday, 14 September 2014 8:32 p.m.
>>> To: Gib Bogle
>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu
>>> Subject: Re: [slicer-devel] BigTIFF
>>>
>>> Hi Gib,
>>>
>>> What do you mean by "reinstalled" ? You should not have to install Slicer
>>> to be able to execute it from the build directory.
>>>
>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option
>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work
>>> out.
>>>
>>> When done building, make sure to start the Slicer launcher:
>>>
>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe
>>>
>>> and not the Slicer executable:
>>>
>>>
>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe
>>>
>>>
>>> By using the launcher, you ensure that the PATH are properly setup and the
>>> expected libraries are loaded.
>>>
>>>
>>> Hth
>>> Jc
>>>
>>>
>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle <g.bogle at auckland.ac.nz>
>>> wrote:
>>>>
>>>> I hope I understand correctly. I added the line as shown to
>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake:
>>>> ...
>>>> # ZLIB
>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON
>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT}
>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR}
>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY}
>>>> # Big TIFF
>>>> -DITK_USE_64_BITS_IDS:BOOL=ON
>>>> ...
>>>>
>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I
>>>> presume this is the "superbuild". I then redid ALL_BUILD in
>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still
>>>> crashes with the big tiff. Is there somewhere I can check in the project
>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took
>>>> effect?
>>>>
>>>> Thanks
>>>> Gib
>>>> ________________________________
>>>> From: Steve Pieper [pieper at isomics.com]
>>>> Sent: Sunday, 14 September 2014 1:36 p.m.
>>>>
>>>> To: Gib Bogle
>>>> Cc: slicer-devel at bwh.harvard.edu
>>>> Subject: Re: [slicer-devel] BigTIFF
>>>>
>>>> Hey Gib -
>>>>
>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the
>>>> ITK build process [1] during the superbuild. I don't think much else was
>>>> required except turning off the IKTv3 parts.
>>>>
>>>> [1]
>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68
>>>>
>>>> -Steve
>>>>
>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get
>>>> it on TV). So the Jo'berg game should be a great rematch!
>>>>
>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle <g.bogle at auckland.ac.nz>
>>>> wrote:
>>>>>
>>>>> You did warn me.
>>>>>
>>>>> Here is the list of options not ticked:
>>>>>
>>>>> Slicer_BUILD_BRAINSTOOLS
>>>>> _LEGACY_CLI
>>>>> _LandmarkRegistration
>>>>> _TESTING_EXTENSIONS
>>>>> _UPDATE_TRANSLATION
>>>>> _USE_GIT_PROTOCOL
>>>>> _OpenIGTLink
>>>>> _PYTHONQT_WITH_OPENSSL
>>>>> _PYTHONQT_WITH_TCL
>>>>> _QtTesting
>>>>> _SimpleITK
>>>>> _VTK_DEBUG_LINKS
>>>>> Slicer_WITH_LIBRARY_VERSION
>>>>>
>>>>> USE_BRAINS*
>>>>> USE_ConvertBetweenFileFormats
>>>>> USE_DWIConvert
>>>>> USE_DebugImageViewer
>>>>> USE_GTRACT
>>>>> USE_ICCDEF
>>>>> USE_ImageCalculator
>>>>> USE_ReferenceAtlas
>>>>>
>>>>> -------
>>>>>
>>>>> Progress! Process Monitor showed me that the exit code was C0000139,
>>>>> which means a DLL was not found. I then realized that I have different
>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this
>>>>> prompted me to look more carefully at the PATH environment variable. I just
>>>>> tested with all the new paths at the start of the PATH string, and Slicer
>>>>> starts successfully! I can load a tiff! But ... it still crashes when I
>>>>> attempt to load a 4 GB tiff.
>>>>>
>>>>> I am now wondering (belatedly!) about the way I tried to build with big
>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as
>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked
>>>>> for directions before doing this - now I'm wondering if that switch actually
>>>>> had any effect. Is that the right thing to do, and if not, what is?
>>>>>
>>>>> Thanks
>>>>> Gib
>>>>> ________________________________
>>>>> From: Steve Pieper [pieper at isomics.com]
>>>>> Sent: Sunday, 14 September 2014 10:02 a.m.
