[vtkusers] [vtk-developers] vtkDICOMImageReader

[Mathieu Malaterre]

[changing from vtk-dev to vtkusers to avoid extra pollution]

No GDCM does not rely on vtkMPEGencoder (grep the source), you must
have turned the option on your own.

2cts
-Mathieu

On Tue, Jul 22, 2008 at 1:01 AM, Bartosz Wiklak <bwiklak at gmail.com> wrote:
> oh, it is patanted - is there any chance to get rit of it?
>
> On Tue, Jul 22, 2008 at 12:45 AM, Bartosz Wiklak <bwiklak at gmail.com> wrote:
>> Does gdcm rely on libvtkMPEGencoder?
>> I don't have it (dont't know why) but when I'm running my simple app
>> that uses vtkGDCMImageReader I'm getting error that tis shared lib is
>> not found.
>>
>> On Tue, Jul 22, 2008 at 12:18 AM, Bartosz Wiklak <bwiklak at gmail.com> wrote:
>>> Ok, :), I looked into examples dir and google and found nothing,
>>> funny, all day had it on my computer.
>>>
>>> Thanks a lot
>>>
>>> On Tue, Jul 22, 2008 at 12:09 AM, Mathieu Malaterre
>>> <mathieu.malaterre at gmail.com> wrote:
>>>> svn co https://gdcm.svn.sourceforge.net/svnroot/gdcm/trunk
>>>>
>>>> $ grep -lr vtkGDCMImageReader *  | grep Testing | grep -v .svn
>>>> Utilities/VTK/Testing/Cxx/TestvtkGDCMImageReader4.cxx
>>>> Utilities/VTK/Testing/Cxx/TestvtkGDCMImageReader3.cxx
>>>> Utilities/VTK/Testing/Cxx/TestvtkGDCMImageWriter.cxx
>>>> Utilities/VTK/Testing/Cxx/CMakeLists.txt
>>>> Utilities/VTK/Testing/Cxx/TestvtkGDCMImageActor.cxx
>>>> Utilities/VTK/Testing/Cxx/TestvtkGDCMImageWriter2.cxx
>>>> Utilities/VTK/Testing/Cxx/TestvtkGDCMImageReader.cxx
>>>> Utilities/VTK/Testing/Cxx/TestvtkGDCMThreadedImageReader2.cxx
>>>> Utilities/VTK/Testing/Cxx/TestvtkGDCMImageReader2.cxx
>>>> Utilities/VTK/Testing/Cxx/TestvtkGDCMThreadedImageReader.cxx
>>>> Utilities/VTK/Testing/Python/CMakeLists.txt
>>>> Utilities/VTK/Testing/Python/TestvtkGDCMImageWriter.py
>>>> Utilities/VTK/Testing/Python/TestvtkGDCMImageReader.py
>>>>
>>>> Hopefully this will be enough now :)
>>>>
>>>>
>>>> -Mathieu
>>>> Ps: please post to gdcm mailing list instead:
>>>> https://lists.sourceforge.net/lists/listinfo/gdcm-developers
>>>>
>>>> On Mon, Jul 21, 2008 at 11:51 PM, Bartosz Wiklak <bwiklak at gmail.com> wrote:
>>>>> Thank you for whole help and info.
>>>>> Could you please give me some examples how to user gdcm
>>>>> vtkGDCMImageReader and connect data to renderer/mapper?
>>>>> I cant find any.
>>>>>
>>>>> Bartek
>>>>>
>>>>> On Mon, Jul 21, 2008 at 4:17 PM, Mathieu Malaterre
>>>>> <mathieu.malaterre at gmail.com> wrote:
>>>>>> GDCM has recently integrated Part 3 and it does support J2K from Part
>>>>>> 5. This is IMHO the biggest advantage in using GDCM over dcmtk. The
>>>>>> main drawback would be a missing network implementation.
>>>>>>
>>>>>> -Mathieu
>>>>>>
>>>>>> On Mon, Jul 21, 2008 at 2:55 PM, Bartosz Wiklak <bwiklak at gmail.com> wrote:
>>>>>>> Thanks a lot,
>>>>>>> I have big experience in DCMTK. Of course it does implement much more
>>>>>>> than Dicom Part5 standard but it would be nice not to include to many
>>>>>>> different implementations of the same standard in one application.
>>>>>>> I have heard that some people include dcmdata pixels (f.e. decoded
>>>>>>> using dcmtk) into VTK object.
>>>>>>> Does anyone have experience in this field?
>>>>>>>
>>>>>>> Bartek
>>>>>>>
>>>>>>> On Mon, Jul 21, 2008 at 1:47 PM, Mathieu Malaterre
>>>>>>> <mathieu.malaterre at gmail.com> wrote:
>>>>>>>> If you have a chance give a try to GDCM:
>>>>>>>>
