[vtkusers] displaying dicom images with the right orientation
David Gobbi
david.gobbi at gmail.com
Thu Mar 17 15:51:17 EDT 2011
For the original orientation, it's fine to use vtkImageReslice to extract
the slices (assuming that the reslice transformation is the identity
transform).
The camera is not an either/or thing. Whether or not you use
vtkImageReslice, you will still have to set the camera correctly.
- David
On Thu, Mar 17, 2011 at 1:30 PM, Lic. José M. Rodriguez Bacallao
<jmrbcu at gmail.com> wrote:
> in my program, the very first thing I need to show is the series of
> images in it's original orientation, then, if the user want, sow
> orthogonal slices. So, for viewing the images in their original
> orientation, what is better, the camera method or the reslice method?
> and for the MPR view (ortho slices) the image reslice method no?
>
> PS: until now I was using vtkImageReslice to view the images in their
> original orientation and for MPR too, my code is based in example:
> Examples/ImageProcessing/Python/ImageSlicing.py
>
> On 3/17/11, David Gobbi <david.gobbi at gmail.com> wrote:
>> For extracting slices in the orthogonal directions, it is not enough
>> to just use the camera unless you are using the new classes
>> (vtkImageSliceMapper, vtkImageResliceMapper) that I mentioned.
>>
>> Without these classes, there are several ways that the orthogonal
>> slices can be extracted, and vtkImageReslice is my favorite. But
>> it is also possible to use vtkImageActor::SetDisplayExtent() or to
>> use a combination of vtkImageClip and vtkImagePermute.
>>
>> See the following wiki page for the new vtkImageSliceMapper and
>> vtkImageResliceMapper classes:
>> http://www.vtk.org/Wiki/VTK/Image_Rendering_Classes
>>
>> - David
>>
>>
>> On Thu, Mar 17, 2011 at 12:09 PM, Lic. José M. Rodriguez Bacallao
>> <jmrbcu at gmail.com> wrote:
>>> oohh, I am understanding better now, for example, if I need to view
>>> ortho slices (MPR) I need to use vtkImageReslice, just one question,
>>> this cannot be achieved with camera as well?
>>> for axial slice viewing with camera is sufficient no?
>>>
>>> PS: vtkImageSliceMapper and vtkImageResliceMapper? what are they for?
>>>
>>> On 3/17/11, David Gobbi <david.gobbi at gmail.com> wrote:
>>>> Use the camera (but also see below). In the VTK development head,
>>>> I added a method to the vtkInteractorStyleImage class that makes it
>>>> easier to set the camera orientation:
>>>>
>>>> SetImageOrientation(double leftToRight[3], double bottomToTop[3]);
>>>>
>>>> This method sets the vectors that correspond to the window "up" and
>>>> "right"
>>>> directions, i.e. bottomToTop is exactly the same as the camera ViewUp.
>>>>
>>>>
>>>> When I say "use the camera" it is not quite as simple as just that,
>>>> unless you are only viewing axial slices. For other orientations,
>>>> look at e.g. Examples/ImageProcessing/Python/ImageSlicing.py
>>>> or even better get the VTK development head and use the new
>>>> classes vtkImageSliceMapper and vtkImageResliceMapper.
>>>>
>>>> I only use vtkImageReslice to transform a whole image if that is
>>>> what I really need, for example if I am reslicing an image after
>>>> doing an image registration. For general image visualization
>>>> pipelines, I use vtkImageReslice to extract single slices in the view
>>>> orientations that I need. But it is not something so simple that I can
>>>> explain it in an email, that is why there are examples like
>>>> ImageSlicing.py.
>>>>
>>>> - David
>>>>
>>>>
>>>> On Thu, Mar 17, 2011 at 10:28 AM, Lic. José M. Rodriguez Bacallao
>>>> <jmrbcu at gmail.com> wrote:
>>>>> well, I give up vtkIMageViewer2 long time ago. Right now I am reading
>>>>> all my images with FileLoewerLeftOn to maintain the dicom coordinates
>>>>> system. So my question is, which is better, to use the camera to
>>>>> achive the right orientation or to use vtkImageReslice?
