def PlotMembershipFunctions( membershipFunctions, min, max, steps ):
step = float( max - min ) / steps
# Setting up the array of values
chartNode = slicer.vtkMRMLChartNode()
chartNode.SetScene( slicer.mrmlScene )
slicer.mrmlScene.AddNode( chartNode )
for i in range( len( membershipFunctions ) ):
arrayNode = slicer.vtkMRMLDoubleArrayNode()
arrayNode.SetScene( slicer.mrmlScene )
slicer.mrmlScene.AddNode( arrayNode )
array = arrayNode.GetArray()
array.SetNumberOfTuples( int( ( max - min ) / step ) )
for j in range( array.GetNumberOfTuples() ):
array.SetComponent( j, 0, min + j * step )
array.SetComponent( j, 1, membershipFunctions[ i ].Evaluate( min + j * step ) )
array.SetComponent( j, 2, 0 )
# Add array into a chart node
chartNode.AddArray( "Membership Function " + str( i ), arrayNode.GetID() )
chartNode.SetProperty( 'default', 'title', 'Membership Functions' )
chartNode.SetProperty( 'default', 'xAxisLabel', 'Membership Value' )
chartNode.SetProperty( 'default', 'yAxisLabel', 'Element' )
# Set the chart in the chart view node
chartViewNode = slicer.mrmlScene.GetNthNodeByClass( 0, "vtkMRMLChartViewNode" )
if ( chartViewNode is None ):
chartViewNode = slicer.vtkMRMLChartViewNode()
chartViewNode.SetScene( slicer.mrmlScene )
slicer.mrmlScene.AddNode( chartViewNode )
chartViewNode.SetChartNodeID( chartNode.GetID() )
def showChart(self, samples, names):
print("Logic showing chart")
lm = slicer.app.layoutManager()
lm.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpQuantitativeView)
doubleArrays = []
for sample in samples:
arrayNode = slicer.mrmlScene.AddNode(
slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
nDataPoints = sample.GetNumberOfTuples()
array.SetNumberOfTuples(nDataPoints)
array.SetNumberOfComponents(3)
for i in range(nDataPoints):
array.SetComponent(i, 0, i)
array.SetComponent(i, 1, sample.GetTuple1(i))
array.SetComponent(i, 2, 0)
doubleArrays.append(arrayNode)
cvNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
cvNodes.SetReferenceCount(cvNodes.GetReferenceCount() - 1)
cvNodes.InitTraversal()
cvNode = cvNodes.GetNextItemAsObject()
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
for pairs in zip(names, doubleArrays):
chartNode.AddArray(pairs[0], pairs[1].GetID())
cvNode.SetChartNodeID(chartNode.GetID())
return
def section_ChartRole(self):
self.delayDisplay("Chart role", self.delayMs)
# Create sample chart node
chartNode = slicer.vtkMRMLChartNode()
slicer.mrmlScene.AddNode(chartNode)
chartNode.SetName(self.sampleChartName)
# Add node to subject hierarchy
from vtkSlicerSubjectHierarchyModuleMRML import vtkMRMLSubjectHierarchyNode
studyNode = slicer.util.getNode(
self.studyName + slicer.vtkMRMLSubjectHierarchyConstants.GetSubjectHierarchyNodeNamePostfix()
)
self.assertTrue(studyNode != None)
chartShNode = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(
slicer.mrmlScene,
studyNode,
slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMLevelSeries(),
self.sampleChartName,
chartNode,
)
self.assertTrue(chartShNode != None)
self.assertTrue(chartShNode.GetParentNode() == studyNode)
self.assertTrue(chartShNode.GetOwnerPluginName() == "Charts")
def run(self, segmentationVolume, falseNegativeLine, truePositiveRegion, dilationFactor):
"""
Run the actual algorithm
"""
logging.info('Processing started')
if (not self.isValidDilateValue(dilationFactor)):
slicer.util.errorDisplay("The dilation value must be an integer.")
return False
if (not self.hasImageData(segmentationVolume)):
slicer.util.errorDisplay("The segmentation is not valid.")
