<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:"Nimbus Roman No9 L [urw]", serif;font-size:12pt"><DIV>Hello Luis,<BR></DIV><DIV></DIV><DIV>I'm sorry, I have understood you wrong. Change of pixel-type in code does not work. I always get MET_ULONG_LONG. Also, Yes, I work with 64-bit machine.</DIV><DIV>Am I doing something wrong in code?</DIV><DIV></DIV><DIV><BR> typedef float InternalPixelType;<BR> typedef unsigned long OutputPixelType;<BR> const unsigned int Dimension = 3;<BR><BR> typedef itk::OrientedImage< InternalPixelType, Dimension > ImageType;<BR><BR> typedef itk::ImageSeriesReader< ImageType > ReaderType;<BR> ReaderType::Pointer reader = ReaderType::New();<BR><BR> typedef itk::GDCMImageIO ImageIOType;<BR> ImageIOType::Pointer dicomIO = ImageIOType::New();<BR><BR> reader->SetImageIO( dicomIO );<BR><BR> typedef itk::GDCMSeriesFileNames
NamesGeneratorType;<BR> NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();<BR><BR> nameGenerator->SetUseSeriesDetails( true );<BR> nameGenerator->AddSeriesRestriction("0008|0021" );<BR><BR> nameGenerator->SetDirectory( selectedDirectory);<BR><BR> typedef std::vector< std::string > SeriesIdContainer;<BR> <BR> const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();<BR> <BR> SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();<BR> SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();<BR> while( seriesItr != seriesEnd )<BR> {<BR> seriesItr++;<BR> }<BR><BR> std::string seriesIdentifier;<BR><BR> seriesIdentifier = seriesUID.begin()->c_str();<BR><BR> typedef std::vector< std::string > FileNamesContainer;<BR> FileNamesContainer fileNames;<BR><BR> fileNames = nameGenerator->GetFileNames( seriesIdentifier
);<BR><BR> reader->SetFileNames( fileNames );<BR> reader->Update();<BR> <BR> reader->GetOutput()->Print( std::cout );<BR><BR> typedef itk::Image< InternalPixelType, Dimension > InternalImageType;<BR> typedef itk::Image< OutputPixelType, Dimension > OutputImageType;<BR> <BR> typedef itk::GradientMagnitudeRecursiveGaussianImageFilter<InternalImageType,InternalImageType> GradientMagnitudeFilterType;<BR> GradientMagnitudeFilterType::Pointer gradienMagnitudeFilter = GradientMagnitudeFilterType::New();<BR> gradienMagnitudeFilter->SetInput( reader->GetOutput() );<BR> gradienMagnitudeFilter->SetSigma( 1.0 );<BR> <BR> typedef itk::WatershedImageFilter<InternalImageType> WatershedFilterType;<BR> WatershedFilterType::Pointer watershedFilter =
WatershedFilterType::New();<BR> watershedFilter->SetInput(gradienMagnitudeFilter->GetOutput());<BR> watershedFilter->SetThreshold(this->sliderThresholdWatershed->value());<BR> watershedFilter->SetLevel(this->sliderLevelWatershed->value());<BR>// typedef WatershedFilterType::OutputImageType LabeledImageType;<BR> <BR> typedef itk::ImageFileWriter< OutputImageType > WriterType;<BR> WriterType::Pointer writer = WriterType::New();<BR> writer->SetInput( watershedFilter->GetOutput() );<BR> writer->SetFileName("Watershed.mhd");<BR> writer->Write();<BR><BR> typedef itk::VTKImageExport< OutputImageType > ExportFilter2Type;<BR> ExportFilter2Type::Pointer itkExporter2 = ExportFilter2Type::New();<BR> <BR> itkExporter2->SetInput( watershedFilter->GetOutput() );<BR><BR> vtkImageImport* vtkImporter2 = vtkImageImport::New(); <BR> ConnectPipelines(itkExporter2,