>>>>>
>>>>> On 3/17/11, David Gobbi <david.gobbi at gmail.com> wrote:
>>>>>> There is no "VTK system" per se when it comes to patient coordinate
>>>>>> systems. That is just a vicious rumor. The problem lies almost
>>>>>> entirely
>>>>>> in vtkImageViewer2, which cannot provide the view orientations needed
>>>>>> for DICOM.
>>>>>>
>>>>>> If someone wrote a new image viewer, i.e. "vtkMedicalImageViewer",
>>>>>> that provides proper DICOM view orientations then the problem will go
>>>>>> away, as long as people use FileLowerLeftOn() when reading images.
>>>>>> Changing the coordinate system of the image so that it "works" with
>>>>>> vtkImageViewer2 is a bad thing, because vtkImageViewer2 is broken
>>>>>> with respect to DICOM.
>>>>>>
>>>>>> Until someone writes a new image viewer, I will continue to advise
>>>>>> people to use vtkImageActor when viewing medical images.
>>>>>>
>>>>>> - David
>>>>>>
>>>>>>
>>>>>> On Thu, Mar 17, 2011 at 9:03 AM, Jothy <jothybasu at gmail.com> wrote:
>>>>>>> If you use vtkImageReslice you will be doing the transformation with
>>>>>>> vtkImageReslice (indirectly). But again you will have problems with
>>>>>>> different Image Orientation patient.
>>>>>>>
>>>>>>> By transforming , I am not modifying the pixel values, its only the
>>>>>>> coordinates to match the vtk system.
>>>>>>>
>>>>>>> Jothy
>>>>>>>
>>>>>>> On Thu, Mar 17, 2011 at 2:53 PM, Lic. José M. Rodriguez Bacallao
>>>>>>> <jmrbcu at gmail.com> wrote:
>>>>>>>> well, I think it could be done that way but I have read in some place
>>>>>>>> (the book from BioImage) that one never should modify the original
>>>>>>>> image, that's why I am asking. In one pipeline I use the camera, in
>>>>>>>> the other one I use vtkImageReslice, which one is more suited to what
>>>>>>>> I need to achieve.
>>>>>>>>
>>>>>>>> On 3/17/11, Jothy <jothybasu at gmail.com> wrote:
>>>>>>>>> Hi Lic
>>>>>>>>>
>>>>>>>>> I uses vtkTransform to transform the vtkImageData rather than
>>>>>>>>> transforming the camera. Because I wanted to overlay the RT dose on
>>>>>>>>> the image. It works very well. The only problem is the the
>>>>>>>>> coordinates too get transformed. I mean if you have +30, -50, it
>>>>>>>>> will
>>>>>>>>> become -30,50.
>>>>>>>>>
>>>>>>>>> Jothy
>>>>>>>>>
>>>>>>>>> On Thu, Mar 17, 2011 at 1:59 PM, Lic. José M. Rodriguez Bacallao
>>>>>>>>> <jmrbcu at gmail.com> wrote:
>>>>>>>>>> so, no one at all?
>>>>>>>>>>
>>>>>>>>>> On 3/14/11, Lic. José M. Rodriguez Bacallao <jmrbcu at gmail.com>
>>>>>>>>>> wrote:
>>>>>>>>>>> any ideas?
>>>>>>>>>>>
>>>>>>>>>>> On 3/14/11, Lic. José M. Rodriguez Bacallao <jmrbcu at gmail.com>
>>>>>>>>>>> wrote:
>>>>>>>>>>>> i folks, I just finished two versions of a pipeline for
>>>>>>>>>>>> displaying
>>>>>>>>>>>> dicom images with the right display position and orientation. I
>>>>>>>>>>>> am
>>>>>>>>>>>> using gdcm vtkGDCMImageReader to read the images (and IPPSort to
>>>>>>>>>>>> sort). In both pipelines I set the reader's FileLoewerLeft to
>>>>>>>>>>>> "On"
>>>>>>>>>>>> and
>>>>>>>>>>>> in both I achieve the desired result. The question is which
>>>>>>>>>>>> pipeline
>>>>>>>>>>>> is better for wat I am trying to do (display the images the right
>>>>>>>>>>>> way
>>>>>>>>>>>> and later display a MPR view) or use one for display simple
>>>>>>>>>>>> slices
>>>>>>>>>>>> and
>>>>>>>>>>>> the other one to make a MPR. One pipeline version is using the
>>>>>>>>>>>> camera
>>>>>>>>>>>> to achieve the right visualization and the other one is using
>>>>>>>>>>>> vtkImageReslice.
