def attribute_dict(i, name):
"""Returns a dict with the attribute values in keys and a list of the
corresponding objects in value
i: the input LabelImage
name: the name of the attribute
"""
import itk
i = itk.output(i)
relabel = itk.StatisticsRelabelLabelMapFilter[i].New(i,
Attribute=name,
ReverseOrdering=True,
InPlace=False)
relabel.UpdateLargestPossibleRegion()
r = relabel.GetOutput()
d = {}
# required because range is overloaded in this module
from builtins import range
for i in range(1, r.GetNumberOfLabelObjects() + 1):
lo = r.GetLabelObject(i)
v = lo.__getattribute__("Get" + name)()
l_list = d.get(v, [])
l_list.append(lo)
d[v] = l_list
return d
def Show(self, itkIm, title="noname") :
""" Display an image, with optional title
If different titles are used then multiple images will be available in imview.
Flip between them with the menu or space bar
"""
import itk
#itkIm = itk.image(itkIm)
itkIm = itk.output(itkIm)
if not self.connected :
# do the login now that we have an image type
self.imviewObj = itk.Imview[itkIm]
self.Connection = self.imviewObj.ImviewLogin(self.portNum)
self.connected = True
print "Connected"
print self.Connection
self.ImageTemp = itk.template(itkIm)[1]
else:
if itk.template(itkIm)[1] != self.ImageTemp:
self.ImageTemp = itk.template(itkIm)[1]
self.imviewObj = itk.Imview[itkIm]
# transmit the image
status = self.imviewObj.ImviewPutImage(itkIm, self.Connection, title)
if (status != 0):
# Failed to send image. Assume that imview has died
self.__StartImview__()
status = self.imviewObj.ImviewPutImage(itkIm, self.Connection, title)
if (status != 0):
print "Something seriously wrong - give up on this Imview instance"
def attributes_list(i, names):
"""Returns a list of the specified attributes for the objects in the image.
i: the input LabelImage
name: the attribute name
"""
import itk
i = itk.output(i)
relabel = itk.StatisticsRelabelLabelMapFilter[i].New(i,
Attribute=names[0],
ReverseOrdering=True,
InPlace=False)
relabel.UpdateLargestPossibleRegion()
r = relabel.GetOutput()
l_list = []
# required because range is overloaded in this module
from builtins import range
for i in range(1, r.GetNumberOfLabelObjects() + 1):
attrs = []
for name in names:
attrs.append(r.GetLabelObject(i).__getattribute__("Get" + name)())
l_list.append(tuple(attrs))
return l_list
def view(image):
have_imglyb = False
try:
import imglyb
have_imglyb = True
except ImportError:
pass
have_vtk = False
try:
import vtk
have_vtk = True
except ImportError:
pass
viewer = Viewer()
if is_arraylike(image):
arr = np.asarray(image)
image_from_array = itk.GetImageViewFromArray(arr)
viewer.image = image_from_array
elif have_vtk and isinstance(image, vtk.vtkImageData):
from vtk.util import numpy_support as vtk_numpy_support
array = vtk_numpy_support.vtk_to_numpy(image.GetPointData().GetScalars())
array.shape = tuple(image.GetDimensions())[::-1]
image_from_array = itk.GetImageViewFromArray(array)
image_from_array.SetSpacing(image.GetSpacing())
image_from_array.SetOrigin(image.GetOrigin())
viewer.image = image_from_array
elif have_imglyb and isinstance(image,
imglyb.util.ReferenceGuardingRandomAccessibleInterval):
image_array = imglyb.to_numpy(image)
image_from_array = itk.GetImageViewFromArray(image_array)
else:
# an itk.Image
viewer.image = itk.output(image)
return viewer
def number_of_objects(i):
"""Returns the number of objets in the image.
