def transform(self, dataset, amount=0.5, threshold=0.0, sigma=1.0):
"""This filter performs anisotropic diffusion on an image using
the classic Perona-Malik, gradient magnitude-based equation.
"""
# Initial progress
self.progress.value = 0
self.progress.maximum = 100
# Approximate percentage of work completed after each step in the
# transform
step_pct = iter([10, 20, 90, 100])
try:
import itk
from tomviz import itkutils
except Exception as exc:
print("Could not import necessary module(s)")
raise exc
try:
self.progress.message = "Converting data to ITK image"
self.progress.value = 0
# Get the ITK image.
itk_image = itkutils.dataset_to_itk_image(dataset)
self.progress.value = next(step_pct)
self.progress.message = "Running filter"
self.progress.value = next(step_pct)
unsharp_mask = \
itk.UnsharpMaskImageFilter.New(Input=itk_image)
unsharp_mask.SetAmount(amount)
unsharp_mask.SetThreshold(threshold)
unsharp_mask.SetSigma(sigma)
itkutils.observe_filter_progress(self,
unsharp_mask, self.progress.value,
next(step_pct))
try:
unsharp_mask.Update()
except RuntimeError:
return
self.progress.message = "Saving results"
itkutils.set_itk_image_on_dataset(unsharp_mask.GetOutput(),
dataset)
self.progress.value = next(step_pct)
except Exception as exc:
print("Problem encountered while running %s" %
self.__class__.__name__)
raise exc
def transform(self, dataset):
"""Define this method for Python operators that transform the input
array. This example uses an ITK filter to add 10 to each voxel value."""
# Try imports to make sure we have everything that is needed
try:
from tomviz import itkutils
import itk
except Exception as exc:
print("Could not import necessary module(s)")
raise exc
self.progress.value = 0
self.progress.maximum = 100
# Add a try/except around the ITK portion. ITK exceptions are
# passed up to the Python layer, so we can at least report what
# went wrong with the script, e.g., unsupported image type.
try:
self.progress.value = 0
self.progress.message = "Converting data to ITK image"
# Get the ITK image
itk_image = itkutils.dataset_to_itk_image(dataset)
itk_input_image_type = type(itk_image)
self.progress.value = 30
self.progress.message = "Running filter"
# ITK filter
filter = itk.AddImageFilter[itk_input_image_type, # Input 1
itk_input_image_type, # Input 2
itk_input_image_type].New() # Output
filter.SetInput1(itk_image)
filter.SetConstant2(10)
itkutils.observe_filter_progress(self, filter, 30, 70)
try:
filter.Update()
except RuntimeError: # Exception thrown when ITK filter is aborted
return
self.progress.message = "Saving results"
itkutils.set_itk_image_on_dataset(filter.GetOutput(), dataset)
self.progress.value = 100
except Exception as exc:
print("Problem encountered while running %s" %
self.__class__.__name__)
raise exc
def transform(self,
dataset,
stencil_radius=2,
iterations=10,
threshold=50.0):
"""This filter smooths a binary image by evolving a level set with a
curvature-based speed function. The Stencil Radius determines the scale
of the noise to remove. The Threshold determines the iso-contour
brightness to discriminate between two pixel classes.
"""
# Initial progress
self.progress.value = 0
self.progress.maximum = 100
# Approximate percentage of work completed after each step in the
# transform
STEP_PCT = [10, 20, 30, 70, 80, 90, 100]
try:
import itk
import itkTypes
from tomviz import itkutils
except Exception as exc:
print("Could not import necessary module(s)")
