[vtkusers] displaying dicom images with the right orientation
Lic. José M. Rodriguez Bacallao
jmrbcu at gmail.com
Thu Mar 17 16:06:40 EDT 2011
yes, for either way I need to setup the camera, difference arise in
the method for setting it up. I will later send my final pipeline for
images in they original orientation.
On Thu, Mar 17, 2011 at 2:51 PM, David Gobbi <david.gobbi at gmail.com> wrote:
> 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
>> -----------------------------------------------------------------
>>
>
--
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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