<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>Hi,</div><div>I managed to find the problem on my code involving LabelOverlayFiltering and was related to an other third party IO class that wrote to disc the resulting image.</div><div><br></div><div>However, I wanted to comment on this to avoid future misunderstanding. One of my doubts raised from the fact that the filter seems to add transparency and it still the resulting image is RGB and not RGBA. After discussing with the filter author (thanks alot for your help), this is the answer on that issue:</div><div><br></div><div><meta http-equiv="content-type" content="text/html; charset=utf-8"><span class="Apple-style-span" style="font-family: arial, helvetica, sans-serif; font-size: 13px; ">The transparency is only for the overlay layer. The produced image is still 100%
opaque.</span></div><div><span class="Apple-style-span" style="font-family: arial, helvetica, sans-serif; font-size: 13px; "><br></span></div><div><span class="Apple-style-span" style="font-family: arial, helvetica, sans-serif; font-size: 13px; ">Maria</span></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 size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">De:</span></b> "insight-users-request@itk.org" <insight-users-request@itk.org><br><b><span style="font-weight: bold;">Para:</span></b> insight-users@itk.org<br><b><span style="font-weight: bold;">Enviado:</span></b> mié,30 marzo, 2011 18:00<br><b><span style="font-weight: bold;">Asunto:</span></b> Insight-users Digest, Vol 83, Issue 56<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> <a href="http://www.itk.org/mailman/listinfo/insight-users" target="_blank">http://www.itk.org/mailman/listinfo/insight-users</a><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. Re: LabelShapeOpeningImageFilter Attribute input =?<br> (Richard Beare)<br> 2.
Re: LabelShapeOpeningImageFilter Attribute input<br> (Ella Maria Kadas)<br> 3. Re: Possible bug in Label Overlay Filter (Ga?tan Lehmann)<br> 4. Re: LabelShapeOpeningImageFilter Attribute input (Ga?tan Lehmann)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Wed, 30 Mar 2011 23:03:14 +1100<br>From: Richard Beare <<a ymailto="mailto:richard.beare@gmail.com" href="mailto:richard.beare@gmail.com">richard.beare@gmail.com</a>><br>Subject: Re: [Insight-users] LabelShapeOpeningImageFilter Attribute<br> input =?<br>To: Ella Maria Kadas <<a ymailto="mailto:ella_kadas@yahoo.com" href="mailto:ella_kadas@yahoo.com">ella_kadas@yahoo.com</a>><br>Cc: "<a ymailto="mailto:insight-users@itk.org" href="mailto:insight-users@itk.org">insight-users@itk.org</a>" <<a ymailto="mailto:insight-users@itk.org"
href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>Message-ID:<br> <AANLkTi=<a ymailto="mailto:WeCa3nrZ1B0U2QP54Lsme3gryouXpe_g8EF6g@mail.gmail.com" href="mailto:WeCa3nrZ1B0U2QP54Lsme3gryouXpe_g8EF6g@mail.gmail.com">WeCa3nrZ1B0U2QP54Lsme3gryouXpe_g8EF6g@mail.gmail.com</a>><br>Content-Type: text/plain; charset="utf-8"<br><br>There is a convenience class in the Review directory that is derived from<br>this contribution called itk::BinaryShapeOpeningImageFilter. This includes<br>all of the labelling and conversion to and from label maps. You just need to<br>call the SetAttribute and SetForegroundValue appropriately. It should work<br>fine for 3D. If you look inside that class you should also find the standard<br>combination of steps you need to go through to use the LabelMap filters.<br><br>On Wed, Mar 30, 2011 at 9:09 PM, Ella Maria Kadas <<a ymailto="mailto:ella_kadas@yahoo.com"
href="mailto:ella_kadas@yahoo.com">ella_kadas@yahoo.com</a>>wrote:<br><br>> Hi all,<br>><br>> I am trying to remove some objects from a 3D image that have a volume<br>> lower then a specific value.<br>> I tried to use the Label object representation and manipulation with<br>> ITK that Gae ?tan Lehmann<br>> implemented but i still don't know what that attribute parameter should<br>> look like. (in the python example it looks a s it would be a char<br>> size =<br>> itk.ShapeOpeningLabelMapFilter[LabelMapType].New(stats,Attribute=?Size?,<br>> Lambda=100)<br>> I want to use the ShapeLabelObject, and it's attributes to do a<br>> LabelShapeOpeningFilter.<br>> As i was getting no result i tried to do it in 2D first.<br>> This is my code:<br>> First i use the ConnectedComponentImageFilter, then<br>> RelabelComponentImageFilter and create a ShapeLabelMap from the