>>>>>
>>>>> To: Gib Bogle
>>>>> Cc: slicer-devel at bwh.harvard.edu
>>>>> Subject: Re: [slicer-devel] BigTIFF
>>>>>
>>>>> Yes, well, don't say I didn't warn you! ; )
>>>>>
>>>>> You do need loadable modules and you probably do want python (a lot of
>>>>> core stuff is in python, like the editor).
>>>>>
>>>>> BRAINSTools should be off for now, since it needs ITKv3.
>>>>>
>>>>> I'm not sure either what to do next, but I suggest maybe trying the
>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when
>>>>> it exited. But that may be a longshot.
>>>>>
>>>>> -Steve
>>>>>
>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle <g.bogle at auckland.ac.nz>
>>>>> wrote:
>>>>>>
>>>>>> Hi Steve,
>>>>>>
>>>>>> That was an interesting exercise. I managed to build Slicer without
>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program
>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit
>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I
>>>>>> built it again, this time selecting most things except BRAINTools. The
>>>>>> build took a long time, partly because I turned on the Python option, which
>>>>>> I don't need. This time there were no errors, except for a couple of
>>>>>> occasions where the attempt to create a directory failed - this was because
>>>>>> the directory already existed, and was easily solved by deleting the
>>>>>> directory and building again. I installed everything that wanted to be
>>>>>> installed, and modified the environment variables to suit.
>>>>>>
>>>>>> My sense of satisfaction was short-lived, however. When Slicer is
>>>>>> invoked the Acknowledgements screen flashes up briefly then the program
>>>>>> exits. There are no error messages. Dependency Walker shows that all the
>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not
>>>>>> knowing what it is).
>>>>>>
>>>>>> I sense that I must be close to getting it working, but I'm not sure
>>>>>> what to do next.
>>>>>>
>>>>>> Cheers
>>>>>> Gib
>>>>>> ________________________________
>>>>>> From: Steve Pieper [pieper at isomics.com]
>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m.
>>>>>>
>>>>>> To: Gib Bogle
>>>>>> Cc: slicer-devel at bwh.harvard.edu
>>>>>> Subject: Re: [slicer-devel] BigTIFF
>>>>>>
>>>>>> Hi Gib -
>>>>>>
>>>>>> A lot of the building goes on in parallel so you need to review the
>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build
>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output
>>>>>> window and then paste it into a text editor to look for issues. Definitely
>>>>>> you don't want to be editing any of the visual studio files, since they are
>>>>>> generated by cmake every configure -- much better to sort out what is going
>>>>>> on at the cmake flag level.
>>>>>>
>>>>>> Best,
>>>>>> Steve
>>>>>>
>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle <g.bogle at auckland.ac.nz>
>>>>>> wrote:
>>>>>>>
>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice
>>>>>>> something odd. Here is a snippet from the list of Linker > Input >
>>>>>>> Additional Dependencies:
>>>>>>>
>>>>>>> ...
>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib
>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib
>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib
>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib
>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib
>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib
>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib
>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib
>>>>>>> ITKCommon.lib
>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib
>>>>>>> ...
>>>>>>>
>>>>>>> For some reason ITKCommon.lib is treated differently from all the
>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this?
>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly
>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this
>>>>>>> 40+ times.
>>>>>>>
>>>>>>> Thanks again
>>>>>>> Gib
>>>>>>> ________________________________
>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu
>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle
>>>>>>> [g.bogle at auckland.ac.nz]
>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m.
>>>>>>>
>>>>>>> To: Steve Pieper
>>>>>>> Cc: slicer-devel at bwh.harvard.edu
>>>>>>> Subject: Re: [slicer-devel] BigTIFF
>>>>>>>
>>>>>>> Hi Steve,
>>>>>>>
>>>>>>> All goes well until the point where the qSlicer*.lib get made. The
>>>>>>> first error, while building qSlicerBaseQTCore.lib, is:
>>>>>>>
>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib'
>>>>>>>
>>>>>>> I don't know how to interpret this. I am guessing that it wants to
>>>>>>> link the ITK library that was just built, i.e.:
>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib
>>>>>>> This is the first of about 40 such link errors.
>>>>>>>
>>>>>>> I'm not sure if ITK really needed to be built, since it is already
>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping
>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set
>>>>>>> ITK_DIR appropriately?
