def ShowSlice(self, index = 0):
dicom = self.dicom_list[index]
# UPDATE GUI
## Text related to size
value = STR_SIZE %(dicom.image.size[0], dicom.image.size[1])
self.text_image_size.SetValue(value)
## Text related to slice position
if not(dicom.image.spacing):
value1 = ''
else:
value1 = STR_SPC %(dicom.image.spacing[2])
if dicom.image.orientation_label == 'AXIAL':
value2 = STR_LOCAL %(dicom.image.position[2])
elif dicom.image.orientation_label == 'CORONAL':
value2 = STR_LOCAL %(dicom.image.position[1])
elif dicom.image.orientation_label == 'SAGITTAL':
value2 = STR_LOCAL %(dicom.image.position[0])
else:
value2 = ''
value = "%s\n%s" %(value1, value2)
self.text_image_location.SetValue(value)
## Text related to patient/ acquisiiton data
value = STR_PATIENT %(dicom.patient.id,\
dicom.acquisition.protocol_name)
self.text_patient.SetValue(value)
## Text related to acquisition date and time
value = STR_ACQ % (dicom.acquisition.date,
dicom.acquisition.time)
self.text_acquisition.SetValue(value)
rdicom = vtkgdcm.vtkGDCMImageReader()
rdicom.SetFileName(dicom.image.file)
rdicom.Update()
# ADJUST CONTRAST
window_level = dicom.image.level
window_width = dicom.image.window
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInputConnection(rdicom.GetOutputPort())
colorer.SetWindow(float(window_width))
colorer.SetLevel(float(window_level))
colorer.Update()
if self.actor is None:
self.actor = vtk.vtkImageActor()
self.renderer.AddActor(self.actor)
# PLOT IMAGE INTO VIEWER
self.actor.SetInputData(colorer.GetOutput())
self.renderer.ResetCamera()
self.interactor.Render()
# Setting slider position
self.slider.SetValue(index)
def SetInput(self, imagedata, mask_dict):
print "SETINPUT!"
self.imagedata = imagedata
self.extent = imagedata.GetExtent()
imagedata_bg = self.__create_background(imagedata)
if not mask_dict:
imagedata_mask = self.__build_mask(imagedata, create=True)
else:
self.__load_masks(imagedata, mask_dict)
imagedata_mask = self.img_colours_mask.GetOutput()
mask_opacity = self.current_mask.opacity
# blend both imagedatas, so it can be inserted into viewer
blend_filter = vtk.vtkImageBlend()
blend_filter.SetBlendModeToNormal()
blend_filter.SetOpacity(0, 1)
if self.current_mask.is_shown:
blend_filter.SetOpacity(1, mask_opacity)
else:
blend_filter.SetOpacity(1, 0)
blend_filter.SetInput(0, imagedata_bg)
blend_filter.SetInput(1, imagedata_mask)
blend_filter.SetBlendModeToNormal()
blend_filter.GetOutput().ReleaseDataFlagOn()
self.blend_filter = blend_filter
self.window_level = vtk.vtkImageMapToWindowLevelColors()
self.window_level.SetInput(self.imagedata)
def ShowSlice(self, index=0):
dicom = self.dicom_list[index]
# UPDATE GUI
## Text related to size
value = STR_SIZE % (dicom.image.size[0], dicom.image.size[1])
self.text_image_size.SetValue(value)
## Text related to slice position
if not (dicom.image.spacing):
value1 = ''
else:
value1 = STR_SPC % (dicom.image.spacing[2])
if dicom.image.orientation_label == 'AXIAL':
value2 = STR_LOCAL % (dicom.image.position[2])
elif dicom.image.orientation_label == 'CORONAL':
value2 = STR_LOCAL % (dicom.image.position[1])
elif dicom.image.orientation_label == 'SAGITTAL':
value2 = STR_LOCAL % (dicom.image.position[0])
else:
value2 = ''
value = "%s\n%s" % (value1, value2)
self.text_image_location.SetValue(value)
## Text related to patient/ acquisiiton data
value = STR_PATIENT %(dicom.patient.id,\
dicom.acquisition.protocol_name)
self.text_patient.SetValue(value)
## Text related to acquisition date and time
value = STR_ACQ % (dicom.acquisition.date, dicom.acquisition.time)
self.text_acquisition.SetValue(value)
rdicom = vtkgdcm.vtkGDCMImageReader()
rdicom.SetFileName(dicom.image.file)
rdicom.Update()
# ADJUST CONTRAST
window_level = dicom.image.level
window_width = dicom.image.window
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInputConnection(rdicom.GetOutputPort())
colorer.SetWindow(float(window_width))
colorer.SetLevel(float(window_level))
colorer.Update()
if self.actor is None:
self.actor = vtk.vtkImageActor()
self.renderer.AddActor(self.actor)
# PLOT IMAGE INTO VIEWER
self.actor.SetInputData(colorer.GetOutput())
self.renderer.ResetCamera()
self.interactor.Render()
# Setting slider position
self.slider.SetValue(index)
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkImageMapToWindowLevelColors(),
'Processing.', ('vtkImageData', ),
('vtkImageData', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def do_ww_wl(self, image):
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInputData(image)
colorer.SetWindow(self.ww)
colorer.SetLevel(self.wl)
colorer.SetOutputFormatToRGB()
colorer.Update()
return colorer.GetOutput()
def do_ww_wl(self, image):
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInput(image)
colorer.SetWindow(self.window_width)
colorer.SetLevel(self.window_level)
colorer.SetOutputFormatToRGB()
colorer.Update()
return colorer.GetOutput()
def setImage(self, dicomfile):
logging.debug("In VTKImageView::setImage()")
if dicomfile:
if os.path.exists(dicomfile):
self.reader = vtkgdcm.vtkGDCMImageReader()
self.reader.SetFileName(dicomfile)
self.reader.Update()
vtkImageData = self.reader.GetOutput()
vtkImageData.UpdateInformation()
srange = vtkImageData.GetScalarRange()
cast = vtk.vtkImageCast()
cast.SetInput(vtkImageData)
cast.SetOutputScalarType(4)
cast.Update()
cast.GetOutput().SetUpdateExtentToWholeExtent()
table = vtk.vtkLookupTable()
table.SetNumberOfColors(256)
table.SetHueRange(0.0, 0.0)
table.SetSaturationRange(0.0, 0.0)
table.SetValueRange(0.0, 1.0)
table.SetAlphaRange(1.0, 1.0)
table.SetRange(srange)
table.SetRampToLinear()
table.Build()
color = vtk.vtkImageMapToColors()
color.SetLookupTable(table)
color.SetInputConnection(cast.GetOutputPort())
color.Update()
self.cast = vtk.vtkImageMapToWindowLevelColors()
self.cast.SetOutputFormatToLuminance()
self.cast.SetInputConnection(color.GetOutputPort())
self.cast.SetWindow(255.0)
self.cast.SetLevel(127.0)
self.cast.Update()
self.cast.UpdateWholeExtent()
self.render.RemoveActor(self.actor)
self.actor = vtk.vtkImageActor()
self.actor.SetInput(self.cast.GetOutput())
self.render.AddActor(self.actor)
self.render.ResetCamera()
self.Render()
else:
self.render.RemoveActor(self.actor)
self.Render()
else:
self.render.RemoveActor(self.actor)
self.Render()
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self,
module_manager,
vtk.vtkImageMapToWindowLevelColors(),
"Processing.",
("vtkImageData",),
("vtkImageData",),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None,
)
def ShowSlice(self, index = 0):