relabel's<br>> output.<br>><br>> typedef unsigned long LabelType;<br>><br>> typedef itk::ShapeLabelObject< LabelType, dim > LabelObjectType;<br>><br>> typedef itk::LabelMap< LabelObjectType > LabelMapType;<br>><br>><br>><br>> typedef itk::LabelImageToShapeLabelMapFilter< LabelImageType,<br>> LabelMapType > ConverterType;<br>><br>> ConverterType::Pointer converter = ConverterType::New();<br>><br>> converter->SetInput( relabel->GetOutput() );<br>><br>> converter->Update();<br>><br>> !!!! Why does it not work if i use this part of code from the journal<br>><br>> /*<br>><br>> and valuate the attributes with the dedicated filter: ShapeLabelMapFilter<br>><br>> typedef itk::ShapeLabelMapFilter< LabelMapType > ShapeFilterType;<br>> ShapeFilterType::Pointer shape = ShapeFilterType::New();
shape->SetInput(<br>> converter->GetOutput() );<br>><br>> update the shape filter, so its output will be up to date<br>><br>> shape->Update();<br>><br>> */<br>><br>><br>> LabelMapType::Pointer labelMap = converter->GetOutput();<br>><br>> std::cout<<"nr of label<br>> objects"<<labelMap->GetNumberOfLabelObjects()<<std::endl;<br>><br>><br>> for( unsigned int label=1; label<=labelMap->GetNumberOfLabelObjects();<br>> label++ )<br>><br>> {<br>><br>><br>><br>> const LabelObjectType * labelObject = labelMap->GetLabelObject( label<br>> );<br>><br>> std::cout << label << "\t" << labelObject->GetPhysicalSize() << "\t" <<<br>> labelObject->GetCentroid() << std::endl;<br>><br>> }<br>><br>><br>> typedef
itk::LabelShapeOpeningImageFilter< LabelImageType ><br>> LabelOpeningType;<br>><br>> LabelOpeningType::Pointer opening = LabelOpeningType::New();<br>><br>> opening->SetInput( relabel->GetOutput());<br>><br>> opening->SetBackgroundValue(0);<br>><br>> opening->SetLambda( 100 );<br>><br>> opening->SetReverseOrdering( false );<br>><br>> //NO IDEA About the Attribute<br>><br>> //I thought it should be the labelMap->Size()) should be as attribute<br>><br>> opening->SetAttribute("PERIMETER");<br>><br>> itk::SimpleFilterWatcher watcher(opening, "filter");<br>><br>> Then i would like to get back the binary image and see it but i can't get<br>> the proper image types as input to LabelMapToLabelIamgeFilter....So the<br>> commented part is not working<br>><br>><br>> /*typedef itk::LabelMapToLabelImageFilter< LabelImageType, LabelImageType<br>> >
L2IType;<br>><br>> L2IType::Pointer l2i = L2IType::New();<br>><br>> l2i->SetInput( opening->GetOutput() );<br>><br>> typedef itk::ImageFileWriter< LabelImageType > WriterType;<br>><br>> WriterType::Pointer writer = WriterType::New();<br>><br>> writer->SetInput( l2i->GetOutput() );<br>><br>> writer->SetFileName( "/Users/ellaK/Documents/Morphology/Opening.gipl");<br>><br>> writer->Update();*/<br>><br>> std::getchar();<br>><br>><br>><br>> Maybe i am doing this the wrong way, and i can't use it for 3D images.<br>> If anybody already already worked with this filters please give me a hint<br>> to what i am doing wrong.<br>> Thanks,<br>> Ella<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>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://www.itk.org/pipermail/insight-users/attachments/20110330/26682abb/attachment-0001.htm"
target="_blank">http://www.itk.org/pipermail/insight-users/attachments/20110330/26682abb/attachment-0001.htm</a>><br><br>------------------------------<br><br>Message: 2<br>Date: Wed, 30 Mar 2011 13:51:23 +0100 (BST)<br>From: Ella Maria Kadas <<a ymailto="mailto:ella_kadas@yahoo.com" href="mailto:ella_kadas@yahoo.com">ella_kadas@yahoo.com</a>><br>Subject: Re: [Insight-users] LabelShapeOpeningImageFilter Attribute<br> input<br>To: <a ymailto="mailto:Richard.Beare@ieee.org" href="mailto:Richard.Beare@ieee.org">Richard.Beare@ieee.org</a><br>Cc: "<a ymailto="mailto:insight-users@itk.org" href="mailto:insight-users@itk.org">insight-users@itk.org</a>" <<a ymailto="mailto:insight-users@itk.org" href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>Message-ID: <<a ymailto="mailto:259184.90324.qm@web29617.mail.ird.yahoo.com"
href="mailto:259184.90324.qm@web29617.mail.ird.yahoo.com">259184.90324.qm@web29617.mail.ird.yahoo.com</a>><br>Content-Type: text/plain; charset="utf-8"<br><br>Hi,<br>?Yes i already tried that and in the by default the Attribute value is "Size", which as far as i understood is the Perimeter of the shape that has a specific label (length-coding)-don't know how that applies to 3D images, but trying to apply the itkBinaryShapeOpeningImageFilter i get the following error (my input image is a float one).Start BinaryShapeOpeningImageFilter "filter" BinaryShapeOpeningImageFilter (0x402d160)<br>? RTTI typeinfo: ? itk::BinaryShapeOpeningImageFilter<itk::Image<float, 3u> ><br>? Reference Count: 3<br>? Modified Time: 1082<br>? Debug: Off<br>? Observers:?<br>? ? StartEvent(SimpleMemberCommand)<br>? ? EndEvent(SimpleMemberCommand)<br>? ? ProgressEvent(SimpleMemberCommand)<br>? ? IterationEvent(SimpleMemberCommand)<br>? ?
