<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>Hello All,<br><br> By default the itk::RelabelComponentImageFilter seems to be sorting the labels by size. I would like the label to be number according to their raster position. Is there a way to turn off the sorting ?<br><br>Thank you,<br>Emma<br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: arial,helvetica,sans-serif; font-size: 13px;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> "insight-users-request@itk.org" <insight-users-request@itk.org><br><b><span style="font-weight: bold;">To:</span></b> insight-users@itk.org<br><b><span style="font-weight: bold;">Sent:</span></b> Mon, August 9, 2010 12:42:15 PM<br><b><span style="font-weight:
bold;">Subject:</span></b> Insight-users Digest, Vol 76, Issue 24<br></font><br>
Send Insight-users mailing list submissions to<br> <a ymailto="mailto:insight-users@itk.org" href="mailto:insight-users@itk.org">insight-users@itk.org</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br><span> <a target="_blank" href="http://www.itk.org/mailman/listinfo/insight-users">http://www.itk.org/mailman/listinfo/insight-users</a></span><br>or, via email, send a message with subject or body 'help' to<br> <a ymailto="mailto:insight-users-request@itk.org" href="mailto:insight-users-request@itk.org">insight-users-request@itk.org</a><br><br>You can reach the person managing the list at<br> <a ymailto="mailto:insight-users-owner@itk.org" href="mailto:insight-users-owner@itk.org">insight-users-owner@itk.org</a><br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of Insight-users digest..."<br><br><br>Today's
Topics:<br><br> 1. Tcon Agenda Posted (Tuesday 1pm EST) (Luis Ibanez)<br> 2. Re: Tcon Agenda Posted (Tuesday 1pm EST) (Bradley Lowekamp)<br> 3. Re: [Insight-developers] Tcon Agenda Posted (Tuesday 1pm EST)<br> (Arnaud GELAS)<br> 4. itk::BilateralImageFilter extremely slow (Oleksandr Dzyubak)<br> 5. Re: Problem with passing images to functions (habibbaluwala2010)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Mon, 9 Aug 2010 14:35:09 -0400<br>From: Luis Ibanez <<a ymailto="mailto:luis.ibanez@kitware.com" href="mailto:luis.ibanez@kitware.com">luis.ibanez@kitware.com</a>><br>Subject: [Insight-users] Tcon Agenda Posted (Tuesday 1pm EST)<br>To: itk <<a ymailto="mailto:Insight-users@itk.org" href="mailto:Insight-users@itk.org">Insight-users@itk.org</a>>, Insight Developers<br>
<<a ymailto="mailto:Insight-developers@itk.org" href="mailto:Insight-developers@itk.org">Insight-developers@itk.org</a>><br>Message-ID:<br> <AANLkTi=OgJ1OyJRuRDOqY=<a ymailto="mailto:t70iSYpWT1JAVZcj_5HC5Y@mail.gmail.com" href="mailto:t70iSYpWT1JAVZcj_5HC5Y@mail.gmail.com">t70iSYpWT1JAVZcj_5HC5Y@mail.gmail.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>The Agenda for tomorrow's tcon has been posted at:<br><br><span><a target="_blank" href="http://www.itk.org/Wiki/Agenda%26Status_081010">http://www.itk.org/Wiki/Agenda%26Status_081010</a></span><br><br>As discussed in the last tcon,<br>we are inverting the order of the agenda,<br>in order to address some topics for which<br>we have run out of time in previous calls.<br><br>Please feel free to add any topics of your interest.<br><br><br> Luis<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br><span>URL: <<a
target="_blank" href="http://www.itk.org/pipermail/insight-users/attachments/20100809/286a83b3/attachment-0001.htm">http://www.itk.org/pipermail/insight-users/attachments/20100809/286a83b3/attachment-0001.htm</a>></span><br><br>------------------------------<br><br>Message: 2<br>Date: Mon, 9 Aug 2010 15:06:45 -0400<br>From: Bradley Lowekamp <<a ymailto="mailto:blowekamp@mail.nih.gov" href="mailto:blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a>><br>Subject: Re: [Insight-users] Tcon Agenda Posted (Tuesday 1pm EST)<br>To: Luis Ibanez <<a ymailto="mailto:luis.ibanez@kitware.com" href="mailto:luis.ibanez@kitware.com">luis.ibanez@kitware.com</a>><br>Cc: itk <<a ymailto="mailto:Insight-users@itk.org" href="mailto:Insight-users@itk.org">Insight-users@itk.org</a>>, Insight Developers<br> <<a ymailto="mailto:Insight-developers@itk.org"