bitmap = self.bitmap_list[index]
# UPDATE GUI
## Text related to size
value = STR_SIZE %(bitmap[3], bitmap[4])
self.text_image_size.SetValue(value)
value1 = ''
value2 = ''
value = "%s\n%s" %(value1, value2)
self.text_image_location.SetValue(value)
#self.text_patient.SetValue(value)
self.text_patient.SetValue('')
#self.text_acquisition.SetValue(value)
self.text_acquisition.SetValue('')
n_array = bitmap_reader.ReadBitmap(bitmap[0])
image = converters.to_vtk(n_array, spacing=(1,1,1),\
slice_number=1, orientation="AXIAL")
# ADJUST CONTRAST
window_level = n_array.max()/2
window_width = n_array.max()
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInputData(image)
colorer.SetWindow(float(window_width))
colorer.SetLevel(float(window_level))
colorer.Update()
if self.actor is None:
self.actor = vtk.vtkImageActor()
self.renderer.AddActor(self.actor)
# PLOT IMAGE INTO VIEWER
self.actor.SetInputData(colorer.GetOutput())
self.renderer.ResetCamera()
self.interactor.Render()
# Setting slider position
self.slider.SetValue(index)
def ShowSlice(self, index = 0):
bitmap = self.bitmap_list[index]
# UPDATE GUI
## Text related to size
value = STR_SIZE %(bitmap[3], bitmap[4])
self.text_image_size.SetValue(value)
value1 = ''
value2 = ''
value = "%s\n%s" %(value1, value2)
self.text_image_location.SetValue(value)
#self.text_patient.SetValue(value)
self.text_patient.SetValue('')
#self.text_acquisition.SetValue(value)
self.text_acquisition.SetValue('')
n_array = bitmap_reader.ReadBitmap(bitmap[0])
image = converters.to_vtk(n_array, spacing=(1,1,1),\
slice_number=1, orientation="AXIAL")
# ADJUST CONTRAST
window_level = n_array.max()/2
window_width = n_array.max()
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInputData(image)
colorer.SetWindow(float(window_width))
colorer.SetLevel(float(window_level))
colorer.Update()
if self.actor is None:
self.actor = vtk.vtkImageActor()
self.renderer.AddActor(self.actor)
# PLOT IMAGE INTO VIEWER
self.actor.SetInputData(colorer.GetOutput())
self.renderer.ResetCamera()
self.interactor.Render()
# Setting slider position
self.slider.SetValue(index)
def iniVTK(self):
self.last_added_sphere_ren1 = None
self.newed_spheres = vtk.vtkCollection()
self.sphere_radius_ren1 = 2.0
self.bouttons_spheres = []
self.slice_assembly = None
self.image_roi = None
self.im_importer = vtk.vtkImageImport()
self.sphere = vtk.vtkSphereSource()
self.sphere.SetRadius(2.0)
self.sphere_mapper = vtk.vtkPolyDataMapper()
self.sphere_mapper.SetInputConnection(self.sphere.GetOutputPort())
self.sphere_actor_ren2 = vtk.vtkActor()
self.sphere.SetCenter(show_height / 2, show_width / 2, 0)
self.sphere_actor_ren2.SetMapper(self.sphere_mapper)
self.sphere_actor_ren2.GetProperty().SetColor(255.0, 0, 0)
self.vtk_widget.GetRenderWindow().SetSize(800, 400)
self.image_actor = vtk.vtkImageActor()
self.ren1 = vtk.vtkRenderer()
self.ren2 = vtk.vtkRenderer()
self.interactorStyle = BouttonInteractorStyle()
self.vtk_widget.SetInteractorStyle(self.interactorStyle)
self.vtk_widget.GetRenderWindow().AddRenderer(self.ren1)
self.vtk_widget.GetRenderWindow().AddRenderer(self.ren2)
self.ren1.SetViewport(0.0, 0.0, 0.5, 1.0)
self.ren2.SetViewport(0.5, 0.0, 1.0, 1.0)
self.ren2.AddActor(self.sphere_actor_ren2)
self.imageLevelFilter = vtk.vtkImageMapToWindowLevelColors()
self.imageLevelFilter.SetLevel(400)
self.imageLevelFilter.SetWindow(800)
self.im_importer.SetNumberOfScalarComponents(1)
self.im_importer.SetDataScalarTypeToUnsignedShort()
self.im_importer.SetDataExtent(0, show_width - 1, 0, show_height - 1,
0, 0)
self.im_importer.SetWholeExtent(0, show_width - 1, 0, show_height - 1,
0, 0)
self.imageLevelFilter.SetInputConnection(
self.im_importer.GetOutputPort())
self.image_actor.SetInput(self.imageLevelFilter.GetOutput())
self.ren1_sphere_actors = vtk.vtkActorCollection()
self.pointPicker = vtk.vtkPointPicker()
self.actorPicker = vtk.vtkPropPicker()
self.pickedActor = None
self.ren1.AddActor(self.image_actor)
self.ren2.AddActor(self.image_actor)
def preview(self):
if self._preview:
return self._preview
else:
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInput(self.dicom.image.imagedata)
colorer.SetWindow(float(self.dicom.image.window))
colorer.SetLevel(float(self.dicom.image.level))
colorer.SetOutputFormatToRGB()
colorer.Update()
width, height, z = colorer.GetOutput().GetDimensions()
r = colorer.GetOutput().GetPointData().GetScalars()
ni = numpy_support.vtk_to_numpy(r)
self.img = wx.ImageFromBuffer(width, height, ni)
self._preview = self.img.Mirror(False)
return self._preview
def iniVTK(self):
self.last_added_sphere_ren1 = None
self.newed_spheres = vtk.vtkCollection()
self.sphere_radius_ren1 = 2.0
self.bouttons_spheres = []
self.slice_assembly = None
self.image_roi = None
self.im_importer = vtk.vtkImageImport()
self.sphere = vtk.vtkSphereSource()
self.sphere.SetRadius(2.0)
self.sphere_mapper = vtk.vtkPolyDataMapper()
self.sphere_mapper.SetInputConnection(self.sphere.GetOutputPort())
self.sphere_actor_ren2 = vtk.vtkActor()
self.sphere.SetCenter(show_height / 2, show_width / 2, 0)
self.sphere_actor_ren2.SetMapper(self.sphere_mapper)
self.sphere_actor_ren2.GetProperty().SetColor(255.0, 0, 0)
self.vtk_widget.GetRenderWindow().SetSize(800, 400)
self.image_actor = vtk.vtkImageActor()
self.ren1 = vtk.vtkRenderer()
self.ren2 = vtk.vtkRenderer()
self.interactorStyle = BouttonInteractorStyle()
self.vtk_widget.SetInteractorStyle(self.interactorStyle)
self.vtk_widget.GetRenderWindow().AddRenderer(self.ren1)
self.vtk_widget.GetRenderWindow().AddRenderer(self.ren2)
self.ren1.SetViewport(0.0, 0.0, 0.5, 1.0)
self.ren2.SetViewport(0.5, 0.0, 1.0, 1.0)
self.ren2.AddActor(self.sphere_actor_ren2)
self.imageLevelFilter = vtk.vtkImageMapToWindowLevelColors()
self.imageLevelFilter.SetLevel(400)
self.imageLevelFilter.SetWindow(800)
self.im_importer.SetNumberOfScalarComponents(1)
self.im_importer.SetDataScalarTypeToUnsignedShort()
self.im_importer.SetDataExtent(0, show_width - 1, 0, show_height - 1, 0, 0)
self.im_importer.SetWholeExtent(0, show_width - 1, 0, show_height - 1, 0, 0)
self.imageLevelFilter.SetInputConnection(self.im_importer.GetOutputPort())
self.image_actor.SetInput(self.imageLevelFilter.GetOutput())
self.ren1_sphere_actors = vtk.vtkActorCollection()
self.pointPicker = vtk.vtkPointPicker()
self.actorPicker = vtk.vtkPropPicker()
self.pickedActor = None
self.ren1.AddActor(self.image_actor)
self.ren2.AddActor(self.image_actor)
def enhance(self):
"""
Enhance a b&w picture using the laplacian, enhancing high-freq edges.
