def getSlide(self, slideNumber = None, **kwargs):
rc = kwargs['renderingProperties']
tc = kwargs['tracingProperties']
newSlide = barTracedSlideRenderer(\
rendererConfiguration = rc,\
tracingConfiguration = tc)
newSlide.slideNumber = slideNumber
if slideNumber == None:
for contour in self._contours:
newSlide.addPath(contour.getBarPath())
for marker in self._markers:
newSlide.addLabel(marker.getLabel())
for textElem in self._textElems:
newSlide.addLabel(textElem.getLabel())
if slideNumber is not None:
# Choose slide element corresponding to provided slide number:
# elementKey = self.slideRange[slideNumber]
# coordElemList = self._zindex[elementKey]
coordElemList = self._zindex[self.slideRange[slideNumber]]
for contour in coordElemList.paths:
newSlide.addPath(contour.getBarPath())
for labelEl in coordElemList.labels:
newSlide.addLabel(labelEl.getLabel())
newSlide.updateMetadata(barBregmaMetadataElement(coordElemList.zCoord))
transformationMatrixTuple=(\
self._scaling[0], self._coord[0],
self._scaling[1], self._coord[1])
newSlide.updateMetadata =\
(barTransfMatrixMetadataElement(transformationMatrixTuple))
return newSlide
def _getSlide(self, slideNumber):
"""
@type slideNumber: C{int}
@param slideNumber: Number of slide to extract
@rtype: L{barTracedSlideRenderer<barTracedSlideRenderer>}
@return: Traced slide with given number.
"""
# Get PIL bitmap image containing slide with given slideNumber
# It is assumed that image is provided in RGB mode.
sourceImage = self._getSourceImage(slideNumber)
# Extract list of uniqe colours from source slide image
# list of tuples in rgbformat
uniqeColours = self._getUniqeColours(sourceImage)
# Create traced slide:
# Use customized slide tempate if provided
try:
self.slideTemplate
customSlideTemplate = self.slideTemplate
except:
customSlideTemplate = None
retSlide = barTracedSlideRenderer(
slideTemplate=customSlideTemplate,
rendererConfiguration=self.renderingProperties,
tracingConfiguration=self.tracingProperties)
retSlide.slideNumber = slideNumber
# Remove background color from the set of colours in the bitmap
uniqeColours.remove(self.backgroundColor)
# Iterate over all uniqe colours and create set of paths basing on
# every uniqe colour:
for imageColour in uniqeColours:
map(retSlide.addPath,
self._processStructure(sourceImage, imageColour))
# Append metadata to newly created slide:
spatialLocation = [
barTransfMatrixMetadataElement(
self._getSpatialTransfMatrix(slideNumber)),
barBregmaMetadataElement(self._getZCoord(slideNumber))
]
retSlide.updateMetadata(spatialLocation)
return retSlide
def _getSlide(self, slideNumber):
"""
@type slideNumber: C{int}
@param slideNumber: Number of slide to extract
@rtype: L{barTracedSlideRenderer<barTracedSlideRenderer>}
@return: Traced slide with given number.
"""
