def main():
if len(sys.argv) < 10:
errMsg = "Missing parameters\n" \
"Usage: %s\n" % (sys.argv[0],) + \
" inputImage outputImage\n" \
" seedX seedY InitialDistance\n" \
" Sigma SigmoidAlpha SigmoidBeta\n" \
" PropagationScaling\n"
print >> sys.stderr, errMsg
return
# We're going to build the following pipelines:
# 1. reader -> smoothing -> gradientMagnitude -> sigmoid -> FI
# 2. fastMarching -> geodesicActiveContour(FI) -> thresholder -> writer
# The output of pipeline 1 is a feature image that is used by the
# geodesicActiveContour object. Also see figure 9.18 in the ITK
# Software Guide.
reader = itk.itkImageFileReaderF2_New()
reader.SetFileName(sys.argv[1])
writer = itk.itkImageFileWriterUS2_New()
writer.SetFileName(sys.argv[2])
smoothing = itk.itkCurvatureAnisotropicDiffusionImageFilterF2F2_New()
gM = itk.itkGradientMagnitudeRecursiveGaussianImageFilterF2F2_New()
gradientMagnitude = gM
sigmoid = itk.itkSigmoidImageFilterF2F2_New()
sigmoid.SetOutputMinimum( 0.0 )
sigmoid.SetOutputMaximum( 1.0 )
fastMarching = itk.itkFastMarchingImageFilterF2F2_New()
gAC = itk.itkGeodesicActiveContourLevelSetImageFilterF2F2_New()
geodesicActiveContour = gAC
propagationScaling = float(sys.argv[9])
geodesicActiveContour.SetPropagationScaling( propagationScaling );
geodesicActiveContour.SetCurvatureScaling( 1.0 );
geodesicActiveContour.SetAdvectionScaling( 1.0 );
geodesicActiveContour.SetMaximumRMSError( 0.02 );
geodesicActiveContour.SetNumberOfIterations( 800 );
smoothing.SetInput( reader.GetOutput() );
gradientMagnitude.SetInput( smoothing.GetOutput() );
sigmoid.SetInput( gradientMagnitude.GetOutput() );
geodesicActiveContour.SetInput( fastMarching.GetOutput() );
geodesicActiveContour.SetFeatureImage( sigmoid.GetOutput() );
thresholder = itk.itkBinaryThresholdImageFilterF2US2_New()
thresholder.SetLowerThreshold( -1000.0 );
thresholder.SetUpperThreshold( 0.0 );
thresholder.SetOutsideValue( 0 );
thresholder.SetInsideValue( 65535 );
thresholder.SetInput( geodesicActiveContour.GetOutput() );
writer.SetInput( thresholder.GetOutput() );
smoothing.SetTimeStep( 0.125 );
smoothing.SetNumberOfIterations( 5 );
smoothing.SetConductanceParameter( 3.0 );
sigma = float(sys.argv[6])
gradientMagnitude.SetSigma(sigma);
alpha = float(sys.argv[7])
beta = float(sys.argv[8])
sigmoid.SetAlpha(alpha)
sigmoid.SetBeta(beta)
# same as image
seedPosition = itk.itkIndex2()
seedPosition.SetElement(0, int(sys.argv[3]))
seedPosition.SetElement(1, int(sys.argv[4]))
initialDistance = float(sys.argv[5])
seedValue = - initialDistance
node = itk.itkLevelSetNodeF2()
node.SetValue(seedValue)
node.SetIndex(seedPosition)
seeds = itk.itkNodeContainerF2_New()
seeds.Initialize()
seeds.InsertElement(0, node)
fastMarching.SetTrialPoints(seeds.GetPointer())
fastMarching.SetSpeedConstant(1.0)
caster1 = itk.itkRescaleIntensityImageFilterF2US2_New()
writer1 = itk.itkImageFileWriterUS2_New()
caster1.SetInput( smoothing.GetOutput() );
writer1.SetInput( caster1.GetOutput() );
writer1.SetFileName("GeodesicActiveContourImageFilterOutput1.png");
caster1.SetOutputMinimum( 0 );
caster1.SetOutputMaximum( 65535 );
writer1.Update();
caster2 = itk.itkRescaleIntensityImageFilterF2US2_New()
writer2 = itk.itkImageFileWriterUS2_New()
caster2.SetInput( gradientMagnitude.GetOutput() );
writer2.SetInput( caster2.GetOutput() );
writer2.SetFileName("GeodesicActiveContourImageFilterOutput2.png");
caster2.SetOutputMinimum( 0 );
caster2.SetOutputMaximum( 65535 );
writer2.Update();
caster3 = itk.itkRescaleIntensityImageFilterF2US2_New()
writer3 = itk.itkImageFileWriterUS2_New()
caster3.SetInput( sigmoid.GetOutput() );