>>>>>>>>>>>>
>>>>>>>>>>>> here is an example program with the two pipelines (left: Camera,
>>>>>>>>>>>> right: vtkImageReslice)
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> def get_left_renderer(input, dir_cosines):
>>>>>>>>>>>> image_actor = vtk.vtkImageActor()
>>>>>>>>>>>> image_actor.SetInput(input.GetOutput())
>>>>>>>>>>>>
>>>>>>>>>>>> ren_left = vtk.vtkRenderer()
>>>>>>>>>>>> ren_left.SetViewport(0.0, 0.0, 0.5, 1.0)
>>>>>>>>>>>> ren_left.AddActor(image_actor)
>>>>>>>>>>>>
>>>>>>>>>>>> camera_left = ren_left.GetActiveCamera()
>>>>>>>>>>>> axial_matrix = vtk.vtkMatrix4x4()
>>>>>>>>>>>> axial_matrix.DeepCopy(dir_cosines)
>>>>>>>>>>>> axial_matrix.SetElement(1, 1, -1)
>>>>>>>>>>>> t = vtk.vtkTransform()
>>>>>>>>>>>> t.Identity()
>>>>>>>>>>>> t.Concatenate(axial_matrix)
>>>>>>>>>>>> camera_left.SetUserTransform(t)
>>>>>>>>>>>> ren_left.ResetCamera()
>>>>>>>>>>>>
>>>>>>>>>>>> return ren_left
>>>>>>>>>>>>
>>>>>>>>>>>> def get_right_renderer(input):
>>>>>>>>>>>> image = input.GetOutput()
>>>>>>>>>>>> (x_min, x_max, y_min, y_max, z_min, z_max) =
>>>>>>>>>>>> image.GetWholeExtent()
>>>>>>>>>>>> (x_spacing, y_spacing, z_spacing) = image.GetSpacing()
>>>>>>>>>>>> (x0, y0, z0) = image.GetOrigin()
>>>>>>>>>>>>
>>>>>>>>>>>> center = (
>>>>>>>>>>>> x0 + x_spacing * 0.5 * (x_min + x_max),
>>>>>>>>>>>> y0 + y_spacing * 0.5 * (y_min + y_max),
>>>>>>>>>>>> z0
>>>>>>>>>>>> )#+ z_spacing * 0.5 * (z_min + z_max))
>>>>>>>>>>>>
>>>>>>>>>>>> axial = vtk.vtkMatrix4x4()
>>>>>>>>>>>> axial.DeepCopy((
>>>>>>>>>>>> 1, 0, 0, center[0],
>>>>>>>>>>>> 0, -1, 0, center[1],
>>>>>>>>>>>> 0, 0, 1, center[2],
>>>>>>>>>>>> 0, 0, 0, 1
>>>>>>>>>>>> ))
>>>>>>>>>>>>
>>>>>>>>>>>> reslice = vtk.vtkImageReslice()
>>>>>>>>>>>> reslice.SetInput(input.GetOutput())
>>>>>>>>>>>> reslice.SetOutputDimensionality(3)
>>>>>>>>>>>> reslice.SetAutoCropOutput(True)
>>>>>>>>>>>> reslice.SetResliceAxes(axial)
>>>>>>>>>>>>
>>>>>>>>>>>> image_actor = vtk.vtkImageActor()
>>>>>>>>>>>> image_actor.SetInput(reslice.GetOutput())
>>>>>>>>>>>>
>>>>>>>>>>>> ren_right = vtk.vtkRenderer()
>>>>>>>>>>>> ren_right.SetViewport(0.5, 0.0, 1.0, 1.0)
>>>>>>>>>>>>
>>>>>>>>>>>> ren_right.AddActor(image_actor)
>>>>>>>>>>>> ren_right.ResetCamera()
>>>>>>>>>>>>
>>>>>>>>>>>> return ren_right
>>>>>>>>>>>>
>>>>>>>>>>>> import vtk, vtkgdcm, sys
>>>>>>>>>>>> from PyQt4 import QtGui
>>>>>>>>>>>>
>>>>>>>>>>>> if __name__ == '__main__':
>>>>>>>>>>>> app = QtGui.QApplication(sys.argv)
>>>>>>>>>>>>
>>>>>>>>>>>> isi = vtk.vtkInteractorStyleImage()
>>>>>>>>>>>> vtk_widget = vtk.QVTKWidget()