vtkImporter2);<BR> <BR> vtkImporter2->Update();<BR><BR> this->displayImage3D->show();<BR> this->displayImage3D->redraw();<BR><BR> mode3D = vtkInteractorStyleTrackballCamera::New();</DIV><DIV><BR> renderer3D = vtkRenderer::New();<BR><BR> renderWindow3D = vtkRenderWindow::New();<BR> renderWindow3D->AddRenderer(renderer3D);<BR><BR> displayImage3D->SetRenderWindow(renderWindow3D);<BR> displayImage3D->SetInteractorStyle(mode3D);<BR> displayImage3D->Initialize();<BR><BR> contourWatershed = vtkContourFilter::New();<BR> contourWatershed->SetInput( vtkImporter2->GetOutput() );<BR> contourWatershed->SetValue(-1000, 4096); // edges of a binary image with values 0,255<BR> <BR> mapperWatershed = vtkPolyDataMapper::New();<BR> mapperWatershed->SetInput(contourWatershed->GetOutput());<BR> mapperWatershed->ScalarVisibilityOff();<BR> <BR> propertyWatershed =
vtkProperty::New();<BR> propertyWatershed->SetAmbient(0.3);<BR> propertyWatershed->SetDiffuse(1.0);<BR> propertyWatershed->SetSpecular(0.2);<BR> propertyWatershed->SetSpecularPower(10.0);<BR> propertyWatershed->SetColor(1 ,1, 1);<BR> propertyWatershed->SetRepresentationToSurface();<BR> <BR> polyActorWatershed = vtkActor::New();<BR> polyActorWatershed->SetMapper(mapperWatershed);<BR> polyActorWatershed->SetProperty(propertyWatershed);<BR> <BR> camera3D = vtkCamera::New();<BR> camera3D->SetViewUp(0, 0, -1);<BR> camera3D->SetPosition(0, 1, 0);<BR> camera3D->SetFocalPoint(0, 0, 0);<BR> camera3D->ComputeViewPlaneNormal();<BR> camera3D->Azimuth(20);<BR> <BR> renderer3D->AddActor(polyActorWatershed);<BR> renderer3D->SetActiveCamera(camera3D);<BR> renderer3D->ResetCamera();<BR> camera3D->Dolly(1.3);<BR> renderer3D->ResetCameraClippingRange();<BR> </DIV><DIV></DIV><DIV><BR>Thank
you.<BR></DIV><DIV style="font-family:times new roman, new york, times, serif;font-size:12pt"><BR><DIV style="font-family:times new roman, new york, times, serif;font-size:12pt"><FONT size="2" face="Tahoma"><HR size="1"><B><SPAN style="font-weight: bold;">Von:</SPAN></B> Luis Ibanez <luis.ibanez@kitware.com><BR><B><SPAN style="font-weight: bold;">An:</SPAN></B> Yusuf OEZBEK <nasil122002@yahoo.de><BR><B><SPAN style="font-weight: bold;">CC:</SPAN></B> ITK Mailinglist <insight-users@itk.org>; VTK Mailinglist <vtkusers@vtk.org>; nasil122002@gmail.com<BR><B><SPAN style="font-weight: bold;">Gesendet:</SPAN></B> Freitag, den 28. Mai 2010, 16:52:20 Uhr<BR><B><SPAN style="font-weight: bold;">Betreff:</SPAN></B> Re: [Insight-users] visualization-problem after segmentation and cropping<BR></FONT><BR><BR>Hi Yusuf,<BR><BR><BR> Manually modifying the pixel type tag in the <BR> metaimage header will not do the trick.<BR><BR> (in
your modified image, the pixel type doesn't<BR> match the content of the pixel buffer, which <BR>
explains the distorted appearance of the image).<BR><BR><BR> My apologies if my instructions were not clear.<BR><BR><BR><BR> What I suggested you to do, was to change<BR> the pixel type in your code, and then to run<BR>
the code again.<BR><BR><BR> Please do so, <BR> and let us know what you find.<BR><BR><BR> Thanks<BR><BR><BR> Luis <BR><BR><BR><BR>--------------------------------------------------<BR><DIV class="gmail_quote">
On Wed, May 26, 2010 at 9:10 PM, Yusuf OEZBEK <SPAN dir="ltr"><<A rel="nofollow" ymailto="mailto:nasil122002@yahoo.de" target="_blank" href="mailto:nasil122002@yahoo.de">nasil122002@yahoo.de</A>></SPAN> wrote:<BR><BLOCKQUOTE class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex;">