>>>>>>>
>>>>>>> Thanks
>>>>>>> Gib
>>>>>>> ________________________________
>>>>>>> From: Steve Pieper [pieper at isomics.com]
>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m.
>>>>>>> To: Gib Bogle
>>>>>>> Cc: slicer-devel at bwh.harvard.edu
>>>>>>> Subject: Re: [slicer-devel] BigTIFF
>>>>>>>
>>>>>>> Hi Gib -
>>>>>>>
>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is
>>>>>>> quite reasonable, and would be workable. But if you haven't built a big
>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git,
>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just
>>>>>>> right. That said, slicer is actually quite well supported on windows,
>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the
>>>>>>> trickiest platform in my experience.
>>>>>>>
>>>>>>> -Steve
>>>>>>>
>>>>>>>
>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle <g.bogle at auckland.ac.nz>
>>>>>>> wrote:
>>>>>>>>
>>>>>>>> Hi Steve,
>>>>>>>>
>>>>>>>> Do you think I would be able to build Slicer myself, with
>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that
>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this
>>>>>>>> point is simply for a 3D viewer that can handle big images.
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>> Gib
>>>>>>>> ________________________________
>>>>>>>> From: Gib Bogle
>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m.
>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper
>>>>>>>> Cc: slicer-devel at bwh.harvard.edu
>>>>>>>> Subject: RE: [slicer-devel] BigTIFF
>>>>>>>>
>>>>>>>> Hi Jean-Christophe,
>>>>>>>>
>>>>>>>> Any idea when 4.5 will enter the world?
>>>>>>>>
>>>>>>>> Cheers
>>>>>>>> Gib
>>>>>>>> ________________________________
>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu
>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe
>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com]
>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m.
>>>>>>>> To: Steve Pieper
>>>>>>>> Cc: slicer-devel at bwh.harvard.edu
>>>>>>>> Subject: Re: [slicer-devel] BigTIFF
>>>>>>>>
>>>>>>>> Hi Folks,
>>>>>>>>
>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on
>>>>>>>> either ITKDeprecated or ITKV3Compatibility.
>>>>>>>>
>>>>>>>> That said, BRAINSTools and some extensions are still depending on
>>>>>>>> these module. All details are captured here:
>>>>>>>>
>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486
>>>>>>>>
>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The
>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is
>>>>>>>> planned for 4.5.
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>> Jc
>>>>>>>>
>>>>>>>>
>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper <pieper at isomics.com>
>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>> Hi Matt -
>>>>>>>>>
>>>>>>>>> Thanks, that's helpful.
>>>>>>>>>
>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK,
>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty
>>>>>>>>> straightforward.
>>>>>>>>>
>>>>>>>>> But there's no reason to start that until we know that BRAINSTools
>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated.
>>>>>>>>>
>>>>>>>>> -Steve
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick
>>>>>>>>> <matt.mccormick at kitware.com> wrote:
>>>>>>>>>>
>>>>>>>>>> Here is what the process would look like:
>>>>>>>>>>
>>>>>>>>>> 0) Start with a clean software quality dashboard.
>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in
>>>>>>>>>> Superbuild/External_ITKv4.cmake
>>>>>>>>>> 2) Rebuild and encounter errors and test failures.
>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and
>>>>>>>>>> the
>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes
>>>>>>>>>> (minor modifications to the API, etc).
>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON.
>>>>>>>>>> 5) Profit.
>>>>>>>>>>
>>>>>>>>>> HTH,
>>>>>>>>>> Matt
>>>>>>>>>>
>>>>>>>>>> [1] http://itk.org/migrationv4/
>>>>>>>>>>
>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html
>>>>>>>>>>
>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper <pieper at isomics.com>
>>>>>>>>>> wrote:
>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists,
>>>>>>>>>> > but it's
>>>>>>>>>> > looking like there's a fair amount of code to retrofit.
>>>>>>>>>> >
>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just
>>>>>>>>>> > what is
>>>>>>>>>> > involved?
>>>>>>>>>> >
>>>>>>>>>> > -Steve
>>>>>>>>>> >
>>>>>>>>>> >
>>>>>>>>>> >
>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle
>>>>>>>>>> > <g.bogle at auckland.ac.nz> wrote:
>>>>>>>>>> >>
>>>>>>>>>> >> :( I imagine that people are increasingly working with very
>>>>>>>>>> >> large
>>>>>>>>>> >> datasets, so the number of people who would like to have this
>>>>>>>>>> >> capability
>>>>>>>>>> >> will grow. I, alas, am not an ITK expert.
