def rescaleAndWrite(filter, fileName):
caster = itk.RescaleIntensityImageFilter[InternalImageType,
OutputImageType].New(
filter,
OutputMinimum=0,
OutputMaximum=255)
itk.write(caster, fileName)
def rescaleAndWrite(filter, fileName):
caster = itk.RescaleIntensityImageFilter[
InternalImageType,
OutputImageType].New(
filter,
OutputMinimum=0,
OutputMaximum=255)
itk.write(caster, fileName)
def shellActiveContourWrapper(image1, seedList, contour, inputVolume):
"""
Performs level set operation that fills in a shell-shaped object.
Parameters:
image1: volume to guide the level set operation
seedList: list of points from which operation will start
contour: deprecated parameter
inputVolume: deprecated parameter
"""
InternalPixelType = itk.F
Dimension = 3
ImageType = itk.Image[InternalPixelType, Dimension]
converter = itk.PyBuffer[ImageType]
IT = itk.Image.F3
#img = IT.New(Regions=[inputVolume1.shape[2], inputVolume1.shape[1], inputVolume1.shape[0]])
#img.Allocate()
#img.FillBuffer(0)
InternalImageType = IT
OutputImageType = IT
# Writing and reading from file works around a WrapITK bug
itk.write(image1, os.path.join(default_path.defaultOutputPath, "hello1.nrrd"))
itk.write(image1, os.path.join(default_path.defaultOutputPath, "hello2.nrrd"))
#seedPosition = numpyToItkPoint(center)
# test code
argv[1:] = ["O:\\images\\HPFcere_vol\\HPF_rotated_tif\\median_then_gaussian_8bit_classified_pixels\\median_then_gaussian_8bit_classified_pixels.nrrd", "o:\\temp\\fastmarch3d.nrrd", 81, 114, 1.0, -0.5, 3.0, 0.4, 0.4]
if( len(argv) < 10 ):
print >> stderr, """Missing Parameters
Usage: FastMarchingImageFilter.py inputImage outputImage seedX seedY Sigma SigmoidAlpha SigmoidBeta TimeThreshold StoppingValue"""
exit(1)
#end of test code
NodeType = itk.LevelSetNode[InternalPixelType, Dimension]
NodeContainer = itk.VectorContainer[itk.UI, NodeType]
itkSeedList = []
for point in seedList:
itkSeedList.append(numpyToItkPoint(point))
resultItkArray = shellActiveContour(inputImage=image1,
seedPoints=itkSeedList,
#advectionScaling=80.0,
advectionScaling=160.0,
#curvatureScaling=0.75,
curvatureScaling=6.75,
dimensions=3,
propagationScaling=1)
#advectionScaling=20.0,
#curvatureScaling=1.2,
return resultItkArray
def rescaleAndWrite(filter, fileName):
"""Rescale and write ITK filter output to file."""
InternalPixelType = itk.F
Dimension = 2
InternalImageType = itk.Image[InternalPixelType, Dimension]
OutputPixelType = itk.UC
OutputImageType = itk.Image[OutputPixelType, Dimension]
caster = itk.RescaleIntensityImageFilter[InternalImageType, OutputImageType].New(filter,
OutputMinimum=0,
OutputMaximum=255)
itk.write(caster, fileName)
# perform a simple binarization. Note that the Otsu filter does not use the same convention as usual : the white part is outside. otsu = itk.OtsuThresholdImageFilter[ImageType, ImageType].New(nuclei, OutsideValue=255, InsideValue=0) # split the nuclei maurer = itk.SignedMaurerDistanceMapImageFilter[ImageType, DistanceImageType].New(otsu) watershed = itk.MorphologicalWatershedImageFilter[DistanceImageType, ImageType].New(maurer, Level=60, MarkWatershedLine=False) mask = itk.MaskImageFilter[ImageType, ImageType, ImageType].New(watershed, otsu) # now switch to the label map representation and compute the attribute values, including the perimeter and the Feret diameter stats = itk.LabelImageToStatisticsLabelMapFilter[ImageType, ImageType, LabelMapType].New(mask, nuclei) # drop the objects too small to be a nucleus, and the ones on the border size = itk.ShapeOpeningLabelMapFilter[LabelMapType].New(stats, Attribute='Size', Lambda=100) border = itk.ShapeOpeningLabelMapFilter[LabelMapType].New(size, Attribute='SizeOnBorder', Lambda=10, ReverseOrdering=True) # reoder the labels. The objects with the highest mean are the first ones. relabel = itk.StatisticsRelabelLabelMapFilter[LabelMapType].New(border, Attribute='Mean') # for visual validation overlay = itk.LabelMapOverlayImageFilter[LabelMapType, ImageType, RGBImageType].New(relabel, nuclei) itk.write(overlay, "nuclei-overlay.png") spots = itk.ImageFileReader[ImageType].New(FileName="images/spots.png") # mask the spot image to keep only the nucleus zone. The rest of the image is cropped, excepted a border of 2 pixels maskSpots = itk.LabelMapMaskImageFilter[LabelMapType, ImageType].New(relabel, spots, Label=1, Crop=True, CropBorder=2) th = itk.BinaryThresholdImageFilter[ImageType, ImageType].New(maskSpots, LowerThreshold=110) sstats = itk.BinaryImageToStatisticsLabelMapFilter[ImageType, ImageType, LabelMapType].New(th, nuclei) # we know there are 4 spots in the nubleus, so keep the 4 biggest spots skeep = itk.ShapeKeepNObjectsLabelMapFilter[LabelMapType].New(sstats, Attribute='Size', NumberOfObjects=4) # reoder the labels. The bigger objects first. srelabel = itk.StatisticsRelabelLabelMapFilter[LabelMapType].New(skeep, Attribute='Size') # display the values we are interested in:
#
# Copyright Insight Software Consortium
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# 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.
