def getStructureColor(self, structureName, rgb = False):
"""
@param structureName: the name of the structure
@type structureName: str
@param rgb: True if requested colour format is 24-bit RGB (8 bits per
chanel), False otherwise.
@type rgb: bool
@return: the colour suitable for a model of requested structure
@rtype: [int, int, int] | [float, float, float]
"""
ct = HTMLColorToRGB(self.sh.ih.colorMapping[structureName])
#TODO: Get rid of this after implementing automatic, hierarchy based
# colour assignment.
# Dummy patch: when colour is not provided (=structure has gray colour
# defined) choose random one.
if ct[0] == ct[1] == ct[2] == 119:
random.seed(structureName)
ct = map(lambda x: random.randint(0, 255), [0,0,0])
if not rgb:
ct = list(intColourToFloat(ct))
return ct
def getStructureColor(self, structureName, rgb=False):
"""
@param structureName: the name of the structure
@type structureName: str
@param rgb: True if requested colour format is 24-bit RGB (8 bits per
chanel), False otherwise.
@type rgb: bool
@return: the colour suitable for a model of requested structure
@rtype: [int, int, int] | [float, float, float]
"""
ct = HTMLColorToRGB(self.sh.ih.colorMapping[structureName])
#TODO: Get rid of this after implementing automatic, hierarchy based
# colour assignment.
# Dummy patch: when colour is not provided (=structure has gray colour
# defined) choose random one.
if ct[0] == ct[1] == ct[2] == 119:
random.seed(structureName)
ct = map(lambda x: random.randint(0, 255), [0, 0, 0])
if not rgb:
ct = list(intColourToFloat(ct))
return ct
def _basicSetup(self, vtkapp, options):
"""
Constructor code common with derivative classes constructor.
@param vtkapp: C{self.L{vtkapp}} value
@type vtkapp: L{barReconstructionModule} object
@param options: an object containing constructor options as its
attributes:
- C{cameraMovementAngles} - C{self.L{vtkapp}.L{cameraPosition<barReconstructionModule.cameraPosition>}}
and C{self.L{vtkapp}.L{cameraViewUp<barReconstructionModule.cameraViewUp>}}
values encoded as camera movement angles,
- C{parallel} - C{self.L{vtkapp}.L{parallelProjection<barReconstructionModule.parallelProjection>}} value,
- C{background} - C{self.L{vtkapp}.L{background<barReconstructionModule.background>}},
- C{voxelDimensions} - C{(self.L{xyres}, self.L{zres})} value,
- C{exportDir} - C{self.L{exportDir}} value,
- C{generateSubstructures} - C{self.L{depth}} value,
- C{format} - C{self.L{formats}} members list,
- C{show} - C{self.L{show}} value,
- C{brainoutline} - legacy option, indicates if the root
structure of the hierarchy tree has
to be appended to C{self.L{outline}},
- C{outline} - structures to be included in C{self.L{outline}},
- C{composite} - C{self.L{composite}} value; if True
forces C{'exportToVTKPolydata' in self.L{formats}},
- C{ignoreBoundingBox} - C{self.L{ignoreBoundingBox}}.
Overrides bounding box
calculation - bounding box
will be always equal to
hierarchy root element bounding
box. Volumes for all structures
will always have the same size
and origin. This feature
increases memory usage and
reconstruction time.