Example:
.. code-block:: python
import vedo
p = vedo.Picture(vedo.dataurl+'images/dog.jpg').bw()
vedo.show(p, p.clone().enhance(), N=2, mode='image')
"""
img = self._data
scalarRange = img.GetPointData().GetScalars().GetRange()
cast = vtk.vtkImageCast()
cast.SetInputData(img)
cast.SetOutputScalarTypeToDouble()
cast.Update()
laplacian = vtk.vtkImageLaplacian()
laplacian.SetInputData(cast.GetOutput())
laplacian.SetDimensionality(2)
laplacian.Update()
subtr = vtk.vtkImageMathematics()
subtr.SetInputData(0, cast.GetOutput())
subtr.SetInputData(1, laplacian.GetOutput())
subtr.SetOperationToSubtract()
subtr.Update()
colorWindow = scalarRange[1] - scalarRange[0]
colorLevel = colorWindow / 2
originalColor = vtk.vtkImageMapToWindowLevelColors()
originalColor.SetWindow(colorWindow)
originalColor.SetLevel(colorLevel)
originalColor.SetInputData(subtr.GetOutput())
originalColor.Update()
return self._update(originalColor.GetOutput())
def ShowSlice(self, index = 0):
dicom = self.dicom_list[index]
# UPDATE GUI
## Text related to size
value = STR_SIZE %(dicom.image.size[0], dicom.image.size[1])
self.text_image_size.SetValue(value)
## Text related to slice position
value1 = STR_SPC %(dicom.image.spacing[2])
value2 = STR_LOCAL %(dicom.image.position[2])
value = "%s\n%s" %(value1, value2)
self.text_image_location.SetValue(value)
## Text related to patient/ acquisiiton data
value = STR_PATIENT %(dicom.patient.id,\
dicom.acquisition.protocol_name)
self.text_patient.SetValue(value)
## Text related to acquisition date and time
value = STR_ACQ % (dicom.acquisition.date,
dicom.acquisition.time)
self.text_acquisition.SetValue(value)
# ADJUST CONTRAST
window_level = dicom.image.level
window_width = dicom.image.window
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInput(dicom.image.imagedata)
colorer.SetWindow(float(window_width))
colorer.SetLevel(float(window_level))
# PLOT IMAGE INTO VIEWER
self.actor.SetInput(colorer.GetOutput())
self.renderer.ResetCamera()
self.interactor.Render()
# Setting slider position
self.slider.SetValue(index)
def ShowBlackSlice(self, pub_sub):
n_array = numpy.zeros((100, 100))
self.text_image_size.SetValue('')
image = converters.to_vtk(n_array, spacing=(1,1,1),\
slice_number=1, orientation="AXIAL")
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInputData(image)
colorer.Update()
if self.actor is None:
self.actor = vtk.vtkImageActor()
self.renderer.AddActor(self.actor)
# PLOT IMAGE INTO VIEWER
self.actor.SetInputData(colorer.GetOutput())
self.renderer.ResetCamera()
self.interactor.Render()
# Setting slider position
self.slider.SetValue(0)
def ShowBlackSlice(self, pub_sub):
n_array = numpy.zeros((100,100))
self.text_image_size.SetValue('')
image = converters.to_vtk(n_array, spacing=(1,1,1),\
slice_number=1, orientation="AXIAL")
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInputData(image)
colorer.Update()
if self.actor is None:
self.actor = vtk.vtkImageActor()
self.renderer.AddActor(self.actor)
# PLOT IMAGE INTO VIEWER
self.actor.SetInputData(colorer.GetOutput())
self.renderer.ResetCamera()
self.interactor.Render()
# Setting slider position
self.slider.SetValue(0)
def create_dicom_thumbnails(filename, window=None, level=None):
rvtk = vtkgdcm.vtkGDCMImageReader()
rvtk.SetFileName(utils.encode(filename, const.FS_ENCODE))
rvtk.Update()
img = rvtk.GetOutput()
if window is None or level is None:
_min, _max = img.GetScalarRange()
window = _max - _min
level = _min + window / 2
dx, dy, dz = img.GetDimensions()
if dz > 1:
thumbnail_paths = []
for i in range(dz):
img_slice = ExtractVOI(img, 0, dx-1, 0, dy-1, i, i+1)
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInputData(img_slice)
colorer.SetWindow(window)
colorer.SetLevel(level)
colorer.SetOutputFormatToRGB()
colorer.Update()
resample = vtk.vtkImageResample()
resample.SetInputData(colorer.GetOutput())
resample.SetAxisMagnificationFactor ( 0, 0.25 )
resample.SetAxisMagnificationFactor ( 1, 0.25 )
resample.SetAxisMagnificationFactor ( 2, 1 )
resample.Update()
thumbnail_path = tempfile.mktemp()
write_png = vtk.vtkPNGWriter()
write_png.SetInputData(resample.GetOutput())
write_png.SetFileName(thumbnail_path)
write_png.Write()
thumbnail_paths.append(thumbnail_path)
return thumbnail_paths
else:
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInputData(img)
colorer.SetWindow(window)
colorer.SetLevel(level)
colorer.SetOutputFormatToRGB()
colorer.Update()
resample = vtk.vtkImageResample()
resample.SetInputData(colorer.GetOutput())
resample.SetAxisMagnificationFactor ( 0, 0.25 )
resample.SetAxisMagnificationFactor ( 1, 0.25 )
resample.SetAxisMagnificationFactor ( 2, 1 )
resample.Update()
thumbnail_path = tempfile.mktemp()
write_png = vtk.vtkPNGWriter()
write_png.SetInputData(resample.GetOutput())
write_png.SetFileName(thumbnail_path)
write_png.Write()
return thumbnail_path
def create_dicom_thumbnails(filename, window=None, level=None):
rvtk = vtkgdcm.vtkGDCMImageReader()
rvtk.SetFileName(filename)
rvtk.Update()
img = rvtk.GetOutput()
if window is None or level is None:
_min, _max = img.GetScalarRange()
window = _max - _min
level = _min + window / 2
dx, dy, dz = img.GetDimensions()
if dz > 1:
thumbnail_paths = []
for i in xrange(dz):
img_slice = ExtractVOI(img, 0, dx-1, 0, dy-1, i, i+1)
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInputData(img_slice)
colorer.SetWindow(window)
colorer.SetLevel(level)
colorer.SetOutputFormatToRGB()
colorer.Update()
resample = vtk.vtkImageResample()
resample.SetInputData(colorer.GetOutput())