#
#==========================================================================*/
#
# Example on the use of the SmoothingRecursiveGaussianImageFilter
#
import itk
from sys import argv
itk.auto_progress(2)
reader = itk.ImageFileReader.IUC2.New(FileName=argv[1])
filter = itk.SmoothingRecursiveGaussianImageFilter.New(
reader,
Sigma=eval(argv[3]))
itk.write(filter, argv[2])
ellipse = itk.EllipseSpatialObject[dim].New(Radius=[10, 5])
ellipse.GetObjectToParentTransform().SetOffset([20, 20])
ellipse.ComputeObjectToWorldTransform()
box = itk.BoxSpatialObject[dim].New(Size=20)
box.GetObjectToParentTransform().SetOffset([20, 40])
box.ComputeObjectToWorldTransform()
gaussian = itk.GaussianSpatialObject[dim].New(Radius=100)
gaussian.GetObjectToParentTransform().SetOffset([60, 60])
gaussian.GetObjectToParentTransform().SetScale(10)
gaussian.ComputeObjectToWorldTransform()
group = itk.GroupSpatialObject[dim].New()
group.AddSpatialObject(ellipse)
group.AddSpatialObject(box)
group.AddSpatialObject(gaussian)
filter = itk.SpatialObjectToImageFilter[SOType, InternalImageType].New(
group, Size=[100, 100], UseObjectValue=True)
filter.Update() # required ?!
rescale = itk.RescaleIntensityImageFilter[
InternalImageType, OutputImageType].New(
filter,
OutputMinimum=itk.NumericTraits[OutputPixelType].NonpositiveMin(),
OutputMaximum=itk.NumericTraits[OutputPixelType].max())
itk.write(rescale, argv[1])
dim = 2 SOType = itk.SpatialObject[dim] InternalImageType = itk.Image[itk.F, dim] OutputPixelType = itk.UC OutputImageType = itk.Image[OutputPixelType, dim] ellipse = itk.EllipseSpatialObject[dim].New( Radius=[10,5] ) ellipse.GetObjectToParentTransform().SetOffset( [20,20] ) ellipse.ComputeObjectToWorldTransform() box = itk.BoxSpatialObject[dim].New( Size=20 ) box.GetObjectToParentTransform().SetOffset( [20,40] ) box.ComputeObjectToWorldTransform() gaussian = itk.GaussianSpatialObject[dim].New( Radius=100 ) gaussian.GetObjectToParentTransform().SetOffset( [60,60] ) gaussian.GetObjectToParentTransform().SetScale( 10 ) gaussian.ComputeObjectToWorldTransform() group = itk.GroupSpatialObject[dim].New() group.AddSpatialObject( ellipse.GetPointer() ) group.AddSpatialObject( box.GetPointer() ) group.AddSpatialObject( gaussian.GetPointer() ) filter = itk.SpatialObjectToImageFilter[SOType, InternalImageType].New( group, Size=[100,100], UseObjectValue=True ) filter.Update() # required ?! rescale = itk.RescaleIntensityImageFilter[InternalImageType, OutputImageType].New( filter, OutputMinimum=itk.NumericTraits[OutputPixelType].NonpositiveMin(), OutputMaximum=itk.NumericTraits[OutputPixelType].max() ) itk.write(rescale, argv[1])
if argv[2] == "Ball":
print "Ball"
strel = itk.FlatStructuringElement[2].Ball( int( argv[3] ) )
elif argv[2] == "Box":
print "Box"
strel = itk.FlatStructuringElement[2].Box( int( argv[3] ) )
elif argv[2] == "FromImage":
print "FromImage"
reader = itk.ImageFileReader.IUC2.New( FileName=argv[3] )
strel = itk.FlatStructuringElement[2].FromImageUC( reader.GetOutput() )
else:
print "invalid arguement: " + argv[2]
exit(1)
img = strel.GetImageUC()
size = itk.size( img )
for y in range(0, size.GetElement(1)):
for x in range(0, size.GetElement(0)):
if img.GetPixel( [x, y] ):
print "X",
else:
print " ",
print "\n",
itk.write( img, argv[1] )
# writer = itk.ImageFileWriter.IUC2.New(FileName=argv[1], Input=img )
# itk.echo(writer)
# writer.Update()
def fastMarch(image1, center, contour, inputVolume):
"""
Fast march. The fast march is seeded by every point of the contour.
Returns fast march result.
"""
InternalPixelType = itk.F
Dimension = 3
ImageType = itk.Image[InternalPixelType, Dimension]
converter = itk.PyBuffer[ImageType]
IT = itk.Image.F3
#img = IT.New(Regions=[inputVolume1.shape[2], inputVolume1.shape[1], inputVolume1.shape[0]])
#img.Allocate()
#img.FillBuffer(0)
InternalImageType = IT
OutputImageType = IT
# test code
itk.write(image1, "/tmp/hello1.nrrd")
itk.write(image1, "/tmp/hello2.nrrd")
# end test code
seedPosition = numpyToItkPoint(center)
argv[1:] = ["O:\\images\\HPFcere_vol\\HPF_rotated_tif\\median_then_gaussian_8bit_classified_pixels\\median_then_gaussian_8bit_classified_pixels.nrrd", "o:\\temp\\fastmarch3d.nrrd", 81, 114, 1.0, -0.5, 3.0, 0.4, 0.4]
if( len(argv) < 10 ):
print >> stderr, """Missing Parameters
Usage: FastMarchingImageFilter.py inputImage outputImage seedX seedY Sigma SigmoidAlpha SigmoidBeta TimeThreshold StoppingValue"""
exit(1)
CastFilterType = itk.RescaleIntensityImageFilter[
InternalImageType,
OutputImageType ]
SmoothingFilterType = itk.CurvatureAnisotropicDiffusionImageFilter[
InternalImageType,
InternalImageType ]
smoothing = SmoothingFilterType.New()
GradientFilterType = itk.GradientMagnitudeRecursiveGaussianImageFilter[
InternalImageType,
InternalImageType ]
SigmoidFilterType = itk.SigmoidImageFilter[
InternalImageType,
InternalImageType ]
gradientMagnitude = GradientFilterType.New();
sigmoid = SigmoidFilterType.New()
sigmoid.SetOutputMinimum( 0.0 )
sigmoid.SetOutputMaximum( 1.0 )
FastMarchingFilterType = itk.FastMarchingUpwindGradientImageFilter[ InternalImageType,
InternalImageType ]
NodeType = itk.LevelSetNode[InternalPixelType, Dimension]
NodeContainer = itk.VectorContainer[itk.UI, NodeType]
stopPoints = NodeContainer.New()
for pointObject in contour.points():
stopPointNode = NodeType()
stopPointNode.SetValue(0) #todo: is this needed
stopPointNode.SetIndex(numpyToItkPoint(pointObject.loc))
stopPoints.InsertElement(0, stopPointNode)
fastMarching = FastMarchingFilterType.New()
fastMarching.SetTargetReachedModeToOneTarget()
fastMarching.SetTargetOffset(0)
fastMarching.SetTargetPoints(stopPoints)
fastMarching.SetInput(image1)
sigma = float( argv[5] )
gradientMagnitude.SetSigma( sigma )
alpha = float( argv[6] )
beta = float( argv[7] )
seeds = NodeContainer.New()
node = NodeType()
seedValue = 0.0
node.SetValue( seedValue )
node.SetIndex( seedPosition )
seeds.Initialize();
seeds.InsertElement( 0, node )
fastMarching.SetTrialPoints( seeds );
fastMarching.SetOutputSize(inputVolume.GetBufferedRegion().GetSize())
stoppingTime = float( argv[9] )
fastMarching.SetStoppingValue( stoppingTime )
print "update"
fastMarching.Update()
print "finished update"
resultItkArray = fastMarching.GetOutput()
return resultItkArray
def quickComputeFillFromEllipseCenters(inputVolume1, contourList, fillMethod):
"""
Uses shellActiveContourWrapper to perform level set initiated at all contours in contourList.
