def __init__(self, *args, **kwargs):
self.logger = logging.getLogger(__name__)
self.featureClasses = getFeatureClasses()
self.settings = {}
self._enabledImagetypes = {}
self._enabledFeatures = {}
if len(args) == 1 and isinstance(args[0], six.string_types):
self.logger.info("Loading parameter file")
self.loadParams(args[0])
else:
# Set default settings and update with and changed settings contained in kwargs
self.settings = self._getDefaultSettings()
if len(kwargs) > 0:
self.logger.info('Applying custom settings')
self.settings.update(kwargs)
else:
self.logger.info('No customized settings, applying defaults')
self.logger.debug("Settings: %s", self.settings)
self._enabledImagetypes = {'Original': {}}
self.logger.info('Enabled image types: %s',
self._enabledImagetypes)
self._enabledFeatures = {}
for featureClassName in self.getFeatureClassNames():
self._enabledFeatures[featureClassName] = []
self.logger.info('Enabled features: %s', self._enabledFeatures)
self._setTolerance()
def __init__(self, *args, **kwargs):
self.logger = logging.getLogger(__name__)
self.featureClasses = getFeatureClasses()
self.inputImages = getInputImageTypes()
self.kwargs = {}
self.inputImages = {}
self.enabledFeatures = {}
if len(args) == 1 and isinstance(args[0], six.string_types):
self.loadParams(args[0])
else:
# Set default settings and update with and changed settings contained in kwargs
self.kwargs = {
'normalize': False,
'normalizeScale': 1,
'removeOutliers': None,
'resampledPixelSpacing': None, # No resampling by default
'interpolator': sitk.sitkBSpline,
'padDistance': 5,
'label': 1,
'verbose': False,
'enableCExtensions': True,
'additionalInfo': True
}
self.kwargs.update(kwargs)
self.inputImages = {'Original': {}}
self.enabledFeatures = {}
for featureClassName in self.getFeatureClassNames():
self.enabledFeatures[featureClassName] = []
def __init__(self):
self.logger = logging.getLogger('radiomics.addBaseline')
self.testUtils = RadiomicsTestUtils()
self.testCases = sorted(self.testUtils.getTests())
self.featureClasses = getFeatureClasses()
dataDir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "data")
self.baselineDir = os.path.join(dataDir, "baseline")
def compute(shape_type):
logger.info('Computing %s', shape_type)
featureNames = enabledFeatures[shape_type]
shapeClass = getFeatureClasses()[shape_type](croppedImage, croppedMask, **kwargs)
if featureNames is not None:
for feature in featureNames:
shapeClass.enableFeatureByName(feature)
for (featureName, featureValue) in six.iteritems(shapeClass.execute()):
newFeatureName = 'original_%s_%s' % (shape_type, featureName)
featureVector[newFeatureName] = featureValue
def get_features_list(results, extractor):
features_list = []
imageTypes = ['original','exponential','gradient','lbp-2D','logarithm','square','squareroot','wavelet']
waveletTypes = ['LLH','LHL','LHH','HLL','HLH','HHL','HHH','LLL']
for waveletType in waveletTypes:
imageTypes.append('wavelet-' + waveletType)
for imageType in imageTypes:
for feature_class in rad.getFeatureClasses().keys():
for feature in extractor.getFeatureNames(feature_class):
feature_name = '_'.join([imageType, feature_class, feature])
if feature_name in results.keys():
features_list.append(feature_name)
return features_list
def computeFeatures(self, image, mask, imageTypeName, **kwargs):
r"""
Compute signature using image, mask and \*\*kwargs settings.
This function computes the signature for just the passed image (original or derived), it does not pre-process or
apply a filter to the passed image. Features / Classes to use for calculation of signature are defined in
``self.enabledFeatures``. See also :py:func:`enableFeaturesByName`.