return False
# Iteratively compute the false negative true positive metrics
falseNegativeResults = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
truePositiveResults = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
falseNegativeArray = falseNegativeResults.GetArray()
truePositiveArray = truePositiveResults.GetArray()
falseNegativeArray.SetNumberOfTuples(int(dilationFactor))
truePositiveArray.SetNumberOfTuples(int(dilationFactor))
for dilateValue in range(int(dilationFactor)):
cliParams = {'truePositiveGroundTruthVolume': truePositiveRegion.GetID(),
'falseNegativeGroundTruthVolume': falseNegativeLine.GetID(),
'dilateValue' : dilateValue,
'segmentedVolume': segmentationVolume.GetID()}
cliNode = slicer.cli.run(slicer.modules.usbonesegmentationevaluator, None, cliParams, wait_for_completion=True)
falseNegativeResult = cliNode.GetParameterAsString("falseNegativePercentage")
falseNegativeArray.SetComponent(dilateValue, 0, dilateValue)
falseNegativeArray.SetComponent(dilateValue, 1, float(falseNegativeResult))
falseNegativeArray.SetComponent(dilateValue, 2, 0)
truePositiveResult = cliNode.GetParameterAsString("truePositivePercentage")
truePositiveArray.SetComponent(dilateValue, 0, dilateValue)
truePositiveArray.SetComponent(dilateValue, 1, float(truePositiveResult))
truePositiveArray.SetComponent(dilateValue, 2, 0)
# Change to layout which has a chart view
layoutNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
layoutNodes.InitTraversal()
layoutNode = layoutNodes.GetNextItemAsObject()
layoutNode.SetViewArrangement(24)
# Create chart node and chart view node
chartViewNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartViewNode())
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
chartNode.AddArray('False Negative Percentage', falseNegativeResults.GetID())
chartNode.AddArray('True Positive Percentage', truePositiveResults.GetID())
chartNode.SetProperty('default', 'xAxisLabel', 'Dilation Value')
chartNode.SetProperty('default', 'yAxisLabel', 'Percentage')
chartNode.SetProperty('default', 'type', 'Scatter')
chartViewNode.SetChartNodeID(chartNode.GetID())
chartNode.Modified()
chartViewNode.Modified()
slicer.mrmlScene.Modified()
layoutNode.Modified()
logging.info('Processing completed')
return True
def createStatsChart(self, labelNode, valueToPlot):
"""Make a MRML chart of the current stats
"""
self.setChartLayout()
chartViewNode = slicer.util.getNode('ChartView')
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
samples = len(self.regionTags)
tuples = samples
array.SetNumberOfTuples(tuples)
tuple = 0
for i in xrange(samples):
index = self.regionTags[i]
array.SetComponent(tuple, 0, i)
array.SetComponent(tuple, 1, self.labelStats[valueToPlot, index])
array.SetComponent(tuple, 2, 0)
tuple += 1
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
chartNode.AddArray(valueToPlot, arrayNode.GetID())
chartViewNode.SetChartNodeID(chartNode.GetID())
chartNode.SetProperty('default', 'title', 'Parenchyma Statistics')
chartNode.SetProperty('default', 'xAxisLabel', 'Label')
chartNode.SetProperty('default', 'yAxisLabel', valueToPlot)
chartNode.SetProperty('default', 'type', 'Bar')
chartNode.SetProperty('default', 'xAxisType', 'categorical')
chartNode.SetProperty('default', 'showLegend', 'off')
# series level properties
if labelNode.GetDisplayNode() != None and labelNode.GetDisplayNode(
).GetColorNode() != None:
colorNode = labelNode.GetDisplayNode().GetColorNode()
newDisplayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
newDisplayNode.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
slicer.mrmlScene.AddNode(newDisplayNode)
newColorNode = newDisplayNode.GetColorNode()
colorNumber = 0
for tag in self.regionTags:
c = [0, 0, 0, 0]
