def checkAndSetLUT(self):
# Default to module color table
self.resourcesPath = os.path.join(slicer.modules.slicerpathology.path.replace(self.moduleName+".py",""), 'Resources')
self.colorFile = os.path.join(self.resourcesPath, "Colors/SlicerPathology.csv")
self.customLUTLabel.setText('Using Default LUT')
try:
self.editorWidget.helper.structureListWidget.merge = None
except AttributeError:
pass
# setup the color table, make sure SlicerPathology LUT is a singleton
allColorTableNodes = slicer.util.getNodes('vtkMRMLColorTableNode*').values()
for ctn in allColorTableNodes:
#print "color: "+ctn.GetName()
if ctn.GetName() == 'SlicerPathologyColor':
slicer.mrmlScene.RemoveNode(ctn)
break
self.SlicerPathologyColorNode = slicer.vtkMRMLColorTableNode()
colorNode = self.SlicerPathologyColorNode
colorNode.SetName('SlicerPathologyColor')
slicer.mrmlScene.AddNode(colorNode)
colorNode.SetTypeToUser()
with open(self.colorFile) as f:
n = sum(1 for line in f)
colorNode.SetNumberOfColors(n-1)
colorNode.NamesInitialisedOn()
import csv
self.structureNames = []
with open(self.colorFile, 'rb') as csvfile:
reader = csv.DictReader(csvfile, delimiter=',')
for index,row in enumerate(reader):
success = colorNode.SetColor(index ,row['Label'],float(row['R'])/255,float(row['G'])/255,float(row['B'])/255,float(row['A']))
if not success:
print "color %s could not be set" % row['Label']
self.structureNames.append(row['Label'])
def fit(self, atlasName='DevelopmentalAtlas', range=[0, 5]):
"""
Create a volume of the slope across the range of years.
least squares notation from:
http://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.lstsq.html
"""
ijkToRAS = vtk.vtkMatrix4x4()
atlasVolume = slicer.util.getNode(atlasName)
atlasVolume.GetIJKToRASMatrix(ijkToRAS)
fitVolume = slicer.vtkMRMLScalarVolumeNode()
fitVolume.SetIJKToRASMatrix(ijkToRAS)
ageRange = str(range).replace('[', '(').replace(']', ')')
fitName = 'Slope_' + ageRange + '_' + atlasName
fitVolume.SetName(fitName)
colorNode = slicer.vtkMRMLColorTableNode()
colorNode.SetTypeToGrey()
slicer.mrmlScene.AddNode(colorNode)
fitDisplayNode = slicer.vtkMRMLScalarVolumeDisplayNode()
fitDisplayNode.SetAutoWindowLevel(False)
fitDisplayNode.SetWindow(10)
fitDisplayNode.SetLevel(45)
slicer.mrmlScene.AddNode(fitDisplayNode)
fitDisplayNode.SetAndObserveColorNodeID(colorNode.GetID())
fitImage = vtk.vtkImageData()
fitImage.ShallowCopy(atlasVolume.GetImageData())
fitImage.AllocateScalars(vtk.VTK_FLOAT, 1)
fitVolume.SetAndObserveImageData(fitImage)
slicer.mrmlScene.AddNode(fitVolume)
fitVolume.SetAndObserveDisplayNodeID(fitDisplayNode.GetID())
fitArray = slicer.util.array(fitName)
atlasArray = slicer.util.array(atlasName)
# make a regression against a scale more or less like the multivolume plot
timePoints = self.agesInYears[range[0]:range[1]]
timePoints = map(lambda x: x * 1000., timePoints)
A = numpy.vstack([timePoints, numpy.ones(len(timePoints))]).T
slices, rows, columns, frames = atlasArray.shape
for slice in xrange(slices):
for row in xrange(rows):
for column in xrange(columns):
if atlasArray[slice, row, column, 0] == 0:
fit = 0
else:
series = atlasArray[slice, row,
column][range[0]:range[1]]
slope, intercept = numpy.linalg.lstsq(A, series)[0]
fit = -1. * numpy.degrees(numpy.arctan(slope))
fitArray[slice, row, column] = fit
return fitVolume
def fit(self,atlasName='DevelopmentalAtlas', range=[0,5]):
"""
Create a volume of the slope across the range of years.
