def SetInput(self, Input):
"""Set the current input image
"""
import itk
img = itk.image( Input )
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()
# release the previous filters
self.clear()
itk.pipeline.SetInput( self, img )
# flip the image to get the same representation than the vtk one
self.connect( itk.FlipImageFilter[img].New() )
axes = self[0].GetFlipAxes()
axes.SetElement(1, True)
self[0].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.connect( itk.ChangeInformationImageFilter[img].New( OutputSpacing=normSpacing, ChangeSpacing=True ) )
# now really convert the data
self.connect( itk.ImageToVTKImageFilter[img].New() )
self.widget.SetInput( self[-1].GetImporter() )
def hist(input, bins=256, log=True, xrange=None, yrange=None, title="WrapITK histogram"):
"""Draw the histogram of the input image using http://gnuplot-py.sourceforge.net/ (http://gnuplot-py.sourceforge.net/).
"""
import Gnuplot, itk, numpy, math
img = itk.image(input)
a = itk.PyBuffer[img].GetArrayFromImage(img)
hist = numpy.histogram(a, bins=bins)
x = hist[1]
y = hist[0]
if log:
y = map(math.log10, y)
if xrange == None:
xrange = ( min(x)-1, max(x)+1 )
g = Gnuplot.Gnuplot()
g.title( title )
g.xlabel('Pixel values')
if log:
g.ylabel('log10( freq )')
else:
g.ylabel('freq')
g('set data style boxes')
g('set style fill solid border -1')
g.set_range( "xrange", xrange )
if yrange != None:
g.set_range( "yrange", yrange )
g.plot( zip( x, y ) )
return g
def hist(input,
bins=256,
log=True,
xrange=None,
yrange=None,
title="WrapITK histogram"):
"""Draw the histogram of the input image using http://gnuplot-py.sourceforge.net/ (http://gnuplot-py.sourceforge.net/).
"""
import Gnuplot, itk, numpy, math
img = itk.image(input)
a = itk.PyBuffer[img].GetArrayFromImage(img)
hist = numpy.histogram(a, bins=bins)
x = hist[1]
y = hist[0]
if log:
y = map(math.log10, y)
if xrange == None:
xrange = (min(x) - 1, max(x) + 1)
g = Gnuplot.Gnuplot()
g.title(title)
g.xlabel('Pixel values')
if log:
g.ylabel('log10( freq )')
else:
g.ylabel('freq')
g('set data style boxes')
g('set style fill solid border -1')
g.set_range("xrange", xrange)
if yrange != None:
g.set_range("yrange", yrange)
g.plot(zip(x, y))
return g
def number_of_objects( i ): """Returns the number of objets in the image. i: the input LabelImage """ i.UpdateLargestPossibleRegion() i = itk.image(i) return i.GetNumberOfLabelObjects()
def SetInput(self, input):
import itk
img = itk.image(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
"""
i = itk.image(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 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
"""
i = itk.image(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 SetInput(self, input) :
import itk
img = itk.image(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 __init__(self, InputImage, sigmaArray, ammount):
"""
Simple workflow implementing unsharp masking.
"""
im = itk.image(InputImage)
InType = itk.class_(im)
self.gaussianSmooth = itk.SmoothingRecursiveGaussianImageFilter[InType,InType].New(\
InputImage,
SigmaArray = sigmaArray)
self.substract = itk.SubtractImageFilter[InType,InType,InType].New(\
Input1 = InputImage,
Input2 = self.gaussianSmooth.GetOutput())
self.shiftScale = itk.ShiftScaleImageFilter[InType,InType].New(\
Input = self.substract.GetOutput(),
Scale = ammount,
Shift = 0)
self.addFilter = itk.AddImageFilter[InType,InType,InType].New(\
Input1 = self.shiftScale.GetOutput(),
Input2 = InputImage)
# 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())
assert s[0] == s[1] == 256.0
# test spacing
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())
assert s[0] == s[1] == 256.0
# test spacing
raise Exception("unknown class should send an exception")
except KeyError:
pass
# test ctype
assert itk.ctype("unsigned short") == itk.US
assert itk.ctype(" unsigned \n short \t ") == itk.US
try:
itk.ctype("dummy")
raise Exception("unknown C type should send an exception")
except KeyError:
pass
# test image
assert repr(itk.image(reader)) == repr(reader.GetOutput().GetPointer())
assert repr(itk.image(reader.GetOutput())) == repr(reader.GetOutput().GetPointer())
assert repr(itk.image(reader.GetOutput().GetPointer())) == repr(reader.GetOutput().GetPointer())
assert itk.image(1) == 1
# 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
