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 _saveTransformationAsMetadata(self, transformation, bregma):
"""
@type transformation: 4 elements array
@param transformation: array holding transformation coefficients in
following orader: [b,a,d,c]. x'=a*x+b, y'=c*y+d
@type bregma: string
@param bregma: bregma coordinate
Puts stereotactic coordinates matrix as SVG metadata
Clues given by Rembrand Bakker:
x'=xy[0]+xy[1]*x
y'=xy[0]+xy[1]*y
"""
# We assume that template is properly defined and empty template
# has precisely one 'metadata' element.
# Appending transformation matrix and bregma coordinate
TransformationMatrix =\
(1*transformation[0][1], transformation[0][0],
1*transformation[1][1], transformation[1][0])
spatialMatrix = barTransfMatrixMetadataElement(TransformationMatrix)
BregmaMetadataElement = barBregmaMetadataElement(bregma)
return (spatialMatrix, BregmaMetadataElement)
def _saveTransformationAsMetadata(self, transformation, bregma):
"""
@type transformation: 4 elements array
@param transformation: array holding transformation coefficients in
following orader: [b,a,d,c]. x'=a*x+b, y'=c*y+d
@type bregma: string
@param bregma: bregma coordinate
Puts stereotactic coordinates matrix as SVG metadata
Clues given by Rembrand Bakker:
x'=xy[0]+xy[1]*x
y'=xy[0]+xy[1]*y
"""
# We assume that template is properly defined and empty template
# has precisely one 'metadata' element.
# Appending transformation matrix and bregma coordinate
TransformationMatrix =\
(1*transformation[0][1], transformation[0][0],
1*transformation[1][1], transformation[1][0])
spatialMatrix = barTransfMatrixMetadataElement(TransformationMatrix)
BregmaMetadataElement = barBregmaMetadataElement(bregma)
return (spatialMatrix, BregmaMetadataElement)
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