>>>>>>>>>>>> vtk_widget.resize(1280,800)
>>>>>>>>>>>> vtk_widget.GetInteractor().SetInteractorStyle(isi)
>>>>>>>>>>>> rwin = vtk_widget.GetRenderWindow()
>>>>>>>>>>>>
>>>>>>>>>>>> # read the image from disk
>>>>>>>>>>>> image_reader = vtkgdcm.vtkGDCMImageReader()
>>>>>>>>>>>>
>>>>>>>>>>>> image_reader.SetFileName('/home/jmrbcu/pictures/workpictures/dicom/IM66.dcm')
>>>>>>>>>>>> image_reader.FileLowerLeftOn()
>>>>>>>>>>>> image_reader.Update()
>>>>>>>>>>>>
>>>>>>>>>>>> # calculate the middle window center and width
>>>>>>>>>>>> image = image_reader.GetOutput()
>>>>>>>>>>>> range = image.GetScalarRange()
>>>>>>>>>>>> center = 0.5 * (range[1] + range[0])
>>>>>>>>>>>> width = range[1] - range[0]
>>>>>>>>>>>>
>>>>>>>>>>>> # create the colormap
>>>>>>>>>>>> colormap = vtkgdcm.vtkImageMapToWindowLevelColors2()
>>>>>>>>>>>> colormap.SetInputConnection(image_reader.GetOutputPort())
>>>>>>>>>>>> colormap.SetWindow(width)
>>>>>>>>>>>> colormap.SetLevel(center)
>>>>>>>>>>>> colormap.Update()
>>>>>>>>>>>>
>>>>>>>>>>>> # create left and right renderers
>>>>>>>>>>>> rwin.AddRenderer(get_left_renderer(colormap,
>>>>>>>>>>>> image_reader.GetDirectionCosines()))
>>>>>>>>>>>> rwin.AddRenderer(get_right_renderer(colormap))
>>>>>>>>>>>>
>>>>>>>>>>>> rwin.Render()
>>>>>>>>>>>> vtk_widget.show()
>>>>>>>>>>>>
>>>>>>>>>>>> app.exec_()
>>>>>>>>>>>>
>>>>>>>>>>>> # ipp = reader.GetImagePositionPatient()
>>>>>>>>>>>> # iop = reader.GetImageOrientationPatient()
>>>>>>>>>>>> # row = iop[:3]
>>>>>>>>>>>> # col = iop[3:]
>>>>>>>>>>>> # slice = [0,0,0]
>>>>>>>>>>>> # vtk.vtkMath().Cross(row, col, slice)
>>>>>>>>>>>> #
>>>>>>>>>>>> # matrix = vtk.vtkMatrix4x4()
>>>>>>>>>>>> # for j in range(3):
>>>>>>>>>>>> # matrix.SetElement(j, 0, row[j])
>>>>>>>>>>>> # matrix.SetElement(j, 1, col[j])
>>>>>>>>>>>> # matrix.SetElement(j, 2, slice[j])
>>>>>>>>>>>> #
>>>>>>>>>>>>
>>>>>>>>>>>> #
>>>>>>>>>>>> # ca.SetUserTransform(t)
>>>>>>>>>>>> # ca.SetViewUp(0, -1, 0)
>>>>>>>>>>>> # ca.SetFocalPoint(0, 0, 1)
>>>>>>>>>>>> # ca.SetPosition(0,0,0)
>>>>>>>>>>>>
>>>>>>>>>>>> # ca.ComputeViewPlaneNormal()
>>>>>>>>>>>> # ca.OrthogonalizeViewUp()
>>>>>>>>>>>> # ca.ParallelProjectionOn()
>>>>>>>>>>>> # ca.SetParallelScale(1)
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> Lic. José M. Rodriguez Bacallao
>>>>>>>>>>>> Centro de Biofisica Medica
>>>>>>>>>>>> -----------------------------------------------------------------
>>>>>>>>>>>> Todos somos muy ignorantes, lo que ocurre es que no todos
>>>>>>>>>>>> ignoramos
>>>>>>>>>>>> lo
>>>>>>>>>>>> mismo.