<DIV><DIV style=""><DIV>Hello Luis,<BR></DIV><DIV><BR></DIV><DIV>I have manually converted the pixel type to unsigned long (ElementType = MET_ULONG) in. mhd file and loaded with 3Dslicer. It works but the 3D-image is not correctly displayed. I get as 3D two axial-view side by side. If I visualize it in my program with vtk, then I get purposeful 3D-image.</DIV>
<DIV><BR></DIV><DIV><BR></DIV><DIV><BR></DIV><DIV>Here are the screenshots:</DIV><DIV><BR></DIV><DIV style="font-family:times new roman, new york, times, serif;font-size:12pt;">Output-Image of watershed on my program (visualized with vtkContourFilter):</DIV>
<DIV style="font-family:times new roman, new york, times, serif;font-size:12pt;"><SPAN><A rel="nofollow" target="_blank" href="http://www.wopsys.com/bilder/watershed_visualizedwithvtk.png">http://www.wopsys.com/bilder/watershed_visualizedwithvtk.png</A></SPAN></DIV>
<DIV style="font-family:times new roman, new york, times, serif;font-size:12pt;"><BR></DIV><DIV style="font-family:times new roman, new york, times, serif;font-size:12pt;"><BR></DIV><DIV style="font-family:times new roman, new york, times, serif;font-size:12pt;">
Output-Image of watershed on 3DSlicer:</DIV><DIV style="font-family:times new roman, new york, times, serif;font-size:12pt;"><SPAN><A rel="nofollow" target="_blank" href="http://www.wopsys.com/bilder/watershed.JPG">http://www.wopsys.com/bilder/watershed.JPG</A></SPAN></DIV>
<DIV style="font-family:times new roman, new york, times, serif;font-size:12pt;"><BR></DIV><DIV style="font-family:times new roman, new york, times, serif;font-size:12pt;"><BR></DIV><DIV style="font-family:times new roman, new york, times, serif;font-size:12pt;">
Output-Image of DicomSeriesReadImageWrite2,
so before segmentation:</DIV><DIV style="font-family:times new roman, new york, times, serif;font-size:12pt;"><SPAN><A rel="nofollow" target="_blank" href="http://www.wopsys.com/bilder/before_segmentation.png">http://www.wopsys.com/bilder/before_segmentation.png</A></SPAN></DIV>
<DIV style="font-family:times new roman, new york, times, serif;font-size:12pt;"><BR></DIV><DIV style="font-family:times new roman, new york, times, serif;font-size:12pt;"><BR></DIV><DIV style="font-family:times new roman, new york, times, serif;font-size:12pt;">
<BR></DIV><DIV style="font-family:times new roman, new york, times, serif;font-size:12pt;">Thank you.</DIV><DIV style="font-family:times new roman, new york, times, serif;font-size:12pt;"><BR><DIV style="font-family:times new roman, new york, times, serif;font-size:12pt;">
<FONT face="Tahoma" size="2"><DIV class="im"><HR size="1"><B><SPAN style="font-weight:bold;">Von:</SPAN></B> Luis Ibanez <<A rel="nofollow" ymailto="mailto:luis.ibanez@kitware.com" target="_blank" href="mailto:luis.ibanez@kitware.com">luis.ibanez@kitware.com</A>><BR><B><SPAN style="font-weight:bold;">An:</SPAN></B> Yusuf OEZBEK <<A rel="nofollow" ymailto="mailto:nasil122002@yahoo.de" target="_blank" href="mailto:nasil122002@yahoo.de">nasil122002@yahoo.de</A>><BR>
<B><SPAN style="font-weight:bold;">CC:</SPAN></B> ITK Mailinglist <<A rel="nofollow" ymailto="mailto:insight-users@itk.org" target="_blank" href="mailto:insight-users@itk.org">insight-users@itk.org</A>>; VTK Mailinglist <<A rel="nofollow" ymailto="mailto:vtkusers@vtk.org" target="_blank" href="mailto:vtkusers@vtk.org">vtkusers@vtk.org</A>>; <A rel="nofollow" ymailto="mailto:nasil122002@gmail.com" target="_blank" href="mailto:nasil122002@gmail.com">nasil122002@gmail.com</A><BR>