writer3.SetInput( caster3.GetOutput() );
writer3.SetFileName("GeodesicActiveContourImageFilterOutput3.png");
caster3.SetOutputMinimum( 0 );
caster3.SetOutputMaximum( 65535 );
writer3.Update();
caster4 = itk.itkRescaleIntensityImageFilterF2US2_New()
writer4 = itk.itkImageFileWriterUS2_New()
caster4.SetInput( fastMarching.GetOutput() );
writer4.SetInput( caster4.GetOutput() );
writer4.SetFileName("GeodesicActiveContourImageFilterOutput4.png");
caster4.SetOutputMinimum( 0 );
caster4.SetOutputMaximum( 65535 );
fastMarching.SetOutputSize(
reader.GetOutput().GetBufferedRegion().GetSize())
writer.Update()
# Print out some useful information
print "\n"
print "Max. no. iterations: %d" % (gAC.GetNumberOfIterations())
print "Max. RMS error: %.3f" % (gAC.GetMaximumRMSError())
print "No. elapsed iterations: %d" % (gAC.GetElapsedIterations())
print "RMS change: %.3f" % (gAC.GetRMSChange())
writer4.Update()
mapWriter = itk.itkImageFileWriterF2_New()
mapWriter.SetInput(fastMarching.GetOutput())
mapWriter.SetFileName("GeodesicActiveContourImageFilterOutput4.mha")
mapWriter.Update()
speedWriter = itk.itkImageFileWriterF2_New()
speedWriter.SetInput( sigmoid.GetOutput() )
speedWriter.SetFileName("GeodesicActiveContourImageFilterOutput3.mha")
speedWriter.Update()
gradientWriter = itk.itkImageFileWriterF2_New()
gradientWriter.SetInput( gradientMagnitude.GetOutput() )
gradientWriter.SetFileName("GeodesicActiveContourImageFilterOutput2.mha")
gradientWriter.Update();
# You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0.txt # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # # ==========================================================================*/ import InsightToolkit as itk import sys reader = itk.itkImageFileReaderF2_New() reader.SetFileName(sys.argv[1]) diffusion = itk.itkGradientAnisotropicDiffusionImageFilterF2F2_New() diffusion.SetInput(reader.GetOutput()) diffusion.SetTimeStep(0.0625) diffusion.SetConductanceParameter(9.0) diffusion.SetNumberOfIterations(5) gradient = itk.itkGradientMagnitudeImageFilterF2F2_New() gradient.SetInput(diffusion.GetOutput()) watershed = itk.itkWatershedImageFilterF2_New() watershed.SetInput(gradient.GetOutput()) watershed.SetThreshold(0.01) watershed.SetLevel(0.2)
# it has to be a single component, itk::VTKImageImport doesn't support more lum = vtk.vtkImageLuminance() lum.SetInput(reader.GetOutput()) # let's cast the output to float imageCast = vtk.vtkImageCast() imageCast.SetOutputScalarTypeToFloat() imageCast.SetInput(lum.GetOutput()) # the end-point of this VTK pipeline segment is a vtkImageExport vtkExporter = vtk.vtkImageExport() vtkExporter.SetInput(imageCast.GetOutput()) # it connects to the itk::VTKImageImport at the beginning of # the subsequent ITK pipeline; two-dimensional float type itkImporter = itk.itkVTKImageImportF2_New() # Call the magic function that connects the two. This will only be # available if you built ITK with ITK_CSWIG_CONNECTVTKITK set to ON. CVIPy.ConnectVTKToITKF2(vtkExporter, itkImporter.GetPointer()) # perform a canny edge detection and rescale the output canny = itk.itkCannyEdgeDetectionImageFilterF2F2_New() rescaler = itk.itkRescaleIntensityImageFilterF2US2_New() canny.SetInput(itkImporter.GetOutput()) rescaler.SetInput(canny.GetOutput()) rescaler.SetOutputMinimum(0) rescaler.SetOutputMaximum(65535) # this is to show off the new PyCommand functionality. :) def progressEvent():
def main():
if len(sys.argv) < 10:
errMsg = "Missing parameters\n" \
"Usage: %s\n" % (sys.argv[0],) + \
" inputImage outputImage\n" \
" seedX seedY InitialDistance\n" \
" Sigma SigmoidAlpha SigmoidBeta\n" \
" PropagationScaling\n"