AbortEvent(SimpleMemberCommand)<br>? Number Of Required Inputs: 1<br>? Number Of Required Outputs: 1<br>? Number Of Threads: 8<br>? ReleaseDataFlag: Off<br>? ReleaseDataBeforeUpdateFlag: Off<br>? Input 0: (0x402cde0)<br>? Output 0: (0x402d380)<br>? AbortGenerateData: Off<br>? Progress: 0<br>? Multithreader:?<br>? ? RTTI typeinfo: ? itk::MultiThreader<br>? ? Reference Count: 1<br>? ? Modified Time: 1069<br>? ? Debug: Off<br>? ? Observers:?<br>? ? ? none<br>? ? Thread Count: 8<br>? ? Global Maximum Number Of Threads: 128<br>? ? Global Default Number Of Threads: 8<br>? FullyConnected: 0<br>? BackgroundValue: 0<br>? ForegroundValue: 255<br>? Lambda: 500<br>? ReverseOrdering: 0<br>? Attribute: Size (0)<br>Progress? | 0 | 0.00292969 | 0.00585938 | 0.00878906 | 0.0117188 | 0.0146484 | 0.0175781 | 0.0205078 | 0.0234375 | 0.0263672<br>?| 0.0292969 | 0.0322266 | 0.0351562 | 0.0380859 | 0.0410156 | 0.0439453 | 0.046875 | 0.0498047 | 0.0527344 | 0.0556641<br>?|
0.0585938 | 0.0615234 | 0.0644531 | 0.0673828 | 0.0703125 | 0.0732422 | 0.0761719 | 0.0791016 | 0.0820312 | 0.0849609<br>?| 0.0878906 | 0.0908203 | 0.09375 | 0.0966797 | 0.0996094 | 0.102539 | 0.105469 | 0.108398 | 0.111328 | 0.114258<br>?| 0.117188 | 0.120117 | 0.123047 | 0.125977 | 0.128906 | 0.131836 | 0.134766 | 0.137695 | 0.140625 | 0.143555<br>?| 0.146484 | 0.149414 | 0.152344 | 0.155273 | 0.158203 | 0.161133 | 0.164062 | 0.166992 | 0.169922 | 0.172852<br>?| 0.175781 | 0.178711 | 0.181641 | 0.18457 | 0.1875 | 0.19043 | 0.193359 | 0.196289 | 0.199219 | 0.202148<br>?| 0.205078 | 0.208008 | 0.210938 | 0.213867 | 0.216797 | 0.219727 | 0.222656 | 0.225586 | 0.228516 | 0.231445<br>?| 0.234375 | 0.237305 | 0.240234 | 0.243164 | 0.246094 | 0.249023 | 0.251953 | 0.254883 | 0.257812 | 0.260742<br>?| 0.263672 | 0.266602 | 0.269531 | 0.272461 | 0.275391 | 0.27832 | 0.28125 | 0.28418 | 0.287109 | 0.290039<br>?| 0.292969 | 0.295898 |
0.298828Brain(6480,0xa0047540) malloc: *** mmap(size=4263636992) failed (error code=12)<br>*** error: can't allocate region<br>*** set a breakpoint in malloc_error_break to debug<br>?| 0.3<br>--- Richard Beare <<a ymailto="mailto:richard.beare@gmail.com" href="mailto:richard.beare@gmail.com">richard.beare@gmail.com</a>> schrieb am Mi, 30.3.2011:<br><br>Von: Richard Beare <<a ymailto="mailto:richard.beare@gmail.com" href="mailto:richard.beare@gmail.com">richard.beare@gmail.com</a>><br>Betreff: Re: [Insight-users] LabelShapeOpeningImageFilter Attribute input<br>An: "Ella Maria Kadas" <<a ymailto="mailto:ella_kadas@yahoo.com" href="mailto:ella_kadas@yahoo.com">ella_kadas@yahoo.com</a>><br>CC: "<a ymailto="mailto:insight-users@itk.org" href="mailto:insight-users@itk.org">insight-users@itk.org</a>" <<a ymailto="mailto:insight-users@itk.org" href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>Datum: Mittwoch, 30. M?rz,