resample.SetAxisMagnificationFactor ( 0, 0.25 )
resample.SetAxisMagnificationFactor ( 1, 0.25 )
resample.SetAxisMagnificationFactor ( 2, 1 )
resample.Update()
thumbnail_path = tempfile.mktemp()
write_png = vtk.vtkPNGWriter()
write_png.SetInputData(resample.GetOutput())
write_png.SetFileName(thumbnail_path)
write_png.Write()
thumbnail_paths.append(thumbnail_path)
return thumbnail_paths
else:
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInputData(img)
colorer.SetWindow(window)
colorer.SetLevel(level)
colorer.SetOutputFormatToRGB()
colorer.Update()
resample = vtk.vtkImageResample()
resample.SetInputData(colorer.GetOutput())
resample.SetAxisMagnificationFactor ( 0, 0.25 )
resample.SetAxisMagnificationFactor ( 1, 0.25 )
resample.SetAxisMagnificationFactor ( 2, 1 )
resample.Update()
thumbnail_path = tempfile.mktemp()
write_png = vtk.vtkPNGWriter()
write_png.SetInputData(resample.GetOutput())
write_png.SetFileName(thumbnail_path)
write_png.Write()
return thumbnail_path
def __init__(self,
dimx=600,
dimy=600,
renWin=None,
iren=None,
ren=None,
debug=False):
'''creates the rendering pipeline'''
# Handle arguments
if renWin is not None:
self.renWin = renWin
else:
self.renWin = vtk.vtkRenderWindow()
if iren is not None:
self.iren = iren
else:
self.iren = vtk.vtkRenderWindowInteractor()
# create a rendering window and renderer
if ren is not None:
self.ren = ren
else:
self.ren = vtk.vtkRenderer()
self.renWin.SetSize(dimx, dimy)
self.renWin.AddRenderer(self.ren)
# img 3D as slice
self.img3D = None
self.slicenos = [0, 0, 0]
self.sliceOrientation = SLICE_ORIENTATION_XY
self.sliceActor = vtk.vtkImageActor()
self.voi = vtk.vtkExtractVOI()
self.wl = vtk.vtkImageMapToWindowLevelColors()
self.ia = vtk.vtkImageHistogramStatistics()
self.sliceActorNo = 0
# Viewer Event manager
self.event = ViewerEventManager()
# create a renderwindowinteractor
self.style = CILInteractorStyle(self)
self.iren.SetInteractorStyle(self.style)
self.iren.SetRenderWindow(self.renWin)
# Render decimation
self.decimate = vtk.vtkDecimatePro()
self.ren.SetBackground(.1, .2, .4)
self.actors = {}
# Help text
self.helpActor = vtk.vtkActor2D()
self.helpActor.GetPositionCoordinate(
).SetCoordinateSystemToNormalizedDisplay()
self.helpActor.GetPositionCoordinate().SetValue(0.1, 0.5)
self.helpActor.VisibilityOff()
self.ren.AddActor(self.helpActor)
# volume render
volumeMapper = vtk.vtkSmartVolumeMapper()
#volumeMapper = vtk.vtkFixedPointVolumeRayCastMapper()
self.volume_mapper = volumeMapper
volumeProperty = vtk.vtkVolumeProperty()
self.volume_property = volumeProperty
# The volume holds the mapper and the property and
# can be used to position/orient the volume.
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)
self.volume = volume
self.volume_render_initialised = False
# axis orientation widget
om = vtk.vtkAxesActor()
ori = vtk.vtkOrientationMarkerWidget()
ori.SetOutlineColor(0.9300, 0.5700, 0.1300)
ori.SetInteractor(self.iren)
ori.SetOrientationMarker(om)
ori.SetViewport(0.0, 0.0, 0.4, 0.4)
ori.SetEnabled(1)
ori.InteractiveOff()
self.orientation_marker = ori
self.iren.Initialize()
def ShowSlice(self, index=0):
try:
dicom = self.dicom_list[index]
except IndexError:
dicom = self.dicom_list[0]
if self.actor is None:
self.__init_vtk()
# UPDATE GUI
## Text related to size
value = STR_SIZE % (dicom.image.size[0], dicom.image.size[1])
self.text_image_size.SetValue(value)
## Text related to slice position
if not (dicom.image.spacing):
value1 = ''
else:
value1 = STR_SPC % (dicom.image.spacing[2])
if dicom.image.orientation_label == 'AXIAL':
value2 = STR_LOCAL % (dicom.image.position[2])
elif dicom.image.orientation_label == 'CORONAL':
value2 = STR_LOCAL % (dicom.image.position[1])
elif dicom.image.orientation_label == 'SAGITTAL':
value2 = STR_LOCAL % (dicom.image.position[0])
else:
value2 = ''
value = "%s\n%s" % (value1, value2)
self.text_image_location.SetValue(value)
## Text related to patient/ acquisiiton data
value = STR_PATIENT %(dicom.patient.id,\
dicom.acquisition.protocol_name)
self.text_patient.SetValue(value)
## Text related to acquisition date and time
value = STR_ACQ % (dicom.acquisition.date, dicom.acquisition.time)
self.text_acquisition.SetValue(value)
if isinstance(dicom.image.thumbnail_path, list):
reader = vtk.vtkPNGReader()
if _has_win32api:
reader.SetFileName(
win32api.GetShortPathName(
dicom.image.thumbnail_path[index]).encode(
const.FS_ENCODE))
else:
reader.SetFileName(dicom.image.thumbnail_path[index])
reader.Update()
image = reader.GetOutput()
else:
filename = dicom.image.file
if _has_win32api:
filename = win32api.GetShortPathName(filename).encode(
const.FS_ENCODE)
np_image = imagedata_utils.read_dcm_slice_as_np2(filename)
vtk_image = converters.to_vtk(np_image, dicom.image.spacing, 0,
'AXIAL')
# ADJUST CONTRAST
window_level = dicom.image.level
window_width = dicom.image.window
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInputData(vtk_image)
colorer.SetWindow(float(window_width))
colorer.SetLevel(float(window_level))
colorer.Update()
image = colorer.GetOutput()
flip = vtk.vtkImageFlip()
flip.SetInputData(image)
flip.SetFilteredAxis(1)
flip.FlipAboutOriginOn()
flip.ReleaseDataFlagOn()
flip.Update()
if self.actor is None:
self.actor = vtk.vtkImageActor()
self.renderer.AddActor(self.actor)
self.canvas.modified = True
# PLOT IMAGE INTO VIEWER
self.actor.SetInputData(flip.GetOutput())
self.renderer.ResetCamera()
self.interactor.Render()
# Setting slider position
self.slider.SetValue(index)
def run(self):
grouper = self.grouper
