How to use iType method in fMBT

Best Python code snippet using fMBT_python

module2module.py

Source:module2module.py

1#==========================================================================2#3#   Copyright Insight Software Consortium4#5#   Licensed under the Apache License, Version 2.0 (the "License");6#   you may not use this file except in compliance with the License.7#   You may obtain a copy of the License at8#9#          http://www.apache.org/licenses/LICENSE-2.0.txt10#11#   Unless required by applicable law or agreed to in writing, software12#   distributed under the License is distributed on an "AS IS" BASIS,13#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.14#   See the License for the specific language governing permissions and15#   limitations under the License.16#17#==========================================================================*/18# def custom_callback(name):19#   print "loading %s submodule..." % name20# import itkConfig21# itkConfig.ImportCallback = custom_callback22import itk, sys23import ITKCommon24import ITKBinaryMathematicalMorphology25import ITKImageStatistics26import ITKSmoothing27import ITKDistanceMap28import ITKImageIntensity29import ITKIOImageBase30import ITKThresholding31import ITKImageGrid32PType = itk.UC33dim = 234IType = itk.Image[PType, dim]35kernel = itk.strel(2, 1)36# create the reader37reader = itk.ImageFileReader[IType].New(FileName=sys.argv[1])38sources = []39image = ITKCommon.Image[PType, dim].New()40r = itk.ImageRegion._2()41r.SetSize((10, 10))42image.SetRegions(r)43image.Allocate()44sources.append(("ITKCommon", image))45sources.append(("ITKIOImageBase", reader.GetOutput()))46otsu = ITKThresholding.OtsuThresholdImageFilter[IType, IType].New(reader)47sources.append(("ITKThresholding", otsu.GetOutput()))48flip = ITKImageGrid.FlipImageFilter[IType].New(reader)49sources.append(("ITKImageGrid", flip.GetOutput()))50abs = ITKImageIntensity.AbsImageFilter[IType, IType].New(reader)51sources.append(("ITKImageIntensity", abs.GetOutput()))52bdilate = ITKBinaryMathematicalMorphology.BinaryDilateImageFilter[IType, IType, kernel].New(reader, Kernel=kernel)53sources.append(("ITKBinaryMathematicalMorphology", bdilate.GetOutput()))54minmax = ITKImageStatistics.MinimumMaximumImageFilter[IType].New(reader)55sources.append(("ITKImageStatistics", minmax.GetOutput()))56median = ITKSmoothing.MedianImageFilter[IType, IType].New(reader)57sources.append(("ITKSmoothing", median.GetOutput()))58distance = ITKDistanceMap.DanielssonDistanceMapImageFilter[IType, IType].New(reader)59sources.append(("ITKDistanceMap", distance.GetOutput()))60# sobel = EdgesAndContours.SobelEdgeDetectionImageFilter[IType, IType].New(reader)61# sources.append(("EdgesAndContours", sobel.GetOutput()))62# laplacian = Filtering.LaplacianImageFilter[IType, IType].New(reader)63# sources.append(("Filtering", laplacian.GetOutput()))64dests = []65dotsu = ITKThresholding.OtsuThresholdImageFilter[IType, IType].New(reader)66dests.append(("ITKThresholding", dotsu))67dflip = ITKImageGrid.FlipImageFilter[IType].New()68dests.append(("ITKImageGrid", dflip))69dabs = ITKImageIntensity.AbsImageFilter[IType, IType].New()70dests.append(("ITKImageIntensity", dabs))71dbdilate = ITKBinaryMathematicalMorphology.BinaryDilateImageFilter[IType, IType, kernel].New(Kernel=kernel)72dests.append(("ITKBinaryMathematicalMorphology", dbdilate))73dminmax = ITKImageStatistics.MinimumMaximumImageFilter[IType].New()74dests.append(("ITKImageStatistics", dminmax))75dmedian = ITKSmoothing.MedianImageFilter[IType, IType].New()76dests.append(("ITKSmoothing", dmedian))77ddistance = ITKDistanceMap.DanielssonDistanceMapImageFilter[IType, IType].New()78dests.append(("ITKDistanceMap", ddistance))79# dsobel = EdgesAndContours.SobelEdgeDetectionImageFilter[IType, IType].New()80# dests.append(("EdgesAndContours", dsobel))81# dlaplacian = Filtering.LaplacianImageFilter[IType, IType].New()82# dests.append(("Filtering", dlaplacian))83writer = ITKIOImageBase.ImageFileWriter[IType].New(FileName='out.png')84dests.append(("ITKIOImageBase", writer))85nb = 086failList = []87for sname, s in sources:88  for dname, d in dests:89    nb += 190    d.SetInput( s )91    try:92      d.Update()93      print "%s -> %s pass" % (sname, dname)94    except RuntimeError, e:95      print "%s -> %s fail" % (sname, dname)96      failList.append((sname, dname))97print98print "%i tests succeed" % (nb - len(failList))99print "%i tests failed" % len(failList)...