</DIV><B><SPAN style="font-weight:bold;">Gesendet:</SPAN></B> Mittwoch, den 26. Mai 2010, 19:56:18 Uhr<DIV><DIV class="h5"><BR><B><SPAN style="font-weight:bold;">Betreff:</SPAN></B> Re: [Insight-users] visualization-problem after segmentation and cropping<BR>
</DIV></DIV></FONT><DIV><DIV class="h5"><BR><BR>Hi Yusuf,<BR><BR>Excellent.<BR><BR>Thanks for posting the screenshots.<BR><BR><BR>They illustrate that the pipeline is working correctly<BR>up to the output of the region growing filter.<BR>
<BR><BR>You can now focus on getting the Watershed <BR>
filter to work correctly by using as output image<BR>an image of pixel type "unsigned long" and <BR>making sure that it doesn't turn into "long long"<BR>in your 64 bits machine.<BR><BR>Please post the screenshot of the Watershed<BR>
output once you get it to work.<BR><BR><BR> Thanks<BR><BR><BR> Luis<BR><BR><BR>-------------------------------------------------------------------<BR><DIV class="gmail_quote">On Tue, May 25, 2010 at 4:14 PM, Yusuf OEZBEK <SPAN dir="ltr"><<A rel="nofollow" ymailto="mailto:nasil122002@yahoo.de" target="_blank" href="mailto:nasil122002@yahoo.de">nasil122002@yahoo.de</A>></SPAN> wrote:<BR>
<BLOCKQUOTE class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex;"><DIV><DIV><DIV>Hello Luis,<BR></DIV><DIV><BR></DIV><DIV>I have the.mhd files loaded with 3DSlicer. Here are the screenshots:</DIV>
<DIV><BR></DIV><DIV>Output-Image of Region Growing:</DIV><DIV><SPAN><A rel="nofollow" target="_blank" href="http://www.wopsys.com/bilder/regiongrowing_notcropped.JPG">http://www.wopsys.com/bilder/regiongrowing_notcropped.JPG</A></SPAN></DIV>
<DIV><SPAN><A rel="nofollow" target="_blank" href="http://www.wopsys.com/bilder/regiongrowing_cropped.JPG">http://www.wopsys.com/bilder/regiongrowing_cropped.JPG</A></SPAN></DIV><DIV><BR></DIV><DIV><BR></DIV><DIV>Output-Image of DicomSeriesReadImageWrite2:</DIV>
<DIV><SPAN><A rel="nofollow" target="_blank" href="http://www.wopsys.com/bilder/DicomSeriesReadImageWrite2.JPG">http://www.wopsys.com/bilder/DicomSeriesReadImageWrite2.JPG</A></SPAN></DIV><DIV><BR></DIV><DIV><BR></DIV><DIV>
<BR></DIV><DIV>
<BR></DIV><DIV style="font-family:times new roman, new york, times, serif;font-size:12pt;">Thanks.<BR><DIV style="font-family:arial, helvetica, sans-serif;font-size:10pt;"><FONT face="Tahoma" size="2"><DIV><HR size="1">
<B><SPAN style="font-weight:bold;">Von:</SPAN></B> Luis Ibanez <<A rel="nofollow" ymailto="mailto:luis.ibanez@kitware.com" target="_blank" href="mailto:luis.ibanez@kitware.com">luis.ibanez@kitware.com</A>><BR><B><SPAN style="font-weight:bold;">An:</SPAN></B> Yusuf OEZBEK <<A rel="nofollow" ymailto="mailto:nasil122002@yahoo.de" target="_blank" href="mailto:nasil122002@yahoo.de">nasil122002@yahoo.de</A>><BR>
</DIV><B><SPAN style="font-weight:bold;">CC:</SPAN></B> ITK Mailinglist <<A rel="nofollow" ymailto="mailto:insight-users@itk.org" target="_blank" href="mailto:insight-users@itk.org">insight-users@itk.org</A>>; VTK Mailinglist <<A rel="nofollow" ymailto="mailto:vtkusers@vtk.org" target="_blank" href="mailto:vtkusers@vtk.org">vtkusers@vtk.org</A>>; <A rel="nofollow" ymailto="mailto:vtkusers-request@vtk.org" target="_blank" href="mailto:vtkusers-request@vtk.org">vtkusers-request@vtk.org</A>; <A rel="nofollow" ymailto="mailto:nasil122002@gmail.com" target="_blank" href="mailto:nasil122002@gmail.com">nasil122002@gmail.com</A><BR>