Parameters:
inputVolume1: guides the level set operation
contourList: list of seed contours
fillMethod: specifies the fill method, use 'shellActiveContour'
"""
global numpyBufferFromPyBufferClass
global img
InternalPixelType = itk.F
Dimension = 3
ImageType = itk.Image[InternalPixelType, Dimension]
converter = itk.PyBuffer[ImageType]
IT = itk.Image.F3
img = IT.New(Regions=[inputVolume1.shape[2], inputVolume1.shape[1], inputVolume1.shape[0]])
img.Allocate()
img.FillBuffer(0)
InternalImageType = IT
OutputImageType = IT
numpyBufferFromPyBufferClass = itk.PyBuffer[IT].GetArrayFromImage(img)
numpyBufferFromPyBufferClass[:, :, :] = inputVolume1
centerList = []
contourCount = 0
print "number of contours", len(contourList)
erodedContoursNode = GroupNode('ErodedContours')
#file = open("o:\\temp\\contours.txt", 'w')
for contour in contourList:
center = contour.bestFitEllipse.center
#centerList.append(center)
#print "starting erosion", contourCount
#print dir(copy_module)
#locations = copy_module.deepcopy(contour.locations())
#print locations
#file.write(str(locations))
#print "number of points", len(locations)
erodedContourSet = erosion.erosion_polygon(contour.locations(), 10)
erodedContourSet = erodedContourSet +\
erosion.erosion_polygon(contour.locations(), 20)
#print "completed erosion"
for erodedContour in erodedContourSet:
erodedContourObject = Contour()
erodedContourObject.addNumpyPoints(erodedContour)
erodedContoursNode.addObject(erodedContourObject)
#for point in contour.locations():
for point in erodedContour:
#centerList.append(((array(point) - array(center)) / 2.0) + array(center))
centerList.append(array(point))
contourCount += 1
#file.close()
count = 0
#todo: check if this center variable needs to be here
if len(contourList) > 0:
center = contour.bestFitEllipse.center
print "compute fill", count, "total", len(contourList)
inputVolume = converter.GetImageFromArray(numpyBufferFromPyBufferClass)
inputVolumeFileName = os.path.join(default_path.defaultOutputPath, "hello.nrrd")
# Writing and reading from file works around a WrapITK bug
itk.write(inputVolume, inputVolumeFileName)
reader1 = itk.ImageFileReader[InternalImageType].New(FileName=inputVolumeFileName)
image1 = reader1.GetOutput()
if fillMethod == 'fastMarch':
#resultItkArray = fastMarch(image1, center, contour, inputVolume)
raise Exception, "not implemented"
elif fillMethod == 'shellActiveContour':
#resultItkArray = shellActiveContourWrapper(image1, centerList, contour, inputVolume)
resultItkArray = shellActiveContourWrapper(image1, centerList, None, inputVolume)
else: raise Exception, "Invalid fill method"
tempFileName = os.path.join(default_path.defaultOutputPath, "fillResult.nrrd")
print "writing file", tempFileName
itk.write(resultItkArray, tempFileName)
resultVolume = numpy.array(converter.GetArrayFromImage(resultItkArray))
if 1:
#contour.features['fastMarchFromEllipseCenter'] = resultVolume
blob = Blob()
#binaryResult = resultVolume < 10000000
binaryResult = resultVolume < 0.5
if 0:
print "starting flood fill"
pointList = floodFill(binaryResult, center)
print "flood fill finished"
blob.setPoints(pointList)
if count == 0:
sumVolume = (1.0 * binaryResult)
else:
sumVolume += (1.0 * binaryResult)
#contour.features['fastMarchBlobFromEllipseCenter'] = blob
print "result volume"
count += 1
return sumVolume, erodedContoursNode
def computeFillFromEllipseCenters(inputVolume1, contourList, fillMethod):
"""
Uses shellActiveContourWrapper to perform level set separately at each contour.
Nolonger using this function.