href="mailto:Insight-developers@itk.org">Insight-developers@itk.org</a>><br>Message-ID: <<a ymailto="mailto:3640D14E-D614-41AA-BE09-5223002184CB@mail.nih.gov" href="mailto:3640D14E-D614-41AA-BE09-5223002184CB@mail.nih.gov">3640D14E-D614-41AA-BE09-5223002184CB@mail.nih.gov</a>><br>Content-Type: text/plain; charset="us-ascii"<br><br>Hello Luis,<br><br>Looking over the agenda for tomorrow, I can't help but think that the Microscopy should be a break out t-con (unless I missed it, and this is a summary). I have had experience with streaming and many related issues to the large datasets complications, so I would like to participate in such a break out.<br><br>Perhaps the agenda item should just be to schedule such a meeting?<br><br>Brad<br><br>On Aug 9, 2010, at 2:35 PM, Luis Ibanez wrote:<br><br>> <br>> The Agenda for tomorrow's tcon has been posted at:<br>> <br>> <a href="http://www.itk.org/Wiki/Agenda%26Status_081010"
target="_blank">http://www.itk.org/Wiki/Agenda%26Status_081010</a><br>> <br>> As discussed in the last tcon, <br>> we are inverting the order of the agenda,<br>> in order to address some topics for which<br>> we have run out of time in previous calls.<br>> <br>> Please feel free to add any topics of your interest.<br>> <br>> <br>> Luis<br>> <br>> <br>> <ATT00001..txt><br><br>========================================================<br>Bradley Lowekamp <br>Lockheed Martin Contractor for<br>Office of High Performance Computing and Communications<br>National Library of Medicine <br><a ymailto="mailto:blowekamp@mail.nih.gov" href="mailto:blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a><br><br><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br><span>URL: <<a target="_blank"
href="http://www.itk.org/pipermail/insight-users/attachments/20100809/bd7b55cd/attachment-0001.htm">http://www.itk.org/pipermail/insight-users/attachments/20100809/bd7b55cd/attachment-0001.htm</a>></span><br><br>------------------------------<br><br>Message: 3<br>Date: Mon, 9 Aug 2010 15:16:54 -0400<br>From: Arnaud GELAS <<a ymailto="mailto:arnaud_gelas@hms.harvard.edu" href="mailto:arnaud_gelas@hms.harvard.edu">arnaud_gelas@hms.harvard.edu</a>><br>Subject: Re: [Insight-users] [Insight-developers] Tcon Agenda Posted<br> (Tuesday 1pm EST)<br>To: Bradley Lowekamp <<a ymailto="mailto:blowekamp@mail.nih.gov" href="mailto:blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a>><br>Cc: itk <<a ymailto="mailto:Insight-users@itk.org" href="mailto:Insight-users@itk.org">Insight-users@itk.org</a>>, Insight Developers<br> <<a ymailto="mailto:Insight-developers@itk.org"
href="mailto:Insight-developers@itk.org">Insight-developers@itk.org</a>>, Luis Ibanez <<a ymailto="mailto:luis.ibanez@kitware.com" href="mailto:luis.ibanez@kitware.com">luis.ibanez@kitware.com</a>>,<br> "Megason, Sean" <<a ymailto="mailto:Sean_Megason@hms.harvard.edu" href="mailto:Sean_Megason@hms.harvard.edu">Sean_Megason@hms.harvard.edu</a>><br>Message-ID: <<a ymailto="mailto:4C605426.4080103@hms.harvard.edu" href="mailto:4C605426.4080103@hms.harvard.edu">4C605426.4080103@hms.harvard.edu</a>><br>Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"<br><br> Hi Brad,<br><br>I think we should do both, first to present problems from the microscopy <br>community. At least everyone can understand some of the related problems <br>in terms of design. Then interested people and people that have ideas on <br>how to address these issues can then meet in another break out