2011 15:03 Uhr<br><br>There is a convenience class in the Review directory that is derived from this contribution called itk::BinaryShapeOpeningImageFilter. This includes all of the labelling and conversion to and from label maps. You just need to call the SetAttribute and SetForegroundValue appropriately. It should work fine for 3D. If you look inside that class you should also find the standard combination of steps you need to go through to use the LabelMap filters.<br><br><br>On Wed, Mar 30, 2011 at 9:09 PM, Ella Maria Kadas <<a ymailto="mailto:ella_kadas@yahoo.com" href="mailto:ella_kadas@yahoo.com">ella_kadas@yahoo.com</a>> wrote:<br><br>Hi all,<br>?? ?I am trying to remove some objects from a 3D image that have a volume lower then a specific value.<br>?? I tried to use the?Label object representation and manipulation with ITK that?Gae ?tan Lehmann<br>implemented but i still don't know what that attribute parameter should look like. (in the
python example it looks a s it would be a<br> char?size = itk.ShapeOpeningLabelMapFilter[LabelMapType].New(stats,Attribute=?Size?, Lambda=100)?<br>?I want to use the ShapeLabelObject, and it's attributes to do a LabelShapeOpeningFilter.?As i was getting no result i tried to do it in 2D first.<br>?This is my code:First i use the ConnectedComponentImageFilter, then RelabelComponentImageFilter and create a ShapeLabelMap from the relabel's output.<br><br><br>typedef unsigned long LabelType;<br>? typedef itk::ShapeLabelObject< LabelType, dim > LabelObjectType;<br>? typedef itk::LabelMap< LabelObjectType > LabelMapType;<br><br><br><br><br>? typedef itk::LabelImageToShapeLabelMapFilter< LabelImageType, LabelMapType > ConverterType;<br>? ConverterType::Pointer converter = ConverterType::New();<br>? converter->SetInput( relabel->GetOutput() );<br>? converter->Update();<br>!!!! Why does it not work if i use this part of code from the
journal <br> /*and valuate the attributes with the dedicated filter: ShapeLabelMapFilter<br><br>typedef itk::ShapeLabelMapFilter< LabelMapType > ShapeFilterType; ShapeFilterType::Pointer shape = ShapeFilterType::New(); shape->SetInput( converter->GetOutput() );<br><br>update the shape filter, so its output will be up to date<br>shape->Update();<br>*/<br>??LabelMapType::Pointer labelMap = converter->GetOutput();<br><br>std::cout<<"nr of label objects"<<labelMap->GetNumberOfLabelObjects()<<std::endl;<br><br><br>? for( unsigned int label=1; label<=labelMap->GetNumberOfLabelObjects(); label++ )<br>? ? {<br>? ??<br>? ? const LabelObjectType * labelObject = labelMap->GetLabelObject( label );<br>? ? std::cout << label << "\t" << labelObject->GetPhysicalSize() << "\t" << labelObject->GetCentroid() << std::endl;<br><br>? ?