value = self.valuesDictionary[tag]
if value[0] == value[1]:
colorNode.SetColorName(value[0], tag)
colorNode.GetColor(value[0], c)
newColorNode.SetColor(colorNumber, c[0], c[1], c[2])
newColorNode.SetColorName(colorNumber, tag)
colorNumber += 1
# chartNode.SetProperty(valueToPlot, 'lookupTable', labelNode.GetDisplayNode().GetColorNodeID())
chartNode.SetProperty(valueToPlot, 'lookupTable',
newColorNode.GetID())
def createStatsChart(self, labelNode, valueToPlot, ignoreZero=False):
"""Make a MRML chart of the current stats
"""
layoutNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
layoutNodes.SetReferenceCount(layoutNodes.GetReferenceCount() - 1)
layoutNodes.InitTraversal()
layoutNode = layoutNodes.GetNextItemAsObject()
layoutNode.SetViewArrangement(
slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalQuantitativeView)
chartViewNodes = slicer.mrmlScene.GetNodesByClass(
'vtkMRMLChartViewNode')
chartViewNodes.SetReferenceCount(chartViewNodes.GetReferenceCount() -
1)
chartViewNodes.InitTraversal()
chartViewNode = chartViewNodes.GetNextItemAsObject()
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
samples = len(self.labelStats["Labels"])
tuples = samples
if ignoreZero and self.labelStats["Labels"].__contains__(0):
tuples -= 1
array.SetNumberOfTuples(tuples)
tuple = 0
for i in xrange(samples):
index = self.labelStats["Labels"][i]
if not (ignoreZero and index == 0):
array.SetComponent(tuple, 0, index)
array.SetComponent(tuple, 1, self.labelStats[index,
valueToPlot])
array.SetComponent(tuple, 2, 0)
tuple += 1
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
state = chartNode.StartModify()
chartNode.AddArray(valueToPlot, arrayNode.GetID())
chartViewNode.SetChartNodeID(chartNode.GetID())
chartNode.SetProperty('default', 'title', 'Label Statistics')
chartNode.SetProperty('default', 'xAxisLabel', 'Label')
chartNode.SetProperty('default', 'yAxisLabel', valueToPlot)
chartNode.SetProperty('default', 'type', 'Bar')
chartNode.SetProperty('default', 'xAxisType', 'categorical')
chartNode.SetProperty('default', 'showLegend', 'off')
# series level properties
if labelNode.GetDisplayNode() != None and labelNode.GetDisplayNode(
).GetColorNode() != None:
chartNode.SetProperty(valueToPlot, 'lookupTable',
labelNode.GetDisplayNode().GetColorNodeID())
chartNode.EndModify(state)
def ChartRepresentationRotation(self, rotationX,rotationY,rotationZ, timeStamp):
# Switch to a layout (24) that contains a Chart View to initiate the construction of the widget and Chart View Node
lns = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
lns.InitTraversal()
ln = lns.GetNextItemAsObject()
ln.SetViewArrangement(506)
# Get the Chart View Node
cvns = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
cvns.InitTraversal()
cvn = cvns.GetNextItemAsObject()
# Create an Array Node and add some data
dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn.GetArray()
a.SetNumberOfTuples(len(rotationX))
t=range(0,len(rotationX))
for i in t:
a.SetComponent(i, 0, i)
a.SetComponent(i, 1, rotationX[i])
a.SetComponent(i, 2, 0)
# Create a second Array node
dn2 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
b = dn2.GetArray()
b.SetNumberOfTuples(len(rotationY))
for i in t:
b.SetComponent(i, 0, i)
b.SetComponent(i, 1, rotationY[i])
b.SetComponent(i, 2, 0)
# Create a second Array node
dn3 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
c = dn3.GetArray()
c.SetNumberOfTuples(len(rotationZ))
for i in t:
c.SetComponent(i, 0, i)
c.SetComponent(i, 1, rotationZ[i])
c.SetComponent(i, 2, 0)
# Create a Chart Node.
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add the Array Nodes to the Chart. The first argument is a string used for the legend and to refer to the Array when setting properties.