t-con.<br><br>It seems to be important to discuss at least in the main t-conf:<br><br> * how to deal with time?<br> * how to deal with channels? (Note that for one channel, the pixel<br> type could be a scalar, vector or tensor)...<br><br>Then we could discuss other details in the break out one...<br><br>Arnaud<br><br>On 08/09/2010 03:06 PM, Bradley Lowekamp wrote:<br>> Hello Luis,<br>><br>> Looking over the agenda for tomorrow, I can't help but think that the <br>> Microscopy should be a break out t-con (unless I missed it, and this <br>> is a summary). I have had experience with streaming and many related <br>> issues to the large datasets complications, so I would like to <br>> participate in such a break out.<br>><br>> Perhaps the agenda item should just be to schedule such a meeting?<br>><br>> Brad<br>><br>> On Aug 9, 2010, at 2:35 PM, Luis Ibanez
wrote:<br>><br>>><br>>> The Agenda for tomorrow's tcon has been posted at:<br>>><br>>> <a href="http://www.itk.org/Wiki/Agenda%26Status_081010" target="_blank">http://www.itk.org/Wiki/Agenda%26Status_081010</a><br>>><br>>> As discussed in the last tcon,<br>>> we are inverting the order of the agenda,<br>>> in order to address some topics for which<br>>> we have run out of time in previous calls.<br>>><br>>> Please feel free to add any topics of your interest.<br>>><br>>><br>>> Luis<br>>><br>>><br>>> <ATT00001..txt><br>><br>> ========================================================<br>><br>> Bradley Lowekamp<br>><br>> Lockheed Martin Contractor for<br>><br>> Office of High Performance Computing and Communications<br>><br>> National Library of Medicine<br>><br>> <a
ymailto="mailto:blowekamp@mail.nih.gov" href="mailto:blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a> <mailto:<a ymailto="mailto:blowekamp@mail.nih.gov" href="mailto:blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a>><br>><br>><br>><br><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br><span>URL: <<a target="_blank" href="http://www.itk.org/pipermail/insight-users/attachments/20100809/424eaff2/attachment-0001.htm">http://www.itk.org/pipermail/insight-users/attachments/20100809/424eaff2/attachment-0001.htm</a>></span><br><br>------------------------------<br><br>Message: 4<br>Date: Mon, 09 Aug 2010 14:35:37 -0500<br>From: Oleksandr Dzyubak <<a ymailto="mailto:adzyubak@gmail.com" href="mailto:adzyubak@gmail.com">adzyubak@gmail.com</a>><br>Subject: [Insight-users] itk::BilateralImageFilter extremely slow<br>To: insight-users <<a ymailto="mailto:Insight-users@itk.org"
href="mailto:Insight-users@itk.org">Insight-users@itk.org</a>><br>Message-ID: <<a ymailto="mailto:4C605889.6020103@gmail.com" href="mailto:4C605889.6020103@gmail.com">4C605889.6020103@gmail.com</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br><br>Dear ITK users and developers,<br><br>A while ago for my experiments I ran into a need of using<br>a narrow kernel bilateral filter so I decided to give<br>the itk:: BilateralImageFilter class a try.<br>After some pre-tests with small test images, I ran a filter on real images.<br>Well, my first impression is somewhat discouraging.<br>But it might be that I am doing some terrible mistake which I do not see.<br><br>My setup.<br>1) Hardware: 4x4 core server with 64 bit Debian Linux.<br>2) ITK-3.18 with p-threads support ON.<br>3) Image 561x561x478.<br><br>I followed the recommendations from the ITK user guide<br>and below are results.<br><br>dzyubak@helium:
/H61_Mo_721Views_July_31_2009$ time <br>./Bilateral_LessAgressive h61_with_psf.hdr h61_with_psf_ds05_rs4.hdr 0.5 4.0<br><br>With all 16 CPUs 100% busy after 1241m29.741s it was still running.<br>Thus I should cancel the run not having an output.<br><br>real 1241m29.741s<br>user 19600m14.380s<br>sys 6m33.993s<br><br>After I changed the parameters, I got something but it was not what I <br>wanted.<br><br>dzyubak@helium: /H61_Mo_721Views_July_31_2009$ time <br>./Bilateral_LessAgressive h61_with_psf.hdr h61_with_psf_ds005_rs4.hdr <br>0.05 4.0<br><br>real 63m46.774s<br>user 764m24.782s<br>sys 0m18.849s<br><br>Since this filter worked extremely slow even with 16 horses under the hood,<br>I started digging the Insight Journal and found the contribution<br>"A Fast Approximation to the Bilateral Filter for ITK" by J. Woehr.<br><br>I was attracted by the word "Fast" since it quite often