<B><SPAN style="font-weight:bold;">Gesendet:</SPAN></B> Dienstag, den 25. Mai 2010, 17:00:30 Uhr<BR><B><SPAN style="font-weight:bold;">Betreff:</SPAN></B> Re: [Insight-users]
visualization-problem after segmentation and cropping<BR></FONT><DIV><DIV><BR>Hi Yusuf,<BR><BR><BR>When you are debugging a pipeline you should<BR>start by verifying that the data has been properly<BR>
loaded in memory, and then you should proceed<BR>to check out the output of every intermediate filter<BR>in order: from source to final output.<BR><BR><BR>Please start by doing the following:<BR><BR><BR> Verify that you succeeded reading the DICOM series.<BR>
<BR> Simply write the output of the Series reader to<BR> an output file.<BR><BR> This essentially the code that you will see in<BR> the example:<BR><BR><BR> Insight/Examples/IO/<BR> DicomSeriesReadImageWrite2.cxx<BR>
<BR><BR> Open that file with any visualization software<BR><BR> For example:<BR><BR> 1) Paraview. (<A rel="nofollow" target="_blank" href="http://www.paraview.org">http://www.paraview.org</A>) or<BR> 2) Slicer, (<A rel="nofollow" target="_blank" href="http://www.slicer.org">http://www.slicer.org</A>) or<BR>
3) SNAP, (<A rel="nofollow" target="_blank" href="http://sourceforge.net/projects/itk-snap/">http://sourceforge.net/projects/itk-snap/</A>) or<BR> 4) VV (<A rel="nofollow" target="_blank" href="http://www.creatis.insa-lyon.fr/rio/vv">http://www.creatis.insa-lyon.fr/rio/vv</A>)<BR>
<BR><BR>Please let us know if you manage to do that initial<BR>test, (it will be great if you post a screen shot of<BR>that output image)<BR><BR>and then we will guide you to the next step.<BR><BR><BR><BR> Regards,<BR>
<BR><BR> Luis<BR><BR><BR>--------------------------------------------------<BR>On Mon, May 24, 2010 at 10:26 PM, Yusuf OEZBEK <<A rel="nofollow" ymailto="mailto:nasil122002@yahoo.de" target="_blank" href="mailto:nasil122002@yahoo.de">nasil122002@yahoo.de</A>> wrote:<BR>
> Hello,<BR>><BR>> I have a problem with cut (cropping) and visualization a 3D image, which I<BR>> produced by the segmentation-method “watershed and region
growing”. In the<BR>> beginning I read the DICOM images with itkImageSeriesReader, then I run<BR>> watershed or region growing algorithm, in order to connect itk with vtk and<BR>> a 3D image produce and for the displaying of segmentation I use<BR>
> vtkContourFilter. After segmentation for cropping the images I use<BR>> vtkBoxClipDataSet and vtkDataSetSurfaceFilter, but the result is a black<BR>> screen. When I read the images with vtkDICOMImageReader or<BR>
> itkImageSeriesReader and then segmented with volume rendering, marching<BR>> cubes watershed and region growing, then it works completely well. The<BR>> problem arises only when cut for watershed and region growing algorithm.<BR>
> What am I doing wrong?<BR>><BR>> To understand my problem better, please see my screenshots on the following<BR>> link.<BR>><BR>><BR>><BR>> <A rel="nofollow" target="_blank" href="http://www.wopsys.com/bilder/segmentation.html">http://www.wopsys.com/bilder/segmentation.html</A><BR>
><BR>><BR>><BR>> To determine whether there missing of any geometrical informations. I had<BR>> sent the following outputs of tests.<BR>><BR>> <A rel="nofollow" target="_blank" href="http://www.wopsys.com/Outputs/Output_MarchingCubes.txt">http://www.wopsys.com/Outputs/Output_MarchingCubes.txt</A><BR>
