def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._image_logic = vtk.vtkImageLogic()
module_utils.setup_vtk_object_progress(self, self._image_logic,
'Performing image logic')
self._image_cast = vtk.vtkImageCast()
module_utils.setup_vtk_object_progress(
self, self._image_cast, 'Casting scalar type before image logic')
self._config.operation = 0
self._config.output_true_value = 1.0
# 'choice' widget with 'base:int' type will automatically get cast
# to index of selection that user makes.
config_list = [
('Operation:', 'operation', 'base:int',
'choice', 'The operation that should be performed.',
tuple(self._operations)),
('Output true value:', 'output_true_value', 'base:float', 'text',
'Output voxels that are TRUE will get this value.')
]
ScriptedConfigModuleMixin.__init__(self, config_list, {
'Module (self)': self,
'vtkImageLogic': self._image_logic
})
self.sync_module_logic_with_config()
def __init__(self, inputs = (2, 2)): """ Initialization """ lib.ProcessingFilter.ProcessingFilter.__init__(self, inputs) self.vtkfilter = vtk.vtkImageLogic() self.vtkfilter.SetOutputTrueValue(255)
def __init__(self, inputs=(2, 2)):
"""
Initialization
"""
lib.ProcessingFilter.ProcessingFilter.__init__(self, inputs)
self.vtkfilter = vtk.vtkImageLogic()
self.vtkfilter.SetOutputTrueValue(255)
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkImageLogic(), 'Processing.',
('vtkImageData', 'vtkImageData'), ('vtkImageData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def VTKImageLogic(x1,x2=None,op="or",numret=False):
if type(x1) == np.ndarray: i1 = NumToVTKImage(x1)
else: i1 = x1
if type(x2) == np.ndarray: i2 = NumToVTKImage(x2)
elif x2: i2 = x2
m = vtk.vtkImageLogic()
numops = [ "and","or","xor","nand","nor","not"]
vtkops = [ m.SetOperationToAnd, m.SetOperationToOr, m.SetOperationToXor, m.SetOperationToNand, m.SetOperationToNor, m.SetOperationToNot]
m.SetOutputTrueValue(1.0)
vtkops[numops.index(op)]()
m.SetInput1Data(i1)
if x2 is not None: m.SetInput2Data(i2)
o = m.GetOutput()
m.Update()
if numret: return VTKImageToNum(o)
else: return o
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._image_logic = vtk.vtkImageLogic()
module_utils.setup_vtk_object_progress(self, self._image_logic, "Performing image logic")
self._image_cast = vtk.vtkImageCast()
module_utils.setup_vtk_object_progress(self, self._image_cast, "Casting scalar type before image logic")
self._config.operation = 0
self._config.output_true_value = 1.0
# 'choice' widget with 'base:int' type will automatically get cast
# to index of selection that user makes.
config_list = [
(
"Operation:",
"operation",
"base:int",
"choice",
"The operation that should be performed.",
tuple(self._operations),
),
(
"Output true value:",
"output_true_value",
"base:float",
"text",
"Output voxels that are TRUE will get this value.",
),
]
ScriptedConfigModuleMixin.__init__(
self, config_list, {"Module (self)": self, "vtkImageLogic": self._image_logic}
)
self.sync_module_logic_with_config()
def removeIslandsMorphologyDecruft(self,
image,
foregroundLabel,
backgroundLabel,
iterations=1):
#
# make binary mask foregroundLabel->1, backgroundLabel->0
#
binThresh = vtk.vtkImageThreshold()
binThresh.SetInputData(image)
binThresh.ThresholdBetween(foregroundLabel, foregroundLabel)
binThresh.SetInValue(1)
binThresh.SetOutValue(0)
binThresh.Update()
#
# first, erode iterations number of times
#
eroder = slicer.vtkImageErode()
eroderImage = vtk.vtkImageData()
eroderImage.DeepCopy(binThresh.GetOutput())
eroder.SetInputData(eroderImage)
for iteration in range(iterations):