"""
global numpyBufferFromPyBufferClass
global img
InternalPixelType = itk.F
Dimension = 3
ImageType = itk.Image[InternalPixelType, Dimension]
converter = itk.PyBuffer[ImageType]
IT = itk.Image.F3
img = IT.New(Regions=[inputVolume1.shape[2], inputVolume1.shape[1], inputVolume1.shape[0]])
img.Allocate()
img.FillBuffer(0)
InternalImageType = IT
OutputImageType = IT
numpyBufferFromPyBufferClass = itk.PyBuffer[IT].GetArrayFromImage(img)
numpyBufferFromPyBufferClass[:, :, :] = inputVolume1
count = 0
for contour in contourList:
center = contour.bestFitEllipse.center
print "compute fill", count, "total", len(contourList)
inputVolume = converter.GetImageFromArray(numpyBufferFromPyBufferClass)
inputVolumeFileName = os.path.join(default_path.defaultOutputPath, "hello.nrrd")
# Writing and reading from file works around a WrapITK bug
itk.write(inputVolume, inputVolumeFileName)
reader1 = itk.ImageFileReader[InternalImageType].New(FileName=inputVolumeFileName)
image1 = reader1.GetOutput()
if fillMethod == 'fastMarch':
resultItkArray = fastMarch(image1, center, contour, inputVolume)
elif fillMethod == 'shellActiveContour':
resultItkArray = shellActiveContourWrapper(image1, center, contour, inputVolume)
else: raise Exception, "Invalid fill method"
tempFileName = os.path.join(default_path.defaultOutputPath, "fillResult.nrrd")
print "writing file", tempFileName
itk.write(resultItkArray, tempFileName)
resultVolume = numpy.array(converter.GetArrayFromImage(resultItkArray))
if 1:
#contour.features['fastMarchFromEllipseCenter'] = resultVolume
blob = Blob()
#binaryResult = resultVolume < 10000000
binaryResult = resultVolume < 0.5
if 0:
print "starting flood fill"
pointList = floodFill(binaryResult, center)
print "flood fill finished"
blob.setPoints(pointList)
if count == 0:
sumVolume = (1.0 * binaryResult)
else:
sumVolume += (1.0 * binaryResult)
#contour.features['fastMarchBlobFromEllipseCenter'] = blob
print "result volume"
count += 1
return sumVolume
def shellActiveContourWrapper_old(seedPositionNumpyArray, numpyTargetPointList):
"""Deprecated"""
if 1:
seedPosition = numpyToItkPoint(seedPositionNumpyArray)
ImageType = itk.Image[itk.F, 3]
converter = itk.PyBuffer[ImageType]
print "fast march inputNumpyVolume", numpyBufferFromPyBufferClass
inputVolume = converter.GetImageFromArray(numpyBufferFromPyBufferClass)
print "fast march inputVolume", inputVolume
itk.write(inputVolume, "/tmp/hello.nrrd")
argv[1:] = ["O:\\images\\HPFcere_vol\\HPF_rotated_tif\\median_then_gaussian_8bit_classified_pixels\\median_then_gaussian_8bit_classified_pixels.nrrd", "o:\\temp\\fastmarch3d.nrrd", 81, 114, 1.0, -0.5, 3.0, 0.4, 0.4]
if( len(argv) < 10 ):
print >> stderr, """Missing Parameters
Usage: FastMarchingImageFilter.py inputImage outputImage seedX seedY Sigma SigmoidAlpha SigmoidBeta TimeThreshold StoppingValue"""
exit(1)
InternalPixelType = itk.F
Dimension = 3
InternalImageType = itk.Image[ InternalPixelType, Dimension ]
OutputPixelType = itk.UC
OutputImageType = itk.Image[ OutputPixelType, Dimension ]
CastFilterType = itk.RescaleIntensityImageFilter[
InternalImageType,
OutputImageType ]
SmoothingFilterType = itk.CurvatureAnisotropicDiffusionImageFilter[
InternalImageType,
InternalImageType ]
smoothing = SmoothingFilterType.New()
GradientFilterType = itk.GradientMagnitudeRecursiveGaussianImageFilter[
InternalImageType,
InternalImageType ]
SigmoidFilterType = itk.SigmoidImageFilter[
InternalImageType,
InternalImageType ]
gradientMagnitude = GradientFilterType.New();
sigmoid = SigmoidFilterType.New()
sigmoid.SetOutputMinimum( 0.0 )
sigmoid.SetOutputMaximum( 1.0 )
FastMarchingFilterType = itk.FastMarchingUpwindGradientImageFilter[ InternalImageType,
InternalImageType ]
NodeType = itk.LevelSetNode[InternalPixelType, Dimension]
NodeContainer = itk.VectorContainer[itk.UI, NodeType]
numpyStopPointList = numpyTargetPointList
stopPoints = NodeContainer.New()
for pointObject in numpyStopPointList:
stopPointNode = NodeType()
stopPointNode.SetValue(0) #todo: is this needed
stopPointNode.SetIndex(numpyToItkPoint(pointObject.loc))
stopPoints.InsertElement(0, stopPointNode)
fastMarching = FastMarchingFilterType.New()
fastMarching.SetTargetReachedModeToOneTarget()
fastMarching.SetTargetOffset(0)
fastMarching.SetTargetPoints(stopPoints)
fastMarching.SetInput(inputVolume)
sigma = float( argv[5] )
gradientMagnitude.SetSigma( sigma )
alpha = float( argv[6] )
beta = float( argv[7] )
seeds = NodeContainer.New()
node = NodeType()
seedValue = 0.0
node.SetValue( seedValue )
node.SetIndex( seedPosition )
seeds.Initialize();
seeds.InsertElement( 0, node )
fastMarching.SetTrialPoints( seeds );
fastMarching.SetOutputSize(inputVolume.GetBufferedRegion().GetSize())
stoppingTime = float( argv[9] )
fastMarching.SetStoppingValue( stoppingTime )
fastMarching.Update()
resultItkArray = fastMarching.GetOutput()
print "inputVolume2", inputVolume
itk.write(inputVolume, "/tmp/result_something.nrrd")
def fastMarch_old(seedPositionNumpyArray, numpyTargetPointList):
"""Deprecated"""
if 1:
seedPosition = numpyToItkPoint(seedPositionNumpyArray)
ImageType = itk.Image[itk.F, 3]
converter = itk.PyBuffer[ImageType]
#UCImageType = itk.Image[itk.UC, 3]
#UCConverter = itk.PyBuffer[UCImageType]
print "fast march inputNumpyVolume", numpyBufferFromPyBufferClass
inputVolume = converter.GetImageFromArray(numpyBufferFromPyBufferClass)
print "fast march inputVolume", inputVolume
itk.write(inputVolume, "/tmp/hello.nrrd")
#argv[1:] = ["O:\\software\\InsightToolkit-3.12.0\\Wrapping\\WrapITK\\images\\BrainProtonDensitySlice.png", "o:\\temp\\fastmarch2d.png", 81, 114, 1.0, -0.5, 3.0, 100, 100]
#argv[1:] = ["O:\\temp\\3dvolume\\3d.nrrd", "o:\\temp\\fastmarch3d.nrrd", 81, 114, 1.0, -0.5, 3.0, 100, 100]
