def __getColorMapping(self):
# Structure name -> structure colour mapping
# The mapping has to be assigned to the parser as well as to the indexer separately
# This procedure should be simplified in the future.
filename = os.path.join(self.inputDirectory, CONF_COLOR_MAPPING_FILE)
mapping = getDictionaryFromFile(filename)
return mapping
def __getColorMapping(self):
# set structure name -> structure colour mapping
# We need to set this mapping here because parser needs to know what
# colors have to be assigned to paths
colorMappingFile = os.path.join(self.inputDirectory, COLOR_MAPPING_FN)
structureColours = getDictionaryFromFile(colorMappingFile, 0, 2)
return structureColours
def __init__(self, inputDirectory, outputDirectory, **kwargs):
# Extend passed properties and invoke uperclass constuctor
kwargs.update(atlasparserProperties)
bar.barBitmapParser.__init__(self, **kwargs)
self.inputDirectory = inputDirectory
self.outputDirectory = outputDirectory
# Define source dataset location and initialize parser by loading
# source dataset
sourceFilename = 'atlas.nii'
self._loadVolume(sourceFilename)
# Some properties cannot be predefined, adding them now:
self.setProperty('outputDirectory', outputDirectory)
# structure name -> structure colour mapping
fullnameMappingFile = os.path.join(self.inputDirectory,
'fullnames.txt')
structureColours = getDictionaryFromFile(fullnameMappingFile, 0, 2)
self.setProperty('structureColours', structureColours)
self.indexer.colorMapping = structureColours
self._defineSlideRange(antPostAxis=3)
self._pathNumber = 0
# Set indexer properties
self.indexer.updateProperties(indexerProperties)
def __getColorMapping(self):
# set structure name -> structure colour mapping
# We need to set this mapping here because parser needs to know what
# colors have to be assigned to paths
colorMappingFile = os.path.join(self.inputDirectory, COLOR_MAPPING_FN)
structureColours = getDictionaryFromFile(colorMappingFile, 0, 2)
return structureColours
def __init__(self, inputDirectory, outputDirectory, **kwargs):
# Extend passed properties and invoke uperclass constuctor
kwargs.update(atlasparserProperties)
bar.barBitmapParser.__init__(self, **kwargs)
self.inputDirectory = inputDirectory
self.outputDirectory= outputDirectory
# Define source dataset location and initialize parser by loading
# source dataset
sourceFilename = 'canon_labels_r.nii'
volumetricFile = os.path.join(inputDirectory,sourceFilename)
self._volumeSrc = nifti.NiftiImage(volumetricFile)
self._volume = self._volumeSrc.data[0]
#Some properties cannot be predefined, adding them now:
self.setProperty('outputDirectory', outputDirectory)
# set structure name -> structure colour mapping
fullnameMappingFile = os.path.join(self.inputDirectory,'fullnames.txt')
structureColours = getDictionaryFromFile(fullnameMappingFile, 0, 2)
self.setProperty('structureColours', structureColours)
self.indexer.colorMapping=structureColours
self.slideRange = map(lambda x: 1023 - x, range(0,1024))
self._pathNumber = 0
# Set indexer properties
self.indexer.updateProperties(indexerProperties)
def __getLabelIndexToNameMapping(self):
# Load pixelValue to structureName mapping:
# This mapping is required to assign structure's name to the given label's index
filename = os.path.join(self.inputDirectory, CONF_VOLUME_LABEL_MAPPING_FILE)
mapping = getDictionaryFromFile(filename)
mapping = dict(map(lambda (k,v): (int(k),v), mapping.iteritems()))
return mapping
def __getColorMapping(self):