means "faster <br>performance".<br>Even though I did not like the author's note "it is single threaded",<br>I decided to eventually try it and, to be fair,<br>I used exactly the same parameters as for itk:: BilateralImageFilter.<br><br>dzyubak@helium: /H61_Mo_721Views_July_31_2009$ time <br>./FastBilateral_LessAgressive h61_with_psf.hdr h61_with_psf_ds05_rs4.hdr <br>0.5 4.0<br>ImageFileName: h61_with_psf.img<br><br>real 4m49.325s<br>user 4m35.085s<br>sys 0m5.804s<br><br>In the submission description J. Woehr said that FastBilateral<br>performs poorer for the narrow kernels thus if someone is<br>in a need of such cases (it is exactly me!),<br>then the itk:: BilateralImageFilter should be used instead.<br><br>Well, I would like to but FastBilateral performed 200 times<br>as much vs itk:: BilateralImageFilter.<br>And in addition to that, for some kernel sizes it never<br>went out of the loop.<br><br>What am I
missing here?<br>Did someone experience the same filter behaver?<br>Is it wrong conditional causing such a "prolongated" loop?<br>Is there any recipe I could used to shorten<br>such unacceptable long run time of itk:: BilateralImageFilter?<br><br>I appreciate any suggestions/discussions on this matter.<br><br>Regards,<br><br>Alex<br><br><br>------------------------------<br><br>Message: 5<br>Date: Mon, 9 Aug 2010 12:42:12 -0700 (PDT)<br>From: habibbaluwala2010 <<a ymailto="mailto:habibbaluwala@gmail.com" href="mailto:habibbaluwala@gmail.com">habibbaluwala@gmail.com</a>><br>Subject: Re: [Insight-users] Problem with passing images to functions<br>To: <a ymailto="mailto:insight-users@itk.org" href="mailto:insight-users@itk.org">insight-users@itk.org</a><br>Message-ID: <<a ymailto="mailto:29391440.post@talk.nabble.com" href="mailto:29391440.post@talk.nabble.com">29391440.post@talk.nabble.com</a>><br>Content-Type: text/plain;
charset=UTF-8<br><br><br>Hello Sergio, <br> Can you give me an example of how to use this in context<br>with the syntax? I am really thankful for the help. <br><br><br>Kind regards, <br><br>Habib Baluwala<br><br><br><br><br>Sergio Vera wrote:<br>> <br>> Following advices from Luis Iba?ez in a previous mail of the list, we now<br>> use the following rules:<br>> <br>> const ITKImgType *ImgIn when images are input to a method and<br>> <br>> ITKImgType::Pointer &ImgOut when the image will be created inside the<br>> function<br>> <br>> regards<br>> <br>> 2010/8/6 D?enan Zuki? <<a ymailto="mailto:dzenanz@gmail.com" href="mailto:dzenanz@gmail.com">dzenanz@gmail.com</a>><br>> <br>>> Use ImageType::Pointer. Here is an example:<br>>><br>>> void calc2DJointHistogram(VisualizingImageType::Pointer x,<br>>>
VisualizingImageType::Pointer y, std::string savefilename)<br>>> {<br>>> ...<br>>> }<br>>><br>>> //calling it<br>>> VisualizingImageType::Pointer lVis, hVis;<br>>> ...<br>>> hVis=hReader->GetOutput();<br>>> calc2DJointHistogram(lVis, hVis, fnNoExt+"_LH.png");<br>>><br>>> D?enan<br>>><br>>> On Fri, Aug 6, 2010 at 15:32, habibbaluwala2010<br>>> <<a ymailto="mailto:habibbaluwala@gmail.com" href="mailto:habibbaluwala@gmail.com">habibbaluwala@gmail.com</a>>wrote:<br>>><br>>>><br>>>> Hi Everyone,<br>>>> I am a biot confused on how can i pass an image with<br>>>> smart<br>>>> pointers to an outside function . I basically need this to avoid<br>>>> reproducing<br>>>> the code again and again and also to avoid composite filters. It