#argv[1:] = ["O:\\images\\HPFcere_vol\\HPF_rotated_tif\\median_then_gaussian_filter.nrrd", "o:\\temp\\fastmarch3d.nrrd", 81, 114, 1.0, -0.5, 3.0, 100, 100]
#argv[1:] = ["O:\\images\\HPFcere_vol\\HPF_rotated_tif\\median_then_gaussian_filter.nrrd", "o:\\temp\\fastmarch3d.nrrd", 81, 114, 1.0, -0.5, 3.0, 1, 1]
#argv[1:] = ["O:\\images\\HPFcere_vol\\HPF_rotated_tif\\median_then_gaussian_8bit_classified_pixels\\median_then_gaussian_8bit_classified_pixels.nrrd", "o:\\temp\\fastmarch3d.nrrd", 81, 114, 1.0, -0.5, 3.0, 0.1, 0.1]
argv[1:] = ["O:\\images\\HPFcere_vol\\HPF_rotated_tif\\median_then_gaussian_8bit_classified_pixels\\median_then_gaussian_8bit_classified_pixels.nrrd", "o:\\temp\\fastmarch3d.nrrd", 81, 114, 1.0, -0.5, 3.0, 0.4, 0.4]
if( len(argv) < 10 ):
print >> stderr, """Missing Parameters
Usage: FastMarchingImageFilter.py inputImage outputImage seedX seedY Sigma SigmoidAlpha SigmoidBeta TimeThreshold StoppingValue"""
exit(1)
#itk.auto_progress(2)
InternalPixelType = itk.F
Dimension = 3
InternalImageType = itk.Image[ InternalPixelType, Dimension ]
OutputPixelType = itk.UC
OutputImageType = itk.Image[ OutputPixelType, Dimension ]
CastFilterType = itk.RescaleIntensityImageFilter[
InternalImageType,
OutputImageType ]
SmoothingFilterType = itk.CurvatureAnisotropicDiffusionImageFilter[
InternalImageType,
InternalImageType ]
smoothing = SmoothingFilterType.New()
GradientFilterType = itk.GradientMagnitudeRecursiveGaussianImageFilter[
InternalImageType,
InternalImageType ]
SigmoidFilterType = itk.SigmoidImageFilter[
InternalImageType,
InternalImageType ]
gradientMagnitude = GradientFilterType.New();
sigmoid = SigmoidFilterType.New()
sigmoid.SetOutputMinimum( 0.0 )
sigmoid.SetOutputMaximum( 1.0 )
FastMarchingFilterType = itk.FastMarchingUpwindGradientImageFilter[ InternalImageType,
InternalImageType ]
#FastMarchingFilterType = itk.FastMarchingImageFilter[ InternalImageType,
# InternalImageType ]
NodeType = itk.LevelSetNode[InternalPixelType, Dimension]
NodeContainer = itk.VectorContainer[itk.UI, NodeType]
#numpyStopPointList = [array(seedPosition) + array([10,10,10])]
numpyStopPointList = numpyTargetPointList
#print numpyStopPointList
stopPoints = NodeContainer.New()
for pointObject in numpyStopPointList:
stopPointNode = NodeType()
stopPointNode.SetValue(0) #todo: is this needed
stopPointNode.SetIndex(numpyToItkPoint(pointObject.loc))
stopPoints.InsertElement(0, stopPointNode)
fastMarching = FastMarchingFilterType.New()
fastMarching.SetTargetReachedModeToOneTarget()
fastMarching.SetTargetOffset(0)
fastMarching.SetTargetPoints(stopPoints)
fastMarching.SetInput(inputVolume)
sigma = float( argv[5] )
gradientMagnitude.SetSigma( sigma )
alpha = float( argv[6] )
beta = float( argv[7] )
##sigmoid.SetAlpha( alpha )
##sigmoid.SetBeta( beta )
seeds = NodeContainer.New()
#seedPosition = [10, 10, 10]
node = NodeType()
seedValue = 0.0
node.SetValue( seedValue )
node.SetIndex( seedPosition )
#print "fastmarch seed position", seedPosition
seeds.Initialize();
seeds.InsertElement( 0, node )
fastMarching.SetTrialPoints( seeds );
#fastMarching.SetOutputSize(
# reader.GetOutput().GetBufferedRegion().GetSize() )
fastMarching.SetOutputSize(inputVolume.GetBufferedRegion().GetSize())
stoppingTime = float( argv[9] )
#stoppingTime = float(1000000)
fastMarching.SetStoppingValue( stoppingTime )
#writer.Update()
#return UCConverter.GetArrayFromImage(thresholder.GetOutput())
fastMarching.Update()
resultItkArray = fastMarching.GetOutput()
#itk.write(resultItkArray, "/tmp/result.nrrd")
print "inputVolume2", inputVolume
itk.write(inputVolume, "/tmp/result_something.nrrd")
#
# Example on the use of the MeanImageFilter
#
import itk
from sys import argv
dim = 2
PixelType = itk.F
ImageType = itk.Image[PixelType, dim]
reader = itk.ImageFileReader[ImageType].New(FileName=argv[1])
fftFilter = itk.FFTWRealToComplexConjugateImageFilter[PixelType,
dim].New(reader)
fftFilter2 = itk.FFTWComplexConjugateToRealImageFilter[PixelType,
dim].New(fftFilter)
cast = itk.CastImageFilter[ImageType, itk.Image[itk.UC, dim]].New(fftFilter2)
itk.write(cast, argv[2])
print itk.size(fftFilter).GetElement(0), itk.size(fftFilter).GetElement(1)
if argv[2] == "Ball":
print "Ball"
strel = itk.FlatStructuringElement[2].Ball(int(argv[3]))
elif argv[2] == "Box":
print "Box"
strel = itk.FlatStructuringElement[2].Box(int(argv[3]))
elif argv[2] == "FromImage":
print "FromImage"
reader = itk.ImageFileReader.IUC2.New(FileName=argv[3])
strel = itk.FlatStructuringElement[2].FromImageUC(reader.GetOutput())
else:
print "invalid arguement: " + argv[2]
exit(1)
img = strel.GetImageUC()
size = itk.size(img)
for y in range(0, size.GetElement(1)):
for x in range(0, size.GetElement(0)):
if img.GetPixel([x, y]):
print "X",
else:
print " ",
print "\n",
itk.write(img, argv[1])
# writer = itk.ImageFileWriter.IUC2.New(FileName=argv[1], Input=img )
# itk.echo(writer)
# writer.Update()
#==========================================================================*/
#
# Example on the use of the CannyEdgeDetectionImageFilter
#
from __future__ import print_function
import itk
from sys import argv, stderr, exit
itk.auto_progress(2)
if len(argv) < 3:
print(("Usage: CannyEdgeDetectionImageFilter.py inputImage outputImage "
"[variance]"),
file=stderr)
exit(1)
variance = 2.0
if len(argv) > 3:
variance = float(argv[3])
print(variance)
reader = itk.ImageFileReader.IF2.New(FileName=argv[1])
filter = itk.CannyEdgeDetectionImageFilter.IF2IF2.New(reader,
Variance=variance)
outputCast = itk.RescaleIntensityImageFilter.IF2IUC2.New(filter,
OutputMinimum=0,
OutputMaximum=255)
itk.write(outputCast, argv[2])