reader = gdcm.ImageReader()
reader.SetFileName(self.filepath)
if (reader.Read()):
file = reader.GetFile()
# Retrieve data set
dataSet = file.GetDataSet()
# Retrieve header
header = file.GetHeader()
stf = gdcm.StringFilter()
field_dict = {}
data_dict = {}
tag = gdcm.Tag(0x0008, 0x0005)
ds = reader.GetFile().GetDataSet()
if ds.FindDataElement(tag):
encoding_value = str(ds.GetDataElement(tag).GetValue()).split('\\')[0]
if encoding_value.startswith("Loaded"):
encoding = "ISO_IR 100"
else:
try:
encoding = const.DICOM_ENCODING_TO_PYTHON[encoding_value]
except KeyError:
encoding = 'ISO_IR 100'
else:
encoding = "ISO_IR 100"
# Iterate through the Header
iterator = header.GetDES().begin()
while (not iterator.equal(header.GetDES().end())):
dataElement = iterator.next()
stf.SetFile(file)
tag = dataElement.GetTag()
data = stf.ToStringPair(tag)
stag = tag.PrintAsPipeSeparatedString()
group = str(tag.GetGroup())
field = str(tag.GetElement())
tag_labels[stag] = data[0]
if not group in data_dict.keys():
data_dict[group] = {}
if not(utils.VerifyInvalidPListCharacter(data[1])):
data_dict[group][field] = data[1].decode(encoding)
else:
data_dict[group][field] = "Invalid Character"
# Iterate through the Data set
iterator = dataSet.GetDES().begin()
while (not iterator.equal(dataSet.GetDES().end())):
dataElement = iterator.next()
stf.SetFile(file)
tag = dataElement.GetTag()
data = stf.ToStringPair(tag)
stag = tag.PrintAsPipeSeparatedString()
group = str(tag.GetGroup())
field = str(tag.GetElement())
tag_labels[stag] = data[0]
if not group in data_dict.keys():
data_dict[group] = {}
if not(utils.VerifyInvalidPListCharacter(data[1])):
data_dict[group][field] = data[1].decode(encoding, 'replace')
else:
data_dict[group][field] = "Invalid Character"
# -------------- To Create DICOM Thumbnail -----------
rvtk = vtkgdcm.vtkGDCMImageReader()
rvtk.SetFileName(self.filepath)
rvtk.Update()
try:
data = data_dict[str(0x028)][str(0x1050)]
level = [float(value) for value in data.split('\\')][0]
data = data_dict[str(0x028)][str(0x1051)]
window = [float(value) for value in data.split('\\')][0]
except(KeyError):
level = 300.0
window = 2000.0
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInput(rvtk.GetOutput())
colorer.SetWindow(float(window))
colorer.SetLevel(float(level))
colorer.SetOutputFormatToRGB()
colorer.Update()
resample = vtk.vtkImageResample()
resample.SetInput(colorer.GetOutput())
resample.SetAxisMagnificationFactor ( 0, 0.25 )
resample.SetAxisMagnificationFactor ( 1, 0.25 )
resample.SetAxisMagnificationFactor ( 2, 1 )
resample.Update()
thumbnail_path = tempfile.mktemp()
write_png = vtk.vtkPNGWriter()
write_png.SetInput(resample.GetOutput())
write_png.SetFileName(thumbnail_path)
write_png.Write()
#------ Verify the orientation --------------------------------
img = reader.GetImage()
direc_cosines = img.GetDirectionCosines()
orientation = gdcm.Orientation()
try:
type = orientation.GetType(tuple(direc_cosines))
except TypeError:
type = orientation.GetType(direc_cosines)
label = orientation.GetLabel(type)
# ---------- Refactory --------------------------------------
data_dict['invesalius'] = {'orientation_label' : label}
# -------------------------------------------------------------
dict_file[self.filepath] = data_dict
#---------- Verify is DICOMDir -------------------------------
is_dicom_dir = 1
try:
if (data_dict[str(0x002)][str(0x002)] != "1.2.840.10008.1.3.10"): #DICOMDIR
is_dicom_dir = 0
except(KeyError):
is_dicom_dir = 0
if not(is_dicom_dir):
parser = dicom.Parser()
parser.SetDataImage(dict_file[self.filepath], self.filepath, thumbnail_path)
dcm = dicom.Dicom()
#self.l.acquire()
dcm.SetParser(parser)
grouper.AddFile(dcm)
def main():
colors = vtk.vtkNamedColors()
fileName = get_program_parameters()
# Read the image.
readerFactory = vtk.vtkImageReader2Factory()
reader = readerFactory.CreateImageReader2(fileName)
reader.SetFileName(fileName)
reader.Update()
fft = vtk.vtkImageFFT()
fft.SetInputConnection(reader.GetOutputPort())
idealHighPass = vtk.vtkImageIdealHighPass()
idealHighPass.SetInputConnection(fft.GetOutputPort())
idealHighPass.SetXCutOff(0.1)
idealHighPass.SetYCutOff(0.1)
idealRfft = vtk.vtkImageRFFT()
idealRfft.SetInputConnection(idealHighPass.GetOutputPort())
idealReal = vtk.vtkImageExtractComponents()
idealReal.SetInputConnection(idealRfft.GetOutputPort())
idealReal.SetComponents(0)
butterworthHighPass = vtk.vtkImageButterworthHighPass()
butterworthHighPass.SetInputConnection(fft.GetOutputPort())
butterworthHighPass.SetXCutOff(0.1)
butterworthHighPass.SetYCutOff(0.1)
butterworthRfft = vtk.vtkImageRFFT()
butterworthRfft.SetInputConnection(butterworthHighPass.GetOutputPort())
butterworthReal = vtk.vtkImageExtractComponents()
butterworthReal.SetInputConnection(butterworthRfft.GetOutputPort())
butterworthReal.SetComponents(0)
# Create the actors.
idealColor = vtk.vtkImageMapToWindowLevelColors()
idealColor.SetWindow(500)
idealColor.SetLevel(0)
idealColor.SetInputConnection(idealReal.GetOutputPort())
idealActor = vtk.vtkImageActor()
idealActor.GetMapper().SetInputConnection(idealColor.GetOutputPort())
idealActor.GetProperty().SetInterpolationTypeToNearest()
butterworthColor = vtk.vtkImageMapToWindowLevelColors()
butterworthColor.SetWindow(500)
butterworthColor.SetLevel(0)
butterworthColor.SetInputConnection(butterworthReal.GetOutputPort())
butterworthActor = vtk.vtkImageActor()
butterworthActor.GetMapper().SetInputConnection(butterworthColor.GetOutputPort())
butterworthActor.GetProperty().SetInterpolationTypeToNearest()