eroder.SetForeground(1)
eroder.SetBackground(0)
eroder.SetNeighborTo8()
eroder.Update()
eroderImage.DeepCopy(eroder.GetOutput())
#
# now save only islands bigger than a specified size
#
# note that island operation happens in unsigned long space
# but the slicer editor works in Short
castIn = vtk.vtkImageCast()
castIn.SetInputConnection(eroder.GetInputConnection(0, 0))
castIn.SetOutputScalarTypeToUnsignedLong()
# now identify the islands in the inverted volume
# and find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
islandMath.SetInputConnection(castIn.GetOutputPort())
islandMath.SetFullyConnected(self.fullyConnected)
islandMath.SetMinimumSize(self.minimumSize)
# note that island operation happens in unsigned long space
# but the slicer editor works in Short
castOut = vtk.vtkImageCast()
castOut.SetInputConnection(islandMath.GetOutputPort())
castOut.SetOutputScalarTypeToShort()
castOut.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
print("%d islands created (%d ignored)" %
(islandCount, ignoredIslands))
#
# now map everything back to 0 and 1
#
thresh = vtk.vtkImageThreshold()
thresh.SetInputConnection(castOut.GetOutputPort())
thresh.ThresholdByUpper(1)
thresh.SetInValue(1)
thresh.SetOutValue(0)
thresh.Update()
#
# now, dilate back (erode background) iterations_plus_one number of times
#
dilater = slicer.vtkImageErode()
dilaterImage = vtk.vtkImageData()
dilaterImage.DeepCopy(thresh.GetOutput())
dilater.SetInputData(dilaterImage)
for iteration in range(1 + iterations):
dilater.SetForeground(0)
dilater.SetBackground(1)
dilater.SetNeighborTo8()
dilater.Update()
dilaterImage.DeepCopy(dilater.GetOutput())
#
# only keep pixels in both original and dilated result
#
logic = vtk.vtkImageLogic()
logic.SetInputConnection(0, dilater.GetInputConnection(0, 0))
logic.SetInputConnection(1, binThresh.GetOutputPort())
#if foregroundLabel == 0:
# logic.SetOperationToNand()
#else:
logic.SetOperationToAnd()
logic.SetOutputTrueValue(1)
logic.Update()
#
# convert from binary mask to 1->foregroundLabel, 0->backgroundLabel
#
unbinThresh = vtk.vtkImageThreshold()
unbinThresh.SetInputConnection(logic.GetOutputPort())
unbinThresh.ThresholdBetween(1, 1)
unbinThresh.SetInValue(foregroundLabel)
unbinThresh.SetOutValue(backgroundLabel)
unbinThresh.Update()
image.DeepCopy(unbinThresh.GetOutput())
def removeIslandsMorphologyDecruft(self,image,foregroundLabel,backgroundLabel,iterations=1):
#
# make binary mask foregroundLabel->1, backgroundLabel->0
#
binThresh = vtk.vtkImageThreshold()
binThresh.SetInputData( image )
binThresh.ThresholdBetween(foregroundLabel,foregroundLabel)
binThresh.SetInValue( 1 )
binThresh.SetOutValue( 0 )
binThresh.Update()
#
# first, erode iterations number of times
#
eroder = slicer.vtkImageErode()
eroderImage = vtk.vtkImageData()
eroderImage.DeepCopy(binThresh.GetOutput())
eroder.SetInputData(eroderImage)
for iteration in range(iterations):
eroder.SetForeground( 1 )
eroder.SetBackground( 0 )
eroder.SetNeighborTo8()
eroder.Update()
eroderImage.DeepCopy(eroder.GetOutput())
#
# now save only islands bigger than a specified size
#
# note that island operation happens in unsigned long space
# but the slicer editor works in Short
castIn = vtk.vtkImageCast()
castIn.SetInputConnection( eroder.GetInputConnection(0,0) )
castIn.SetOutputScalarTypeToUnsignedLong()
# now identify the islands in the inverted volume
# and find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
islandMath.SetInputConnection( castIn.GetOutputPort() )
islandMath.SetFullyConnected( self.fullyConnected )