>>>>>>>>>> >> ________________________________
>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com]
>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m.
>>>>>>>>>> >>
>>>>>>>>>> >> To: Gib Bogle
>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu
>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF
>>>>>>>>>> >>
>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even
>>>>>>>>>> >> configure
>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module,
>>>>>>>>>> >> like vtkITK
>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK
>>>>>>>>>> >> experts are
>>>>>>>>>> >> going to need to dig in before this mode can be enabled.
>>>>>>>>>> >>
>>>>>>>>>> >> -Steve
>>>>>>>>>> >>
>>>>>>>>>> >>
>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle
>>>>>>>>>> >> <g.bogle at auckland.ac.nz> wrote:
>>>>>>>>>> >>>
>>>>>>>>>> >>> I await the results with interest...
>>>>>>>>>> >>> ________________________________
>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu
>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve
>>>>>>>>>> >>> Pieper
>>>>>>>>>> >>> [pieper at isomics.com]
>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m.
>>>>>>>>>> >>> To: Bradley Lowekamp
>>>>>>>>>> >>>
>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu
>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF
>>>>>>>>>> >>>
>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out
>>>>>>>>>> >>> a lot of
>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places
>>>>>>>>>> >>> ITKV3_COMPATIBILITY was
>>>>>>>>>> >>> required? I kicked off a build to see what will happen.
>>>>>>>>>> >>>
>>>>>>>>>> >>> -Steve
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp
>>>>>>>>>> >>> <blowekamp at mail.nih.gov>
>>>>>>>>>> >>> wrote:
>>>>>>>>>> >>>>
>>>>>>>>>> >>>> Steve,
>>>>>>>>>> >>>>
>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been
>>>>>>>>>> >>>> configured in
>>>>>>>>>> >>>> Slicer.
>>>>>>>>>> >>>>
>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY
>>>>>>>>>> >>>> needs to
>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer
>>>>>>>>>> >>>> be used. I have
>>>>>>>>>> >>>> brought these issue up before and offered assistance but no
>>>>>>>>>> >>>> one wanted to
>>>>>>>>>> >>>> champion changing these configuration flags.
>>>>>>>>>> >>>>
>>>>>>>>>> >>>> Brad
>>>>>>>>>> >>>>
>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper <pieper at isomics.com>
>>>>>>>>>> >>>> wrote:
>>>>>>>>>> >>>>
>>>>>>>>>> >>>> Hi Brad -
>>>>>>>>>> >>>>
>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was
>>>>>>>>>> >>>> able to
>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's
>>>>>>>>>> >>>> vtkNRRDWriter
>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file
>>>>>>>>>> >>>> with ITK's NRRD
>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with
>>>>>>>>>> >>>> default options
>>>>>>>>>> >>>> on win7 64bit.
>>>>>>>>>> >>>>
>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just
>>>>>>>>>> >>>> something nobody
>>>>>>>>>> >>>> has tried?
>>>>>>>>>> >>>>
>>>>>>>>>> >>>> -Steve
>>>>>>>>>> >>>>
>>>>>>>>>> >>>>
>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp
>>>>>>>>>> >>>> <blowekamp at mail.nih.gov> wrote:
>>>>>>>>>> >>>>>
>>>>>>>>>> >>>>> Steve,
>>>>>>>>>> >>>>>
>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on
>>>>>>>>>> >>>>> windows 64?
>>>>>>>>>> >>>>>
>>>>>>>>>> >>>>> There should be some image source filters in the
>>>>>>>>>> >>>>> SimpleFilters modules
>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff
>>>>>>>>>> >>>>> specific.
>>>>>>>>>> >>>>>
>>>>>>>>>> >>>>> Bread
>>>>>>>>>> >>>>>
>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper
>>>>>>>>>> >>>>> <pieper at isomics.com> wrote:
>>>>>>>>>> >>>>>
>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib!
>>>>>>>>>> >>>>>
>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and
>>>>>>>>>> >>>>> pasted in
>>>>>>>>>> >>>>> a stack trace and put a link to the data.