print >> sys.stderr, errMsg
return
# We're going to build the following pipelines:
# 1. reader -> smoothing -> gradientMagnitude -> sigmoid -> FI
# 2. fastMarching -> geodesicActiveContour(FI) -> thresholder -> writer
# The output of pipeline 1 is a feature image that is used by the
# geodesicActiveContour object. Also see figure 9.18 in the ITK
# Software Guide.
reader = itk.itkImageFileReaderF2_New()
reader.SetFileName(sys.argv[1])
writer = itk.itkImageFileWriterUS2_New()
writer.SetFileName(sys.argv[2])
smoothing = itk.itkCurvatureAnisotropicDiffusionImageFilterF2F2_New()
gM = itk.itkGradientMagnitudeRecursiveGaussianImageFilterF2F2_New()
gradientMagnitude = gM
sigmoid = itk.itkSigmoidImageFilterF2F2_New()
sigmoid.SetOutputMinimum(0.0)
sigmoid.SetOutputMaximum(1.0)
fastMarching = itk.itkFastMarchingImageFilterF2F2_New()
gAC = itk.itkGeodesicActiveContourLevelSetImageFilterF2F2_New()
geodesicActiveContour = gAC
propagationScaling = float(sys.argv[9])
geodesicActiveContour.SetPropagationScaling(propagationScaling)
geodesicActiveContour.SetCurvatureScaling(1.0)
geodesicActiveContour.SetAdvectionScaling(1.0)
geodesicActiveContour.SetMaximumRMSError(0.02)
geodesicActiveContour.SetNumberOfIterations(800)
smoothing.SetInput(reader.GetOutput())
gradientMagnitude.SetInput(smoothing.GetOutput())
sigmoid.SetInput(gradientMagnitude.GetOutput())
geodesicActiveContour.SetInput(fastMarching.GetOutput())
geodesicActiveContour.SetFeatureImage(sigmoid.GetOutput())
thresholder = itk.itkBinaryThresholdImageFilterF2US2_New()
thresholder.SetLowerThreshold(-1000.0)
thresholder.SetUpperThreshold(0.0)
thresholder.SetOutsideValue(0)
thresholder.SetInsideValue(65535)
thresholder.SetInput(geodesicActiveContour.GetOutput())
writer.SetInput(thresholder.GetOutput())
smoothing.SetTimeStep(0.125)
smoothing.SetNumberOfIterations(5)
smoothing.SetConductanceParameter(3.0)
sigma = float(sys.argv[6])
gradientMagnitude.SetSigma(sigma)
alpha = float(sys.argv[7])
beta = float(sys.argv[8])
sigmoid.SetAlpha(alpha)
sigmoid.SetBeta(beta)
# same as image
seedPosition = itk.itkIndex2()
seedPosition.SetElement(0, int(sys.argv[3]))
seedPosition.SetElement(1, int(sys.argv[4]))
initialDistance = float(sys.argv[5])
seedValue = -initialDistance
node = itk.itkLevelSetNodeF2()
node.SetValue(seedValue)
node.SetIndex(seedPosition)
seeds = itk.itkNodeContainerF2_New()
seeds.Initialize()
seeds.InsertElement(0, node)
fastMarching.SetTrialPoints(seeds.GetPointer())
fastMarching.SetSpeedConstant(1.0)
caster1 = itk.itkRescaleIntensityImageFilterF2US2_New()
writer1 = itk.itkImageFileWriterUS2_New()
caster1.SetInput(smoothing.GetOutput())
writer1.SetInput(caster1.GetOutput())
writer1.SetFileName("GeodesicActiveContourImageFilterOutput1.png")
caster1.SetOutputMinimum(0)
caster1.SetOutputMaximum(65535)
writer1.Update()
caster2 = itk.itkRescaleIntensityImageFilterF2US2_New()
writer2 = itk.itkImageFileWriterUS2_New()
caster2.SetInput(gradientMagnitude.GetOutput())
writer2.SetInput(caster2.GetOutput())
writer2.SetFileName("GeodesicActiveContourImageFilterOutput2.png")
caster2.SetOutputMinimum(0)
caster2.SetOutputMaximum(65535)
writer2.Update()
caster3 = itk.itkRescaleIntensityImageFilterF2US2_New()
writer3 = itk.itkImageFileWriterUS2_New()
caster3.SetInput(sigmoid.GetOutput())
writer3.SetInput(caster3.GetOutput())
writer3.SetFileName("GeodesicActiveContourImageFilterOutput3.png")