raise exc
# Return values
returnValue = None
# Add a try/except around the ITK portion. ITK exceptions are
# passed up to the Python layer, so we can at least report what
# went wrong with the script, e.g,, unsupported image type.
try:
self.progress.value = STEP_PCT[0]
self.progress.message = "Converting data to ITK image"
# Get the ITK image
itk_image = itkutils.dataset_to_itk_image(dataset)
itk_input_image_type = type(itk_image)
self.progress.message = "Casting input to float type"
itk_filter_image_type = itk.Image[itkTypes.F,
itk_image.GetImageDimension()]
caster = itk.CastImageFilter[itk_input_image_type,
itk_filter_image_type].New()
caster.SetInput(itk_image)
itkutils.observe_filter_progress(self, caster, STEP_PCT[1],
STEP_PCT[2])
try:
caster.Update()
except RuntimeError:
return
self.progress.message = "Running filter"
smoothing_filter = itk.BinaryMinMaxCurvatureFlowImageFilter[
itk_filter_image_type, itk_filter_image_type].New()
smoothing_filter.SetThreshold(threshold)
smoothing_filter.SetStencilRadius(stencil_radius)
smoothing_filter.SetNumberOfIterations(iterations)
smoothing_filter.SetTimeStep(0.0625)
smoothing_filter.SetInput(caster)
itkutils.observe_filter_progress(self, smoothing_filter,
STEP_PCT[2], STEP_PCT[3])
try:
smoothing_filter.Update()
except RuntimeError:
return
itk_image_data = smoothing_filter.GetOutput()
# Cast output to the input type
self.progress.message = "Casting output to input type"
caster = itk.CastImageFilter[itk_filter_image_type,
itk_input_image_type].New()
caster.SetInput(itk_image_data)
itkutils.observe_filter_progress(self, caster, STEP_PCT[3],
STEP_PCT[4])
try:
caster.Update()
except RuntimeError:
return
itk_image_data = caster.GetOutput()
self.progress.value = STEP_PCT[5]
self.progress.message = "Saving results"
itkutils.set_itk_image_on_dataset(itk_image_data, dataset)
self.progress.value = STEP_PCT[6]
except Exception as exc:
print("Problem encountered while running %s" %
self.__class__.__name__)
raise exc
return returnValue
def transform(self,
dataset,
structuring_element_id=0,
radius=1,
object_label=1,
background_label=0):
"""Erode segmented objects with a given label by a spherically symmetric
structuring element with a given radius.
"""
# Initial progress
self.progress.value = 0
self.progress.maximum = 100
# Approximate percentage of work completed after each step in the
# transform
STEP_PCT = [10, 20, 90, 100]
try:
import itk
from tomviz import itkutils
except Exception as exc:
print("Could not import necessary module(s)")
raise exc
# Add a try/except around the ITK portion. ITK exceptions are
# passed up to the Python layer, so we can at least report what
# went wrong with the script, e.g,, unsupported image type.
try:
self.progress.value = STEP_PCT[0]
self.progress.message = "Converting data to ITK image"
# Get the ITK image
itk_image = itkutils.dataset_to_itk_image(dataset)
itk_input_image_type = type(itk_image)
itk_kernel_type = itk.FlatStructuringElement[3]
if (structuring_element_id == 0):
itk_kernel = itk_kernel_type.Box(radius)
elif (structuring_element_id == 1):
itk_kernel = itk_kernel_type.Ball(radius)
elif (structuring_element_id == 2):
itk_kernel = itk_kernel_type.Cross(radius)
else:
raise Exception('Invalid kernel shape id %d' %
structuring_element_id)
self.progress.value = STEP_PCT[1]
self.progress.message = "Running filter"
erode_filter = itk.BinaryErodeImageFilter[itk_input_image_type,
itk_input_image_type,
itk_kernel_type].New()
erode_filter.SetErodeValue(object_label)
erode_filter.SetBackgroundValue(background_label)
erode_filter.SetKernel(itk_kernel)
erode_filter.SetInput(itk_image)
itkutils.observe_filter_progress(self, erode_filter, STEP_PCT[1],
STEP_PCT[2])
try:
erode_filter.Update()
except RuntimeError:
return
self.progress.message = "Saving results"
itkutils.set_itk_image_on_dataset(erode_filter.GetOutput(),
dataset)
self.progress.value = STEP_PCT[3]
except Exception as exc:
print("Problem encountered while running %s" %
self.__class__.__name__)
raise exc
def transform(self, dataset, minimum_radius=0.5, maximum_radius=6.):
"""Segment pores. The pore size must be greater than the minimum radius
and less than the maximum radius. Pores will be separated according to
the minimum radius."""
# Initial progress
self.progress.value = 0
self.progress.maximum = 100
# Approximate percentage of work completed after each step in the
# transform
step_pct = iter([5, 5, 5, 5, 5, 5, 5, 5, 5, 30, 10, 5, 5, 5])
try:
import itk
from tomviz import itkutils
import numpy as np
except Exception as exc:
print("Could not import necessary module(s)")