islandMath.SetMinimumSize( self.minimumSize )
# note that island operation happens in unsigned long space
# but the slicer editor works in Short
castOut = vtk.vtkImageCast()
castOut.SetInputConnection( islandMath.GetOutputPort() )
castOut.SetOutputScalarTypeToShort()
castOut.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
print( "%d islands created (%d ignored)" % (islandCount, ignoredIslands) )
#
# now map everything back to 0 and 1
#
thresh = vtk.vtkImageThreshold()
thresh.SetInputConnection( castOut.GetOutputPort() )
thresh.ThresholdByUpper(1)
thresh.SetInValue( 1 )
thresh.SetOutValue( 0 )
thresh.Update()
#
# now, dilate back (erode background) iterations_plus_one number of times
#
dilater = slicer.vtkImageErode()
dilaterImage = vtk.vtkImageData()
dilaterImage.DeepCopy(thresh.GetOutput())
dilater.SetInputData(dilaterImage)
for iteration in range(1+iterations):
dilater.SetForeground( 0 )
dilater.SetBackground( 1 )
dilater.SetNeighborTo8()
dilater.Update()
dilaterImage.DeepCopy(dilater.GetOutput())
#
# only keep pixels in both original and dilated result
#
logic = vtk.vtkImageLogic()
logic.SetInputConnection(0, dilater.GetInputConnection(0,0))
logic.SetInputConnection(1, binThresh.GetOutputPort())
#if foregroundLabel == 0:
# logic.SetOperationToNand()
#else:
logic.SetOperationToAnd()
logic.SetOutputTrueValue(1)
logic.Update()
#
# convert from binary mask to 1->foregroundLabel, 0->backgroundLabel
#
unbinThresh = vtk.vtkImageThreshold()
unbinThresh.SetInputConnection( logic.GetOutputPort() )
unbinThresh.ThresholdBetween( 1,1 )
unbinThresh.SetInValue( foregroundLabel )
unbinThresh.SetOutValue( backgroundLabel )
unbinThresh.Update()
image.DeepCopy(unbinThresh.GetOutput())
def _appendSingle(self, volToAppend, uid):
"""
@type uid: C{int}
@param uid: index to be assigned to this volume.
Method merges proivded volume with existing, cached volume. Following
algorithm is used (e - existing image, n - new image, M - image mask):
e = (n AND (M(n) XOR M(e))) + e
@return: C{None}
"""
# If privided volume is the first one, simply take it as output volume.
if not self.outVol:
self.outVol = volToAppend.GetIndexed(uid)
print >>sys.stderr, "No volume found. Creating initial volume."
return
# Otherwise:
# XOR existing volume with the new
print "...start:"
volCurNewXor = vtk.vtkImageLogic()
volCurNewXor.SetInput1(volToAppend.GetMask())
volCurNewXor.SetInput2(self.GetMask())
volCurNewXor.SetOperationToXor()
# Intersect xored image with the new volume getting the part of the
# volume to be updated
print "...start volXorAndNew:"
volXorAndNew = vtk.vtkImageLogic()
volXorAndNew.SetInput1(volToAppend.GetMask())
volXorAndNew.SetInput2(volCurNewXor.GetOutput())
volXorAndNew.SetOperationToAnd()
# Change the image type
print "...start imgCast:"
cast = vtk.vtkImageCast()
cast.SetInput(volXorAndNew.GetOutput())
cast.SetOutputScalarTypeToUnsignedChar()
# Assign index to the 'new' volume
print "...start volToReplace"
volToReplace = vtk.vtkImageMask()
volToReplace.SetImageInput(volToAppend.GetIndexed(uid))
volToReplace.SetMaskInput(cast.GetOutput())
# Add both volumes
print "...start newSumVol"
newSumVol = vtk.vtkImageMathematics()
newSumVol.SetOperationToAdd()
newSumVol.SetNumberOfThreads(1)
newSumVol.SetInput1(volToReplace.GetOutput())
newSumVol.SetInput2(self.outVol)
# This is funny :)
# In order to not to store mass of the references we create deep copy
# of the result - that gives much speedup.
newSumVol.GetOutput().Update()
self.outVol.DeepCopy(newSumVol.GetOutput())
print "...stop:"
def testAllLogic(self):