i: the input LabelImage
"""
import itk
i.UpdateLargestPossibleRegion()
i = itk.output(i)
return i.GetNumberOfLabelObjects()
def Overlay(self, itkIm, title="noname") :
"""Send an overlay to image with specified title"""
import itk
#itkIm = itk.image(itkIm)
itkIm = itk.output(itkIm)
if not self.connected :
print "No image being viewed - send one first"
else:
if itk.template(itkIm)[1] != self.ImageTemp:
self.ImageTemp = itk.template(itkIm)[1]
self.imviewObj = itk.Imview[itkIm]
status = self.imviewObj.ImviewPutOverlay(itkIm, self.Connection, title)
def to_itk_image(image_like):
if isinstance(image_like, itk.Image):
return image_like
if is_arraylike(image_like):
array = np.asarray(image_like)
can_use_view = array.flags['OWNDATA']
if have_dask and isinstance(image_like, dask.array.core.Array):
can_use_view = False
array = np.ascontiguousarray(array)
# JavaScript does not support 64-bit integers
if array.dtype == np.int64:
array = array.astype(np.float32)
elif array.dtype == np.uint64:
array = array.astype(np.float32)
if can_use_view:
image_from_array = itk.image_view_from_array(array)
else:
image_from_array = itk.image_from_array(array)
return image_from_array
elif have_vtk and isinstance(image_like, vtk.vtkImageData):
from vtk.util import numpy_support as vtk_numpy_support
array = vtk_numpy_support.vtk_to_numpy(
image_like.GetPointData().GetScalars())
array.shape = tuple(image_like.GetDimensions())[::-1]
image_from_array = itk.image_view_from_array(array)
image_from_array.SetSpacing(image_like.GetSpacing())
image_from_array.SetOrigin(image_like.GetOrigin())
return image_from_array
elif have_simpleitk and isinstance(image_like, sitk.Image):
array = sitk.GetArrayViewFromImage(image_like)
image_from_array = itk.image_view_from_array(array)
image_from_array.SetSpacing(image_like.GetSpacing())
image_from_array.SetOrigin(image_like.GetOrigin())
direction = image_like.GetDirection()
npdirection = np.asarray(direction)
npdirection = np.reshape(npdirection, (-1, 3))
itkdirection = itk.matrix_from_array(npdirection)
image_from_array.SetDirection(itkdirection)
return image_from_array
elif have_imagej:
import imglyb
if isinstance(image_like,
imglyb.util.ReferenceGuardingRandomAccessibleInterval):
array = imglyb.to_numpy(image_like)
image_from_array = itk.image_view_from_array(array)
return image_from_array
elif isinstance(image_like, itk.ProcessObject):
return itk.output(image_like)
return None
def SetInput(self, input):
import itk
img = itk.output(input)
self.__input__ = img
if img:
# Update to try to avoid to exit if a c++ exception is throwed
# sadely, it will not prevent the program to exit later...
# a real fix would be to wrap c++ exception in vtk
img.UpdateOutputInformation()
img.Update()
# flip the image to get the same representation than the vtk one
self.__flipper__ = itk.FlipImageFilter[img].New(Input=img)
axes = self.__flipper__.GetFlipAxes()
axes.SetElement(1, True)
self.__flipper__.SetFlipAxes(axes)
# change the spacing while still keeping the ratio to workaround vtk bug
# when spacing is very small
spacing_ = itk.spacing(img)
normSpacing = []
for i in range(0, spacing_.Size()):
normSpacing.append(
spacing_.GetElement(i) / spacing_.GetElement(0))
self.__changeInfo__ = itk.ChangeInformationImageFilter[img].New(
self.__flipper__,
OutputSpacing=normSpacing,
ChangeSpacing=True)
# now really convert the data
self.__itkvtkConverter__ = itk.ImageToVTKImageFilter[img].New(
self.__changeInfo__)
self.__volumeMapper__.SetInput(
self.__itkvtkConverter__.GetOutput())
# needed to avoid warnings
# self.__itkvtkConverter__.GetOutput() must be callable
import vtk
if not self.__outline__:
self.__outline__ = vtk.vtkOutlineFilter()
self.__outline__.SetInput(self.__itkvtkConverter__.GetOutput())
self.__outlineMapper__ = vtk.vtkPolyDataMapper()
self.__outlineMapper__.SetInput(self.__outline__.GetOutput())
self.__outlineActor__ = vtk.vtkActor()
self.__outlineActor__.SetMapper(self.__outlineMapper__)
self.__ren__.AddActor(self.__outlineActor__)
else:
self.__outline__.SetInput(self.__itkvtkConverter__.GetOutput())
self.Render()
def attribute_list( i, name ):
"""Returns a list of the specified attributes for the objects in the image.