cn.AddArray('Rotation in X', dn.GetID())
cn.AddArray('Rotation in Y', dn2.GetID())
cn.AddArray('Rotation in Z', dn3.GetID())
# Set a few properties on the Chart. The first argument is a string identifying which Array to assign the property.
# 'default' is used to assign a property to the Chart itself (as opposed to an Array Node).
cn.SetProperty('default', 'title', 'ROTATION PLOT')
cn.SetProperty('default', 'xAxisLabel', 'Time')
cn.SetProperty('default', 'yAxisLabel', 'Angle (degrees)')
# Tell the Chart View which Chart to display
cvn.SetChartNodeID(cn.GetID())
def showChart(self):
#switch to layout containing a chart viewer
#lm = slicer.app.layoutManager()
#lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpQuantitativeView)
# Switch to a layout (24) that contains a Chart View to initiate the construction of the widget and Chart View Node
lns = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
lns.InitTraversal()
ln = lns.GetNextItemAsObject()
ln.SetViewArrangement(506)
# Get the Chart View Node
cvns = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
cvns.InitTraversal()
cvn = cvns.GetNextItemAsObject()
# Create an Array Node and add some data
dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn.GetArray()
a.SetNumberOfTuples(600)
x = range(0, 600)
for i in range(len(x)):
a.SetComponent(i, 0, x[i]/50.0)
a.SetComponent(i, 1, math.sin(x[i]/50.0))
a.SetComponent(i, 2, 0)
# Create a second Array node
dn2 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn2.GetArray()
a.SetNumberOfTuples(600)
x = range(0, 600)
for i in range(len(x)):
a.SetComponent(i, 0, x[i]/50.0)
a.SetComponent(i, 1, math.cos(x[i]/50.0))
a.SetComponent(i, 2, 0)
# Create a Chart Node.
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add the Array Nodes to the Chart. The first argument is a string used for the legend and to refer to the Array when setting properties.
cn.AddArray('A double array', dn.GetID())
cn.AddArray('Another double array', dn2.GetID())
# Set a few properties on the Chart. The first argument is a string identifying which Array to assign the property.
# 'default' is used to assign a property to the Chart itself (as opposed to an Array Node).
cn.SetProperty('default', 'title', 'A simple chart with 2 curves')
cn.SetProperty('default', 'xAxisLabel', 'Something in x')
cn.SetProperty('default', 'yAxisLabel', 'Something in y')
# Tell the Chart View which Chart to display
cvn.SetChartNodeID(cn.GetID())
def createStatsChart(self, labelNode, valueToPlot, ignoreZero=False):
"""Make a MRML chart of the current stats
"""
layoutNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
layoutNodes.SetReferenceCount(layoutNodes.GetReferenceCount()-1)
layoutNodes.InitTraversal()
layoutNode = layoutNodes.GetNextItemAsObject()
layoutNode.SetViewArrangement(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalQuantitativeView)
chartViewNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
chartViewNodes.SetReferenceCount(chartViewNodes.GetReferenceCount()-1)
chartViewNodes.InitTraversal()
chartViewNode = chartViewNodes.GetNextItemAsObject()
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
samples = len(self.labelStats["Labels"])
tuples = samples
if ignoreZero and self.labelStats["Labels"].__contains__(0):
tuples -= 1
array.SetNumberOfTuples(tuples)
tuple = 0
for i in xrange(samples):
index = self.labelStats["Labels"][i]
if not (ignoreZero and index == 0):
array.SetComponent(tuple, 0, index)
array.SetComponent(tuple, 1, self.labelStats[index,valueToPlot])
array.SetComponent(tuple, 2, 0)
