[vtkusers] displaying dicom images with the right orientation

[Lic. José M. Rodriguez Bacallao]

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
-----------------------------------------------------------------