# Setup the renderers.
idealRenderer = vtk.vtkRenderer()
idealRenderer.SetViewport(0.0, 0.0, 0.5, 1.0)
idealRenderer.AddActor(idealActor)
idealRenderer.ResetCamera()
idealRenderer.SetBackground(colors.GetColor3d("SlateGray"))
butterworthRenderer = vtk.vtkRenderer()
butterworthRenderer.SetViewport(0.5, 0.0, 1.0, 1.0)
butterworthRenderer.AddActor(butterworthActor)
butterworthRenderer.SetActiveCamera(idealRenderer.GetActiveCamera())
butterworthRenderer.SetBackground(colors.GetColor3d("LightSlateGray"))
renderWindow = vtk.vtkRenderWindow()
renderWindow.SetSize(600, 300)
renderWindow.SetWindowName('IdealHighPass')
renderWindow.AddRenderer(idealRenderer)
renderWindow.AddRenderer(butterworthRenderer)
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
style = vtk.vtkInteractorStyleImage()
renderWindowInteractor.SetInteractorStyle(style)
renderWindowInteractor.SetRenderWindow(renderWindow)
idealRenderer.GetActiveCamera().Dolly(1.4)
idealRenderer.ResetCameraClippingRange()
renderWindowInteractor.Initialize()
renderWindowInteractor.Start()
gradInvert.SetOutputScalarTypeToFloat() gradInvert.SetInputConnection( grad.GetOutputPort() ) gradInvert.Update() renderer = vtk.vtkRenderer() renWin = vtk.vtkRenderWindow() renWin.AddRenderer( renderer ) iren = vtk.vtkRenderWindowInteractor() iren.SetRenderWindow( renWin ) style = vtk.vtkInteractorStyleImage() iren.SetInteractorStyle( style ) del style # The color map will accept any scalar image type and convert to # unsigned char for the image actor colorMap = vtk.vtkImageMapToWindowLevelColors() colorMap.SetInputConnection(gradInvert.GetOutputPort()) range = gradInvert.GetOutput().GetScalarRange(); colorMap.SetWindow(1.0) colorMap.SetLevel(0.5) actor = vtk.vtkImageActor() actor.SetInput( colorMap.GetOutput() ) actor.SetDisplayExtent(0, 255, 0, 255, 0, 0) renderer.AddActor( actor ) renderer.SetBackground(0.2, 0.2, 1) renWin.SetSize(400, 400)
def main():
colors = vtk.vtkNamedColors()
fileName = get_program_parameters()
# Read the image.
readerFactory = vtk.vtkImageReader2Factory()
reader = readerFactory.CreateImageReader2(fileName)
reader.SetFileName(fileName)
reader.Update()
# Pipelines
constantPad = vtk.vtkImageConstantPad()
constantPad.SetInputConnection(reader.GetOutputPort())
constantPad.SetConstant(800)
constantPad.SetOutputWholeExtent(-127, 383, -127, 383, 22, 22)
mirrorPad = vtk.vtkImageMirrorPad()
mirrorPad.SetInputConnection(reader.GetOutputPort())
mirrorPad.SetOutputWholeExtent(constantPad.GetOutputWholeExtent())
# Create actors
constantPadColor = vtk.vtkImageMapToWindowLevelColors()
constantPadColor.SetWindow(2000)
constantPadColor.SetLevel(1000)
constantPadColor.SetInputConnection(constantPad.GetOutputPort())
constantPadActor = vtk.vtkImageActor()
constantPadActor.GetMapper().SetInputConnection(
constantPadColor.GetOutputPort())
constantPadActor.GetProperty().SetInterpolationTypeToNearest()
mirrorPadColor = vtk.vtkImageMapToWindowLevelColors()
mirrorPadColor.SetWindow(2000)
mirrorPadColor.SetLevel(1000)
mirrorPadColor.SetInputConnection(mirrorPad.GetOutputPort())
mirrorPadActor = vtk.vtkImageActor()
mirrorPadActor.GetMapper().SetInputConnection(
mirrorPadColor.GetOutputPort())
mirrorPadActor.GetProperty().SetInterpolationTypeToNearest()
# Setup the renderers.
constantPadRenderer = vtk.vtkRenderer()
constantPadRenderer.SetViewport(0.0, 0.0, 0.5, 1.0)
constantPadRenderer.AddActor(constantPadActor)
constantPadRenderer.ResetCamera()
constantPadRenderer.SetBackground(colors.GetColor3d("SlateGray"))
mirrorPadRenderer = vtk.vtkRenderer()
mirrorPadRenderer.SetViewport(0.5, 0.0, 1.0, 1.0)
mirrorPadRenderer.AddActor(mirrorPadActor)
mirrorPadRenderer.SetActiveCamera(constantPadRenderer.GetActiveCamera())
mirrorPadRenderer.SetBackground(colors.GetColor3d("LightSlateGray"))
renderWindow = vtk.vtkRenderWindow()
renderWindow.SetSize(600, 300)
renderWindow.SetWindowName('Pad')
renderWindow.AddRenderer(constantPadRenderer)
renderWindow.AddRenderer(mirrorPadRenderer)
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
style = vtk.vtkInteractorStyleImage()
renderWindowInteractor.SetInteractorStyle(style)
renderWindowInteractor.SetRenderWindow(renderWindow)
constantPadRenderer.GetActiveCamera().Dolly(1.2)
constantPadRenderer.ResetCameraClippingRange()
renderWindowInteractor.Initialize()
renderWindowInteractor.Start()
def __init__(self):
vtkViewImage.__init__(self)
self.FirstRender = 1
self.FirstImage = 1
self.ShowCurrentPoint = True
self.ShowDirections = True
self.ShowSliceNumber = True
self.Orientation = vtkViewImage.AXIAL_ID
self.InteractionStyle = self.SELECT_INTERACTION
self.LeftButtonInteractionStyle = self.SELECT_INTERACTION
self.MiddleButtonInteractionStyle = self.SELECT_INTERACTION
self.RightButtonInteractionStyle = self.SELECT_INTERACTION
self.WheelInteractionStyle = self.SELECT_INTERACTION
self.Conventions = self.RADIOLOGIC
self.InitialParallelScale = 1.0
self.OverlappingImage = None
self.ImageReslice = vtk.vtkImageReslice()
self.ImageActor = vtk.vtkImageActor()
self.WindowLevelForCorner = vtk.vtkImageMapToWindowLevelColors()
self.WindowLevel = vtk.vtkImageMapToColors()
#self.MaskFilter = vtk.vtkImageBlendWithMask()
self.Blender = vtk.vtkImageBlend()
self.HorizontalLineSource = vtk.vtkLineSource()
self.VerticalLineSource = vtk.vtkLineSource()
self.HorizontalLineActor = vtk.vtkActor()
self.VerticalLineActor = vtk.vtkActor()
self.DataSetCutPlane = vtk.vtkPlane()
self.DataSetCutBox = vtk.vtkBox()
self.DataSetCutPlane.SetOrigin(0,0,0)
self.DataSetCutPlane.SetNormal(0,0,1)
self.DataSetCutBox.SetBounds(0, 0, 0, 0, 0, 0)
self.BoxThickness = 2
self.LinkCameraFocalAndPosition = 0
# set the filters properties
self.Blender.SetBlendModeToNormal()
self.Blender.SetOpacity(0, 0.25)
self.Blender.SetOpacity(1, 0.75)
# set up the vtk pipeline
self.ImageReslice.SetOutputDimensionality(2)
self.ImageReslice.InterpolateOff()
self.ImageReslice.SetInputConnection(self.WindowLevel.GetOutputPort())