tuple += 1
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
state = chartNode.StartModify()
chartNode.AddArray(valueToPlot, arrayNode.GetID())
chartViewNode.SetChartNodeID(chartNode.GetID())
chartNode.SetProperty('default', 'title', 'Label Statistics')
chartNode.SetProperty('default', 'xAxisLabel', 'Label')
chartNode.SetProperty('default', 'yAxisLabel', valueToPlot)
chartNode.SetProperty('default', 'type', 'Bar');
chartNode.SetProperty('default', 'xAxisType', 'categorical')
chartNode.SetProperty('default', 'showLegend', 'off')
# series level properties
if labelNode.GetDisplayNode() != None and labelNode.GetDisplayNode().GetColorNode() != None:
chartNode.SetProperty(valueToPlot, 'lookupTable', labelNode.GetDisplayNode().GetColorNodeID());
chartNode.EndModify(state)
def AddSelectedHistograms(self, histogramsList):
histogramViewNode = slicer.util.getNode('HistogramView')
HistNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
for tag in histogramsList:
HistNode.AddArray(tag, self.histogramArrays[tag].GetID())
histogramViewNode.SetChartNodeID(HistNode.GetID())
HistNode.SetProperty('default', 'title', 'Lung Density Histogram')
HistNode.SetProperty('default', 'xAxisLabel', 'Density (HU)')
HistNode.SetProperty('default', 'yAxisLabel', 'Frequency')
HistNode.SetProperty('default', 'type', 'Line')
HistNode.SetProperty('default', 'xAxisType', 'quantitative')
HistNode.SetProperty('default', 'showLegend', 'on')
def compareTRE_FRE():
averages = []
TREs = []
numPoints = range(10, 45, 5)
for i in range(10, 45, 5):
# This is 7 iterations
print "Number of points used: " + str(i)
[alphaPoints, betaPoints, referenceToRas] = createTransformPoints(2.0, i)
alphaToBetaMatrix = computeRegistration(referenceToRas, alphaPoints, betaPoints)
average = avgDistAfterReg(i, alphaPoints, betaPoints, alphaToBetaMatrix)
averages.append(average)
TRE = computeTRE(alphaToBetaMatrix)
TREs.append(TRE)
lns = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
lns.InitTraversal()
ln = lns.GetNextItemAsObject()
ln.SetViewArrangement(24)
# Get the Chart View Node
cvns = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
cvns.InitTraversal()
cvn = cvns.GetNextItemAsObject()
# Create an Array Node and add some data
TRE_dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
arrayNode = TRE_dn.GetArray()
arrayNode.SetNumberOfTuples(7)
FRE_dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
arrayNode2 = FRE_dn.GetArray()
arrayNode2.SetNumberOfTuples(7)
for i in range(len(numPoints)):
arrayNode.SetComponent(i, 0, numPoints[i])
arrayNode.SetComponent(i, 1, TREs[i])
arrayNode.SetComponent(i, 2, 0)
arrayNode2.SetComponent(i, 0, numPoints[i])
arrayNode2.SetComponent(i, 1, averages[i])
arrayNode2.SetComponent(i, 2, 0)
# Create a Chart Node.
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add the Array Nodes to the Chart. The first argument is a string used for the legend and to refer to the Array when setting properties.
cn.AddArray('TRE', TRE_dn.GetID())
cn.AddArray('FRE', FRE_dn.GetID())
# Set a few properties on the Chart. The first argument is a string identifying which Array to assign the property.
# 'default' is used to assign a property to the Chart itself (as opposed to an Array Node).
cn.SetProperty('default', 'title', 'TRE and FRE as a function of the number of points')
cn.SetProperty('default', 'xAxisLabel', 'Number of points')
cn.SetProperty('default', 'yAxisLabel', 'Unit Value')
# Tell the Chart View which Chart to display
cvn.SetChartNodeID(cn.GetID())
def section_ChartRole(self):