# Structure name -> structure colour mapping
# The mapping has to be assigned to the parser as well as to the indexer separately
# This procedure should be simplified in the future.
filename = os.path.join(self.inputDirectory, CONF_COLOR_MAPPING_FILE)
mapping = getDictionaryFromFile(filename)
return mapping
def __getImageToStructureMapping(self):
# set source bitmap colour -> structure name
imagToStructFn =\
os.path.join(self.inputDirectory, IMAGE_TO_STRUCTURE_FN)
imageToStructure = getDictionaryFromFile(imagToStructFn)
imageToStructure = dict(
('#' + k.lower(), v) for k, v in imageToStructure.iteritems())
return imageToStructure
def __getLabelIndexToNameMapping(self):
# Load pixelValue to structureName mapping:
# This mapping is required to assign structure's name to the given label's index
filename = os.path.join(self.inputDirectory,
CONF_VOLUME_LABEL_MAPPING_FILE)
mapping = getDictionaryFromFile(filename)
mapping = dict(map(lambda (k, v): (int(k), v), mapping.iteritems()))
return mapping
def __init__(self, inputDirectory, outputDirectory):
props = {}
props['filenameTemplates'] = filenameTempates
props['slideRange'] = slideRange
colorMapping = getDictionaryFromFile(colorMappingFilename)
props['structureColours'] = colorMapping
props['renderingProperties'] = renderingProperties
props['tracingProperties'] = tracerSettings
props['inputDirectory'] = inputDirectory
props['outputDirectory'] = outputDirectory
bar.barVectorParser.__init__(self, **props)
self.indexer.updateProperties(indexerProps)
def __init__(self, inputDirectory, outputDirectory):
props = {}
props['filenameTemplates'] = filenameTempates
props['slideRange'] = slideRange
colorMapping = getDictionaryFromFile(colorMappingFilename)
props['structureColours'] = colorMapping
props['renderingProperties'] = renderingProperties
props['tracingProperties'] = tracerSettings
props['inputDirectory'] = inputDirectory
props['outputDirectory'] = outputDirectory
bar.barVectorParser.__init__(self, **props)
self.indexer.updateProperties(indexerProps)
def __init__(self, inputDirectory, outputDirectory, **kwargs):
# Extend passed properties and invoke uperclass constuctor
kwargs.update(atlasparserProperties)
bar.barBitmapParser.__init__(self, **kwargs)
self.inputDirectory = inputDirectory
self.outputDirectory= outputDirectory
# Define source dataset location and initialize parser by loading
# source dataset
sourceFilename = 'segmentation_in_uct_space.nii.gz'
volumetricFile = os.path.join(inputDirectory, sourceFilename)
self._volumeSrc = nifti.NiftiImage(volumetricFile)
self._volumeHeader = self._volumeSrc.header
self._volume = self._volumeSrc.data
#Some properties cannot be predefined, adding them now:
self.setProperty('outputDirectory', outputDirectory)
# Assign structure abbreviation --> structure colour mapping
# Assign structure abbreviation --> structure fullname mapping
fullnameMappingFile = os.path.join(self.inputDirectory,'fullnames.txt')
structureColours = getDictionaryFromFile(fullnameMappingFile, 1, 2)
imageToStructure = getDictionaryFromFile(fullnameMappingFile, 0, 1)
imageToStructure = dict( ('#'+k.lower(), v) for k, v in # small
imageToStructure.iteritems()) # correction
self.setProperty('structureColours', structureColours)
self.setProperty('imageToStructure', imageToStructure)
self.indexer.colorMapping = structureColours
self._defineSlideRange(antPostAxis=2)
self._pathNumber = 0
# Set indexer properties
self.indexer.updateProperties(indexerProperties)
def reindex(self):
bar.barBitmapParser.reindex(self)
#Load hierarchy from parents.txt
hierarhySourceFilename = os.path.join(self.inputDirectory, 'parents.txt')
self.indexer.setParentsFromFile(hierarhySourceFilename)
# set structure name -> structure colour mapping
fullnameMappingFile = os.path.join(self.inputDirectory,'fullnames.txt')
structureColours = getDictionaryFromFile(fullnameMappingFile, 0, 2)
self.setProperty('structureColours', structureColours)
self.indexer.colorMapping=structureColours
# Load and use fullname mapping
fullnameMappingFile = os.path.join(self.inputDirectory,'fullnames.txt')
self.indexer.setNameMappingFromFile(fullnameMappingFile, 0 , 1)
self.writeIndex()
def __init__(self, inputDirectory, outputDirectory):