:param image: The cropped (and optionally filtered) SimpleITK.Image object representing the image used
:param mask: The cropped SimpleITK.Image object representing the mask used
:param imageTypeName: String specifying the filter applied to the image, or "original" if no filter was applied.
:param kwargs: Dictionary containing the settings to use for this particular image type.
:return: collections.OrderedDict containing the calculated features for all enabled classes.
If no features are calculated, an empty OrderedDict will be returned.
.. note::
shape descriptors are independent of gray level and therefore calculated separately (handled in `execute`). In
this function, no shape features are calculated.
"""
global logger
featureVector = collections.OrderedDict()
featureClasses = getFeatureClasses()
enabledFeatures = self.enabledFeatures
# Calculate feature classes
for featureClassName, featureNames in six.iteritems(enabledFeatures):
# Handle calculation of shape features separately
if featureClassName.startswith('shape'):
continue
if featureClassName in featureClasses:
logger.info('Computing %s', featureClassName)
featureClass = featureClasses[featureClassName](image, mask,
**kwargs)
if featureNames is not None:
for feature in featureNames:
featureClass.enableFeatureByName(feature)
for (featureName,
featureValue) in six.iteritems(featureClass.execute()):
newFeatureName = '%s_%s_%s' % (
imageTypeName, featureClassName, featureName)
featureVector[newFeatureName] = featureValue
return featureVector
def __init__(self, *args, **kwargs):
global logger
self.settings = {}
self.enabledImagetypes = {}
self.enabledFeatures = {}
self.featureClassNames = list(getFeatureClasses().keys())
if len(args) == 1 and isinstance(args[0], dict):
logger.info("Loading parameter dictionary")
self._applyParams(paramsDict=args[0])
elif len(args) == 1 and (isinstance(args[0], six.string_types)
or isinstance(args[0], pathlib.PurePath)):
if not os.path.isfile(args[0]):
raise IOError("Parameter file %s does not exist." % args[0])
logger.info("Loading parameter file %s", str(args[0]))
self._applyParams(paramsFile=args[0])
else:
# Set default settings and update with and changed settings contained in kwargs
self.settings = self._getDefaultSettings()
logger.info('No valid config parameter, using defaults: %s',
self.settings)
self.enabledImagetypes = {'Original': {}}
logger.info('Enabled image types: %s', self.enabledImagetypes)
for featureClassName in self.featureClassNames:
if featureClassName == 'shape2D': # Do not enable shape2D by default
continue
self.enabledFeatures[featureClassName] = []
logger.info('Enabled features: %s', self.enabledFeatures)
if len(kwargs) > 0:
logger.info('Applying custom setting overrides: %s', kwargs)
self.settings.update(kwargs)
logger.debug("Settings: %s", self.settings)
if self.settings.get('binCount', None) is not None:
logger.warning(
'Fixed bin Count enabled! However, we recommend using a fixed bin Width. See '
'http://pyradiomics.readthedocs.io/en/latest/faq.html#radiomics-fixed-bin-width for more '
'details')
self._setTolerance()
def __init__(self, *args, **kwargs):
self.logger = logging.getLogger(__name__)
self.featureClasses = getFeatureClasses()
self.generalInfo = None
self.settings = {}
self._enabledImagetypes = {}
self._enabledFeatures = {}
if len(args) == 1 and isinstance(
args[0], six.string_types) and os.path.isfile(args[0]):
self.logger.info("Loading parameter file")
self._applyParams(paramsFile=args[0])
elif len(args) == 1 and isinstance(args[0], dict):
self.logger.info("Loading parameter dictionary")
self._applyParams(paramsDict=args[0])
else:
# Set default settings and update with and changed settings contained in kwargs
self.settings = self._getDefaultSettings()
self.logger.info(
'No valid config parameter, applying defaults: %s',
self.settings)
self._enabledImagetypes = {'Original': {}}
self.logger.info('Enabled image types: %s',
self._enabledImagetypes)
self._enabledFeatures = {}
for featureClassName in self.getFeatureClassNames():
if featureClassName == 'shape2D': # Do not enable shape2D by default
continue
self._enabledFeatures[featureClassName] = []
self.logger.info('Enabled features: %s', self._enabledFeatures)
if len(kwargs) > 0:
self.logger.info('Applying custom setting overrides')
self.settings.update(kwargs)
self.logger.debug("Settings: %s", self.settings)
self._setTolerance()
def _addCustomizationSection(self):
customizationCollapsibleButton = ctk.ctkCollapsibleButton()
customizationCollapsibleButton.text = 'Extraction Customization'
customizationCollapsibleButton.collapsed = True
self.layout.addWidget(customizationCollapsibleButton)
customizationFormLayout = qt.QFormLayout(customizationCollapsibleButton)
#
# Radiobuttons to select customization Type
#
self.manualCustomizationRadioButton = qt.QRadioButton()
self.manualCustomizationRadioButton.text = 'Manual Customization'
self.manualCustomizationRadioButton.checked = True
customizationFormLayout.layout().addWidget(self.manualCustomizationRadioButton)
self.parameterFileCustomizationRadioButton = qt.QRadioButton()
self.parameterFileCustomizationRadioButton.text = 'Parameter File Customization'
self.parameterFileCustomizationRadioButton.checked = False
customizationFormLayout.layout().addWidget(self.parameterFileCustomizationRadioButton)
#
# Manual Customization
#
self.manualCustomizationGroupBox = qt.QGroupBox('Manual Customization')
self.manualCustomizationGroupBox.visible = True
# self.manualCustomizationGroupBox.checkable = True
customizationFormLayout.addWidget(self.manualCustomizationGroupBox)
manualCustomizationFormLayout = qt.QFormLayout(self.manualCustomizationGroupBox)
# Feature Class section
featureClassCollapsibleButton = ctk.ctkCollapsibleButton()
featureClassCollapsibleButton.text = 'Feature Classes'
featureClassCollapsibleButton.collapsed = False
manualCustomizationFormLayout.addWidget(featureClassCollapsibleButton)
featureClassLayout = qt.QFormLayout(featureClassCollapsibleButton)
self.featuresLayout = qt.QHBoxLayout()
featureClassLayout.addRow('Features:', self.featuresLayout)
self.featuresButtonGroup = qt.QButtonGroup(self.featuresLayout)
self.featuresButtonGroup.exclusive = False
# Get the feature classes dynamically
self.features = list(getFeatureClasses().keys())
# Create a checkbox for each feature
featureButtons = {}
for feature in self.features:
featureButtons[feature] = qt.QCheckBox(feature)
# TODO: decide which features to enable by default
featureButtons[feature].checked = False
if feature == 'firstorder':
featureButtons[feature].checked = True
self.featuresButtonGroup.addButton(featureButtons[feature])
self.featuresLayout.layout().addWidget(featureButtons[feature])
# set the ID to be the index of this feature in the list
self.featuresButtonGroup.setId(featureButtons[feature], self.features.index(feature))
# Add buttons to select all or none
self.buttonsLayout = qt.QHBoxLayout()
featureClassLayout.addRow('Toggle Features:', self.buttonsLayout)
self.calculateAllFeaturesButton = qt.QPushButton('All Features')
self.calculateAllFeaturesButton.toolTip = 'Calculate all feature classes.'
self.calculateAllFeaturesButton.enabled = True
self.buttonsLayout.addWidget(self.calculateAllFeaturesButton)
self.calculateNoFeaturesButton = qt.QPushButton('No Features')
self.calculateNoFeaturesButton.toolTip = 'Calculate no feature classes.'
