def reindex(self):
# bar.barSBAParser.reindex(self)
# self.indexer.createFlatHierarchy()
self.indexer.colorMapping = dict((cleanStructName(v),k) for k, v in self._sbaImportData['rgb2acr'].iteritems())
self.indexer.fullNameMapping = self._sbaImportData['acr2full']
# And the just store the results into the txt files so they can be
# further preocessed by the volumetric parser.
# Ditry hack stripping all keys and values. It is required as provided
self.indexer.fullNameMapping = dict(
(cleanStructName(k),v )\
for k, v in self.indexer.fullNameMapping.iteritems())
# Define mappings for all the files that will be used in other processings
fullNameMappingPath = os.path.join(self.inputDirectory, CONF_FULLNAME_MAPPING_FILE)
colorMappingPath = os.path.join(self.inputDirectory, CONF_COLOR_MAPPING_FILE)
volIdxToAbbrevPath = os.path.join(self.inputDirectory, CONF_VOLUME_LABEL_MAPPING_FILE)
volIdxToAbbrevSrcPath = os.path.join(self.inputDirectory, CONF_VOLUME_LABEL_MAPPING_SOURCE)
# Load additional mappings from json files
volumeToAbbrevMapping = json.load(open(volIdxToAbbrevSrcPath))
colorToStructureMapping = dict(map(lambda (k,v): \
(str(k), cleanStructName(v)), enumerate(volumeToAbbrevMapping)))
# And then store them into files
self._writeDictionaryToFile(self.indexer.colorMapping, colorMappingPath)
self._writeDictionaryToFile(self.indexer.fullNameMapping, fullNameMappingPath)
self._writeDictionaryToFile(colorToStructureMapping, volIdxToAbbrevPath)
def __getImageToAbbrevMapping(self):
volIdxToAbbrevSrcPath = os.path.join(self.inputDirectory, CONF_VOLUME_LABEL_MAPPING_SOURCE)
volumeToAbbrevMapping = json.load(open(volIdxToAbbrevSrcPath))
mapping = dict( \
(str(k), cleanStructName(v)) \
for k, v \
in enumerate(volumeToAbbrevMapping) )
return mapping
def __getImageToAbbrevMapping(self):
volIdxToAbbrevSrcPath = os.path.join(self.inputDirectory,
CONF_VOLUME_LABEL_MAPPING_SOURCE)
volumeToAbbrevMapping = json.load(open(volIdxToAbbrevSrcPath))
mapping = dict( \
(str(k), cleanStructName(v)) \
for k, v \
in enumerate(volumeToAbbrevMapping) )
return mapping
def __getFullnameMapping(self):
mapping = dict( \
(cleanStructName(k),v )\
for k, v \
in self._sbaImportData['acr2full'].iteritems() )
return mapping
def __getColorMapping(self):
colorMapping = dict(\
(cleanStructName(v), k) \
for k, v \
in self._sbaImportData['rgb2acr'].iteritems() )
return colorMapping
def __getFullnameMapping(self):
mapping = dict( \
(cleanStructName(k),v )\
for k, v \
in self._sbaImportData['acr2full'].iteritems() )
return mapping
def __getColorMapping(self):
colorMapping = dict(\
(cleanStructName(v), k) \
for k, v \
in self._sbaImportData['rgb2acr'].iteritems() )
return colorMapping