i: the input LabelImage
name: the attribute name
"""
import itk
i = itk.output(i)
relabel = itk.StatisticsRelabelLabelMapFilter[i].New(i, Attribute=name, ReverseOrdering=True, InPlace=False)
relabel.UpdateLargestPossibleRegion()
r = relabel.GetOutput()
l = []
for i in range(1, r.GetNumberOfLabelObjects()+1):
l.append( r.GetLabelObject(i).__getattribute__("Get"+name)() )
return l
def SetInput(self, input) :
import itk
img = itk.output(input)
self.__input__ = img
if img :
# Update to try to avoid to exit if a c++ exception is throwed
# sadely, it will not prevent the program to exit later...
# a real fix would be to wrap c++ exception in vtk
img.UpdateOutputInformation()
img.Update()
# flip the image to get the same representation than the vtk one
self.__flipper__ = itk.FlipImageFilter[img].New(Input=img)
axes = self.__flipper__.GetFlipAxes()
axes.SetElement(1, True)
self.__flipper__.SetFlipAxes(axes)
# change the spacing while still keeping the ratio to workaround vtk bug
# when spacing is very small
spacing_ = itk.spacing(img)
normSpacing = []
for i in range(0, spacing_.Size()):
normSpacing.append( spacing_.GetElement(i) / spacing_.GetElement(0) )
self.__changeInfo__ = itk.ChangeInformationImageFilter[img].New(self.__flipper__, OutputSpacing=normSpacing, ChangeSpacing=True)
# now really convert the data
self.__itkvtkConverter__ = itk.ImageToVTKImageFilter[img].New(self.__changeInfo__)
self.__volumeMapper__.SetInput(self.__itkvtkConverter__.GetOutput())
# needed to avoid warnings
# self.__itkvtkConverter__.GetOutput() must be callable
import vtk
if not self.__outline__ :
self.__outline__ = vtk.vtkOutlineFilter()
self.__outline__.SetInput(self.__itkvtkConverter__.GetOutput())
self.__outlineMapper__ = vtk.vtkPolyDataMapper()
self.__outlineMapper__.SetInput(self.__outline__.GetOutput())
self.__outlineActor__ = vtk.vtkActor()
self.__outlineActor__.SetMapper(self.__outlineMapper__)
self.__ren__.AddActor(self.__outlineActor__)
else :
self.__outline__.SetInput(self.__itkvtkConverter__.GetOutput())
self.Render()
def attribute_dict( i, name ):
"""Returns a dict with the attribute values in keys and a list of the corresponding objects in value
i: the input LabelImage
name: the name of the attribute
"""
import itk
i = itk.output(i)
relabel = itk.StatisticsRelabelLabelMapFilter[i].New(i, Attribute=name, ReverseOrdering=True, InPlace=False)
relabel.UpdateLargestPossibleRegion()
r = relabel.GetOutput()
d = {}
for i in range(1, r.GetNumberOfLabelObjects()+1):
lo = r.GetLabelObject(i)
v = lo.__getattribute__("Get"+name)()
l = d.get( v, [] )
l.append( lo )
d[v] = l
return d
def validate(self, obj, value):
self._source_object = value
image_from_array = to_itk_image(value)
if image_from_array:
return image_from_array
try:
# an itk.Image or a filter that produces an Image
# return itk.output(value)
# Working around traitlets / ipywidgets update mechanism to
# force an update. While the result of __eq__ can indicate it is
# the same object, the actual contents may have changed, as
# indicated by image.GetMTime()
value = itk.output(value)