# Update the parser properties dictionary before invoking an instance
# of vector atlas parser (this is the way it works).
props = {}
props['filenameTemplates'] = filenameTempates
props['slideRange'] = slideRange
colorMapping = getDictionaryFromFile(colorMappingFilename)
props['structureColours'] = colorMapping
props['renderingProperties'] = renderingProperties
props['tracingProperties'] = tracerSettings
props['inputDirectory'] = inputDirectory
props['outputDirectory'] = outputDirectory
bar.barVectorParser.__init__(self, **props)
# Add slide tracing and rendering settings to the parser's data
self._tracingConf = tracerSettings
self._rendererConf = renderingProperties
# And now update the parser's indexer configuration (phew...) as
# previously we were updating only properties and configuration of the
# parser itself.
self.indexer.updateProperties(indexerProps)
def __init__(self, inputDirectory, outputDirectory):
# Update the parser properties dictionary before invoking an instance
# of vector atlas parser (this is the way it works).
props = {}
props['filenameTemplates'] = filenameTempates
props['slideRange'] = slideRange
colorMapping = getDictionaryFromFile(colorMappingFilename)
props['structureColours'] = colorMapping
props['renderingProperties'] = renderingProperties
props['tracingProperties'] = tracerSettings
props['inputDirectory'] = inputDirectory
props['outputDirectory'] = outputDirectory
bar.barVectorParser.__init__(self, **props)
# Add slide tracing and rendering settings to the parser's data
self._tracingConf = tracerSettings
self._rendererConf = renderingProperties
# And now update the parser's indexer configuration (phew...) as
# previously we were updating only properties and configuration of the
# parser itself.
self.indexer.updateProperties(indexerProps)
def __getFullnameMapping(self):
filename = os.path.join(self.inputDirectory, CONF_FULLNAME_MAPPING_FILE)
mapping = getDictionaryFromFile(filename)
return mapping
def __getParentChildMapping(self):
mappingFilename = os.path.join(self.inputDirectory, HIERARCHY_FILANEME)
mapping = getDictionaryFromFile(mappingFilename)
return mapping
def __getParentChildMapping(self):
mappingFilename = os.path.join(self.inputDirectory, HIERARCHY_FILANEME)
mapping = getDictionaryFromFile(mappingFilename)
return mapping
def __getFullNameMapping(self):
fullnameMappingFile = os.path.join(self.inputDirectory, FULLNAME_MAPPING_FN)
return getDictionaryFromFile(fullnameMappingFile, 0, 1)
def __getImageToStructureMapping(self):
# set source bitmap colour -> structure name
imagToStructFn = os.path.join(self.inputDirectory, IMAGE_TO_STRUCTURE_FN)
imageToStructure = getDictionaryFromFile(imagToStructFn)
imageToStructure = dict(("#" + k.lower(), v) for k, v in imageToStructure.iteritems())
return imageToStructure
def __getColorMapping(self):
mappingFilename = os.path.join(self.inputDirectory, MAPPING_FILENAME)
mapping = getDictionaryFromFile(mappingFilename, 0, 2)
return mapping
def __getImageToAbbrevMapping(self):
mappingFilename = os.path.join(self.inputDirectory, MAPPING_FILENAME)
mapping = getDictionaryFromFile(mappingFilename, 4, 0)
mapping = dict(map(lambda (k, v): (int(k), v), mapping.iteritems()))
return mapping
def __getFullNameMapping(self):
fullnameMappingFile =\
os.path.join(self.inputDirectory, FULLNAME_MAPPING_FN)
return getDictionaryFromFile(fullnameMappingFile, 0, 1)
def __getImageToAbbrevMapping(self):
mappingFilename = os.path.join(self.inputDirectory, MAPPING_FILENAME)
mapping = getDictionaryFromFile(mappingFilename, 4, 0)
mapping = dict(map(lambda (k,v): (int(k),v), mapping.iteritems()))
return mapping
def __getFullnameMapping(self):
filename = os.path.join(self.inputDirectory,
CONF_FULLNAME_MAPPING_FILE)
mapping = getDictionaryFromFile(filename)
return mapping
def __getColorMapping(self):
mappingFilename = os.path.join(self.inputDirectory, MAPPING_FILENAME)
mapping = getDictionaryFromFile(mappingFilename, 0, 2)
return mapping