least squares notation from:
http://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.lstsq.html
"""
ijkToRAS = vtk.vtkMatrix4x4()
atlasVolume = slicer.util.getNode(atlasName)
atlasVolume.GetIJKToRASMatrix(ijkToRAS)
fitVolume = slicer.vtkMRMLScalarVolumeNode()
fitVolume.SetIJKToRASMatrix(ijkToRAS)
ageRange = str(range).replace('[','(').replace(']',')')
fitName = 'Slope_'+ageRange+'_'+atlasName
fitVolume.SetName(fitName)
colorNode = slicer.vtkMRMLColorTableNode()
colorNode.SetTypeToGrey()
slicer.mrmlScene.AddNode(colorNode)
fitDisplayNode = slicer.vtkMRMLScalarVolumeDisplayNode()
fitDisplayNode.SetAutoWindowLevel(False)
fitDisplayNode.SetWindow(10)
fitDisplayNode.SetLevel(45)
slicer.mrmlScene.AddNode(fitDisplayNode)
fitDisplayNode.SetAndObserveColorNodeID(colorNode.GetID())
fitImage = vtk.vtkImageData()
fitImage.ShallowCopy(atlasVolume.GetImageData())
fitImage.AllocateScalars(vtk.VTK_FLOAT, 1)
fitVolume.SetAndObserveImageData(fitImage)
slicer.mrmlScene.AddNode(fitVolume)
fitVolume.SetAndObserveDisplayNodeID(fitDisplayNode.GetID())
fitArray = slicer.util.array(fitName)
atlasArray = slicer.util.array(atlasName)
# make a regression against a scale more or less like the multivolume plot
timePoints = self.agesInYears[range[0]:range[1]]
timePoints = map(lambda x : x * 1000., timePoints)
A = numpy.vstack([timePoints, numpy.ones(len(timePoints))]).T
slices, rows, columns, frames = atlasArray.shape
for slice in xrange(slices):
for row in xrange(rows):
for column in xrange(columns):
if atlasArray[slice, row, column, 0] == 0:
fit = 0
else:
series = atlasArray[slice, row, column][range[0]:range[1]]
slope, intercept = numpy.linalg.lstsq(A, series)[0]
fit = -1. * numpy.degrees(numpy.arctan(slope))
fitArray[slice, row, column] = fit
return fitVolume
def createFociVisualizationColorMap(self, minimumValue, maximumValue):
if (minimumValue < 0):
numberOfCoolColors = -(minimumValue)
else:
numberOfCoolColors = 0
if (maximumValue > 0):
numberOfHotColors = maximumValue + 1 # includes zero
else:
numberOfHotColors = 0
#print "number of cool colors = " + str(numberOfCoolColors)
#print "number of hot colors (including zero) = " + str(numberOfHotColors)
colorNode = slicer.util.getNode(self.FOCI_DETECTION_COLORMAP_NAME)
if colorNode is None:
colorNode = slicer.vtkMRMLColorTableNode()
slicer.mrmlScene.AddNode(colorNode)
colorNode.SetName(self.FOCI_DETECTION_COLORMAP_NAME)
colorNode.SetTypeToUser()
colorNode.SetNumberOfColors(numberOfCoolColors + numberOfHotColors);
# colorNode.SetColor(0, "zero", 0.0, 0.0, 0.0, 1.0);
# colorNode.SetColor(1, "one", 1.0, 0.0, 0.0, 1.0);
# colorNode.SetColor(2, "two", 0.0, 1.0, 0.0, 1.0);
colorNode.SetNamesFromColors()
''' cool color map in Matlab
r = (0:m-1)'/max(m-1,1);
c = [r 1-r ones(m,1)];
'''
for colorIndex in xrange(0, numberOfCoolColors):
r = np.double(numberOfCoolColors - 1 - colorIndex) / (numberOfCoolColors)
colorNode.SetColor(colorIndex, r, 1 - r, 1, 1.0);
#print "cool color index = " + str(colorIndex)
''' hot color table in Matlab
r = [(1:n)'/n; ones(m-n,1)];
g = [zeros(n,1); (1:n)'/n; ones(m-2*n,1)];
b = [zeros(2*n,1); (1:m-2*n)'/(m-2*n)];
'''
n = 3 * numberOfHotColors / 8 # fix
''' hot color table in Python '''
r = np.concatenate((np.double(range(1, n + 1)) / n , np.ones(numberOfHotColors - n)))
g = np.concatenate((np.zeros(n), np.double(range(1, n + 1)) / n, np.ones(numberOfHotColors - 2 * n)))
b = np.concatenate((np.zeros(2 * n), np.double(range(1, numberOfHotColors - 2 * n + 1)) / (numberOfHotColors - 2 * n)))
for colorIndex in xrange(0, numberOfHotColors):
colorNode.SetColor(numberOfCoolColors + colorIndex, r[colorIndex], g[colorIndex], b[colorIndex], 1.0);
#print "hot color index = " + str(numberOfCoolColors + colorIndex)
colorNode.SetOpacity(numberOfCoolColors, 0);
'''
def createColorTable(self):
""" """