self.delayDisplay("Chart role",self.delayMs)
# Create sample chart node
chartNode = slicer.vtkMRMLChartNode()
slicer.mrmlScene.AddNode(chartNode)
chartNode.SetName(self.sampleChartName)
# Add markups to subject hierarchy
studyNode = slicer.util.getNode(self.studyName)
self.assertIsNotNone( studyNode )
chartShNode = slicer.vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(slicer.mrmlScene, studyNode, slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMLevelSeries(), self.sampleChartName, chartNode)
self.assertIsNotNone( chartShNode )
self.assertEqual( chartShNode.GetParentNode(), studyNode )
self.assertEqual( chartShNode.GetOwnerPluginName(), 'Charts' )
def section_PluginAutoSearch(self):
self.delayDisplay("Plugin auto search",self.delayMs)
# Disable subject hierarchy auto-creation to be able to test plugin auto search
subjectHierarchyWidget = slicer.modules.subjecthierarchy.widgetRepresentation()
subjectHierarchyPluginLogic = subjectHierarchyWidget.pluginLogic()
self.assertIsNotNone( subjectHierarchyWidget )
self.assertIsNotNone( subjectHierarchyPluginLogic )
subjectHierarchyPluginLogic.autoCreateSubjectHierarchy = False
# Test whether the owner plugin is automatically searched when the associated data node changes
chartNode2 = slicer.vtkMRMLChartNode()
chartNode2.SetName(self.sampleChartName + '2')
slicer.mrmlScene.AddNode(chartNode2)
clonedMarkupShNode = slicer.util.getNode(self.sampleMarkupName + self.cloneNodeNamePostfix + slicer.vtkMRMLSubjectHierarchyConstants.GetSubjectHierarchyNodeNamePostfix())
clonedMarkupShNode.SetAssociatedNodeID(chartNode2.GetID())
self.assertEqual( clonedMarkupShNode.GetOwnerPluginName(), 'Charts' )
def section_PluginAutoSearch(self):
self.delayDisplay("Plugin auto search",self.delayMs)
# Disable subject hierarchy auto-creation to be able to test plugin auto search
subjectHierarchyWidget = slicer.modules.subjecthierarchy.widgetRepresentation()
subjectHierarchyPluginLogic = subjectHierarchyWidget.pluginLogic()
self.assertIsNotNone( subjectHierarchyWidget )
self.assertIsNotNone( subjectHierarchyPluginLogic )
subjectHierarchyPluginLogic.autoCreateSubjectHierarchy = False
# Test whether the owner plugin is automatically searched when the associated data node changes
chartNode2 = slicer.vtkMRMLChartNode()
chartNode2.SetName(self.sampleChartName + '2')
slicer.mrmlScene.AddNode(chartNode2)
clonedMarkupShNode = slicer.util.getNode(self.sampleMarkupName + self.cloneNodeNamePostfix + slicer.vtkMRMLSubjectHierarchyConstants.GetSubjectHierarchyNodeNamePostfix())
clonedMarkupShNode.SetAssociatedNodeID(chartNode2.GetID())
self.assertEqual( clonedMarkupShNode.GetOwnerPluginName(), 'Charts' )
def section_ChartRole(self):
self.delayDisplay("Chart role",self.delayMs)
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
self.assertIsNotNone( shNode )
# Create sample chart node
chartNode = slicer.vtkMRMLChartNode()
slicer.mrmlScene.AddNode(chartNode)
chartNode.SetName(self.sampleChartName)
chartShItemID = shNode.GetItemByDataNode(chartNode)
self.assertIsNotNone( chartShItemID )
self.assertEqual( shNode.GetItemOwnerPluginName(chartShItemID), 'Charts' )
# Add chart under study
chartShItemID2 = shNode.CreateItem(self.studyItemID, chartNode)
self.assertEqual( chartShItemID, chartShItemID2 )
self.assertEqual( shNode.GetItemParent(chartShItemID), self.studyItemID )
self.assertEqual( shNode.GetItemOwnerPluginName(chartShItemID), 'Charts' )
def plotMotion(self, relOrigins, contourName):
ln = slicer.util.getNode(pattern='vtkMRMLLayoutNode*')