would<br>>>> be<br>>>> very helpful if you can provide an example which does the job!!! Anyways<br>>>> looking forward to your replies.<br>>>> --<br>>>> View this message in context:<br><span>>>> <a target="_blank" href="http://old.nabble.com/Problem-with-passing-images-to-functions-tp29356451p29356451.html">http://old.nabble.com/Problem-with-passing-images-to-functions-tp29356451p29356451.html</a></span><br>>>> Sent from the ITK - Users mailing list archive at <a target="_blank" href="http://Nabble.com">Nabble.com</a>.<br>>>><br>>>> _____________________________________<br>>>> Powered by <a target="_blank" href="http://www.kitware.com">www.kitware.com</a><br>>>><br>>>> Visit other Kitware open-source projects at<br><span>>>> <a target="_blank"
href="http://www.kitware.com/opensource/opensource.html">http://www.kitware.com/opensource/opensource.html</a></span><br>>>><br>>>> Kitware offers ITK Training Courses, for more information visit:<br><span>>>> <a target="_blank" href="http://www.kitware.com/products/protraining.html">http://www.kitware.com/products/protraining.html</a></span><br>>>><br>>>> Please keep messages on-topic and check the ITK FAQ at:<br><span>>>> <a target="_blank" href="http://www.itk.org/Wiki/ITK_FAQ">http://www.itk.org/Wiki/ITK_FAQ</a></span><br>>>><br>>>> Follow this link to subscribe/unsubscribe:<br><span>>>> <a target="_blank" href="http://www.itk.org/mailman/listinfo/insight-users">http://www.itk.org/mailman/listinfo/insight-users</a></span><br>>>><br>>><br>>><br>>> _____________________________________<br><span>>> Powered by <a target="_blank"
href="http://www.kitware.com">www.kitware.com</a></span><br>>><br>>> Visit other Kitware open-source projects at<br>>> <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>>><br>>> Kitware offers ITK Training Courses, for more information visit:<br>>> <a href="http://www.kitware.com/products/protraining.html" target="_blank">http://www.kitware.com/products/protraining.html</a><br>>><br>>> Please keep messages on-topic and check the ITK FAQ at:<br>>> <a href="http://www.itk.org/Wiki/ITK_FAQ" target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br>>><br>>> Follow this link to subscribe/unsubscribe:<br>>> <a href="http://www.itk.org/mailman/listinfo/insight-users" target="_blank">http://www.itk.org/mailman/listinfo/insight-users</a><br>>><br>>><br>> <br>> <br>> -- <br>> Sergio
Vera<br>> <br>> Alma IT Systems<br>> C/ Vilana, 4B, 4? 1?<br>> 08022 Barcelona<br>> T. (+34) 932 380 592<br>> <a target="_blank" href="http://www.alma3d.com">www.alma3d.com</a><br>> <br>> _____________________________________<br><span>> Powered by <a target="_blank" href="http://www.kitware.com">www.kitware.com</a></span><br>> <br>> Visit other Kitware open-source projects at<br>> <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>> <br>> Kitware offers ITK Training Courses, for more information visit:<br>> <a href="http://www.kitware.com/products/protraining.html" target="_blank">http://www.kitware.com/products/protraining.html</a><br>> <br>> Please keep messages on-topic and check the ITK FAQ at:<br>> <a href="http://www.itk.org/Wiki/ITK_FAQ"
target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br>> <br>> Follow this link to subscribe/unsubscribe:<br>> <a href="http://www.itk.org/mailman/listinfo/insight-users" target="_blank">http://www.itk.org/mailman/listinfo/insight-users</a><br>> <br>> <br><br>-- <br><span>View this message in context: <a target="_blank" href="http://old.nabble.com/Problem-with-passing-images-to-functions-tp29356451p29391440.html">http://old.nabble.com/Problem-with-passing-images-to-functions-tp29356451p29391440.html</a></span><br>Sent from the ITK - Users mailing list archive at Nabble.com.<br><br><br><br>------------------------------<br><br>_______________________________________________<br>Insight-users mailing list<br><a ymailto="mailto:Insight-users@itk.org" href="mailto:Insight-users@itk.org">Insight-users@itk.org</a><br><a href="http://www.itk.org/mailman/listinfo/insight-users"
target="_blank">http://www.itk.org/mailman/listinfo/insight-users</a><br><br><br>End of Insight-users Digest, Vol 76, Issue 24<br>*********************************************<br></div></div>
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