raise exc
# Return values
returnValues = None
# Add a try/except around the ITK portion. ITK exceptions are
# passed up to the Python layer, so we can at least report what
# went wrong with the script, e.g,, unsupported image type.
try:
self.progress.message = "Converting data to ITK image"
# Get the ITK image
itk_input_image = itkutils.dataset_to_itk_image(dataset)
self.progress.value = next(step_pct)
# Reduce noise
smoothed = median_filter(self, step_pct, itk_input_image)
# Enhance pore contrast
enhanced = unsharp_mask(self, step_pct, smoothed)
thresholded = threshold(self, step_pct, enhanced)
dimension = itk_input_image.GetImageDimension()
spacing = itk_input_image.GetSpacing()
closing_radius = itk.Size[dimension]()
closing_radius.Fill(1)
for dim in range(dimension):
radius = int(np.round(maximum_radius / spacing[dim]))
if radius > closing_radius[dim]:
closing_radius[dim] = radius
StructuringElementType = itk.FlatStructuringElement[dimension]
structuring_element = \
StructuringElementType.Ball(closing_radius)
particle_mask = morphological_closing(self, step_pct, thresholded,
structuring_element)
encapsulated = encapsulate(self, step_pct, thresholded,
particle_mask, structuring_element)
distance = get_distance(self, step_pct, encapsulated)
segmented = watershed(self, step_pct, distance, minimum_radius)
inverted = invert(self, step_pct, thresholded)
segmented.DisconnectPipeline()
inverted.DisconnectPipeline()
separated = apply_mask(self, step_pct, segmented, inverted)
separated.DisconnectPipeline()
particle_mask.DisconnectPipeline()
in_particles = apply_mask(self, step_pct, separated, particle_mask)
opening_radius = itk.Size[dimension]()
opening_radius.Fill(1)
for dim in range(dimension):
radius = int(np.round(minimum_radius / spacing[dim]))
if radius > opening_radius[dim]:
opening_radius[dim] = radius
structuring_element = \
StructuringElementType.Ball(opening_radius)
opened = opening_by_reconstruction(self, step_pct, in_particles,
structuring_element)
self.progress.message = "Saving results"
label_map_dataset = dataset.create_child_dataset()
itkutils.set_itk_image_on_dataset(opened, label_map_dataset)
# Set up dictionary to return operator results
returnValues = {}
returnValues["label_map"] = label_map_dataset
except Exception as exc:
print("Problem encountered while running %s" %
self.__class__.__name__)
raise exc
return returnValues
def transform(self, dataset, lower_threshold=40.0, upper_threshold=255.0):
"""This filter computes a binary threshold on the data set and
stores the result in a child data set. It does not modify the dataset
passed in."""
# Initial progress
self.progress.value = 0
self.progress.maximum = 100
# Approximate percentage of work completed after each step in the
# transform
STEP_PCT = [20, 40, 75, 90, 100]
# Set up return value
returnValue = None
# Try imports to make sure we have everything that is needed
try:
self.progress.message = "Loading modules"
import itk
from tomviz import itkutils
except Exception as exc:
print("Could not import necessary module(s)")
raise exc
# Add a try/except around the ITK portion. ITK exceptions are
# passed up to the Python layer, so we can at least report what
# went wrong with the script, e.g,, unsupported image type.
try:
self.progress.value = STEP_PCT[0]
self.progress.message = "Converting data to ITK image"
# Get the ITK image
itk_image = itkutils.dataset_to_itk_image(dataset)
itk_input_image_type = type(itk_image)
self.progress.value = STEP_PCT[1]
self.progress.message = "Running filter"
# We change the output type to unsigned char 3D
# (itk.Image.UC3D) to save memory in the output label map
# representation.
itk_output_image_type = itk.Image.UC3
# ITK's BinaryThresholdImageFilter does the hard work
threshold_filter = itk.BinaryThresholdImageFilter[
itk_input_image_type, itk_output_image_type].New()
python_cast = itkutils.get_python_voxel_type(itk_image)
threshold_filter.SetLowerThreshold(python_cast(lower_threshold))
threshold_filter.SetUpperThreshold(python_cast(upper_threshold))
threshold_filter.SetInsideValue(1)
threshold_filter.SetOutsideValue(0)
threshold_filter.SetInput(itk_image)
itkutils.observe_filter_progress(self, threshold_filter,
STEP_PCT[2], STEP_PCT[3])
try:
threshold_filter.Update()
except RuntimeError:
return returnValue
self.progress.message = "Creating child data set"
# Set the output as a new child data object of the current data set
label_map_dataset = dataset.create_child_dataset()
itkutils.set_itk_image_on_dataset(threshold_filter.GetOutput(),
label_map_dataset)
self.progress.value = STEP_PCT[4]
returnValue = {"thresholded_segmentation": label_map_dataset}
except Exception as exc:
print("Problem encountered while running %s" %
self.__class__.__name__)
raise exc
return returnValue
def transform(self, dataset, minimum_radius=4):
"""Segment spherical particles from a homogeneous, dark background.
Even if the particles have pores, they are segmented as solid
structures.