# append multiple displaced spheres into an RGB image.
# Image pipeline
renWin = vtk.vtkRenderWindow()
logics = ["And", "Or", "Xor", "Nand", "Nor", "Not"]
types = [
"Float", "Double", "UnsignedInt", "UnsignedLong", "UnsignedShort",
"UnsignedChar"
]
sphere1 = list()
sphere2 = list()
logic = list()
mapper = list()
actor = list()
imager = list()
for idx, operator in enumerate(logics):
ScalarType = types[idx]
sphere1.append(vtk.vtkImageEllipsoidSource())
sphere1[idx].SetCenter(95, 100, 0)
sphere1[idx].SetRadius(70, 70, 70)
eval('sphere1[idx].SetOutputScalarTypeTo' + ScalarType + '()')
sphere1[idx].Update()
sphere2.append(vtk.vtkImageEllipsoidSource())
sphere2[idx].SetCenter(161, 100, 0)
sphere2[idx].SetRadius(70, 70, 70)
eval('sphere2[idx].SetOutputScalarTypeTo' + ScalarType + '()')
sphere2[idx].Update()
logic.append(vtk.vtkImageLogic())
logic[idx].SetInput1Data(sphere1[idx].GetOutput())
if operator != "Not":
logic[idx].SetInput2Data(sphere2[idx].GetOutput())
logic[idx].SetOutputTrueValue(150)
eval('logic[idx].SetOperationTo' + operator + '()')
mapper.append(vtk.vtkImageMapper())
mapper[idx].SetInputConnection(logic[idx].GetOutputPort())
mapper[idx].SetColorWindow(255)
mapper[idx].SetColorLevel(127.5)
actor.append(vtk.vtkActor2D())
actor[idx].SetMapper(mapper[idx])
imager.append(vtk.vtkRenderer())
imager[idx].AddActor2D(actor[idx])
renWin.AddRenderer(imager[idx])
imager[0].SetViewport(0, .5, .33, 1)
imager[1].SetViewport(.33, .5, .66, 1)
imager[2].SetViewport(.66, .5, 1, 1)
imager[3].SetViewport(0, 0, .33, .5)
imager[4].SetViewport(.33, 0, .66, .5)
imager[5].SetViewport(.66, 0, 1, .5)
renWin.SetSize(768, 512)
# render and interact with data
iRen = vtk.vtkRenderWindowInteractor()
iRen.SetRenderWindow(renWin)
renWin.Render()
img_file = "TestAllLogic.png"
vtk.test.Testing.compareImage(
iRen.GetRenderWindow(),
vtk.test.Testing.getAbsImagePath(img_file),
threshold=25)
vtk.test.Testing.interact()
def testAllLogic(self):
# append multiple displaced spheres into an RGB image.
# Image pipeline
renWin = vtk.vtkRenderWindow()
logics = ["And", "Or", "Xor", "Nand", "Nor", "Not"]
types = ["Float", "Double", "UnsignedInt", "UnsignedLong", "UnsignedShort", "UnsignedChar"]
sphere1 = list()
sphere2 = list()
logic = list()
mapper = list()
actor = list()
imager = list()
for idx, operator in enumerate(logics):
ScalarType = types[idx]
sphere1.append(vtk.vtkImageEllipsoidSource())
sphere1[idx].SetCenter(95, 100, 0)
sphere1[idx].SetRadius(70, 70, 70)
eval('sphere1[idx].SetOutputScalarTypeTo' + ScalarType + '()')
sphere1[idx].Update()
sphere2.append(vtk.vtkImageEllipsoidSource())
sphere2[idx].SetCenter(161, 100, 0)
sphere2[idx].SetRadius(70, 70, 70)
eval('sphere2[idx].SetOutputScalarTypeTo' + ScalarType + '()')
sphere2[idx].Update()
logic.append(vtk.vtkImageLogic())
logic[idx].SetInput1Data(sphere1[idx].GetOutput())
if operator != "Not":
logic[idx].SetInput2Data(sphere2[idx].GetOutput())
logic[idx].SetOutputTrueValue(150)
eval('logic[idx].SetOperationTo' + operator + '()')
mapper.append(vtk.vtkImageMapper())
mapper[idx].SetInputConnection(logic[idx].GetOutputPort())
mapper[idx].SetColorWindow(255)
mapper[idx].SetColorLevel(127.5)
actor.append(vtk.vtkActor2D())
actor[idx].SetMapper(mapper[idx])
imager.append(vtk.vtkRenderer())
imager[idx].AddActor2D(actor[idx])
renWin.AddRenderer(imager[idx])
imager[0].SetViewport(0, .5, .33, 1)
imager[1].SetViewport(.33, .5, .66, 1)
imager[2].SetViewport(.66, .5, 1, 1)
imager[3].SetViewport(0, 0, .33, .5)
imager[4].SetViewport(.33, 0, .66, .5)
imager[5].SetViewport(.66, 0, 1, .5)
renWin.SetSize(768, 512)
# render and interact with data
iRen = vtk.vtkRenderWindowInteractor()
iRen.SetRenderWindow(renWin);
renWin.Render()
img_file = "TestAllLogic.png"
vtk.test.Testing.compareImage(iRen.GetRenderWindow(), vtk.test.Testing.getAbsImagePath(img_file), threshold=25)
vtk.test.Testing.interact()