self.calculateNoFeaturesButton.enabled = True
self.buttonsLayout.addWidget(self.calculateNoFeaturesButton)
# Resampling and Filtering
filteringCollapsibleButton = ctk.ctkCollapsibleButton()
filteringCollapsibleButton.text = 'Resampling and Filtering'
filteringCollapsibleButton.collapsed = False
manualCustomizationFormLayout.addRow(filteringCollapsibleButton)
# Layout within the dummy collapsible button
filteringFormLayout = qt.QFormLayout(filteringCollapsibleButton)
# Resampling
self.resampledVoxelSize = qt.QLineEdit()
self.resampledVoxelSize.toolTip = 'Three floating-point numbers separated by comma defining the resampled pixel ' \
'size (mm).'
filteringFormLayout.addRow('Resampled voxel size', self.resampledVoxelSize)
# LoG kernel sizes. default to 5 (?)
self.logKernelSizes = qt.QLineEdit()
self.logKernelSizes.toolTip = 'Laplacian of Gaussian filter kernel sizes (mm), separated by comma. ' \
'If empty, no LoG filtering will be applied.'
filteringFormLayout.addRow('LoG kernel sizes', self.logKernelSizes)
# Wavelet
self.waveletCheckBox = qt.QCheckBox()
self.waveletCheckBox.checked = 0
self.waveletCheckBox.toolTip = 'If checked, PyRadiomics will calculate features on the image after applying ' \
'wavelet transformation'
filteringFormLayout.addRow('Wavelet-based features', self.waveletCheckBox)
#
# Feature calculation settings
#
settingsCollapsibleButton = ctk.ctkCollapsibleButton()
settingsCollapsibleButton.text = 'Settings'
settingsCollapsibleButton.collapsed = False
manualCustomizationFormLayout.addWidget(settingsCollapsibleButton)
# Layout within the dummy collapsible button
settingsFormLayout = qt.QFormLayout(settingsCollapsibleButton)
# bin width, defaults to 25
self.binWidthSliderWidget = ctk.ctkSliderWidget()
self.binWidthSliderWidget.singleStep = 1
self.binWidthSliderWidget.decimals = 2
self.binWidthSliderWidget.minimum = 0.01
self.binWidthSliderWidget.maximum = 100
self.binWidthSliderWidget.value = 25
self.binWidthSliderWidget.toolTip = 'Set the bin width'
settingsFormLayout.addRow('Bin Width', self.binWidthSliderWidget)
# symmetricalGLCM flag, defaults to false
self.symmetricalGLCMCheckBox = qt.QCheckBox()
self.symmetricalGLCMCheckBox.checked = 1
self.symmetricalGLCMCheckBox.toolTip = 'Use a symmetrical GLCM matrix'
settingsFormLayout.addRow('Enforce Symmetrical GLCM', self.symmetricalGLCMCheckBox)
#
# Parameter File Customization
#
self.parameterCustomizationGroupBox = qt.QGroupBox('Parameter File Customization')
self.parameterCustomizationGroupBox.visible = False
# self.parameterCustomizationGroupBox.checkable = True
customizationFormLayout.addWidget(self.parameterCustomizationGroupBox)
parameterCustomizationFormLayout = qt.QFormLayout(self.parameterCustomizationGroupBox)
# Path edit to select parameter file
self.parameterFilePathLineEdit = ctk.ctkPathLineEdit()
parameterCustomizationFormLayout.addRow("Parameter File", self.parameterFilePathLineEdit)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Setup a logger for the extension log messages (child logger of pyradiomics)
self.logger = logging.getLogger(radiomics.logger.name + '.slicer')
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = 'Parameters'
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# input volume selector
#
self.inputVolumeSelector = slicer.qMRMLNodeComboBox()
self.inputVolumeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.inputVolumeSelector.selectNodeUponCreation = True
self.inputVolumeSelector.addEnabled = False
self.inputVolumeSelector.removeEnabled = False
self.inputVolumeSelector.noneEnabled = False
self.inputVolumeSelector.showHidden = False
self.inputVolumeSelector.showChildNodeTypes = False
self.inputVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.inputVolumeSelector.setToolTip(
'Pick the input image for the feature calculation.')