self.logging.debug("call")
self.colorTableNode = slicer.vtkMRMLColorTableNode()
self.colorTableNode.SetFileName(os.path.join(__slicer_module__, 'Resources', 'ColorFile', self.colorTable))
self.colorTableNode.SetName(self.colorTable[:-4])
storage = self.colorTableNode.CreateDefaultStorageNode()
slicer.mrmlScene.AddNode(storage)
self.colorTableNode.AddAndObserveStorageNodeID(storage.GetID())
slicer.mrmlScene.AddNode(self.colorTableNode)
storage.SetFileName(self.colorTableNode.GetFileName())
storage.SetReadState(True)
storage.ReadData(self.colorTableNode, True)
def createColorTable(self):
"""
"""
self.colorTableNode = slicer.vtkMRMLColorTableNode()
self.colorTableNode.SetFileName(
os.path.join(__slicer_module__, 'Resources', 'ColorFile',
self.colorTable))
self.colorTableNode.SetName(self.colorTable[:-4])
storage = self.colorTableNode.CreateDefaultStorageNode()
slicer.mrmlScene.AddNode(storage)
self.colorTableNode.AddAndObserveStorageNodeID(storage.GetID())
slicer.mrmlScene.AddNode(self.colorTableNode)
storage.SetFileName(self.colorTableNode.GetFileName())
storage.SetReadState(True)
storage.ReadData(self.colorTableNode, True)
def __init__(self, parent = None):
QCLib.genericPanel.__init__(self,parent)
self.coln=slicer.mrmlScene.GetNodesByClassByName('vtkMRMLColorNode','GMBColorTable').GetItemAsObject(0)
if not self.coln:
self.coln=slicer.vtkMRMLColorTableNode()
self.coln.SetName("GMBColorTable")
self.coln.SetTypeToUser()
self.coln.HideFromEditorsOff()
self.coln.SetNumberOfColors(2)
self.coln.SetColor(0,'bg',0,0,0)
self.coln.SetColor(1,'fg',1,0,0)
self.coln.SetOpacity(0,0)
self.coln.SetOpacity(1,1)
slicer.mrmlScene.AddNode(self.coln)
if not parent:
self.setup()
self.parent.show()
def generateLUT(self):
self.deleteNodeByName('ShapeDistanceAnalyzer Distance Color Table')
colorlow = (0.1, 0.1, 1)
colormid = (1, 1, 1)
colorhigh = (1, 0.1, 0.1)
#should be an odd number
total_number_of_colors = 512
colorTableNode = slicer.vtkMRMLColorTableNode()
colorTableNode.SetName('ShapeDistanceAnalyzer Color Table')
colorTableNode.SetTypeToUser()
colorTableNode.HideFromEditorsOff()
colorTableNode.SaveWithSceneOff()
colorTableNode.SetNumberOfColors(total_number_of_colors)
colorTableNode.GetLookupTable().SetTableRange(
0, total_number_of_colors - 1)
number_of_colors = total_number_of_colors / 2
#from colorlow to colormid
for i in range(number_of_colors):
alpha = float(i) / (number_of_colors - 1)
r = colorlow[0] * (1 - alpha) + colormid[0] * alpha
g = colorlow[1] * (1 - alpha) + colormid[1] * alpha
b = colorlow[2] * (1 - alpha) + colormid[2] * alpha
colorTableNode.AddColor(str(i), r, g, b, 1)
#from colormid to colorhigh
for i in range(number_of_colors):
alpha = float(i) / (number_of_colors - 1)
r = colormid[0] * (1 - alpha) + colorhigh[0] * alpha
g = colormid[1] * (1 - alpha) + colorhigh[1] * alpha
b = colormid[2] * (1 - alpha) + colorhigh[2] * alpha
colorTableNode.AddColor(str(number_of_colors + i), r, g, b, 1)
colorTableNode.SetName('ShapeDistanceAnalyzer Distance Color Table')
slicer.mrmlScene.AddNode(colorTableNode)
def createColorTable(self, outputVolumeNodeName):
""" Creates a colour table with the names of the fiducials
:param str outputVolumeNodeName:
"""
# Need to use and reset WASP label if already their
if slicer.util.getNode("WASP_labels"):
color = slicer.util.getNode("WASP_labels")
color.Reset()
else:
# Setup a new colour table
color = slicer.vtkMRMLColorTableNode()
color.SetNumberOfColors(3)
color.SetName("WASP_labels")
color.SetTypeToLabels()
# Go through the self.final_dict instance attribute and set a new colour map using those names
for name in self.final_dict:
color.SetColorName(self.final_dict[name], name)
# add to scene
slicer.mrmlScene.AddNode(color)
# print for check
colorID = color.GetID()
print outputVolumeNodeName
print "colour", colorID