grafted = value.__New_orig__()
grafted.Graft(value)
return grafted
except:
self.error(obj, value)
def validate(self, obj, value):
if is_arraylike(value):
array = np.asarray(value)
self._source_object = array
if array.flags['OWNDATA']:
image_from_array = itk.GetImageViewFromArray(array)
else:
image_from_array = itk.GetImageFromArray(array)
return image_from_array
elif have_vtk and isinstance(value, vtk.vtkImageData):
from vtk.util import numpy_support as vtk_numpy_support
array = vtk_numpy_support.vtk_to_numpy(
value.GetPointData().GetScalars())
array.shape = tuple(value.GetDimensions())[::-1]
self._source_object = array
image_from_array = itk.GetImageViewFromArray(array)
image_from_array.SetSpacing(value.GetSpacing())
image_from_array.SetOrigin(value.GetOrigin())
return image_from_array
elif have_imglyb and isinstance(
value, imglyb.util.ReferenceGuardingRandomAccessibleInterval):
array = imglyb.to_numpy(value)
self._source_object = array
image_from_array = itk.GetImageViewFromArray(array)
return image_from_array
try:
# an itk.Image or a filter that produces an Image
# return itk.output(value)
# Working around traitlets / ipywidgets update mechanism to
# force an update. While the result of __eq__ can indicate it is
# the same object, the actual contents may have changed, as
# indicated by image.GetMTime()
value = itk.output(value)
self._source_object = value
grafted = value.__New_orig__()
grafted.Graft(value)
return grafted
except:
self.error(obj, value)
def computeRegion(lo, img):
img = itk.output(img)
import math
transform = lo.GetBinaryPrincipalAxesToPhysicalAxesTransform()
invTransform = itk.AffineTransform.D3.New()
transform.GetInverse( invTransform )
region = lo.GetRegion()
outputSpacing = [min(itk.spacing(img))]*3
dummyImg = itk.Image.UC3.New()
dummyImg.SetSpacing( outputSpacing )
idx = region.GetIndex()
size = region.GetSize()
minPoint = [4294967295L]*3
maxPoint = [-4294967295L]*3
for x in [idx[0], idx[0]+size[0]]:
for y in [idx[1], idx[1]+size[1]]:
for z in [idx[2], idx[2]+size[2]]:
inputPoint = img.TransformIndexToPhysicalPoint( [x,y,z] )
outputPoint = invTransform.TransformPoint( inputPoint )
for i in range(0,3):
if minPoint[i] > outputPoint[i]:
minPoint[i] = outputPoint[i]
if maxPoint[i] < outputPoint[i]:
maxPoint[i] = outputPoint[i]
minIdx = dummyImg.TransformPhysicalPointToIndex(minPoint)
maxIdx = dummyImg.TransformPhysicalPointToIndex(maxPoint)
outputIdx = []
outputSize = []
for i in range(0,3):
outputIdx.append(int(minIdx[i]))
outputSize.append( int(maxIdx[i] - minIdx[i]) )
uabc3 = 1.0
for v in itk.spacing(img):
uabc3 *= v
for v in lo.GetEquivalentEllipsoidSize():
uabc3 *= v
uabc3 = math.pow(uabc3, 1/3.0)
spacing2 = [uabc3 / v for v in lo.GetEquivalentEllipsoidSize()]
return (outputIdx, outputSize, outputSpacing, spacing2)