template.py

Source:template.py

1#==========================================================================2#3#   Copyright Insight Software Consortium4#5#   Licensed under the Apache License, Version 2.0 (the "License");6#   you may not use this file except in compliance with the License.7#   You may obtain a copy of the License at8#9#          http://www.apache.org/licenses/LICENSE-2.0.txt10#11#   Unless required by applicable law or agreed to in writing, software12#   distributed under the License is distributed on an "AS IS" BASIS,13#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.14#   See the License for the specific language governing permissions and15#   limitations under the License.16#17#==========================================================================*/18import itk19dim = 220PType = itk.UC21# check the repr string22assert "<itkTemplate itk::Image>" == repr(itk.Image)23# template should work with CType instance and with numbers24IType = itk.Image[PType, dim]25# template should return the same class with a class as parameter26# or with an object of this class, and should also be the same27# with the attribute28# create instances of image for the next tests29im = IType.New()30im2 = IType.New()31readerType = itk.ImageFileReader[IType]32readerType2 = itk.ImageFileReader[im]33readerType3 = itk.ImageFileReader.IUC234assert readerType == readerType2 == readerType335# we should be able to get the template and its parameters from the class36(tpl, parameters) = itk.template( IType )37assert tpl == itk.Image38assert parameters == (PType, dim)39# the template must raise a KeyError exception if the template parameter40# is unknown41try :42  itk.ImageFileReader['unknown parameter']43  raise Exception('no exception sent for unknown parameter')44except KeyError:45  pass46# TODO: test the rest of the dict interface47# TODO: test __eq__, __ne__ and __hash__48# something else ?49# now test the New method50# without parameter51reader = readerType.New()52reader2 = readerType.New()53# with an attribute parameter54reader = readerType.New(FileName='test.png')55assert reader.GetFileName() == 'test.png'56# wwith a wrong attribute name57try :58  reader = readerType.New(WrongName='test.png')59  raise Exception('no exception sent for wrong attribute name')60except AttributeError:61  pass62# wwith a wrong attribute type63try :64  reader = readerType.New(FileName=1)65  raise Exception('no exception sent for wrong attribute type')66except :67  pass68# pass filter as argument for input69# to a filter with SetInput method70median = itk.MedianImageFilter[IType, IType].New(reader)71assert reader.GetOutput() == median.GetInput()72# to a filter with a SetImage method73calculator = itk.MinimumMaximumImageCalculator[IType].New(reader)74# not GetImage() method here to verify it's the right image75# to a filter with several inputs76sub = itk.SubtractImageFilter[IType, IType, IType].New(reader, reader2)77assert reader.GetOutput() == sub.GetInput(0)78assert reader2.GetOutput() == sub.GetInput(1)79# pass image as argument for input80# to a filter with SetInput method81median = itk.MedianImageFilter[IType, IType].New(im)82assert im == median.GetInput()83# to a filter with a SetImage method84calculator = itk.MinimumMaximumImageCalculator[IType].New(im)85# not GetImage() method here to verify it's the right image86# to a filter with several inputs87sub = itk.SubtractImageFilter[IType, IType, IType].New(im, im2)88assert im == sub.GetInput(0)89assert im2 == sub.GetInput(1)90# pass invalid input91try:92  itk.MedianImageFilter[IType, IType].New(1)93  raise Exception('no exception sent for wrong input type')94except:95  pass96try:97  itk.SubtractImageFilter[IType, IType, IType].New(im, "wrong")98  raise Exception('no exception sent for wrong 2nd input type')99except TypeError:100  pass101# pass both input and attribute102recons = itk.ReconstructionByDilationImageFilter[IType, IType].New(reader.GetOutput(), im, FullyConnected=True)103assert reader.GetOutput() == recons.GetInput(0)104assert im == recons.GetInput(1)105assert recons.GetFullyConnected() == True106# pass input to object which do not take one107try:108  IType.New(im)109  raise Exception('no exception sent for object without input')110except AttributeError:111  pass112# TODO: test auto_progress113# but how ?...

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