import itk input = '../../Testing/Data/Input/foot.mha' valt = itk.F imgt = itk.Image[valt, 2] reader = itk.ImageFileReader[imgt].New( FileName=input ) grad_io = itk.VTKImageIO.New() grad_io.SetPixelType( grad_io.VECTOR ) gradient_filter = itk.GradientImageFilter[ imgt, valt, valt ].New() gradient_filter.SetInput( reader.GetOutput() ) gradt = itk.output(gradient_filter) itk.write( gradient_filter, 'foot_GradientImageFilter.mha' ) gradient_mag_filter = itk.GradientToMagnitudeImageFilter[ gradt, imgt ].New() gradient_mag_filter.SetInput( gradient_filter.GetOutput() ) itk.write( gradient_mag_filter, 'foot_GradientImageFilter_magnitude.mha' ) dog_filter = itk.DifferenceOfGaussiansGradientImageFilter[ imgt, valt ].New() dog_filter.SetInput( reader.GetOutput() ) dog_filter.SetWidth( 1 ) itk.write( dog_filter, 'foot_DifferenceOfGaussiansGradientImageFilter.mha' ) dog_mag_filter = itk.GradientToMagnitudeImageFilter[ gradt, imgt ].New() dog_mag_filter.SetInput( dog_filter.GetOutput() ) itk.write( dog_mag_filter, 'foot_DifferenceOfGaussiansGradientImageFilter_magnitude.mha' )
def main():
if len(argv) < 10:
errMsg = "Missing parameters\n" \
"Usage: %s\n" % (argv[0],) + \
" inputImage outputImage\n" \
" seedX seedY InitialDistance\n" \
" Sigma SigmoidAlpha SigmoidBeta\n" \
" PropagationScaling\n"
print >> 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.
# we wan't to know what is happening
# itk.auto_progress(True)
InternalPixelType = itk.F
Dimension = 2
InternalImageType = itk.Image[InternalPixelType, Dimension]
OutputPixelType = itk.UC
OutputImageType = itk.Image[OutputPixelType, Dimension]
reader = itk.ImageFileReader[InternalImageType].New(FileName=argv[1])
# needed to give the size to the fastmarching filter
reader.Update()
smoothing = itk.CurvatureAnisotropicDiffusionImageFilter[
InternalImageType, InternalImageType].New(reader,
TimeStep=0.125,
NumberOfIterations=5,
ConductanceParameter=9.0)
gradientMagnitude = itk.GradientMagnitudeRecursiveGaussianImageFilter[
InternalImageType, InternalImageType].New(smoothing,
Sigma=float(argv[6]))
sigmoid = itk.SigmoidImageFilter[InternalImageType, InternalImageType].New(
gradientMagnitude,
OutputMinimum=0.0,
OutputMaximum=1.1,
Alpha=float(argv[7]),
Beta=float(argv[8]))
seedPosition = itk.Index[2]()
seedPosition.SetElement(0, int(argv[3]))
seedPosition.SetElement(1, int(argv[4]))
node = itk.LevelSetNode[InternalPixelType, Dimension]()
node.SetValue(-float(argv[5]))
node.SetIndex(seedPosition)
seeds = itk.VectorContainer[itk.UI, itk.LevelSetNode[InternalPixelType,
Dimension]].New()
seeds.Initialize()
seeds.InsertElement(0, node)
fastMarching = itk.FastMarchingImageFilter[
InternalImageType, InternalImageType].New(
sigmoid,
TrialPoints=seeds,
SpeedConstant=1.0,
OutputSize=reader.GetOutput().GetBufferedRegion().GetSize())
geodesicActiveContour = itk.GeodesicActiveContourLevelSetImageFilter[
InternalImageType, InternalImageType,
InternalPixelType].New(fastMarching,
sigmoid,
PropagationScaling=float(argv[9]),
CurvatureScaling=1.0,
AdvectionScaling=1.0,
MaximumRMSError=0.02,
NumberOfIterations=800)
thresholder = itk.BinaryThresholdImageFilter[InternalImageType,
OutputImageType].New(
geodesicActiveContour,
LowerThreshold=-1000,
UpperThreshold=0,
OutsideValue=0,
InsideValue=255)
writer = itk.ImageFileWriter[OutputImageType].New(thresholder,
FileName=argv[2])
def rescaleAndWrite(filter, fileName):
caster = itk.RescaleIntensityImageFilter[InternalImageType,
OutputImageType].New(
filter,
OutputMinimum=0,
OutputMaximum=255)
itk.write(caster, fileName)
rescaleAndWrite(smoothing, "GeodesicActiveContourImageFilterOutput1.png")
rescaleAndWrite(gradientMagnitude,
"GeodesicActiveContourImageFilterOutput2.png")
rescaleAndWrite(sigmoid, "GeodesicActiveContourImageFilterOutput3.png")
rescaleAndWrite(fastMarching,
"GeodesicActiveContourImageFilterOutput4.png")
writer.Update()
print
print "Max. no. iterations: %d" % (
geodesicActiveContour.GetNumberOfIterations())
print "Max. RMS error: %.3f" % (geodesicActiveContour.GetMaximumRMSError())
print
print "No. elapsed iterations: %d" % (
geodesicActiveContour.GetElapsedIterations())
print "RMS change: %.3f" % (geodesicActiveContour.GetRMSChange())
itk.write(fastMarching, "GeodesicActiveContourImageFilterOutput4.mha")
itk.write(sigmoid, "GeodesicActiveContourImageFilterOutput3.mha")
itk.write(gradientMagnitude, "GeodesicActiveContourImageFilterOutput2.mha")
v = int( rmaxRelabel[0].GetLabelObject(22).GetMaximum()/2 )
values = [rmaxRelabel[0].GetLabelObject(i+1).GetMaximum() for i in range(11)]
# vmean = mean(values) / 4
# vmedian = median(values) / 4
th.SetLowerThreshold( int(vmedian) )
# auto crop filter is actually buggy - lets force it to see that the input has changed
crop.Modified()
#
# visualisation
obo2()
result.ClearLabels()
window.SetWindowMinimum(int(nucleus.GetMinimum()))
window.SetWindowMaximum(int(nucleus.GetMaximum()))
#
for spot in bi2lm[0]:
cog = spot.GetCenterOfGravity()
idx = bi2lm[0].TransformPhysicalPointToIndex(cog)
result2.SetPixel(idx, l)
print '"'+inputFileName+'"', l, " ".join(str(i) for i in idx), " ".join(str(i) for i in cog)
#
result.PushLabelObject(obo2[0].GetLabelObject(spot.GetLabel()))
#
# push the nucleus shape to the result label map, to see the nucleus border in the image
result.PushLabelObject(obo3.GetOutput().GetLabelObject(l))
# and write the result
itk.write(overlay, inputFileName + "-%s.tif" % l)
itk.write(result2, inputFileName + "-CENP.nrrd", True)
def main():
if len(argv) < 10:
errMsg = "Missing parameters\n" \
"Usage: %s\n" % (argv[0],) + \
" inputImage outputImage\n" \
" seedX seedY InitialDistance\n" \
" Sigma SigmoidAlpha SigmoidBeta\n" \
" PropagationScaling\n"
print >> 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.