# Get PIL bitmap image containing slide with given slideNumber
# It is assumed that image is provided in RGB mode.
sourceImage = self._getSourceImage(slideNumber)
# Extract list of uniqe colours from source slide image
# list of tuples in rgbformat
uniqeColours = self._getUniqeColours(sourceImage)
# Create traced slide:
# Use customized slide tempate if provided
try:
self.slideTemplate
customSlideTemplate = self.slideTemplate
except:
customSlideTemplate = None
retSlide = barTracedSlideRenderer(
slideTemplate=customSlideTemplate,
rendererConfiguration=self.renderingProperties,
tracingConfiguration=self.tracingProperties)
retSlide.slideNumber = slideNumber
# Remove background color from the set of colours in the bitmap
uniqeColours.remove(self.backgroundColor)
# Iterate over all uniqe colours and create set of paths basing on
# every uniqe colour:
for imageColour in uniqeColours:
map(retSlide.addPath, self._processStructure(
sourceImage, imageColour))
# Append metadata to newly created slide:
spatialLocation = [
barTransfMatrixMetadataElement(
self._getSpatialTransfMatrix(slideNumber)),
barBregmaMetadataElement(self._getZCoord(slideNumber))]
retSlide.updateMetadata(spatialLocation)
return retSlide
def getSlide(self, slideNumber=None, **kwargs):
rc = kwargs['renderingProperties']
tc = kwargs['tracingProperties']
newSlide = barTracedSlideRenderer(\
rendererConfiguration = rc,\
tracingConfiguration = tc)
newSlide.slideNumber = slideNumber
if slideNumber == None:
for contour in self._contours:
newSlide.addPath(contour.getBarPath())
for marker in self._markers:
newSlide.addLabel(marker.getLabel())
for textElem in self._textElems:
newSlide.addLabel(textElem.getLabel())
if slideNumber is not None:
# Choose slide element corresponding to provided slide number:
# elementKey = self.slideRange[slideNumber]
# coordElemList = self._zindex[elementKey]
coordElemList = self._zindex[self.slideRange[slideNumber]]
for contour in coordElemList.paths:
newSlide.addPath(contour.getBarPath())
for labelEl in coordElemList.labels:
newSlide.addLabel(labelEl.getLabel())
newSlide.updateMetadata(
barBregmaMetadataElement(coordElemList.zCoord))
transformationMatrixTuple=(\
self._scaling[0], self._coord[0],
self._scaling[1], self._coord[1])
newSlide.updateMetadata =\
(barTransfMatrixMetadataElement(transformationMatrixTuple))
return newSlide
def parse(self, slideNumber,\
generateLabels = True,\
useIndexer = True,\
writeSlide = True):
"""
@param slideNumber: int
@type slideNumber: Number of slide which will be parsed
Creates svg document from JSON file for given slide number.
Slide is created using following workflow:
- Get template of empty slide
- Get list of structures in given slide
- Extract definitions of paths corresponding to structures,
add them into slide
- Extract metadata and put in into SVG slide
- Generate positions of labels corresponding to created paths and
append therm
"""
barExternalParser.parse(self, slideNumber)
tracedSlide = barTracedSlideRenderer(\
slideTemplate = self.slideTemplate,\
rendererConfiguration = self.renderingProperties,\
tracingConfiguration = self.tracingProperties)
# Define string version of current slide number
# I do it because loaded json files are converted to dictionaries
# and integer keys are converted to string keys ( 1 goes to '1')
# so all keys are strings
CurrentSlideNumber = str(slideNumber)
# Extract structures that are defined in slide >CurrentSlideNumber<
# There are two ways of indexing structures: by dictionary (keys are
# slidenumbers) or in list.
# Code belows tries to load data in both ways
try:
CurrentSlideStructures = self._sbaImportData['brainslices'][CurrentSlideNumber]
except TypeError:
CurrentSlideStructures = self._sbaImportData['brainslices'][int(CurrentSlideNumber)]
# CurrentSlideStructures is dictionary that maps color in hexagonal
# format to number of polygon corresponding to given structure
# eg. {'fafafa':[0]}
# so key id color-encoded name of the structure and list is list of
# path indexes stored in self.sbaImportData['svgpaths'] list
# Dump information about structures in given slide
print >>sys.stderr, "Converting slide number:\t%d" % slideNumber
if __debug__:
print >>sys.stderr, "\tThere are %d structures defined." % len(CurrentSlideStructures)
print >>sys.stderr, "\tInitializing structure index."