>>>>>>>>>> >>>>>
>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825
>>>>>>>>>> >>>>>
>>>>>>>>>> >>>>> -Steve
>>>>>>>>>> >>>>>
>>>>>>>>>> >>>>>
>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp
>>>>>>>>>> >>>>> <blowekamp at mail.nih.gov> wrote:
>>>>>>>>>> >>>>>>
>>>>>>>>>> >>>>>> Matt, I was just about to point that out.
>>>>>>>>>> >>>>>>
>>>>>>>>>> >>>>>> The other things is the compatibility flag:
>>>>>>>>>> >>>>>>
>>>>>>>>>> >>>>>>
>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48
>>>>>>>>>> >>>>>>
>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's
>>>>>>>>>> >>>>>> still
>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3.
>>>>>>>>>> >>>>>>
>>>>>>>>>> >>>>>>
>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122
>>>>>>>>>> >>>>>>
>>>>>>>>>> >>>>>> Brad
>>>>>>>>>> >>>>>>
>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper
>>>>>>>>>> >>>>>> <pieper at isomics.com> wrote:
>>>>>>>>>> >>>>>>
>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can
>>>>>>>>>> >>>>>> replicate the
>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects.
>>>>>>>>>> >>>>>>
>>>>>>>>>> >>>>>>
>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick
>>>>>>>>>> >>>>>> <matt.mccormick at kitware.com> wrote:
>>>>>>>>>> >>>>>>>
>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem:
>>>>>>>>>> >>>>>>>
>>>>>>>>>> >>>>>>>
>>>>>>>>>> >>>>>>>
>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb
>>>>>>>>>> >>>>>>>
>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle
>>>>>>>>>> >>>>>>> <g.bogle at auckland.ac.nz>
>>>>>>>>>> >>>>>>> wrote:
>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get
>>>>>>>>>> >>>>>>> > back to this
>>>>>>>>>> >>>>>>> > later.
>>>>>>>>>> >>>>>>> > ________________________________
>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com]
>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m.
>>>>>>>>>> >>>>>>> >
>>>>>>>>>> >>>>>>> > To: Gib Bogle
>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu
>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF
>>>>>>>>>> >>>>>>> >
>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how
>>>>>>>>>> >>>>>>> > to
>>>>>>>>>> >>>>>>> > generate a big
>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable
>>>>>>>>>> >>>>>>> > for any
>>>>>>>>>> >>>>>>> > standard
>>>>>>>>>> >>>>>>> > platform should be fine too.
>>>>>>>>>> >>>>>>> >
>>>>>>>>>> >>>>>>> >
>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle
>>>>>>>>>> >>>>>>> > <g.bogle at auckland.ac.nz>
>>>>>>>>>> >>>>>>> > wrote:
>>>>>>>>>> >>>>>>> >>
>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to
>>>>>>>>>> >>>>>>> >> a
>>>>>>>>>> >>>>>>> >> reasonable size.
>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK
>>>>>>>>>> >>>>>>> >> without
>>>>>>>>>> >>>>>>> >> problems.
>>>>>>>>>> >>>>>>> >> ________________________________
>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com]
>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m.
>>>>>>>>>> >>>>>>> >> To: Gib Bogle
>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu
>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF
>>>>>>>>>> >>>>>>> >>
>>>>>>>>>> >>>>>>> >> Hi -
>>>>>>>>>> >>>>>>> >>
>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this,
>>>>>>>>>> >>>>>>> >> for example
>>>>>>>>>> >>>>>>> >> with a
>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to
>>>>>>>>>> >>>>>>> >> transfer a
>>>>>>>>>> >>>>>>> >> 4.5GB file
>>>>>>>>>> >>>>>>> >> from NZ).
>>>>>>>>>> >>>>>>> >>
>>>>>>>>>> >>>>>>> >> -Steve
>>>>>>>>>> >>>>>>> >>
>>>>>>>>>> >>>>>>> >>
>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle
>>>>>>>>>> >>>>>>> >> <g.bogle at auckland.ac.nz>
>>>>>>>>>> >>>>>>> >> wrote:
>>>>>>>>>> >>>>>>> >>>
>>>>>>>>>> >>>>>>> >>> Hi Brad,
>>>>>>>>>> >>>>>>> >>>
>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7.