self.AuxInput = self.WindowLevel.GetOutput()
self.ResliceInput = self.WindowLevel.GetOutput()
# Interactor Style
self.InitInteractorStyle(self.SELECT_INTERACTION)
# Initialize cursor lines
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(self.HorizontalLineSource.GetOutputPort())
self.HorizontalLineActor.SetMapper(mapper)
self.HorizontalLineActor.GetProperty().SetColor(1.0, 0.0, 0.0)
#del mapper
self.HorizontalLineActor.SetVisibility(0)
mapper2 = vtk.vtkPolyDataMapper()
mapper2.SetInputConnection(self.VerticalLineSource.GetOutputPort())
self.VerticalLineActor.SetMapper(mapper2)
self.VerticalLineActor.GetProperty().SetColor(1.0, 0.0, 0.0)
#del mapper2
self.VerticalLineActor.SetVisibility(0)
self.CornerAnnotation.SetWindowLevel(self.WindowLevelForCorner)
self.SetOrientation(vtkViewImage.AXIAL_ID)
if self.GetViewImage2DDisplayConventions() == 0:
self.SetConventionsToRadiological()
else:
self.SetConventionsToNeurological()
#!/usr/bin/env python import vtk from vtk.test import Testing from vtk.util.misc import vtkGetDataRoot VTK_DATA_ROOT = vtkGetDataRoot() RANGE = 150 MAX_ITERATIONS_1 = RANGE MAX_ITERATIONS_2 = RANGE XRAD = 200 YRAD = 200 mandelbrot1 = vtk.vtkImageMandelbrotSource() mandelbrot1.SetMaximumNumberOfIterations(150) mandelbrot1.SetWholeExtent(0,expr.expr(globals(), locals(),["XRAD","-1"]),0,expr.expr(globals(), locals(),["YRAD","-1"]),0,0) mandelbrot1.SetSampleCX(expr.expr(globals(), locals(),["1.3","/","XRAD"]),expr.expr(globals(), locals(),["1.3","/","XRAD"]),expr.expr(globals(), locals(),["1.3","/","XRAD"]),expr.expr(globals(), locals(),["1.3","/","XRAD"])) mandelbrot1.SetOriginCX(-0.72,0.22,0.0,0.0) mandelbrot1.SetProjectionAxes(0,1,2) mapToWL = vtk.vtkImageMapToWindowLevelColors() mapToWL.SetInputConnection(mandelbrot1.GetOutputPort()) mapToWL.SetWindow(RANGE) mapToWL.SetLevel(expr.expr(globals(), locals(),["RANGE","/","3.0"])) # set the window/level to 255.0/127.5 to view full range viewer = vtk.vtkImageViewer() viewer.SetInputConnection(mapToWL.GetOutputPort()) viewer.SetColorWindow(255.0) viewer.SetColorLevel(127.5) viewer.Render() # --- end of script --
def run(self):
grouper = self.grouper
reader = gdcm.ImageReader()
reader.SetFileName(self.filepath)
if (reader.Read()):
file = reader.GetFile()
# Retrieve data set
dataSet = file.GetDataSet()
# Retrieve header
header = file.GetHeader()
stf = gdcm.StringFilter()
field_dict = {}
data_dict = {}
tag = gdcm.Tag(0x0008, 0x0005)
ds = reader.GetFile().GetDataSet()
if ds.FindDataElement(tag):
encoding_value = str(
ds.GetDataElement(tag).GetValue()).split('\\')[0]
if encoding_value.startswith("Loaded"):
encoding = "ISO_IR 100"
else:
try:
encoding = const.DICOM_ENCODING_TO_PYTHON[
encoding_value]
except KeyError:
encoding = 'ISO_IR 100'
else:
encoding = "ISO_IR 100"
# Iterate through the Header
iterator = header.GetDES().begin()
while (not iterator.equal(header.GetDES().end())):
dataElement = iterator.next()
stf.SetFile(file)
tag = dataElement.GetTag()
data = stf.ToStringPair(tag)
stag = tag.PrintAsPipeSeparatedString()
group = str(tag.GetGroup())
field = str(tag.GetElement())
tag_labels[stag] = data[0]
if not group in data_dict.keys():
data_dict[group] = {}
if not (utils.VerifyInvalidPListCharacter(data[1])):
data_dict[group][field] = data[1].decode(encoding)
else:
data_dict[group][field] = "Invalid Character"
# Iterate through the Data set
iterator = dataSet.GetDES().begin()
while (not iterator.equal(dataSet.GetDES().end())):
dataElement = iterator.next()
stf.SetFile(file)
tag = dataElement.GetTag()
data = stf.ToStringPair(tag)
stag = tag.PrintAsPipeSeparatedString()
group = str(tag.GetGroup())
field = str(tag.GetElement())
tag_labels[stag] = data[0]
if not group in data_dict.keys():
data_dict[group] = {}
if not (utils.VerifyInvalidPListCharacter(data[1])):
data_dict[group][field] = data[1].decode(
encoding, 'replace')
else:
data_dict[group][field] = "Invalid Character"
# -------------- To Create DICOM Thumbnail -----------
rvtk = vtkgdcm.vtkGDCMImageReader()
rvtk.SetFileName(self.filepath)
rvtk.Update()
try:
data = data_dict[str(0x028)][str(0x1050)]
level = [float(value) for value in data.split('\\')][0]
data = data_dict[str(0x028)][str(0x1051)]
window = [float(value) for value in data.split('\\')][0]
except (KeyError):
level = 300.0
window = 2000.0
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInputConnection(rvtk.GetOutputPort())
colorer.SetWindow(float(window))
colorer.SetLevel(float(level))
colorer.SetOutputFormatToRGB()
colorer.Update()
resample = vtk.vtkImageResample()
resample.SetInputConnection(colorer.GetOutputPort())
resample.SetAxisMagnificationFactor(0, 0.25)
resample.SetAxisMagnificationFactor(1, 0.25)
resample.SetAxisMagnificationFactor(2, 1)
resample.Update()
thumbnail_path = tempfile.mktemp()
write_png = vtk.vtkPNGWriter()
write_png.SetInputConnection(resample.GetOutputPort())
write_png.SetFileName(thumbnail_path)
write_png.Write()
#------ Verify the orientation --------------------------------
img = reader.GetImage()
direc_cosines = img.GetDirectionCosines()
orientation = gdcm.Orientation()
try:
type = orientation.GetType(tuple(direc_cosines))
except TypeError:
type = orientation.GetType(direc_cosines)
label = orientation.GetLabel(type)
# ---------- Refactory --------------------------------------
data_dict['invesalius'] = {'orientation_label': label}
# -------------------------------------------------------------
dict_file[self.filepath] = data_dict
#---------- Verify is DICOMDir -------------------------------
is_dicom_dir = 1
try:
if (data_dict[str(0x002)][str(0x002)] !=
"1.2.840.10008.1.3.10"): #DICOMDIR
is_dicom_dir = 0
except (KeyError):
is_dicom_dir = 0
if not (is_dicom_dir):
parser = dicom.Parser()
parser.SetDataImage(dict_file[self.filepath], self.filepath,
thumbnail_path)
dcm = dicom.Dicom()
#self.l.acquire()
dcm.SetParser(parser)
grouper.AddFile(dcm)
def main():
# colors = vtk.vtkNamedColors()
fileName = get_program_parameters()