caster3.SetOutputMinimum(0)
caster3.SetOutputMaximum(65535)
writer3.Update()
caster4 = itk.itkRescaleIntensityImageFilterF2US2_New()
writer4 = itk.itkImageFileWriterUS2_New()
caster4.SetInput(fastMarching.GetOutput())
writer4.SetInput(caster4.GetOutput())
writer4.SetFileName("GeodesicActiveContourImageFilterOutput4.png")
caster4.SetOutputMinimum(0)
caster4.SetOutputMaximum(65535)
fastMarching.SetOutputSize(
reader.GetOutput().GetBufferedRegion().GetSize())
writer.Update()
# Print out some useful information
print "\n"
print "Max. no. iterations: %d" % (gAC.GetNumberOfIterations())
print "Max. RMS error: %.3f" % (gAC.GetMaximumRMSError())
print "No. elapsed iterations: %d" % (gAC.GetElapsedIterations())
print "RMS change: %.3f" % (gAC.GetRMSChange())
writer4.Update()
mapWriter = itk.itkImageFileWriterF2_New()
mapWriter.SetInput(fastMarching.GetOutput())
mapWriter.SetFileName("GeodesicActiveContourImageFilterOutput4.mha")
mapWriter.Update()
speedWriter = itk.itkImageFileWriterF2_New()
speedWriter.SetInput(sigmoid.GetOutput())
speedWriter.SetFileName("GeodesicActiveContourImageFilterOutput3.mha")
speedWriter.Update()
gradientWriter = itk.itkImageFileWriterF2_New()
gradientWriter.SetInput(gradientMagnitude.GetOutput())
gradientWriter.SetFileName("GeodesicActiveContourImageFilterOutput2.mha")
gradientWriter.Update()
# it has to be a single component, itk::VTKImageImport doesn't support more lum = vtk.vtkImageLuminance() lum.SetInput(reader.GetOutput()) # let's cast the output to float imageCast = vtk.vtkImageCast() imageCast.SetOutputScalarTypeToFloat() imageCast.SetInput(lum.GetOutput()) # the end-point of this VTK pipeline segment is a vtkImageExport vtkExporter = vtk.vtkImageExport() vtkExporter.SetInput(imageCast.GetOutput()) # it connects to the itk::VTKImageImport at the beginning of # the subsequent ITK pipeline; two-dimensional float type itkImporter = itk.itkVTKImageImportF2_New() # Call the magic function that connects the two. This will only be # available if you built ITK with ITK_CSWIG_CONNECTVTKITK set to ON. CVIPy.ConnectVTKToITKF2(vtkExporter, itkImporter.GetPointer()) # perform a canny edge detection and rescale the output canny = itk.itkCannyEdgeDetectionImageFilterF2F2_New() rescaler = itk.itkRescaleIntensityImageFilterF2US2_New() canny.SetInput(itkImporter.GetOutput()) rescaler.SetInput(canny.GetOutput()) rescaler.SetOutputMinimum(0) rescaler.SetOutputMaximum(65535) # this is to show off the new PyCommand functionality. :) def progressEvent():
import InsightToolkit as itk import sys reader = itk.itkImageFileReaderF2_New() reader.SetFileName( sys.argv[1] ) diffusion = itk.itkGradientAnisotropicDiffusionImageFilterF2F2_New() diffusion.SetInput(reader.GetOutput()) diffusion.SetTimeStep(0.0625) diffusion.SetConductanceParameter(9.0) diffusion.SetNumberOfIterations( 5 ); gradient = itk.itkGradientMagnitudeImageFilterF2F2_New() gradient.SetInput(diffusion.GetOutput()) watershed = itk.itkWatershedImageFilterF2_New() watershed.SetInput(gradient.GetOutput()) watershed.SetThreshold(0.01) watershed.SetLevel(0.2) # not UL writer available # will wait for LabelToRGBImageFIlter to be integrated in the toolkit # to add this test writer = itk.itkImageFileWriterUL2_New() writer.SetFileName( sys.argv[2] ) writer.SetInput( watershed.GetOutput() ) writer.Update()