}<br><br><br> typedef itk::LabelShapeOpeningImageFilter< LabelImageType > LabelOpeningType;<br><br> LabelOpeningType::Pointer opening = LabelOpeningType::New();<br><br> opening->SetInput( relabel->GetOutput());<br> opening->SetBackgroundValue(0);<br> opening->SetLambda( 100 );<br> opening->SetReverseOrdering( false );<br>//NO IDEA About the Attribute//I thought it should be the labelMap->Size()) should be as attribute<br><br> opening->SetAttribute("PERIMETER");<br> itk::SimpleFilterWatcher watcher(opening, "filter");<br><br> <br>Then i would like to get back the binary image and see it but i can't get the proper image types as input to LabelMapToLabelIamgeFilter....So the commented part is not working<br><br><br> /*typedef
itk::LabelMapToLabelImageFilter< LabelImageType, LabelImageType > L2IType;?<br><br> L2IType::Pointer l2i = L2IType::New();?<br> l2i->SetInput( opening->GetOutput() );<br> <br> typedef itk::ImageFileWriter< LabelImageType > WriterType;<br> WriterType::Pointer writer = WriterType::New();<br> writer->SetInput( l2i->GetOutput() );<br> writer->SetFileName( "/Users/ellaK/Documents/Morphology/Opening.gipl");<br> writer->Update();*/<br> std::getchar();<br><br><br><br>Maybe i am doing this the wrong way, and i can't use it for 3D images.<br>If anybody already already worked with this filters please give me a hint to what i am doing wrong.Thanks,?? Ella<br><br>_____________________________________<br><br><span>Powered by <a target="_blank"
href="http://www.kitware.com">www.kitware.com</a></span><br><br><br><br>Visit other Kitware open-source projects at<br><br><a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br><br><br><br>Kitware offers ITK Training Courses, for more information visit:<br><br><a href="http://www.kitware.com/products/protraining.html" target="_blank">http://www.kitware.com/products/protraining.html</a><br><br><br><br>Please keep messages on-topic and check the ITK FAQ at:<br><br><a href="http://www.itk.org/Wiki/ITK_FAQ" target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br><br><br><br>Follow this link to subscribe/unsubscribe:<br><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>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a
href="http://www.itk.org/pipermail/insight-users/attachments/20110330/c907c66f/attachment-0001.htm" target="_blank">http://www.itk.org/pipermail/insight-users/attachments/20110330/c907c66f/attachment-0001.htm</a>><br><br>------------------------------<br><br>Message: 3<br>Date: Wed, 30 Mar 2011 16:32:07 +0200<br>From: Ga?tan Lehmann <<a ymailto="mailto:gaetan.lehmann@jouy.inra.fr" href="mailto:gaetan.lehmann@jouy.inra.fr">gaetan.lehmann@jouy.inra.fr</a>><br>Subject: Re: [Insight-users] Possible bug in Label Overlay Filter<br>To: Maria Alejandra Zuluaga Valencia <<a ymailto="mailto:mariazulv@yahoo.es" href="mailto:mariazulv@yahoo.es">mariazulv@yahoo.es</a>><br>Cc: ITK list <<a ymailto="mailto:insight-users@itk.org" href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>Message-ID: <<a ymailto="mailto:15A0F6C9-5172-4A2F-9E97-4AEE690AF31B@jouy.inra.fr"
href="mailto:15A0F6C9-5172-4A2F-9E97-4AEE690AF31B@jouy.inra.fr">15A0F6C9-5172-4A2F-9E97-4AEE690AF31B@jouy.inra.fr</a>><br>Content-Type: text/plain; charset="iso-8859-1"; Format="flowed";<br> DelSp="yes"<br><br><br>Hi,<br><br>Could you provide a small code to reproduce that problem?<br><br>Thanks,<br><br>Ga?tan<br><br><br>Le 28 mars 11 ? 16:48, Maria Alejandra Zuluaga Valencia a ?crit :<br><br>> Hello again,<br>><br>> Earlier this morning I posted a message on problems with <br>> ExtractImageFilter (which I put at the end of the message for follow- <br>> up purposes).<br>> I've performed several tests to find the cause of my error. Since, <br>> the input images I was using came from itkLabelOverlayImageFilter, <br>> right now I am under the hypothesis that the latter is the one that <br>> really causes the problem when 3D images are used.<br>><br>> In my pipeline I am