>>>>>>>>>>>>
>>>>>>>>>>>> Recuerda: El arca de Noe fue construida por aficionados, el
>>>>>>>>>>>> titanic
>>>>>>>>>>>> por profesionales
>>>>>>>>>>>> -----------------------------------------------------------------
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Lic. José M. Rodriguez Bacallao
>>>>>>>>>>> Centro de Biofisica Medica
>>>>>>>>>>> -----------------------------------------------------------------
>>>>>>>>>>> Todos somos muy ignorantes, lo que ocurre es que no todos
>>>>>>>>>>> ignoramos
>>>>>>>>>>> lo
>>>>>>>>>>> mismo.
>>>>>>>>>>>
>>>>>>>>>>> Recuerda: El arca de Noe fue construida por aficionados, el
>>>>>>>>>>> titanic
>>>>>>>>>>> por profesionales
>>>>>>>>>>> -----------------------------------------------------------------
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Lic. José M. Rodriguez Bacallao
>>>>>>>>>> Centro de Biofisica Medica
>>>>>>>>>> -----------------------------------------------------------------
>>>>>>>>>> Todos somos muy ignorantes, lo que ocurre es que no todos ignoramos
>>>>>>>>>> lo
>>>>>>>>>> mismo.
>>>>>>>>>>
>>>>>>>>>> Recuerda: El arca de Noe fue construida por aficionados, el titanic
>>>>>>>>>> por profesionales
>>>>>>>>>> -----------------------------------------------------------------
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Powered by www.kitware.com
>>>>>>>>>>
>>>>>>>>>> Visit other Kitware open-source projects at
>>>>>>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>>>>>>
>>>>>>>>>> Please keep messages on-topic and check the VTK FAQ at:
>>>>>>>>>> http://www.vtk.org/Wiki/VTK_FAQ
>>>>>>>>>>
>>>>>>>>>> Follow this link to subscribe/unsubscribe:
>>>>>>>>>> http://www.vtk.org/mailman/listinfo/vtkusers
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Lic. José M. Rodriguez Bacallao
>>>>>>>> Centro de Biofisica Medica
>>>>>>>> -----------------------------------------------------------------
>>>>>>>> Todos somos muy ignorantes, lo que ocurre es que no todos ignoramos
>>>>>>>> lo
>>>>>>>> mismo.
>>>>>>>>
>>>>>>>> Recuerda: El arca de Noe fue construida por aficionados, el titanic
>>>>>>>> por profesionales
>>>>>>>> -----------------------------------------------------------------
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Powered by www.kitware.com
>>>>>>>
>>>>>>> Visit other Kitware open-source projects at
>>>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>>>
>>>>>>> Please keep messages on-topic and check the VTK FAQ at:
>>>>>>> http://www.vtk.org/Wiki/VTK_FAQ
>>>>>>>
>>>>>>> Follow this link to subscribe/unsubscribe:
>>>>>>> http://www.vtk.org/mailman/listinfo/vtkusers
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Lic. José M. Rodriguez Bacallao
>>>>> Centro de Biofisica Medica
>>>>> -----------------------------------------------------------------
>>>>> Todos somos muy ignorantes, lo que ocurre es que no todos ignoramos lo
>>>>> mismo.
>>>>>
>>>>> Recuerda: El arca de Noe fue construida por aficionados, el titanic
>>>>> por profesionales
>>>>> -----------------------------------------------------------------
>>>>>
>>>>
>>>
>>>
>>> --
>>> Lic. José M. Rodriguez Bacallao
>>> Centro de Biofisica Medica
>>> -----------------------------------------------------------------
>>> Todos somos muy ignorantes, lo que ocurre es que no todos ignoramos lo
>>> mismo.
>>>
>>> Recuerda: El arca de Noe fue construida por aficionados, el titanic
>>> por profesionales
>>> -----------------------------------------------------------------
>>>
>>
>
>
> --
> Lic. José M. Rodriguez Bacallao
> Centro de Biofisica Medica
> -----------------------------------------------------------------
> Todos somos muy ignorantes, lo que ocurre es que no todos ignoramos lo mismo.
>
> Recuerda: El arca de Noe fue construida por aficionados, el titanic
> por profesionales
> -----------------------------------------------------------------
>
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