>>>>>>>> http://gdcm.sourceforge.net/wiki/index.php/GDCM_Release_2.0
>>>>>>>>
>>>>>>>> it has a vtkGDCMImageReader and a gdcm::IPPSorter. Pluging them
>>>>>>>> together should do what you want:
>>>>>>>>
>>>>>>>> http://gdcm.sourceforge.net/html/classvtkGDCMImageReader.html
>>>>>>>>
>>>>>>>> http://gdcm.sourceforge.net/html/classgdcm_1_1IPPSorter.html
>>>>>>>>
>>>>>>>> HTH
>>>>>>>> -Mathieu
>>>>>>>>
>>>>>>>> On Mon, Jul 21, 2008 at 1:18 PM, Bartosz Wiklak <bwiklak at gmail.com> wrote:
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> I'm new to VTK but I'm very impressed by it's capabilities.
>>>>>>>>> I'm specially interested in medical 3D visualization (CT,MR,PET).
>>>>>>>>> I have already learned haw to use many VTK methods and also how to
>>>>>>>>> read DICOM data through vtkDICOMImageReader. Here my question begins.
>>>>>>>>>
>>>>>>>>> In many dicom data sets (scans) spacing between slices in not the same
>>>>>>>>> in whole 3D object (f.e series).
>>>>>>>>> To make things worse tags such as SliceLocation,  SpacingBetweenSlices
>>>>>>>>> have comonly bad values.
>>>>>>>>>
>>>>>>>>> Good information about slice positions in 3D is always (in Dicom 3
>>>>>>>>> compilant images) stored in:
>>>>>>>>> Image Orientation (Patient) (0020,0037),
>>>>>>>>> Image Position (Patient) (0020,0032).
>>>>>>>>>
>>>>>>>>> Standard says about this In PS 3.3:
>>>>>>>>>
>>>>>>>>> C.7.6.2.1.1 Image Position And Image Orientation
>>>>>>>>> The Image Position (0020,0032) specifies the x, y, and z coordinates of the
>>>>>>>>> upper left hand
>>>>>>>>> corner of the image; it is the first pixel transmitted. Image Orientation
>>>>>>>>> (0020,0037) specifies the
>>>>>>>>> direction cosines of the first row and the first column with respect to the
>>>>>>>>> patient. These Attributes
>>>>>>>>> shall be provide as a pair. Row value for the x, y, and z axes respectively
>>>>>>>>> followed by the Column
>>>>>>>>> value for the x, y, and z axes respectively.
>>>>>>>>>
>>>>>>>>> The direction of the axes is defined fully by the patient's orientation.
>>>>>>>>> The x-axis is increasing to the
>>>>>>>>> left hand side of the patient. The y-axis is increasing to the posterior
>>>>>>>>> side of the patient. The z-axis
>>>>>>>>> is increasing toward the head of the patient.
>>>>>>>>>
>>>>>>>>> I'm sure that in some of my datasets that not have homogenious spacing
>>>>>>>>> between slices the data shown in VTK is bad.
>>>>>>>>>
>>>>>>>>> I would like to contibute in VTK and help to imporve
>>>>>>>>> vtkDICOMImageReader but I need some help to start.
>>>>>>>>> I need to know how exacly vtkDICOMImageReader creates VTK 3D dataset,
>>>>>>>>> and if there is possibility to construct anisotropic data tor
>>>>>>>>> vizsualiztion without need to use interpolation to force isotropy.
>>>>>>>>>
>>>>>>>>> I have read vtkDICOMImageReader code but after quick look I cant find
>>>>>>>>> place where data is build.
>>>>>>>>>
>>>>>>>>> Maybe someone can help me to make a few first steps?
>>>>>>>>>
>>>>>>>>> Bartek
>>>>>>>>> _______________________________________________
>>>>>>>>> vtk-developers mailing list
>>>>>>>>> vtk-developers at vtk.org
>>>>>>>>> http://www.vtk.org/mailman/listinfo/vtk-developers
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Mathieu
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Mathieu
>>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Mathieu
>>>>
>>>
>>
>



-- 
Mathieu