able of creating a 3D RGB image (mhd/raw format) <br>> and I can visualize it without any problem. However, once I try to <br>> do something with this resulting image I get problems.<br>><br>> At the beginning I was using ExtractImageFilter to obtain a single <br>> slice from the overlaid image. Since it did not work, I performed <br>> the simplest operation which consisted in reading from disk the 3D <br>> RGB image and then writing it again. In every case, the resulting <br>> image contains only noise. If I do this same test with a 2D overlaid <br>> image, it works perfectly.<br>><br>> Has anyone experienced the same problem? is there anyway to solve it?<br>><br>> thanks in advance,<br>><br>> Maria A. Zuluaga<br>><br>> Maybe there are some problems regarding R G B channel interleaving/ <br>> separation?<br>><br>> HTH<br>><br>> On Mon, Mar
28, 2011 at 12:05, Maria Alejandra Zuluaga Valencia <<a ymailto="mailto:mariazulv@yahoo.es" href="mailto:mariazulv@yahoo.es">mariazulv@yahoo.es</a> <br>> > wrote:<br>> Hi,<br>> I am using the ExtractImageFilter to obtain a 2D slice from a 3D <br>> volume. I used the example from the user's guide and it works OK. <br>> However, when I change the pixel type to RGB (I want to do this for <br>> some overlay images) it fails. The resulting slice is completely <br>> noisy. Any idea?<br>><br>> Thanks in advance,<br>><br>> Maria A. Zuluaga<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><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>Ga?tan Lehmann<br>Biologie du D?veloppement et de la Reproduction<br>INRA de Jouy-en-Josas (France)<br>tel: +33 1 34 65 29 66 fax: 01 34 65 29 09<br><a href="http://voxel.jouy.inra.fr" target="_blank">http://voxel.jouy.inra.fr</a> <a href="http://www.itk.org"
target="_blank">http://www.itk.org</a><br><a href="http://www.mandriva.org" target="_blank">http://www.mandriva.org</a> <a href="http://www.bepo.fr" target="_blank">http://www.bepo.fr</a><br><br>-------------- next part --------------<br>A non-text attachment was scrubbed...<br>Name: PGP.sig<br>Type: application/pgp-signature<br>Size: 203 bytes<br>Desc: Ceci est une signature ?lectronique PGP<br>URL: <<a href="http://www.itk.org/pipermail/insight-users/attachments/20110330/b1c65619/attachment-0001.pgp" target="_blank">http://www.itk.org/pipermail/insight-users/attachments/20110330/b1c65619/attachment-0001.pgp</a>><br><br>------------------------------<br><br>Message: 4<br>Date: Wed, 30 Mar 2011 16:44:42 +0200<br>From: Ga?tan Lehmann <<a ymailto="mailto:gaetan.lehmann@jouy.inra.fr" href="mailto:gaetan.lehmann@jouy.inra.fr">gaetan.lehmann@jouy.inra.fr</a>><br>Subject: Re: [Insight-users] LabelShapeOpeningImageFilter
Attribute<br> input<br>To: Ella Maria Kadas <<a ymailto="mailto:ella_kadas@yahoo.com" href="mailto:ella_kadas@yahoo.com">ella_kadas@yahoo.com</a>><br>Cc: "<a ymailto="mailto:insight-users@itk.org" href="mailto:insight-users@itk.org">insight-users@itk.org</a>" <<a ymailto="mailto:insight-users@itk.org" href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>Message-ID: <<a ymailto="mailto:D1ABD4AA-848E-4EFA-9D10-B631159147C9@jouy.inra.fr" href="mailto:D1ABD4AA-848E-4EFA-9D10-B631159147C9@jouy.inra.fr">D1ABD4AA-848E-4EFA-9D10-B631159147C9@jouy.inra.fr</a>><br>Content-Type: text/plain; charset="utf-8"; Format="flowed";<br> DelSp="yes"<br><br>Hi,<br><br><br>Le 30 mars 11 ? 14:51, Ella Maria Kadas a ?crit :<br><br>> Hi,<br>><br>> Yes i already tried that and in the by default the Attribute value <br>> is "Size", which as far as i understood is the Perimeter of the
shape<br><br>This is the number of pixels in the object. It has been renamed in ITK <br>v4 in NumberOfPixels.<br><br>> that has a specific label (length-coding)-don't know how that <br>> applies to 3D images,<br><br>that's still the number of pixels independently of the image <br>dimension :-)<br><br>> but trying to apply the itkBinaryShapeOpeningImageFilter i get the <br>> following error (my input image is a float one).<br><br>Your image should have an integer pixel type. There is no point in <br>using that class with a real pixel type.<br>I'm not sure this is your problem, though. Can you provide a minimum <br>example so we can try to reproduce the problem?<br><br>Regards,<br><br>Ga?tan<br><br>> Start BinaryShapeOpeningImageFilter "filter" <br>> BinaryShapeOpeningImageFilter (0x402d160)<br>> RTTI typeinfo: <br>>
