[vtkusers] displaying dicom images with the right orientation
Lic. José M. Rodriguez Bacallao
jmrbcu at gmail.com
Thu Mar 17 10:53:34 EDT 2011
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
>> -----------------------------------------------------------------
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>
--
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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