# Setup the layers
outputVolumeNode = slicer.util.getNode(str(outputVolumeNodeName))
outputVolumeNode.SetDisplayVisibility(1)
# Set to the output to show. Otherwise a volumeDisplayNode wont
slicer.app.applicationLogic().GetSelectionNode().SetReferenceActiveVolumeID(outputVolumeNode.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection(0)
display = outputVolumeNode.GetVolumeDisplayNode()
display.SetAndObserveColorNodeID(str(colorID))
def onSelectMaster(self):
self.master = self.masterSelector.currentNode()
merge=None
self.overrideROI.enabled=False
self.sliceslider.enabled=False
self.autothr.enabled=False
self.autothreshold()
self.dgp.enabled=False
self.chartButton.enabled=False
self.sides=None
self.diagonals=None
for n in range(8):
self.items[n+2].setText("")
#-----mergeVolume()
if self.master:
self.overrideROI.enabled=True
self.autothr.enabled=True
self.autothreshold()
masterName = self.master.GetName()
mergeName = masterName+self.suffixMergeName
# if we already have a merge and the master hasn't changed, use it
if self.merge and self.master == self.masterWhenMergeWasSet:
mergeNode = slicer.mrmlScene.GetNodeByID(self.merge.GetID())
if mergeNode and mergeNode !="":
merge=self.merge
if not merge:
self.masterWhenMergeWasSemasterWhenMergeWasSet = None
# otherwise pick the merge based on the master name
# - either return the merge volume or empty string
merge = self.getNodeByName(mergeName)
self.merge=merge
#-----
if merge:
if merge.GetClassName() != "vtkMRMLLabelMapVolumeNode":
self.errorDialog("Error: selected merge label volume is not a label volume " + merge.GetClassName())
else:
warnings = self.checkForVolumeWarnings(self.master,self.merge)
if warnings != "":
self.errorDialog( "Warning: %s" % warnings )
else:
# make the source node the active background, and the label node the active label
applicationLogic = slicer.app.applicationLogic()
selectionNode = applicationLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(self.master.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(merge.GetID())
applicationLogic.PropagateVolumeSelection(0)
self.merge = merge
sn=self.qu.getSliceNode()
if sn:
self.sliceslider.setMRMLSliceNode(sn)
self.sliceslider.enabled=True
else:
self.sliceslider.enabled=False
else:
# the master exists, but there is no merge volume yet
volumesLogic = slicer.modules.volumes.logic()
merge = volumesLogic.CreateAndAddLabelVolume(slicer.mrmlScene, self.master, mergeName)
coln=slicer.vtkMRMLColorTableNode()
coln.SetTypeToRandom()
slicer.mrmlScene.AddNode(coln)
merge.GetDisplayNode().SetAndObserveColorNodeID(coln.GetID())
#cl=slicer.vtkMRMLColorLogic()
#cl.SetMRMLScene(slicer.mrmlScene)
#merge.GetDisplayNode().SetAndObserveColorNodeID(cl.GetFileColorNodeID("GenericColors.txt"))
self.merge = merge
self.masterWhenMergeWasSet = self.master
#self.labelSelector.setCurrentNode(self.merge)
self.onSelectMaster()
def __init__(self):
# Member variables
self.outputLabels = None
self.recordedDataBuffer = []
self.record = False
self.reset = False
self.outputObserverTag = -1
self.rigidBodyToTrackerTransformNode = None
self.measurementToMeasurerTransformNode = None
self.parametersToMeasurerTransformNode = None
self.plus = None
self.m = vtk.vtkMatrix4x4()
self.direction = -1
self.ras = [0, 0, 0, 1]
self.d = 0.0
self.snr = 0
self.total = 0
self.LABEL_UPDATE_RATE = 10
self.labelUpdateCount = 0
self.snrThreshold = 40
self.distanceMaximumValue = 1000.0
self.distanceMinimumValue = 0.0
self.lensMaxDistance = 0.0
self.lensMinDistance = 0.0
self.normalizingConstant = 0.0
self.min = -1000.0
self.addColours = True
import Viewpoint # Viewpoint
self.viewpointLogic = Viewpoint.ViewpointLogic()
self.stopWatch = None # StopWatch
# Create style sheets
self.errorStyleSheet = "QLabel { color : #FF0000; \
font: bold 14px}"
self.defaultStyleSheet = "QLabel { color : #000000; \