parametersFormLayout.addRow('Input Image Volume: ',
self.inputVolumeSelector)
#
# input mask volume selector
#
self.inputMaskSelector = slicer.qMRMLNodeComboBox()
self.inputMaskSelector.nodeTypes = ['vtkMRMLLabelMapVolumeNode']
self.inputMaskSelector.selectNodeUponCreation = True
self.inputMaskSelector.addEnabled = False
self.inputMaskSelector.removeEnabled = False
self.inputMaskSelector.noneEnabled = True
self.inputMaskSelector.showHidden = False
self.inputMaskSelector.showChildNodeTypes = False
self.inputMaskSelector.setMRMLScene(slicer.mrmlScene)
self.inputMaskSelector.setToolTip(
'Pick the input mask for the feature calculation.')
parametersFormLayout.addRow('Input LabelMap: ', self.inputMaskSelector)
#
# input segmentation selector
#
self.inputSegmentationSelector = slicer.qMRMLNodeComboBox()
self.inputSegmentationSelector.nodeTypes = ['vtkMRMLSegmentationNode']
self.inputSegmentationSelector.selectNodeUponCreation = True
self.inputSegmentationSelector.addEnabled = False
self.inputSegmentationSelector.removeEnabled = False
self.inputSegmentationSelector.noneEnabled = True
self.inputSegmentationSelector.showHidden = False
self.inputSegmentationSelector.showChildNodeTypes = False
self.inputSegmentationSelector.setMRMLScene(slicer.mrmlScene)
self.inputSegmentationSelector.setToolTip(
'Pick the input segmentation for the feature calculation.')
parametersFormLayout.addRow('Input Segmentation: ',
self.inputSegmentationSelector)
#
# Feature class selection
#
self.featuresLayout = qt.QHBoxLayout()
parametersFormLayout.addRow('Features:', self.featuresLayout)
self.featuresButtonGroup = qt.QButtonGroup(self.featuresLayout)
self.featuresButtonGroup.exclusive = False
# Get the feature classes dynamically
self.features = getFeatureClasses().keys()
# Create a checkbox for each feature
featureButtons = {}
for feature in self.features:
featureButtons[feature] = qt.QCheckBox(feature)
# TODO: decide which features to enable by default
featureButtons[feature].checked = False
if feature == 'firstorder':
featureButtons[feature].checked = True
self.featuresButtonGroup.addButton(featureButtons[feature])
self.featuresLayout.layout().addWidget(featureButtons[feature])
# set the ID to be the index of this feature in the list
self.featuresButtonGroup.setId(featureButtons[feature],
self.features.index(feature))
# Add buttons to select all or none
self.buttonsLayout = qt.QHBoxLayout()
parametersFormLayout.addRow('Toggle Features:', self.buttonsLayout)
self.calculateAllFeaturesButton = qt.QPushButton('All Features')
self.calculateAllFeaturesButton.toolTip = 'Calculate all feature classes.'
self.calculateAllFeaturesButton.enabled = True
self.buttonsLayout.addWidget(self.calculateAllFeaturesButton)
self.calculateNoFeaturesButton = qt.QPushButton('No Features')
self.calculateNoFeaturesButton.toolTip = 'Calculate no feature classes.'