import numpy as np import matplotlib.pyplot as plt # import numpy.fft as fft np.core.arrayprint._line_width = 200 Dimension = 2 RealPixelType = itk.F RealImageType = itk.Image[RealPixelType, Dimension] # Read input Image inputImage = "/home/phc/Software/ITK/build-dev-cpp98/ExternalData/Modules/Remote/IsotropicWavelets/test/Input/checkershadow_Lch_512x512.tiff" reader = itk.ImageFileReader.New(FileName=inputImage) spacing = reader.GetOutput().GetSpacing() origin = reader.GetOutput().GetOrigin() direction = reader.GetOutput().GetDirection() # Perform FFT on input image castFilter = itk.CastImageFilter[itk.output(reader), RealImageType].New(reader) fftFilter = itk.ForwardFFTImageFilter.New(castFilter) fftFilter.Update() ComplexType=itk.output(fftFilter.GetOutput()) npInput = itk.GetArrayFromImage(castFilter) npFFT = itk.GetArrayFromImage(fftFilter) plt.imshow(npInput) itk.show(reader) # plt.show() inputImage3D = "/home/phc/Software/ITK/build-dev-cpp98/ExternalData/Modules/Remote/IsotropicWavelets/test/Input/collagen_21x21x9.tiff" reader3D = itk.ImageFileReader.New(FileName=inputImage) npInput3D = itk.GetArrayFromImage(reader3D)
except KeyError:
pass
# test ctype
assert itk.ctype("unsigned short") == itk.US
assert itk.ctype(" unsigned \n short \t ") == itk.US
assert itk.ctype("signed short") == itk.SS
assert itk.ctype("short") == itk.SS
try:
itk.ctype("dummy")
raise Exception("unknown C type should send an exception")
except KeyError:
pass
# test output
assert itk.output(reader) == reader.GetOutput()
assert itk.output(1) == 1
# test the deprecated image
assert itk.image(reader) == reader.GetOutput()
assert itk.image(1) == 1
# test size
s = itk.size(reader)
assert s[0] == s[1] == 256
s = itk.size(reader.GetOutput())
assert s[0] == s[1] == 256
# test physical size
s = itk.physical_size(reader)
assert s[0] == s[1] == 256.0
s = itk.physical_size(reader.GetOutput())
pass
# test ctype
assert itk.ctype("unsigned short") == itk.US
assert itk.ctype(" unsigned \n short \t ") == itk.US
assert itk.ctype("signed short") == itk.SS
assert itk.ctype("short") == itk.SS
try:
itk.ctype("dummy")
raise Exception("unknown C type should send an exception")
except KeyError:
pass
# test output
assert itk.output(reader) == reader.GetOutput()
assert itk.output(1) == 1
# test the deprecated image
assert itk.image(reader) == reader.GetOutput()
assert itk.image(1) == 1
# test size
s = itk.size(reader)
assert s[0] == s[1] == 256
s = itk.size(reader.GetOutput())
assert s[0] == s[1] == 256
# test physical size
s = itk.physical_size(reader)
assert s[0] == s[1] == 256.0
s = itk.physical_size(reader.GetOutput())
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 checkerboard(image1, image2, pattern=3, invert=False, **viewer_kwargs):
"""Compare two images with a checkerboard pattern.
This is particularly useful for examining registration results.
Parameters
----------
image1 : array_like, itk.Image, or vtk.vtkImageData
First image to use in the checkerboard.
image2 : array_like, itk.Image, or vtk.vtkImageData
Second image to use in the checkerboard.
pattern : int, optional, default: 3
Size of the checkerboard pattern.
invert : bool, optional, default: False
Swap inputs.
viewer_kwargs : optional
Keyword arguments for the viewer. See help(itkwidgets.view).