ln.SetViewArrangement(ln.SlicerLayoutOneUpQuantitativeView )
# Get the first ChartView node
cvn = slicer.util.getNode(pattern='vtkMRMLChartViewNode*')
# Create arrays of data
dn = {}
dim = relOrigins.shape
for i in range(0, 4):
dn[i] = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn[i].GetArray()
a.SetNumberOfTuples(dim[1])
for j in range(0,dim[1]):
a.SetComponent(j, 0, j)
a.SetComponent(j, 1, relOrigins[i, j])
a.SetComponent(j, 2, 0)
# Create the ChartNode,
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the Chart
cn.AddArray('L-R', dn[0].GetID())
cn.AddArray('A-P', dn[1].GetID())
cn.AddArray('I-S', dn[2].GetID())
cn.AddArray('abs', dn[3].GetID())
# Configure properties of the Chart
cn.SetProperty('default', 'title','Relative ' + contourName + ' motion')
cn.SetProperty('default', 'xAxisLabel', 'phase')
cn.SetProperty('default', 'yAxisLabel', 'position [mm]')
cn.SetProperty('default', 'showGrid', 'on')
cn.SetProperty('default', 'xAxisPad', '1')
cn.SetProperty('default', 'showMarkers', 'on')
cn.SetProperty('L-R', 'color', '#0000ff')
cn.SetProperty('A-P', 'color', '#00ff00')
cn.SetProperty('I-S', 'color', '#ff0000')
cn.SetProperty('abs', 'color', '#000000')
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
def createHistogram(self):
self.setHistogramLayout()
histogramViewNode = slicer.util.getNode('HistogramView')
# Show histogram
self.histogramArrays = {}
HistNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
for tag in self.regionTags:
arrayDataNode = slicer.mrmlScene.AddNode(
slicer.vtkMRMLDoubleArrayNode())
arrayData = arrayDataNode.GetArray()
histogram = self.regionHists[tag]
bins = self.regionBins[tag]
dataSamples = histogram.size
dataTuples = dataSamples
arrayData.SetNumberOfTuples(dataTuples)
tuple = 0
for i in xrange(dataSamples):
arrayData.SetComponent(tuple, 0, bins[i])
arrayData.SetComponent(tuple, 1, histogram[i])
arrayData.SetComponent(tuple, 2, 0)
tuple += 1
self.histogramArrays[tag] = arrayDataNode
HistNode.AddArray(tag, arrayDataNode.GetID())
histogramViewNode.SetChartNodeID(HistNode.GetID())
HistNode.SetProperty('default', 'title', 'Lung Density Histogram')
HistNode.SetProperty('default', 'xAxisLabel', 'Density (HU)')
HistNode.SetProperty('default', 'yAxisLabel', 'Frequency')
HistNode.SetProperty('default', 'type', 'Line')
HistNode.SetProperty('default', 'xAxisType', 'quantitative')
HistNode.SetProperty('default', 'showLegend', 'on')
def ChartRepresentationRotation(self, rotationData, timeStamp):
"""
Summary: This functions represents graphically the array rotationData versus time.
"""
# Switch to a layout (24) that contains a Chart View to initiate the construction of the widget and Chart View Node
lns = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
lns.InitTraversal()
ln = lns.GetNextItemAsObject()
ln.SetViewArrangement(506)
# Get the Chart View Node
cvns = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
cvns.InitTraversal()
cvn = cvns.GetNextItemAsObject()
# Create an Array Node and add some data
dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn.GetArray()
a.SetNumberOfTuples(len(rotationData))
t=range(0,len(rotationData))
for i in t:
a.SetComponent(i, 0, i) # Intentar plotear con respecto al TimeStamp
a.SetComponent(i, 1, rotationData[i])
a.SetComponent(i, 2, 0)
# Create a Chart Node.
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
print('Chart Node created')
# Add the Array Nodes to the Chart. The first argument is a string used for the legend and to refer to the Array when setting properties.
cn.AddArray('Rotation', dn.GetID())