# Read the image.
readerFactory = vtk.vtkImageReader2Factory()
reader = readerFactory.CreateImageReader2(fileName)
reader.SetFileName(fileName)
reader.Update()
scalarRange = [0] * 2
scalarRange[0] = reader.GetOutput().GetPointData().GetScalars().GetRange()[0]
scalarRange[1] = reader.GetOutput().GetPointData().GetScalars().GetRange()[1]
print("Range:", scalarRange)
middleSlice = 22
# Work with triple images.
cast = vtk.vtkImageCast()
cast.SetInputConnection(reader.GetOutputPort())
cast.SetOutputScalarTypeToDouble()
cast.Update()
laplacian = vtk.vtkImageLaplacian()
laplacian.SetInputConnection(cast.GetOutputPort())
laplacian.SetDimensionality(3)
enhance = vtk.vtkImageMathematics()
enhance.SetInputConnection(0, cast.GetOutputPort())
enhance.SetInputConnection(1, laplacian.GetOutputPort())
enhance.SetOperationToSubtract()
colorWindow = (scalarRange[1] - scalarRange[0])
colorLevel = colorWindow / 2
# Map the image through the lookup table.
originalColor = vtk.vtkImageMapToWindowLevelColors()
originalColor.SetWindow(colorWindow)
originalColor.SetLevel(colorLevel)
originalColor.SetInputConnection(reader.GetOutputPort())
originalActor = vtk.vtkImageActor()
originalActor.GetMapper().SetInputConnection(originalColor.GetOutputPort())
originalActor.GetProperty().SetInterpolationTypeToNearest()
originalActor.SetDisplayExtent(
reader.GetDataExtent()[0], reader.GetDataExtent()[1],
reader.GetDataExtent()[2], reader.GetDataExtent()[3],
middleSlice, middleSlice)
laplacianColor = vtk.vtkImageMapToWindowLevelColors()
laplacianColor.SetWindow(1000)
laplacianColor.SetLevel(0)
laplacianColor.SetInputConnection(laplacian.GetOutputPort())
laplacianActor = vtk.vtkImageActor()
laplacianActor.GetMapper().SetInputConnection(laplacianColor.GetOutputPort())
laplacianActor.GetProperty().SetInterpolationTypeToNearest()
laplacianActor.SetDisplayExtent(originalActor.GetDisplayExtent())
enhancedColor = vtk.vtkImageMapToWindowLevelColors()
enhancedColor.SetWindow(colorWindow)
enhancedColor.SetLevel(colorLevel)
enhancedColor.SetInputConnection(enhance.GetOutputPort())
enhancedActor = vtk.vtkImageActor()
enhancedActor.GetMapper().SetInputConnection(enhancedColor.GetOutputPort())
enhancedActor.GetProperty().SetInterpolationTypeToNearest()
enhancedActor.SetDisplayExtent(originalActor.GetDisplayExtent())
# Setup the renderers.
originalRenderer = vtk.vtkRenderer()
originalRenderer.AddActor(originalActor)
laplacianRenderer = vtk.vtkRenderer()
laplacianRenderer.AddActor(laplacianActor)
enhancedRenderer = vtk.vtkRenderer()
enhancedRenderer.AddActor(enhancedActor)
renderers = list()
renderers.append(originalRenderer)
renderers.append(laplacianRenderer)
renderers.append(enhancedRenderer)
# Setup viewports for the renderers.
rendererSize = 400
xGridDimensions = 3
yGridDimensions = 1
renderWindow = vtk.vtkRenderWindow()
renderWindow.SetSize(rendererSize * xGridDimensions, rendererSize * yGridDimensions)
for row in range(0, yGridDimensions):
for col in range(xGridDimensions):
index = row * xGridDimensions + col
# (xmin, ymin, xmax, ymax)
viewport = [float(col) / xGridDimensions, float(yGridDimensions - (row + 1)) / yGridDimensions,
float(col + 1) / xGridDimensions, float(yGridDimensions - row) / yGridDimensions]
renderers[index].SetViewport(viewport)
renderWindow.AddRenderer(renderers[index])
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
style = vtk.vtkInteractorStyleImage()
renderWindowInteractor.SetInteractorStyle(style)
renderWindowInteractor.SetRenderWindow(renderWindow)
# Renderers share one camera.
renderWindow.Render()
renderers[0].GetActiveCamera().Dolly(1.5)
renderers[0].ResetCameraClippingRange()
for r in range(1, len(renderers)):
renderers[r].SetActiveCamera(renderers[0].GetActiveCamera())
renderWindowInteractor.Initialize()
renderWindowInteractor.Start()
#!/usr/bin/env python import vtk from vtk.util.misc import vtkGetDataRoot VTK_DATA_ROOT = vtkGetDataRoot() RANGE = 150 MAX_ITERATIONS_1 = RANGE MAX_ITERATIONS_2 = RANGE XRAD = 200 YRAD = 200 mandelbrot1 = vtk.vtkImageMandelbrotSource() mandelbrot1.SetMaximumNumberOfIterations(150) mandelbrot1.SetWholeExtent(0, XRAD - 1, 0, YRAD - 1, 0, 0) mandelbrot1.SetSampleCX(1.3 / XRAD, 1.3 / XRAD, 1.3 / XRAD, 1.3 / XRAD) mandelbrot1.SetOriginCX(-0.72, 0.22, 0.0, 0.0) mandelbrot1.SetProjectionAxes(0, 1, 2) mapToWL = vtk.vtkImageMapToWindowLevelColors() mapToWL.SetInputConnection(mandelbrot1.GetOutputPort()) mapToWL.SetWindow(RANGE) mapToWL.SetLevel(RANGE / 3.0) # set the window/level to 255.0/127.5 to view full range viewer = vtk.vtkImageViewer() viewer.SetInputConnection(mapToWL.GetOutputPort()) viewer.SetColorWindow(255.0) viewer.SetColorLevel(127.5) viewer.Render()