"""
itk_image1 = to_itk_image(image1)
if not itk_image1:
itk_image1 = itk.output(image1)
itk_image2 = to_itk_image(image2)
if not itk_image2:
itk_image2 = itk.output(image2)
input1 = itk_image1
input2 = itk_image2
region_image1 = itk_image1.GetLargestPossibleRegion()
region_image2 = itk_image2.GetLargestPossibleRegion()
same_physical_space = \
np.allclose(np.array(itk_image1.GetOrigin()), np.array(itk_image2.GetOrigin())) and \
np.allclose(np.array(itk_image1.GetSpacing()), np.array(itk_image2.GetSpacing())) and \
itk_image1.GetDirection() == itk_image2.GetDirection() and \
np.allclose(np.array(region_image1.GetIndex()), np.array(region_image2.GetIndex())) and \
np.allclose(np.array(region_image1.GetSize()), np.array(region_image2.GetSize()))
if not same_physical_space:
upsample_image2 = True
if itk_image1.GetSpacing() != itk_image2.GetSpacing():
min1 = min(itk_image1.GetSpacing())
min2 = min(itk_image2.GetSpacing())
if min2 < min1:
upsample_image2 = False
else:
size1 = max(itk.size(itk_image1))
size2 = max(itk.size(itk_image1))
if size2 > size1:
upsample_image2 = False
if upsample_image2:
resampler = itk.ResampleImageFilter.New(itk_image2)
resampler.UseReferenceImageOn()
resampler.SetReferenceImage(itk_image1)
resampler.Update()
input2 = resampler.GetOutput()
else:
resampler = itk.ResampleImageFilter.New(itk_image1)
resampler.UseReferenceImageOn()
resampler.SetReferenceImage(itk_image2)
resampler.Update()
input1 = resampler.GetOutput()
checkerboard_filter = itk.CheckerBoardImageFilter.New(input1, input2)
dimension = itk_image1.GetImageDimension()
checker_pattern = [pattern]*dimension
checkerboard_filter.SetCheckerPattern(checker_pattern)
checkerboard_filter_inverse = itk.CheckerBoardImageFilter.New(input2, input1)
if invert:
checkerboard_filter_inverse.Update()
checkerboard = checkerboard_filter_inverse.GetOutput()
else:
checkerboard_filter.Update()
checkerboard = checkerboard_filter.GetOutput()
if 'annotations' not in viewer_kwargs:
viewer_kwargs['annotations'] = False
if 'interpolation' not in viewer_kwargs:
viewer_kwargs['interpolation'] = False
if 'ui_collapsed' not in viewer_kwargs:
viewer_kwargs['ui_collapsed'] = True
viewer = Viewer(image=checkerboard, **viewer_kwargs)
# Heuristic to specify the max pattern size
max_size1 = int(min(itk.size(itk_image1)) / 8)
max_size1 = max(max_size1, pattern*2)
max_size2 = int(min(itk.size(itk_image2)) / 8)
max_size2 = max(max_size2, pattern*2)
max_size = max(max_size1, max_size2)
pattern_slider = widgets.IntSlider(value=pattern, min=2, max=max_size,
step=1, description='Pattern size:')
invert_checkbox = widgets.Checkbox(value=invert, description = 'Invert')
def update_checkerboard(change):
checker_pattern = [pattern_slider.value]*dimension
checkerboard_filter.SetCheckerPattern(checker_pattern)
checkerboard_filter_inverse.SetCheckerPattern(checker_pattern)
if invert_checkbox.value:
checkerboard_filter_inverse.Update()
viewer.image = checkerboard_filter_inverse.GetOutput()
else:
checkerboard_filter.Update()
viewer.image = checkerboard_filter.GetOutput()
pattern_slider.observe(update_checkerboard, ['value'])
invert_checkbox.observe(update_checkerboard, ['value'])
widget = widgets.VBox([viewer,
widgets.HBox([pattern_slider, invert_checkbox])])
return widget
def to_itk_image(image_like):
if isinstance(image_like, (itk.Image, itk.VectorImage)):
return image_like
if is_arraylike(image_like):
array = np.asarray(image_like)
can_use_view = array.flags['OWNDATA']
if have_dask and isinstance(image_like, dask.array.core.Array):
can_use_view = False
array = np.ascontiguousarray(array)
# JavaScript does not support 64-bit integers
if array.dtype == np.int64:
array = array.astype(np.float32)
elif array.dtype == np.uint64:
array = array.astype(np.float32)