@type options: optparse.Values object
"""
self.vtkapp = vtkapp
# Process options
self.vtkapp.background = intColourToFloat(options.background)
self.cameraMovementAngles = options.cameraMovementAngles
self.parallel = options.parallel
if options.voxelDimensions != None:
self.xyres, self.zres = options.voxelDimensions
if options.exportDir != None:
self.exportDir = options.exportDir
if options.outline:
# check whether every group requested as an outline exists
self.outline = set(options.outline)
invalidGroups = self.outline - set(self.sh.ih.groups)
if len(invalidGroups) > 0:
# if not - report it and try to fix
for name in invalidGroups:
debugOutput("Structure %s not found." % name, error = True)
self.outline -= validGroups
else:
self.outline = set()
if options.brainoutline:
self.outline.add(self.sh.ih.hierarchyRootElementName)
self.depth = options.generateSubstructures
self.formats = set()
if options.format != None:
self.formats = set(options.format)
self.show = options.show
self.composite = options.composite
self.ignoreBoundingBox = options.ignoreBoundingBox
#---------------------- done with options
# Proceed with VTK setup
# Create the RenderWindow and RenderWindowInteractor
self.renWin = vtk.vtkRenderWindow()
self.renWin.SetSize(800,600)
self.vtkapp.addRenderWindow(self.renWin)
self.iren = vtk.vtkRenderWindowInteractor()
self.iren.SetRenderWindow(self.renWin)
self.iren.Initialize()
self._simpleQueue = []
self._compositeQueue = []
def _basicSetup(self, vtkapp, options):
"""
Constructor code common with derivative classes constructor.
@param vtkapp: C{self.L{vtkapp}} value
@type vtkapp: L{barReconstructionModule} object
@param options: an object containing constructor options as its
attributes:
- C{cameraMovementAngles} - C{self.L{vtkapp}.L{cameraPosition<barReconstructionModule.cameraPosition>}}
and C{self.L{vtkapp}.L{cameraViewUp<barReconstructionModule.cameraViewUp>}}
values encoded as camera movement angles,
- C{parallel} - C{self.L{vtkapp}.L{parallelProjection<barReconstructionModule.parallelProjection>}} value,
- C{background} - C{self.L{vtkapp}.L{background<barReconstructionModule.background>}},
- C{voxelDimensions} - C{(self.L{xyres}, self.L{zres})} value,
- C{exportDir} - C{self.L{exportDir}} value,
- C{generateSubstructures} - C{self.L{depth}} value,
- C{format} - C{self.L{formats}} members list,
- C{show} - C{self.L{show}} value,
- C{brainoutline} - legacy option, indicates if the root
structure of the hierarchy tree has
to be appended to C{self.L{outline}},
- C{outline} - structures to be included in C{self.L{outline}},
- C{composite} - C{self.L{composite}} value; if True
forces C{'exportToVTKPolydata' in self.L{formats}},
- C{ignoreBoundingBox} - C{self.L{ignoreBoundingBox}}.
Overrides bounding box
calculation - bounding box
will be always equal to
hierarchy root element bounding
box. Volumes for all structures
will always have the same size
and origin. This feature
increases memory usage and
reconstruction time.
@type options: optparse.Values object
"""
self.vtkapp = vtkapp
# Process options
self.vtkapp.background = intColourToFloat(options.background)
self.cameraMovementAngles = options.cameraMovementAngles
self.parallel = options.parallel
if options.voxelDimensions != None:
self.xyres, self.zres = options.voxelDimensions
if options.exportDir != None:
self.exportDir = options.exportDir
if options.outline:
# check whether every group requested as an outline exists
self.outline = set(options.outline)
invalidGroups = self.outline - set(self.sh.ih.groups)
if len(invalidGroups) > 0:
# if not - report it and try to fix
for name in invalidGroups:
debugOutput("Structure %s not found." % name, error=True)
self.outline -= validGroups
else:
self.outline = set()
if options.brainoutline:
self.outline.add(self.sh.ih.hierarchyRootElementName)
self.depth = options.generateSubstructures
self.formats = set()
if options.format != None:
self.formats = set(options.format)
self.show = options.show
self.composite = options.composite
self.ignoreBoundingBox = options.ignoreBoundingBox
#---------------------- done with options
# Proceed with VTK setup
# Create the RenderWindow and RenderWindowInteractor
self.renWin = vtk.vtkRenderWindow()
self.renWin.SetSize(800, 600)
self.vtkapp.addRenderWindow(self.renWin)
self.iren = vtk.vtkRenderWindowInteractor()
self.iren.SetRenderWindow(self.renWin)
self.iren.Initialize()
self._simpleQueue = []
self._compositeQueue = []