itk::BinaryShapeOpeningImageFilter<itk::Image<float, 3u> ><br>> Reference Count: 3<br>> Modified Time: 1082<br>> Debug: Off<br>> Observers:<br>> StartEvent(SimpleMemberCommand)<br>> EndEvent(SimpleMemberCommand)<br>> ProgressEvent(SimpleMemberCommand)<br>> IterationEvent(SimpleMemberCommand)<br>> AbortEvent(SimpleMemberCommand)<br>> Number Of Required Inputs: 1<br>> Number Of Required Outputs: 1<br>> Number Of Threads: 8<br>> ReleaseDataFlag: Off<br>> ReleaseDataBeforeUpdateFlag: Off<br>> Input 0: (0x402cde0)<br>> Output 0: (0x402d380)<br>> AbortGenerateData: Off<br>> Progress: 0<br>> Multithreader:<br>> RTTI typeinfo: itk::MultiThreader<br>> Reference Count: 1<br>>
Modified Time: 1069<br>> Debug: Off<br>> Observers:<br>> none<br>> Thread Count: 8<br>> Global Maximum Number Of Threads: 128<br>> Global Default Number Of Threads: 8<br>> FullyConnected: 0<br>> BackgroundValue: 0<br>> ForegroundValue: 255<br>> Lambda: 500<br>> ReverseOrdering: 0<br>> Attribute: Size (0)<br>> Progress | 0 | 0.00292969 | 0.00585938 | 0.00878906 | 0.0117188 | <br>> 0.0146484 | 0.0175781 | 0.0205078 | 0.0234375 | 0.0263672<br>> | 0.0292969 | 0.0322266 | 0.0351562 | 0.0380859 | 0.0410156 | <br>> 0.0439453 | 0.046875 | 0.0498047 | 0.0527344 | 0.0556641<br>> | 0.0585938 | 0.0615234 | 0.0644531 | 0.0673828 | 0.0703125 | <br>> 0.0732422 | 0.0761719 | 0.0791016 | 0.0820312 | 0.0849609<br>> | 0.0878906 |
0.0908203 | 0.09375 | 0.0966797 | 0.0996094 | <br>> 0.102539 | 0.105469 | 0.108398 | 0.111328 | 0.114258<br>> | 0.117188 | 0.120117 | 0.123047 | 0.125977 | 0.128906 | 0.131836 | <br>> 0.134766 | 0.137695 | 0.140625 | 0.143555<br>> | 0.146484 | 0.149414 | 0.152344 | 0.155273 | 0.158203 | 0.161133 | <br>> 0.164062 | 0.166992 | 0.169922 | 0.172852<br>> | 0.175781 | 0.178711 | 0.181641 | 0.18457 | 0.1875 | 0.19043 | <br>> 0.193359 | 0.196289 | 0.199219 | 0.202148<br>> | 0.205078 | 0.208008 | 0.210938 | 0.213867 | 0.216797 | 0.219727 | <br>> 0.222656 | 0.225586 | 0.228516 | 0.231445<br>> | 0.234375 | 0.237305 | 0.240234 | 0.243164 | 0.246094 | 0.249023 | <br>> 0.251953 | 0.254883 | 0.257812 | 0.260742<br>> | 0.263672 | 0.266602 | 0.269531 | 0.272461 | 0.275391 | 0.27832 | <br>> 0.28125 | 0.28418 | 0.287109 | 0.290039<br>> | 0.292969 |
0.295898 | 0.298828Brain(6480,0xa0047540) malloc: *** <br>> mmap(size=4263636992) failed (error code=12)<br>> *** error: can't allocate region<br>> *** set a breakpoint in malloc_error_break to debug<br>> | 0.3<br>><br>> --- Richard Beare <<a ymailto="mailto:richard.beare@gmail.com" href="mailto:richard.beare@gmail.com">richard.beare@gmail.com</a>> schrieb am Mi, 30.3.2011:<br>><br>> Von: Richard Beare <<a ymailto="mailto:richard.beare@gmail.com" href="mailto:richard.beare@gmail.com">richard.beare@gmail.com</a>><br>> Betreff: Re: [Insight-users] LabelShapeOpeningImageFilter Attribute <br>> input<br>> An: "Ella Maria Kadas" <<a ymailto="mailto:ella_kadas@yahoo.com" href="mailto:ella_kadas@yahoo.com">ella_kadas@yahoo.com</a>><br>> CC: "<a ymailto="mailto:insight-users@itk.org" href="mailto:insight-users@itk.org">insight-users@itk.org</a>" <<a ymailto="mailto:insight-users@itk.org"
href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>> Datum: Mittwoch, 30. M?rz, 2011 15:03 Uhr<br>><br>> There is a convenience class in the Review directory that is derived <br>> from this contribution called itk::BinaryShapeOpeningImageFilter. <br>> This includes all of the labelling and conversion to and from label <br>> maps. You just need to call the SetAttribute and SetForegroundValue <br>> appropriately. It should work fine for 3D. If you look inside that <br>> class you should also find the standard combination of steps you <br>> need to go through to use the LabelMap filters.<br>><br>> On Wed, Mar 30, 2011 at 9:09 PM, Ella Maria Kadas <<a ymailto="mailto:ella_kadas@yahoo.com" href="mailto:ella_kadas@yahoo.com">ella_kadas@yahoo.com</a> <br>> > wrote:<br>> Hi all,<br>><br>> I am trying to remove some objects from a 3D image that