font: bold 14px}"
# Create rainbow colour table
self.colorTable=slicer.vtkMRMLColorTableNode()
self.colorTable.SetTypeToRainbow ()
# Add MeasurementPoint
self.measurementPointMarkupsFiducialNode = slicer.util.getNode('MeasurementPoint')
if not self.measurementPointMarkupsFiducialNode:
self.measurementPointMarkupsFiducialNode = slicer.vtkMRMLMarkupsFiducialNode()
self.measurementPointMarkupsFiducialNode.SetName('MeasurementPoint')
self.measurementPointMarkupsFiducialNode.AddFiducial(0, 0, 0)
self.measurementPointMarkupsFiducialNode.SetNthFiducialLabel(0, '')
slicer.mrmlScene.AddNode(self.measurementPointMarkupsFiducialNode)
self.measurementPointMarkupsFiducialNode.GetDisplayNode().SetGlyphScale(2.0)
self.measurementPointMarkupsFiducialNode.GetDisplayNode().SetGlyphType(13) # Sphere3D
self.measurementPointMarkupsFiducialNode.GetDisplayNode().SetSelectedColor(1, 0, 0)
# Add RecordedModel
self.recordedModelNode = slicer.util.getNode('RecordedModel')
if not self.recordedModelNode:
recordedPoints = vtk.vtkPoints()
recordedVertices = vtk.vtkCellArray()
recordedPolyData = vtk.vtkPolyData()
recordedPolyData.SetPoints(recordedPoints)
recordedPolyData.SetVerts(recordedVertices)
self.recordedModelNode = self.addModelToScene(recordedPolyData, "RecordedModel")
self.recordedModelNode.GetModelDisplayNode().SetPointSize(3)
# Set up coloured scalars
colorArray = vtk.vtkDoubleArray()
colorArray.SetNumberOfComponents(4)
colorArray.SetName('Colors')
self.recordedModelNode.GetPolyData().GetPointData().SetScalars(colorArray)
# Create share directory
self.pathToCreatedSaveDir = self.createShareDirectory()
# Post-Processing default (for undo)
self.recordedDataBufferDefault = []
def onSelectMaster(self):
self.master = self.masterSelector.currentNode()
merge=None
#-----mergeVolume()
if self.master:
masterName = self.master.GetName()
mergeName = masterName+self.suffixMergeName
# if we already have a merge and the master hasn't changed, use it
if self.merge and self.master == self.masterWhenMergeWasSet:
mergeNode = slicer.mrmlScene.GetNodeByID(self.merge.GetID())
if mergeNode and mergeNode !="":
merge=self.merge
if not merge:
self.masterWhenMergeWasSemasterWhenMergeWasSet = None
# otherwise pick the merge based on the master name
# - either return the merge volume or empty string
merge = self.getNodeByName(mergeName)
self.merge=merge
#-----
if merge:
if merge.GetClassName() != "vtkMRMLLabelMapVolumeNode":
self.errorDialog("Error: selected merge label volume is not a label volume " + merge.GetClassName())
else:
warnings = self.checkForVolumeWarnings(self.master,self.merge)
if warnings != "":
self.errorDialog( "Warning: %s" % warnings )
else:
# make the source node the active background, and the label node the active label
applicationLogic = slicer.app.applicationLogic()
selectionNode = applicationLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(self.master.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(merge.GetID())
applicationLogic.PropagateVolumeSelection(0)
self.merge = merge
else:
# the master exists, but there is no merge volume yet
volumesLogic = slicer.modules.volumes.logic()
merge = volumesLogic.CreateAndAddLabelVolume(slicer.mrmlScene, self.master, mergeName)
coln=slicer.vtkMRMLColorTableNode()
coln.SetTypeToUser()
coln.SetNumberOfColors(9)
coln.SetColor(0,'bg',0,0,0)
coln.SetColor(1,'n',1,0,0)
coln.SetColor(2,'ne',0,1,0)
coln.SetColor(3,'nw',0,0,1)
coln.SetColor(4,'e',1,1,0)
coln.SetColor(5,'w',1,0,1)
coln.SetColor(6,'s',0,1,1)
coln.SetColor(7,'se',1,1,1)
coln.SetColor(8,'sw',1,0.5,0)
coln.SetOpacity(0,0)
for n in range(1,9):
coln.SetOpacity(n,1)
slicer.mrmlScene.AddNode(coln)
merge.GetDisplayNode().SetAndObserveColorNodeID(coln.GetID())
self.merge = merge
self.masterWhenMergeWasSet = self.master
self.onSelectMaster()