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#==========================================================================
#
# 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.
#
#==========================================================================*/
import itk
import tempfile
import os
dim = 2
PixelType = itk.UC
# check the repr string
assert "<itkTemplate itk::Image>" == repr(itk.Image)
# template should work with CType instance and with numbers
ImageType = itk.Image[PixelType, dim]
# template should return the same class with a class as parameter
# or with an object of this class, and should also be the same
# with the attribute
# create instances of image for the next tests
im = ImageType.New()
im2 = ImageType.New()
readerType = itk.ImageFileReader[ImageType]
readerType2 = itk.ImageFileReader[im]
readerType3 = itk.ImageFileReader.IUC2
assert readerType == readerType2 == readerType3
# we should be able to get the template and its parameters from the class
(tpl, parameters) = itk.template(ImageType)
assert tpl == itk.Image
assert parameters == (PixelType, dim)
# the template must raise a KeyError exception if the template parameter
# is unknown
try:
itk.ImageFileReader['unknown parameter']
raise Exception('no exception sent for unknown parameter')
except KeyError:
pass
# TODO: test the rest of the dict interface
# TODO: test __eq__, __ne__ and __hash__
# something else ?
# now test the New method
# without parameter
reader = readerType.New()
reader2 = readerType.New()
# with an attribute parameter
reader = readerType.New(FileName='test.png')
assert reader.GetFileName() == 'test.png'
# wwith a wrong attribute name
try:
reader = readerType.New(WrongName='test.png')
raise Exception('no exception sent for wrong attribute name')
except AttributeError:
pass
# wwith a wrong attribute type
try:
reader = readerType.New(FileName=1)
raise Exception('no exception sent for wrong attribute type')
except:
pass
# pass filter as argument for input
# to a filter with SetInput method
median = itk.MedianImageFilter[ImageType, ImageType].New(reader)
assert reader.GetOutput() == median.GetInput()
# filter type determined by the input passed as an arg
median_args = itk.MedianImageFilter.New(reader.GetOutput())
assert itk.class_(median) == itk.class_(median_args)
# filter type determined by the input passed as a primary method input
median_kwarg = itk.MedianImageFilter.New(Input=reader.GetOutput())
assert itk.class_(median) == itk.class_(median_kwarg)
# to a filter with a SetImage method
calculator = itk.MinimumMaximumImageCalculator[ImageType].New(reader)
# not GetImage() method here to verify it's the right image
# to a filter with several inputs
sub = itk.SubtractImageFilter[ImageType, ImageType, ImageType].New(reader, reader2)
assert reader.GetOutput() == sub.GetInput(0)
assert reader2.GetOutput() == sub.GetInput(1)
# pass image as argument for input
# to a filter with SetInput method
median = itk.MedianImageFilter[ImageType, ImageType].New(im)
assert im == median.GetInput()
# to a filter with a SetImage method
calculator = itk.MinimumMaximumImageCalculator[ImageType].New(im)
# not GetImage() method here to verify it's the right image
# to a filter with several inputs
sub = itk.SubtractImageFilter[ImageType, ImageType, ImageType].New(im, im2)
assert im == sub.GetInput(0)
assert im2 == sub.GetInput(1)
# pass invalid input
try:
itk.MedianImageFilter[ImageType, ImageType].New(1)
raise Exception('no exception sent for wrong input type')
except:
pass
try:
itk.SubtractImageFilter[ImageType, ImageType, ImageType].New(im, "wrong")
raise Exception('no exception sent for wrong 2nd input type')
except TypeError:
pass
# pass both input and attribute
recons = itk.ReconstructionByDilationImageFilter[
ImageType, ImageType].New(reader.GetOutput(), im, FullyConnected=True)
assert reader.GetOutput() == recons.GetInput(0)
assert im == recons.GetInput(1)
assert recons.GetFullyConnected()
# pass input to object which do not take one
try:
ImageType.New(im)
raise Exception('no exception sent for object without input')
except AttributeError:
pass
# pass no attribute to reader and see if it automatically detects input image type.
# Since we cannot easily know which type of images are supported in python, we generate
# a lot of different types and try to create images using these types, create empty images
# that we save, and then try to read them to test the reader.
# We ignore the exception raised for creating types of pixels and images and from trying to
# write the images on the hard disk the first time. We only care about exception raised from
# the reader.
def pixel_type_from_IO(pixel, component, dimension):
import itk
if pixel == 'scalar':
PixelType = component
elif pixel == 'rgb':
PixelType = itk.RGBPixel[component]
elif pixel == 'rgba':
PixelType = itk.RGBAPixel[component]
elif pixel == 'offset':
PixelType = itk.Offset[dimension]
elif pixel == 'vector':
PixelType = itk.Vector[component, dimension]
elif pixel == 'point':
PixelType = itk.Point[component, dimension]
elif pixel == 'covariant_vector':
PixelType = itk.CovariantVector[component, dimension]
elif pixel == 'symmetric_second_rank_tensor':
PixelType = itk.SymmetricSecondRankTensor[component, dimension]
elif pixel == 'diffusion_tensor_3D':
PixelType = itk.DiffusionTensor3D[component]
elif pixel == 'complex':
PixelType = itk.complex[component]
elif pixel == 'fixed_array':
PixelType = itk.FixedArray[component, dimension]
elif pixel == 'matrix':
PixelType = itk.Matrix[component, dimension, dimension]
else:
raise RuntimeError("Unknown pixel type %s." % pixel)
return PixelType
dimensions = [2, 3]
component_type_dic= {"float":itk.F, "double":itk.D,
"unsigned_char":itk.UC, "unsigned_short":itk.US, "unsigned_int":itk.UI,
"unsigned_long":itk.UL, "char":itk.SC, "short":itk.SS,
"int":itk.SI, "long":itk.SL, "bool":itk.B}
pixel_types = ['scalar', 'rgb', 'rgba', 'offset', 'vector', 'point',
'covariant_vector', 'symmetric_second_rank_tensor',
'diffusion_tensor_3D', 'complex', 'fixed_array', 'matrix']
dir_name=tempfile.mkdtemp()
pixel_type_error = []
image_error = []
other_error = []
writer_error = []
reader_error = []
pixel_fill_error = []
for dim in dimensions:
for p in pixel_types:
for c, cv in component_type_dic.items():
try:
PixelType = pixel_type_from_IO(p, cv, dim)
except Exception as ex:
pixel_type_error.append(ex)
continue
try:
ImageType=itk.Image[PixelType, dim]
im=ImageType.New()
except Exception as ex:
image_error.append(ex)
continue
try:
zero_value = itk.NumericTraits[PixelType].ZeroValue()
except:
try:
zero_value = PixelType()
zero_value.Fill(0)
except:
try:
zero_value = PixelType(0)
except Exception as ex:
pixel_fill_error.append(ex)
try:
im.SetRegions(5)
im.Allocate()
im.FillBuffer( zero_value )
filename = os.path.join(dir_name, "_".join([p,c,str(dim)]) + ".nrrd")
except Exception as ex:
other_error.append(ex)
continue
try:
writer = itk.ImageFileWriter.New(Input=im, FileName=filename)
writer.Update()
except Exception as ex:
writer_error.append(str(ex) + " - " + str([p, c, dim]))
continue
try:
reader = itk.ImageFileReader.New(FileName=filename)
reader.Update()
print("Dimension: %i ; Pixel Type: %s ; Component Type: %s - OK" % (dim, p, c))
except Exception as ex:
reader_error.append(ex)
continue
if reader_error or other_error:
print("PixelType error: %s" % pixel_type_error)
print("Image error: %s" % image_error)
print("Other error: %s" % other_error)
print("Writer error: %s" % writer_error)
print("Pixel Fill error: %s" % pixel_fill_error)
print("Reader error: %s" % reader_error)
raise AssertionError()
# Test that ImageFileWriter can be called with filter given as input
# with 'Input' keyword.
reader=itk.ImageFileReader[itk.Image[itk.F,3]].New()
try:
writer = itk.ImageFileWriter.New(Input=reader, FileName=filename)
except TypeError:
raise Exception("Writer doesn't accept filter with 'Input' keyword")
# TODO: test auto_progress
# but how ?
# something else ?
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