have a <br>> volume lower then a specific value.<br>> I tried to use the Label object representation and manipulation <br>> with ITK that Gae ?tan Lehmann<br>> implemented but i still don't know what that attribute parameter <br>> should look like. (in the python example it looks a s it would be a <br>> char<br>> size = <br>> itk <br>> .ShapeOpeningLabelMapFilter <br>> [LabelMapType].New(stats,Attribute=?Size?, Lambda=100)<br>> I want to use the ShapeLabelObject, and it's attributes to do a <br>> LabelShapeOpeningFilter.<br>> As i was getting no result i tried to do it in 2D first.<br>> This is my code:<br>> First i use the ConnectedComponentImageFilter, then <br>> RelabelComponentImageFilter and create a ShapeLabelMap from the <br>> relabel's output.<br>><br>> typedef unsigned long LabelType;<br>> typedef
itk::ShapeLabelObject< LabelType, dim > LabelObjectType;<br>> typedef itk::LabelMap< LabelObjectType > LabelMapType;<br>><br>><br>> typedef itk::LabelImageToShapeLabelMapFilter< LabelImageType, <br>> LabelMapType > ConverterType;<br>> ConverterType::Pointer converter = ConverterType::New();<br>> converter->SetInput( relabel->GetOutput() );<br>> converter->Update();<br>> !!!! Why does it not work if i use this part of code from the journal<br>> /*<br>><br>> and valuate the attributes with the dedicated filter: <br>> ShapeLabelMapFilter<br>> typedef itk::ShapeLabelMapFilter< LabelMapType > ShapeFilterType; <br>> ShapeFilterType::Pointer shape = ShapeFilterType::New(); shape- <br>> >SetInput( converter->GetOutput() );<br>> update the shape filter, so its output will be up to date<br>>
shape->Update();<br>><br>> */<br>><br>><br>> LabelMapType::Pointer labelMap = converter->GetOutput();<br>> std::cout<<"nr of label objects"<<labelMap- <br>> >GetNumberOfLabelObjects()<<std::endl;<br>><br>> for( unsigned int label=1; label<=labelMap- <br>> >GetNumberOfLabelObjects(); label++ )<br>> {<br>><br>> const LabelObjectType * labelObject = labelMap- <br>> >GetLabelObject( label );<br>> std::cout << label << "\t" << labelObject->GetPhysicalSize() << <br>> "\t" << labelObject->GetCentroid() << std::endl;<br>> }<br>><br>> typedef itk::LabelShapeOpeningImageFilter< LabelImageType > <br>> LabelOpeningType;<br>> LabelOpeningType::Pointer opening = LabelOpeningType::New();<br>> opening->SetInput(
relabel->GetOutput());<br>> opening->SetBackgroundValue(0);<br>> opening->SetLambda( 100 );<br>> opening->SetReverseOrdering( false );<br>> //NO IDEA About the Attribute<br>> //I thought it should be the labelMap->Size()) should be as attribute<br>> opening->SetAttribute("PERIMETER");<br>> itk::SimpleFilterWatcher watcher(opening, "filter");<br>><br>> Then i would like to get back the binary image and see it but i <br>> can't get the proper image types as input to <br>> LabelMapToLabelIamgeFilter....So the commented part is not working<br>><br>> /*typedef itk::LabelMapToLabelImageFilter< LabelImageType, <br>> LabelImageType > L2IType;<br>> L2IType::Pointer l2i = L2IType::New();<br>> l2i->SetInput( opening->GetOutput() );<br>><br>> typedef itk::ImageFileWriter< LabelImageType > WriterType;<br>> WriterType::Pointer writer =
WriterType::New();<br>> writer->SetInput( l2i->GetOutput() );<br>> writer->SetFileName( "/Users/ellaK/Documents/Morphology/ <br>> Opening.gipl");<br>> writer->Update();*/<br>> std::getchar();<br>><br>><br>><br>> Maybe i am doing this the wrong way, and i can't use it for 3D images.<br>> If anybody already already worked with this filters please give me a <br>> hint to what i am doing wrong.<br>> Thanks,<br>> Ella<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><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>Ga?tan Lehmann<br>Biologie du D?veloppement et de la Reproduction<br>INRA de Jouy-en-Josas (France)<br>tel: +33 1 34 65 29 66 fax: 01 34 65 29 09<br><a href="http://voxel.jouy.inra.fr" target="_blank">http://voxel.jouy.inra.fr</a> <a href="http://www.itk.org" target="_blank">http://www.itk.org</a><br><a href="http://www.mandriva.org" target="_blank">http://www.mandriva.org</a> <a href="http://www.bepo.fr"
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