# we wan't to know what is happening
# itk.auto_progress(True)
InternalPixelType = itk.F
Dimension = 2
InternalImageType = itk.Image[InternalPixelType, Dimension]
OutputPixelType = itk.UC
OutputImageType = itk.Image[OutputPixelType, Dimension]
reader = itk.ImageFileReader[InternalImageType].New(FileName=argv[1])
# needed to give the size to the fastmarching filter
reader.Update()
smoothing = itk.CurvatureAnisotropicDiffusionImageFilter[InternalImageType, InternalImageType].New(reader,
TimeStep=0.125,
NumberOfIterations=5,
ConductanceParameter=9.0)
gradientMagnitude = itk.GradientMagnitudeRecursiveGaussianImageFilter[InternalImageType, InternalImageType].New(smoothing,
Sigma=float(argv[6]))
sigmoid = itk.SigmoidImageFilter[InternalImageType, InternalImageType].New(gradientMagnitude,
OutputMinimum=0.0,
OutputMaximum=1.1,
Alpha=float(argv[7]),
Beta=float(argv[8]))
seedPosition = itk.Index[2]()
seedPosition.SetElement(0, int(argv[3]))
seedPosition.SetElement(1, int(argv[4]))
node = itk.LevelSetNode[InternalPixelType, Dimension]()
node.SetValue(-float(argv[5]))
node.SetIndex(seedPosition)
seeds = itk.VectorContainer[itk.UI, itk.LevelSetNode[InternalPixelType, Dimension]].New()
seeds.Initialize()
seeds.InsertElement(0, node)
fastMarching = itk.FastMarchingImageFilter[InternalImageType, InternalImageType].New(sigmoid,
TrialPoints=seeds,
SpeedConstant=1.0,
OutputSize=reader.GetOutput().GetBufferedRegion().GetSize() )
geodesicActiveContour = itk.GeodesicActiveContourLevelSetImageFilter[InternalImageType, InternalImageType, InternalPixelType].New(fastMarching, sigmoid,
PropagationScaling=float(argv[9]),
CurvatureScaling=1.0,
AdvectionScaling=1.0,
MaximumRMSError=0.02,
NumberOfIterations=800
)
thresholder = itk.BinaryThresholdImageFilter[InternalImageType, OutputImageType].New(geodesicActiveContour,
LowerThreshold=-1000,
UpperThreshold=0,
OutsideValue=0,
InsideValue=255)
writer = itk.ImageFileWriter[OutputImageType].New(thresholder, FileName=argv[2])
def rescaleAndWrite(filter, fileName):
caster = itk.RescaleIntensityImageFilter[InternalImageType, OutputImageType].New(filter,
OutputMinimum=0,
OutputMaximum=255)
itk.write(caster, fileName)
rescaleAndWrite(smoothing, "GeodesicActiveContourImageFilterOutput1.png")
rescaleAndWrite(gradientMagnitude, "GeodesicActiveContourImageFilterOutput2.png")
rescaleAndWrite(sigmoid, "GeodesicActiveContourImageFilterOutput3.png")
rescaleAndWrite(fastMarching, "GeodesicActiveContourImageFilterOutput4.png")
writer.Update()
print
print "Max. no. iterations: %d" % (geodesicActiveContour.GetNumberOfIterations())
print "Max. RMS error: %.3f" % (geodesicActiveContour.GetMaximumRMSError())
print
print "No. elapsed iterations: %d" % (geodesicActiveContour.GetElapsedIterations())
print "RMS change: %.3f" % (geodesicActiveContour.GetRMSChange())
itk.write(fastMarching, "GeodesicActiveContourImageFilterOutput4.mha")
itk.write(sigmoid, "GeodesicActiveContourImageFilterOutput3.mha")
itk.write(gradientMagnitude, "GeodesicActiveContourImageFilterOutput2.mha")
# a function to produce a full image from a cropped label image
def fullLabelImage( f ):
padLabels.SetInput( f.GetOutput() )
lm2li.UpdateLargestPossibleRegion()
i = lm2li.GetOutput()
imgDuplicator = itk.ImageDuplicator[i].New(i)
imgDuplicator.Update()
return imgDuplicator.GetOutput()
# the list to store the images of the wap and caseins spots
caseins = []
waps = []
# v = itk.show(labels, MaxOpacity=0.05)
itk.write(overlayNuclei, readerNuclei.GetFileName()+"-nuclei.tif") #, True)
# let start, really
statisticsLabelMapRobustNuclei.Update()
shapeLabelMapNuclei.Update()
otsuNuclei.Compute()
if opts.visualValidation:
padLabels.SetRegion( readerNuclei.GetOutput().GetLargestPossibleRegion() )
if opts.saveSegmentation:
itk.write( labelRobustNuclei, readerNuclei.GetFileName()+"-nuclei-segmentation.nrrd", True)
# test strel # should work with the image type, an image instance or a filter # and should work with a list, a tuple, an int or an itk.Size for s in [2, (2, 2), [2, 2], itk.Size[2](2)] : st = itk.strel(dim, s) (tpl, param) = itk.template(st) assert tpl == itk.FlatStructuringElement assert param[0] == dim assert st.GetRadius().GetElement(0) == st.GetRadius().GetElement(1) == 2 # test size s = itk.size(reader) assert s.GetElement(0) == s.GetElement(1) == 256 s = itk.size(reader.GetOutput()) assert s.GetElement(0) == s.GetElement(1) == 256 s = itk.size(reader.GetOutput().GetPointer()) assert s.GetElement(0) == s.GetElement(1) == 256 # test range assert itk.range(reader) == (0, 255) assert itk.range(reader.GetOutput()) == (0, 255) assert itk.range(reader.GetOutput().GetPointer()) == (0, 255) # test write itk.write(reader, sys.argv[2])
seeds.Initialize()
seeds.InsertElement(0, node)
fastMarching.SetTrialPoints(seeds)
