[vtk-developers] vtkDICOMImageReader broken in vtk 5.0 and up

Tue May 2 18:00:05 EDT 2006

Hi Mathieu,

Must have been my weird IP setup at work. I tried at home and got it all,
configured and compiled fine with the vtk cvs version from 22MAR06 and
Python 2.4

Two things that seem to not work are 

- the gdcm.pth file that gets written into the python site-packages
directory has a entry to gdcm\bin. Tried to run demo\vtkGdcmReader.py,
didn't find gdcm. So I changed the .pth entries to \gdcm and
\gdcm\bin\release, then the packages do get found by the import command.

- but now it complains that it cannot find vtkCommon.dll! So I checked
vtkgdcmPython.dll with the Windows dependency walker, and it loads
vtkCommon.dll from the correct location!! I can also do an "import vtk" just
fine!

So I guess I must have the paths somehow wrong, thanks for your help so far
too.

- Sven

-----Original Message-----
From: Mathieu Malaterre [mailto:mathieu.malaterre at kitware.com] 
Sent: Saturday, April 29, 2006 5:21 AM
To: Sven Prevrhal; 'Karthik Krishnan'
Cc: 'Mathieu Malaterre'
Subject: Re: RE: [vtk-developers] vtkDICOMImageReader broken in vtk 5.0 and

Hi Sven,

   I am looking at yesterday dashbaord and the cvs update happen as
expected. Are you sure you did not do a mistake in the cvs url ? Pay
particular attention to the cvs port: 2402. There are some known issues with
the cvs command in with panther/MacOSX (you need the cvs command from fink,
for example).

HTH
Mathieu

>  up?
> 
> Karthik and Mathieu,
> 
> Thanks I'll look into gdcm - their win binaries are compiled with an older
> vtk, so I want to get their stuff from cvs and rebuild. Unfortunately
their
> cvs server seems to be down (checked again today).
> 
> - Sven
> 
> 
> -----Original Message-----
> From: Karthik Krishnan [mailto:Karthik.Krishnan at kitware.com] 
> Sent: Thursday, April 27, 2006 11:49 AM
> To: Sven Prevrhal
> Cc: vtk-developers at vtk.org; 'Nikolaus Heger'
> Subject: Re: [vtk-developers] vtkDICOMImageReader broken in vtk 5.0 and
up?
> 
> Mathieu will have more to say, but have you tried using vtkgdcmViewer. I 
> use it all the time cause its in sync with gdcm cvs and usually tells me 
> if things are fixed in gdcm cvs (where things are fixed more often).
> 
> cvs -d:pserver:anonymous at cvs.creatis.insa-lyon.fr:2402/cvs/public co gdcm
> 
> build with cmake as usual
> 
> vtkgdcmViewer file.dcm
> vtkgdcmSerieViewer seriesdirectory
> 
> bye
> -karthik
> 
> Sven Prevrhal wrote:
> 
> >Hi Mathieu and others:
> >
> >vtkDICOMImageReader or vtkImageViewer2 from 5.0 up seems to have a memory
> >problem with bigger files - I have a digitized X-ray of 10MB, and older
vtk
> >versions are leaky, at least the python wrappers. This is a potential
> >showstopper for me 
> >
> >I see two ways out - 
> >1. fix vtkDICOMImageReader and/or vtkImageViewer2 
> >2. find a tool that converts to 16-bit JPEG or other format (I don't know
> >any) and try to read that. 
> >
> >Can you point me to where the problem might lie? I will try implementing
a
> >bug fix then.
> >
> >The DICOM file that causes a crash in my configuration is on
>
>ftp://ftp.mrsc.ucsf.edu/pub/sven/SC.1.3.6.1.4.1.9590.100.1.1.58158724011060
> 9
> >28131648073180919160033  
> >
> >The JPEG version (only 8bit!) is ftp://ftp.mrsc.ucsf.edu/pub/sven/x.jpg