if can_use_view:
image_from_array = itk.image_view_from_array(array)
else:
image_from_array = itk.image_from_array(array)
return image_from_array
elif have_vtk and isinstance(image_like, vtk.vtkImageData):
from vtk.util import numpy_support as vtk_numpy_support
array = vtk_numpy_support.vtk_to_numpy(
image_like.GetPointData().GetScalars())
dims = list(image_like.GetDimensions())
spacing = list(image_like.GetSpacing())
origin = list(image_like.GetOrigin())
# Check for zdim==1
zdim = dims.pop()
if zdim > 1:
# zdim>1, put it back in the dims array
dims.append(zdim)
else:
#zdim==1, remove z-spacing and z-origin
spacing.pop()
origin.pop()
array.shape = dims[::-1]
image_from_array = itk.image_view_from_array(array)
image_from_array.SetSpacing(spacing)
image_from_array.SetOrigin(origin)
return image_from_array
elif have_simpleitk and isinstance(image_like, sitk.Image):
array = sitk.GetArrayViewFromImage(image_like)
image_from_array = itk.image_view_from_array(array)
image_from_array.SetSpacing(image_like.GetSpacing())
image_from_array.SetOrigin(image_like.GetOrigin())
direction = image_like.GetDirection()
npdirection = np.asarray(direction)
npdirection = np.reshape(npdirection, (-1, image_like.GetDimension()))
itkdirection = itk.matrix_from_array(npdirection)
image_from_array.SetDirection(itkdirection)
return image_from_array
elif have_imagej:
import imglyb
if isinstance(image_like,
imglyb.util.ReferenceGuardingRandomAccessibleInterval):
array = imglyb.to_numpy(image_like)
image_from_array = itk.image_view_from_array(array)
return image_from_array
elif isinstance(image_like, itk.ProcessObject):
return itk.output(image_like)
return None
if len(sys.argv) != 5:
print "Usage: " + sys.argv[0] + " inputImage outputImage High_sub_bands levels"
sys.exit(1)
print ("Generating Wavelet Space for input image %s" % sys.argv[1])
inputImage = sys.argv[1]
outputImage = sys.argv[2]
high_sub_bands = int(sys.argv[3])
levels = int(sys.argv[4])
print "Reading image"
reader = itk.ImageFileReader.New(FileName=inputImage)
reader.Update()
spacing = reader.GetOutput().GetSpacing()
origin = reader.GetOutput().GetOrigin()
direction = reader.GetOutput().GetDirection()
castFilter = itk.CastImageFilter[itk.output(reader),itk.Image[itk.F,3]].New(reader)
print "Perform FFT on input image"
fftFilter = itk.ForwardFFTImageFilter.New(castFilter)
fftFilter.Update()
ComplexType=itk.output(fftFilter.GetOutput())
RealImageType = itk.Image[itk.F,3]
inverseFFT = itk.InverseFFTImageFilter[ ComplexType, RealImageType].New()
print "Create Forward Filter Bank"
PointType=itk.Point[itk.D,3]
SimoncelliType = itk.SimoncelliIsotropicWavelet[itk.F,3,PointType]
forwardFilterBankType = itk.WaveletFrequencyFilterBankGenerator[ComplexType,SimoncelliType]
forwardFilterBank = forwardFilterBankType.New()
forwardFilterBank.SetHighPassSubBands( high_sub_bands )
forwardFilterBank.SetSize( fftFilter.GetOutput().GetLargestPossibleRegion().GetSize() )
forwardFilterBank.Update()
castImageFilter.Update() filter2 = itk.ConnectedThresholdImageFilter.New(castImageFilter.GetOutput()) filter2.SetReplaceValue(255) filter2.SetLower(900) filter2.SetUpper(1600) index = itk.Index[dimension]() index[0] = 83 index[1] = 80 index[2] = 109 filter2.SetSeed(index) filter2.Update() in_type = itk.output(filter2) output_type = itk.Image[PixelType, dimension] rescaler = itk.RescaleIntensityImageFilter[in_type, output_type].New(filter2) rescaler.SetOutputMinimum(0) rescaler.SetOutputMaximum(255) rescaler.Update() itk.imwrite(filter2, os.path.join(filepath, itk_output_filename)) ren = vtk.vtkRenderer() renWin = vtk.vtkRenderWindow() renWin.AddRenderer(ren) iren = vtk.vtkRenderWindowInteractor() iren.SetRenderWindow(renWin) reader = vtk.vtkMetaImageReader()