fastMarching.SetOutputSize(reader.GetOutput().GetBufferedRegion().GetSize())
stoppingTime = float(argv[9])
fastMarching.SetStoppingValue(stoppingTime)
writer.Update()
# other outputs
def rescaleAndWrite(filter, fileName):
caster = itk.RescaleIntensityImageFilter[InternalImageType,
OutputImageType].New(
filter,
OutputMinimum=0,
OutputMaximum=255)
itk.write(caster, fileName)
rescaleAndWrite(smoothing, "FastMarchingFilterOutput1.png")
rescaleAndWrite(gradientMagnitude, "FastMarchingFilterOutput2.png")
rescaleAndWrite(sigmoid, "FastMarchingFilterOutput3.png")
rescaleAndWrite(fastMarching, "FastMarchingFilterOutput4.png")
#internal outputs
itk.write(fastMarching, "FastMarchingFilterOutput4.mha")
itk.write(sigmoid, "FastMarchingFilterOutput3.mha")
itk.write(gradientMagnitude, "FastMarchingFilterOutput2.mha")
# # Example on the use of the MeanImageFilter # import itk from sys import argv dim = 2 PixelType = itk.F ImageType = itk.Image[PixelType, dim] reader = itk.ImageFileReader[ImageType].New( FileName=argv[1] ) fftFilter = itk.FFTWRealToComplexConjugateImageFilter[PixelType, dim].New(reader) fftFilter2 = itk.FFTWComplexConjugateToRealImageFilter[PixelType, dim].New(fftFilter) cast = itk.CastImageFilter[ImageType, itk.Image[itk.UC, dim]].New( fftFilter2 ) itk.write(cast, argv[2]) print itk.size(fftFilter).GetElement(0), itk.size(fftFilter).GetElement(1)
maskCENP.SetLabel( l )
# search the spots
thCENP.SetLowerThreshold( 1 )
statsCENP.UpdateLargestPossibleRegion()
while number_of_objects(statsCENP) > 44:
thCENP.SetLowerThreshold( thCENP.GetLowerThreshold() + 1 )
statsCENP.Update()
# some basic outputs about nuclei
nucleusLabelObject = borderNuclei.GetOutput().GetLabelObject(l)
print >> nucleiFile, '"'+readerNuclei.GetFileName()+'"', l, nucleusLabelObject.GetPhysicalSize(), nucleusLabelObject.GetRegionElongation(), number_of_objects(statsCENP), ' '.join([str(i) for i in itk.physical_point_to_index(borderNuclei, nucleusLabelObject.GetCentroid())])
for l2 in range(1, statsCENP.GetOutput().GetNumberOfLabelObjects()+1):
lo = statsCENP.GetOutput().GetLabelObject(l2)
cog = lo.GetCenterOfGravity()
idx = itk.physical_point_to_index(cenpSpotsImg, cog)
cenpSpotsImg.SetPixel(idx, 255)
# copy label objects
cplo = itk.StatisticsLabelObject.UL3.New()
cplo.CopyDataFrom( lo )
cenpImg.PushLabelObject( cplo )
print >> genesFile, '"'+readerNuclei.GetFileName()+'"', l, " ".join(str(i) for i in idx), " ".join(str(i) for i in cog)
if opts.saveSegmentation:
itk.write(lm2iNuclei, readerNuclei.GetFileName()+"-nuclei.nrrd", True)
itk.write(cenpSpotsImg, readerNuclei.GetFileName()+"-CENP.nrrd", True)
if opts.visualValidation:
itk.write(overlayNuclei, readerNuclei.GetFileName()+"-nuclei.tif") #, True)
itk.write(overlayCENP, readerNuclei.GetFileName()+"-CENP.tif") #, True)
# # 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. # #==========================================================================*/ # # Example on the use of the CannyEdgeDetectionImageFilter # import itk from sys import argv, stderr, exit itk.auto_progress(2) if len(argv) < 3: print >> stderr, "Usage: CannyEdgeDetectionImageFilter.py inputImage outputImage [variance]" exit(1) variance = 2.0 if len(argv) > 3: variance = float( argv[3] ) print variance reader = itk.ImageFileReader.IF2.New( FileName=argv[1] ) filter = itk.CannyEdgeDetectionImageFilter.IF2IF2.New( reader, Variance=variance ) outputCast = itk.RescaleIntensityImageFilter.IF2IUC2.New( filter, OutputMinimum=0, OutputMaximum=255 ) itk.write( outputCast, argv[2] )
stats = itk.LabelImageToStatisticsLabelMapFilter[ImageType, ImageType,
LabelMapType].New(
mask, nuclei)
# drop the objects too small to be a nucleus, and the ones on the border
size = itk.ShapeOpeningLabelMapFilter[LabelMapType].New(stats,
Attribute='Size',
Lambda=100)
border = itk.ShapeOpeningLabelMapFilter[LabelMapType].New(
size, Attribute='SizeOnBorder', Lambda=10, ReverseOrdering=True)
# reoder the labels. The objects with the highest mean are the first ones.
relabel = itk.StatisticsRelabelLabelMapFilter[LabelMapType].New(
border, Attribute='Mean')
# for visual validation
overlay = itk.LabelMapOverlayImageFilter[LabelMapType, ImageType,
RGBImageType].New(relabel, nuclei)
itk.write(overlay, "nuclei-overlay.png")
spots = itk.ImageFileReader[ImageType].New(FileName="images/spots.png")
# mask the spot image to keep only the nucleus zone. The rest of the image is cropped, excepted a border of 2 pixels
maskSpots = itk.LabelMapMaskImageFilter[LabelMapType,
ImageType].New(relabel,
spots,
Label=1,
Crop=True,
CropBorder=2)
th = itk.BinaryThresholdImageFilter[ImageType,
ImageType].New(maskSpots,
LowerThreshold=110)
sstats = itk.BinaryImageToStatisticsLabelMapFilter[ImageType, ImageType,
LabelMapType].New(
th, nuclei)