>>>>>>>>>> >>>>>>> >>> I can load
>>>>>>>>>> >>>>>>> >>> a tiff
>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000),
>>>>>>>>>> >>>>>>> >>> but a couple
>>>>>>>>>> >>>>>>> >>> of bigger
>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about
>>>>>>>>>> >>>>>>> >>> 4.5 GB
>>>>>>>>>> >>>>>>> >>> (actually when I
>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes
>>>>>>>>>> >>>>>>> >>> immediately,
>>>>>>>>>> >>>>>>> >>> exception
>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half
>>>>>>>>>> >>>>>>> >>> this size
>>>>>>>>>> >>>>>>> >>> is the
>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different -
>>>>>>>>>> >>>>>>> >>> I see the
>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the
>>>>>>>>>> >>>>>>> >>> windows greys
>>>>>>>>>> >>>>>>> >>> out.
>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button
>>>>>>>>>> >>>>>>> >>> on the
>>>>>>>>>> >>>>>>> >>> popup, and the
>>>>>>>>>> >>>>>>> >>> program crashes.
>>>>>>>>>> >>>>>>> >>>
>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I
>>>>>>>>>> >>>>>>> >>> installed
>>>>>>>>>> >>>>>>> >>> Slicer is
>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very
>>>>>>>>>> >>>>>>> >>> good but
>>>>>>>>>> >>>>>>> >>> BigTIFFs
>>>>>>>>>> >>>>>>> >>> are not enabled.
>>>>>>>>>> >>>>>>> >>>
>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with
>>>>>>>>>> >>>>>>> >>> different
>>>>>>>>>> >>>>>>> >>> build
>>>>>>>>>> >>>>>>> >>> options?
>>>>>>>>>> >>>>>>> >>>
>>>>>>>>>> >>>>>>> >>> Thanks
>>>>>>>>>> >>>>>>> >>> Gib
>>>>>>>>>> >>>>>>> >>> ________________________________
>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov]
>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m.
>>>>>>>>>> >>>>>>> >>> To: Gib Bogle
>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu
>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF
>>>>>>>>>> >>>>>>> >>>
>>>>>>>>>> >>>>>>> >>> Hello,
>>>>>>>>>> >>>>>>> >>>
>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3,
>>>>>>>>>> >>>>>>> >>> and the
>>>>>>>>>> >>>>>>> >>> associated
>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you
>>>>>>>>>> >>>>>>> >>> please
>>>>>>>>>> >>>>>>> >>> provide more
>>>>>>>>>> >>>>>>> >>> detail about your issue?
>>>>>>>>>> >>>>>>> >>>
>>>>>>>>>> >>>>>>> >>> Brad
>>>>>>>>>> >>>>>>> >>>
>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle
>>>>>>>>>> >>>>>>> >>> <g.bogle at auckland.ac.nz>
>>>>>>>>>> >>>>>>> >>> wrote:
>>>>>>>>>> >>>>>>> >>>
>>>>>>>>>> >>>>>>> >>> Hi,
>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does
>>>>>>>>>> >>>>>>> >>> not
>>>>>>>>>> >>>>>>> >>> handle
>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability?
>>>>>>>>>> >>>>>>> >>> Thanks
>>>>>>>>>> >>>>>>> >>> Gib
>>>>>>>>>> >>>>>>> >>> _______________________________________________
>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list
>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu
>>>>>>>>>> >>>>>>> >>>
>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to
>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with
>>>>>>>>>> >>>>>>> >>> unsubscribe as
>>>>>>>>>> >>>>>>> >>> the
>>>>>>>>>> >>>>>>> >>> subject
>>>>>>>>>> >>>>>>> >>>
>>>>>>>>>> >>>>>>> >>>
>>>>>>>>>> >>>>>>> >>>
>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ
>>>>>>>>>> >>>>>>> >>>
>>>>>>>>>> >>>>>>> >>>
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>>>>>>>>>> >>>>>>> >
>>>>>>>>>> >>>>>>> > _______________________________________________
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>>>>>>>>>> >>>>>> _______________________________________________
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>>>>>>>>>> >>>
>>>>>>>>>> >>
>>>>>>>>>> >
>>>>>>>>>> >
>>>>>>>>>> > _______________________________________________
>>>>>>>>>> > slicer-devel mailing list
>>>>>>>>>> > slicer-devel at bwh.harvard.edu
>>>>>>>>>> > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
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>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
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>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> +1 919 869 8849
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
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