> <A rel="nofollow" target="_blank" href="http://www.wopsys.com/Outputs/Output_VolumeRendering.txt">http://www.wopsys.com/Outputs/Output_VolumeRendering.txt</A><BR>> <A rel="nofollow" target="_blank" href="http://www.wopsys.com/Outputs/Output_Watershed.txt">http://www.wopsys.com/Outputs/Output_Watershed.txt</A><BR>
> <A rel="nofollow" target="_blank" href="http://www.wopsys.com/Outputs/Output_RegionGrowing.txt">http://www.wopsys.com/Outputs/Output_RegionGrowing.txt</A><BR>><BR>> Thanks.<BR>><BR>><BR>> ________________________________<BR>
> Von: Luis Ibanez <<A rel="nofollow" ymailto="mailto:luis.ibanez@kitware.com" target="_blank" href="mailto:luis.ibanez@kitware.com">luis.ibanez@kitware.com</A>><BR>> An: Yusuf OEZBEK <<A rel="nofollow" ymailto="mailto:nasil122002@yahoo.de" target="_blank" href="mailto:nasil122002@yahoo.de">nasil122002@yahoo.de</A>><BR>
> CC: ITK Mailinglist <<A rel="nofollow" ymailto="mailto:insight-users@itk.org" target="_blank" href="mailto:insight-users@itk.org">insight-users@itk.org</A>>; VTK Mailinglist<BR>> <<A rel="nofollow" ymailto="mailto:vtkusers@vtk.org" target="_blank" href="mailto:vtkusers@vtk.org">vtkusers@vtk.org</A>>; <A rel="nofollow" ymailto="mailto:nasil122002@gmail.com" target="_blank" href="mailto:nasil122002@gmail.com">nasil122002@gmail.com</A><BR>
> Gesendet: Sonntag, den 18. April 2010, 1:12:33 Uhr<BR>> Betreff: Re: [Insight-users] Cropping Problem<BR>><BR>><BR>> Hi Yusuf,<BR>><BR>><BR>> You should start by separating the segmentation<BR>> problem from the visualization problem.<BR>
><BR>><BR>> Please do the following:<BR>><BR>> 0) Just after you call:<BR>><BR>>
reader->SetFileNames( fileNames );<BR>> reader->Update();<BR>><BR>> add<BR>><BR>> reader->GetOutput()->Print( std::cout );<BR>><BR>> then<BR>><BR>> 1) Run the ITK segmentation pipeline until you<BR>
> get the segmented image, and save it as a<BR>> MetaImage file (with extension .mhd)<BR>><BR>><BR>> 2) Post the content of the resulting .mhd file<BR>> back to the list, as well as the print out of<BR>
> the statement:<BR>><BR>> reader->GetOutput()->Print( std::cout );<BR>><BR>><BR><SPAN>> 3) Use Paraview (<A rel="nofollow" target="_blank" href="http://www.paraview.org">www.paraview.org</A>) to load the</SPAN><BR>
> resulting image and extracting an iso-surface.<BR>> Compare that iso-surface with the one that<BR>> you get by directly from the DICOM image.<BR>> (and let us know what you
find).<BR>><BR>><BR>> With the information from (2) we should be<BR>> able to identify if any geometrical information<BR>> is missing from the ITK processing pipeline.<BR>><BR>><BR>> Thanks<BR>
><BR>><BR>> Luis<BR>><BR>><BR>><BR>><BR>><BR>> _____________________________________<BR><SPAN>> Powered by <A rel="nofollow" target="_blank" href="http://www.kitware.com">www.kitware.com</A></SPAN><BR>
><BR>> Visit other Kitware open-source projects at<BR>> <A rel="nofollow" target="_blank" href="http://www.kitware.com/opensource/opensource.html">http://www.kitware.com/opensource/opensource.html</A><BR>><BR>
> Kitware offers ITK Training Courses, for more information visit:<BR>
> <A rel="nofollow" target="_blank" href="http://www.kitware.com/products/protraining.html">http://www.kitware.com/products/protraining.html</A><BR>><BR>> Please keep messages on-topic and check the ITK FAQ at:<BR>
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