self.calculateNoFeaturesButton.enabled = True
self.buttonsLayout.addWidget(self.calculateNoFeaturesButton)
#
# Feature calculation options
#
optionsCollapsibleButton = ctk.ctkCollapsibleButton()
optionsCollapsibleButton.text = 'Options'
optionsCollapsibleButton.collapsed = True
self.layout.addWidget(optionsCollapsibleButton)
# Layout within the dummy collapsible button
optionsFormLayout = qt.QFormLayout(optionsCollapsibleButton)
# bin width, defaults to 25
self.binWidthSliderWidget = ctk.ctkSliderWidget()
self.binWidthSliderWidget.singleStep = 1
self.binWidthSliderWidget.decimals = 0
self.binWidthSliderWidget.minimum = 1
self.binWidthSliderWidget.maximum = 100
self.binWidthSliderWidget.value = 25
self.binWidthSliderWidget.toolTip = 'Set the bin width'
optionsFormLayout.addRow('Bin Width', self.binWidthSliderWidget)
# symmetricalGLCM flag, defaults to false
self.symmetricalGLCMCheckBox = qt.QCheckBox()
self.symmetricalGLCMCheckBox.checked = 1
self.symmetricalGLCMCheckBox.toolTip = 'Use a symmetrical GLCM matrix'
optionsFormLayout.addRow('Enforce Symmetrical GLCM',
self.symmetricalGLCMCheckBox)
# label for the mask, defaults to 1
self.labelSliderWidget = ctk.ctkSliderWidget()
self.labelSliderWidget.singleStep = 1
self.labelSliderWidget.decimals = 0
self.labelSliderWidget.minimum = 0
self.labelSliderWidget.maximum = 255
self.labelSliderWidget.value = 1
self.labelSliderWidget.toolTip = 'Set the label to use for masking the image'
# optionsFormLayout.addRow('Label', self.labelSliderWidget)
# debug logging flag, defaults to false
self.debuggingCheckBox = qt.QCheckBox()
self.debuggingCheckBox.checked = 0
self.debuggingCheckBox.toolTip = \
'If checked, PyRadiomics log messages from level DEBUG and higher will be added to the slicer log'
optionsFormLayout.addRow('Store debug log', self.debuggingCheckBox)
#
# Output table
#
outputCollapsibleButton = ctk.ctkCollapsibleButton()
outputCollapsibleButton.text = 'Output'
self.layout.addWidget(outputCollapsibleButton)
outputFormLayout = qt.QFormLayout(outputCollapsibleButton)
self.outputTableSelector = slicer.qMRMLNodeComboBox()
self.outputTableSelector.nodeTypes = ['vtkMRMLTableNode']
self.outputTableSelector.addEnabled = True
self.outputTableSelector.selectNodeUponCreation = True
self.outputTableSelector.renameEnabled = True
self.outputTableSelector.removeEnabled = True
self.outputTableSelector.noneEnabled = False
self.outputTableSelector.setMRMLScene(slicer.mrmlScene)
self.outputTableSelector.toolTip = \
'Select the table where features will be saved, resets feature values on each run.'
outputFormLayout.addRow('Output table:', self.outputTableSelector)
#
# Apply Button
#
self.applyButton = qt.QPushButton('Apply')
self.applyButton.toolTip = 'Run the algorithm.'
self.applyButton.enabled = False
self.layout.addWidget(self.applyButton)
# connections
self.calculateAllFeaturesButton.connect(
'clicked(bool)', self.onCalculateAllFeaturesButton)
self.calculateNoFeaturesButton.connect(
'clicked(bool)', self.onCalculateNoFeaturesButton)
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.inputVolumeSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onSelect)
self.inputMaskSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onSelect)
self.inputSegmentationSelector.connect(
'currentNodeChanged(vtkMRMLNode*)', self.onSelect)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelect()
import logging
import os
from nose_parameterized import parameterized
import numpy
import six
from radiomics import getFeatureClasses
from testUtils import custom_name_func, RadiomicsTestUtils
testUtils = RadiomicsTestUtils()
tests = sorted(testUtils.getTests())
featureClasses = getFeatureClasses()
class TestMatrices:
def generate_scenarios():
global tests, featureClasses
for testCase in tests:
for className, featureClass in six.iteritems(featureClasses):
assert (featureClass is not None)
if "_calculateMatrix" in dir(featureClass):
logging.debug('generate_scenarios: featureClass = %s',
className)
yield testCase, className
@parameterized.expand(generate_scenarios(),