> >
> >
> >Sven Prevrhal
> >
> >
> >-----Original Message-----
> >From: Sven Prevrhal [mailto:sven.prevrhal at radiology.ucsf.edu] 
> >Sent: Wednesday, March 15, 2006 1:24 PM
> >To: 'Mathieu Malaterre'
> >Subject: RE: [vtkusers] vtkDICOMImageReader broken in vtk 5.0 and up?
> >
> >Great! From where do I pull the cvs sources? 
> >:pserver:anonymous at public.kitware.com:/cvsroot/VTK or, as your text
> >suggests, somehow form ParaView?
> >
> >- Sven
> >
> >
> >-----Original Message-----
> >From: Mathieu Malaterre [mailto:mathieu.malaterre at kitware.com]
> >Sent: Wednesday, March 15, 2006 12:15 PM
> >To: Sven Prevrhal
> >Subject: Re: [vtkusers] vtkDICOMImageReader broken in vtk 5.0 and up?
> >
> >Sven,
> >
> >	I believe the seg fault you saw is fixed in current VTK CVS.
> >
> >	Please give it a try if you can. Thanks for the data to reproduce
> >the problem.
> >
> >
> >$ cvs ci -m"BUG: DICOM spec do not enforce value to be present for Slice 
> >Number" 
> >/cvsroot/ParaView/ParaView/VTK/Utilities/DICOMParser/DICOMAppHelper.cxx,v

> >  <--  DICOMAppHelper.cxx
> >new revision: 1.23; previous revision: 1.22
> >/cvsroot/ParaView/ParaView/VTK/Utilities/DICOMParser/DICOMParser.cxx,v 
> ><--  DICOMParser.cxx
> >new revision: 1.15; previous revision: 1.14
> >
> >HTH
> >Mathieu
> >Ps: You may want to contact your DICOM vendor as the DICOM has a very 
> >bizarre 0008,0008 Image Type value: "Vidar" ??? Whereas it should be 
> >something like:
> >
> >DERIVED/SECONDARY
> >
> >Sven Prevrhal wrote:
> >  
> >
> >>Hi Mathieu,
> >>
> >>You can grab the images from ftp://ftp.mrsc.ucsf.edu/pub/sven. The setup
> >>file is unrelated!
> >>
> >>Thanks for looking at this!
> >>
> >>sven
> >>
> >>Sven Prevrhal, Ph.D.
> >>Department of Radiology
> >>University of California, San Francisco
> >>
> >>185 Berry St, Suite 350, San Francisco, CA 94107
> >>ph 415-353-9404, fax 415-353-3438
> >>
> >>Faculty Assistant: Jessica.Mapes at radiology.ucsf.edu
> >>
> >>
> >>-----Original Message-----
> >>From: Mathieu Malaterre [mailto:mathieu.malaterre at kitware.com] 
> >>Sent: Friday, March 10, 2006 12:49 PM
> >>To: Sven Prevrhal
> >>Cc: vtkusers at vtk.org
> >>Subject: Re: [vtkusers] vtkDICOMImageReader broken in vtk 5.0 and up?
> >>
> >>Sven Prevrhal wrote:
> >>
> >>    
> >>
> >>>I have DICOM images that vtk 4.4 will read just fine, but vtk 5.0 and
up 
> >>>and nightly builds will crash.  (I built vtk with python 2.4). Anybody 
> >>>experiencing similar behavior?
> >>>      
> >>>
> >>Can you send me a sample data to reproduce the problem ?
> >>
> >>Thanks
> >>Mathieu
> >>
> >>
> >>
> >>
> >>    
> >>
> >
> >
> >  
> >
> >------------------------------------------------------------------------
> >
> >import vtk
> >
> ># This script is for testing the 3D Sobel filter.
> ># Displays the 3 components using color.
> >
> >format = 'DICOM'
> ># Image pipeline
> >if format == 'DICOM':
> >    reader = vtk.vtkDICOMImageReader()
> >
>
reader.SetFileName("C:/temp/SC.1.3.6.1.4.1.9590.100.1.1.58158724011060928131
> 648073180919160033")
> >    win = 400000
> >    lev = 400000
> >else:
> >    reader = vtk.vtkJPEGReader()
> >    reader.SetFileName("C:/temp/x.jpg")
> >    win = 4000
> >    lev = 0
> >    
> >viewer = vtk.vtkImageViewer()
> >viewer.SetInputConnection( reader.GetOutputPort() )
> >viewer.SetColorWindow(win)
> >viewer.SetColorLevel(lev)
> >viewer.Render()
> >
> >viewer2 = vtk.vtkImageViewer2()
> >viewer2.SetInputConnection( reader.GetOutputPort() )
> >viewer2.SetColorWindow(win)
> >viewer2.SetColorLevel(lev)
> >viewer2.Render()
> >
> >iren = vtk.vtkRenderWindowInteractor()
> >viewer2.SetupInteractor(iren)
> >iren.Initialize()
> >
> >
> >
> >
> >
> >
> >
> >
> >  
> >
> >------------------------------------------------------------------------
> >
> >_______________________________________________
> >vtk-developers mailing list
> >vtk-developers at vtk.org
> >http://www.vtk.org/mailman/listinfo/vtk-developers
> >  
> >
> 
> 
> 
> 