# Now we iterate over all structures in given slide
for structure in CurrentSlideStructures.keys():
# TODO come up with idea how to do it better
# Now two thing are passed structureID, and list of path indexes
# Create path definition
map(tracedSlide.addPath,
self._parseSingleStructure(structure, CurrentSlideStructures[structure]))
# Extract stereoraxic transformation matrix and put it into SVG slide
offsets=[\
self._sbaImportData['xyscaling'][str(CurrentSlideNumber)][0:2],
self._sbaImportData['xyscaling'][str(CurrentSlideNumber)][2:]]
spatialData = self._saveTransformationAsMetadata(offsets,\
self._sbaImportData['bregma'][slideNumber])
tracedSlide.updateMetadata(spatialData)
corrArray = np.array([[0.1,0,0],[0,0.1,0],[0,0,0]])
tracedSlide.affineTransform(corrArray)
# Perform additional actions if requested
if generateLabels:
tracedSlide.generateLabels()
if writeSlide: tracedSlide.writeXMLtoFile(self._getOutputFilename(slideNumber))
if useIndexer: self.indexer.indexSingleSlide(tracedSlide, slideNumber)
return tracedSlide
def parse(self, slideNumber,\
generateLabels = True,\
useIndexer = True,\
writeSlide = True):
"""
@param slideNumber: int
@type slideNumber: Number of slide which will be parsed
Creates svg document from JSON file for given slide number.
Slide is created using following workflow:
- Get template of empty slide
- Get list of structures in given slide
- Extract definitions of paths corresponding to structures,
add them into slide
- Extract metadata and put in into SVG slide
- Generate positions of labels corresponding to created paths and
append therm
"""
barExternalParser.parse(self, slideNumber)
tracedSlide = barTracedSlideRenderer(\
slideTemplate = self.slideTemplate,\
rendererConfiguration = self.renderingProperties,\
tracingConfiguration = self.tracingProperties)
# Define string version of current slide number
# I do it because loaded json files are converted to dictionaries
# and integer keys are converted to string keys ( 1 goes to '1')
# so all keys are strings
CurrentSlideNumber = str(slideNumber)
# Extract structures that are defined in slide >CurrentSlideNumber<
# There are two ways of indexing structures: by dictionary (keys are
# slidenumbers) or in list.
# Code belows tries to load data in both ways
try:
CurrentSlideStructures = self._sbaImportData['brainslices'][
CurrentSlideNumber]
except TypeError:
CurrentSlideStructures = self._sbaImportData['brainslices'][int(
CurrentSlideNumber)]
# CurrentSlideStructures is dictionary that maps color in hexagonal
# format to number of polygon corresponding to given structure
# eg. {'fafafa':[0]}
# so key id color-encoded name of the structure and list is list of
# path indexes stored in self.sbaImportData['svgpaths'] list
# Dump information about structures in given slide
print >> sys.stderr, "Converting slide number:\t%d" % slideNumber
if __debug__:
print >> sys.stderr, "\tThere are %d structures defined." % len(
CurrentSlideStructures)
print >> sys.stderr, "\tInitializing structure index."
# Now we iterate over all structures in given slide
for structure in CurrentSlideStructures.keys():
# TODO come up with idea how to do it better
# Now two thing are passed structureID, and list of path indexes
# Create path definition
map(
tracedSlide.addPath,
self._parseSingleStructure(structure,
CurrentSlideStructures[structure]))
# Extract stereoraxic transformation matrix and put it into SVG slide
offsets=[\
self._sbaImportData['xyscaling'][str(CurrentSlideNumber)][0:2],
self._sbaImportData['xyscaling'][str(CurrentSlideNumber)][2:]]
spatialData = self._saveTransformationAsMetadata(offsets,\
self._sbaImportData['bregma'][slideNumber])
tracedSlide.updateMetadata(spatialData)
corrArray = np.array([[0.1, 0, 0], [0, 0.1, 0], [0, 0, 0]])
tracedSlide.affineTransform(corrArray)
# Perform additional actions if requested
if generateLabels:
tracedSlide.generateLabels()
if writeSlide:
tracedSlide.writeXMLtoFile(self._getOutputFilename(slideNumber))
if useIndexer: self.indexer.indexSingleSlide(tracedSlide, slideNumber)
return tracedSlide