"""
# Initial progress
self.progress.value = 0
self.progress.maximum = 100
# Approximate percentage of work completed after each step in the
# transform
step_pct = iter([10, 10, 10, 10, 10, 10, 10, 10, 10, 10])
try:
import itk
from tomviz import itkutils
except Exception as exc:
print("Could not import necessary module(s)")
raise exc
# Return values
returnValues = None
# Add a try/except around the ITK portion. ITK exceptions are
# passed up to the Python layer, so we can at least report what
# went wrong with the script, e.g,, unsupported image type.
try:
self.progress.message = "Converting data to ITK image"
# Get the ITK image
itk_input_image = itkutils.dataset_to_itk_image(dataset)
self.progress.value = next(step_pct)
smoothed = median_filter(self, step_pct, itk_input_image)
Dimension = 3
StructuringElementType = itk.FlatStructuringElement[Dimension]
structuring_element = StructuringElementType.Ball(minimum_radius)
# Reduces reconstruction streak artifact effects and artifacts far
# from the center of the image.
opened = opening_by_reconstruction(self, step_pct, smoothed,
structuring_element)
thresholded = threshold(self, step_pct, opened)
# Removes structures smaller than the structuring element while
# retaining particle shape
# Grayscale implementation is faster than binary
cleaned = opening_by_reconstruction(self, step_pct, thresholded,
structuring_element)
# Fill in pores
# Grayscale implementation is faster than binary
closed = morphological_closing(self, step_pct, cleaned,
structuring_element)
# Fill in pores
# Grayscale implementation is faster than binary
filled = fill_holes(self, step_pct, closed)
# Disconnect separate particles and reduce reconstruction
opening = morphological_opening(self, step_pct, filled,
structuring_element)
self.progress.message = "Saving results"
label_map_dataset = dataset.create_child_dataset()
itkutils.set_itk_image_on_dataset(opening,
label_map_dataset,
dtype=type(itk_input_image))
# Set up dictionary to return operator results
returnValues = {}
returnValues["label_map"] = label_map_dataset
except Exception as exc:
print("Problem encountered while running %s" %
self.__class__.__name__)
raise exc
return returnValues
def transform(self,
dataset,
number_of_thresholds=1,
enable_valley_emphasis=False):
"""This filter performs semi-automatic multithresholding of a data set.
Voxels are automatically classified into a chosen number of classes such
that inter-class variance of the voxel values is minimized. The output
is a label map with one label per voxel class.
"""
# Initial progress
self.progress.value = 0
self.progress.maximum = 100
# Approximate percentage of work completed after each step in the
# transform
STEP_PCT = [10, 20, 70, 90, 100]
try:
import itk
import itkExtras
import itkTypes
from tomviz import itkutils
except Exception as exc:
print("Could not import necessary module(s)")
raise exc
# Return values
returnValues = None
# Add a try/except around the ITK portion. ITK exceptions are
# passed up to the Python layer, so we can at least report what
# went wrong with the script, e.g,, unsupported image type.
try:
self.progress.value = STEP_PCT[0]
self.progress.message = "Converting data to ITK image"
# Get the ITK image
itk_image = itkutils.dataset_to_itk_image(dataset)
itk_input_image_type = type(itk_image)
# OtsuMultipleThresholdsImageFilter's wrapping requires that the
# input and output image types be the same.
itk_threshold_image_type = itk_input_image_type
# Otsu multiple threshold filter
otsu_filter = itk.OtsuMultipleThresholdsImageFilter[
itk_input_image_type, itk_threshold_image_type].New()
otsu_filter.SetNumberOfThresholds(number_of_thresholds)
otsu_filter.SetValleyEmphasis(enable_valley_emphasis)
otsu_filter.SetInput(itk_image)
itkutils.observe_filter_progress(self, otsu_filter, STEP_PCT[1],
STEP_PCT[2])
try:
otsu_filter.Update()
except RuntimeError:
return
print("Otsu threshold(s): %s" % (otsu_filter.GetThresholds(), ))
itk_image_data = otsu_filter.GetOutput()
# Cast threshold output to an integral type if needed.
py_buffer_type = itk_threshold_image_type
voxel_type = itkExtras.template(itk_threshold_image_type)[1][0]
if voxel_type is itkTypes.F or voxel_type is itkTypes.D:
self.progress.message = "Casting output to integral type"
# Unsigned char supports 256 labels, or 255 threshold levels.
# This should be sufficient for all but the most unusual use
# cases.
py_buffer_type = itk.Image.UC3
caster = itk.CastImageFilter[itk_threshold_image_type,
py_buffer_type].New()
caster.SetInput(itk_image_data)
itkutils.observe_filter_progress(self, caster, STEP_PCT[2],
STEP_PCT[3])
try:
caster.Update()
except RuntimeError:
return
itk_image_data = caster.GetOutput()
self.progress.value = STEP_PCT[3]
self.progress.message = "Saving results"
label_map_dataset = dataset.create_child_dataset()
itkutils.set_itk_image_on_dataset(itk_image_data,
label_map_dataset,
dtype=py_buffer_type)
self.progress.value = STEP_PCT[4]
# Set up dictionary to return operator results
returnValues = {}
returnValues["label_map"] = label_map_dataset
except Exception as exc:
print("Problem encountered while running %s" %
self.__class__.__name__)
raise exc
return returnValues