# Set a few properties on the Chart. The first argument is a string identifying which Array to assign the property.
# 'default' is used to assign a property to the Chart itself (as opposed to an Array Node).
cn.SetProperty('default', 'title', self.prename + ' Rotation Plot')
cn.SetProperty('default', 'xAxisLabel', 'Sample Number')
cn.SetProperty('default', 'yAxisLabel', 'Angle (degrees)')
# Tell the Chart View which Chart to display
cvn.SetChartNodeID(cn.GetID())
def showChart(self, samples, names):
print('Logic showing chart\n')
# S2. Switch to a layout containing a chart viewer
lm = slicer.app.layoutManager()
lm.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpQuantitativeView)
# Initialise double array MRML node for each sample list
# since this is what chart view MRML node needs
doubleArrays = []
for sample in samples:
arrayNode = slicer.mrmlScene.AddNode(
slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
nDataPoints = sample.GetNumberOfTuples()
array.SetNumberOfTuples(nDataPoints)
array.SetNumberOfComponents(3)
for i in range(nDataPoints):
array.SetComponent(i, 0, i)
array.SetComponent(i, 1, sample.GetTuple1(i))
array.SetComponent(i, 2, 0)
doubleArrays.append(arrayNode)
# S3. Get the chart view MRML node
cvNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
cvNodes.SetReferenceCount(cvNodes.GetReferenceCount()-1)
cvNodes.InitTraversal()
cvNode = cvNodes.GetNextItemAsObject()
# Create a new chart node
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
for pairs in zip(names, doubleArrays):
chartNode.AddArray(pairs[0], pairs[1].GetID())
cvNode.SetChartNodeID(chartNode.GetID())
return
def PlotMembershipFunctions(membershipFunctions, min, max, steps):
step = float(max - min) / steps
# Setting up the array of values
chartNode = slicer.vtkMRMLChartNode()
chartNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(chartNode)
for i in range(len(membershipFunctions)):
arrayNode = slicer.vtkMRMLDoubleArrayNode()
arrayNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(arrayNode)
array = arrayNode.GetArray()
array.SetNumberOfTuples(int((max - min) / step))
for j in range(array.GetNumberOfTuples()):
array.SetComponent(j, 0, min + j * step)
array.SetComponent(
j, 1, membershipFunctions[i].Evaluate(min + j * step))
array.SetComponent(j, 2, 0)
# Add array into a chart node
chartNode.AddArray("Membership Function " + str(i),
arrayNode.GetID())
chartNode.SetProperty('default', 'title', 'Membership Functions')
chartNode.SetProperty('default', 'xAxisLabel', 'Membership Value')
chartNode.SetProperty('default', 'yAxisLabel', 'Element')
# Set the chart in the chart view node
chartViewNode = slicer.mrmlScene.GetNthNodeByClass(
0, "vtkMRMLChartViewNode")
if (chartViewNode is None):
chartViewNode = slicer.vtkMRMLChartViewNode()
chartViewNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(chartViewNode)
chartViewNode.SetChartNodeID(chartNode.GetID())
def showChart(self, samples, names):
print("Logic showing chart")
#Switch to a layout containing a chart viewer
lm = slicer.app.layoutManager()
lm.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpQuantitativeView)
#initialize double array MRML node for each sample list, since this is what chart view MRML node needs
doubleArrays = []
for sample in samples:
arrayNode = slicer.mrmlScene.AddNode(
slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
nDataPoints = sample.GetNumberOfTuples()
array.SetNumberOfTuples(nDataPoints)
array.SetNumberOfComponents(3)
for i in range(nDataPoints):
array.SetComponent(i, 0, i)
array.SetComponent(i, 1, sample.GetTuple1(i))
array.SetComponent(i, 2, 0)
doubleArrays.append(arrayNode)
#Get the chart view mrml node
cvNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
cvNodes.SetReferenceCount(cvNodes.GetReferenceCount() - 1)
cvNodes.InitTraversal()
cvNode = cvNodes.GetNextItemAsObject()
#Create a new chart node
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
for pairs in zip(names, doubleArrays):
chartNode.AddArray(pairs[0], pairs[1].GetID())
cvNode.SetChartNodeID(chartNode.GetID())
return
def section_ChartRole(self):
self.delayDisplay("Chart role", self.delayMs)
# Create sample chart node
chartNode = slicer.vtkMRMLChartNode()
slicer.mrmlScene.AddNode(chartNode)
chartNode.SetName(self.sampleChartName)
# Add markups to subject hierarchy
from vtkSlicerSubjectHierarchyModuleMRML import vtkMRMLSubjectHierarchyNode
studyNode = slicer.util.getNode(self.studyName +
slicer.vtkMRMLSubjectHierarchyConstants
.GetSubjectHierarchyNodeNamePostfix())
self.assertTrue(studyNode != None)
chartShNode = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(
slicer.mrmlScene, studyNode,
slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMLevelSeries(),
self.sampleChartName, chartNode)
self.assertTrue(chartShNode != None)
self.assertTrue(chartShNode.GetParentNode() == studyNode)
self.assertTrue(chartShNode.GetOwnerPluginName() == 'Charts')
def test_Charting1(self):
""" Testing charting
"""
self.delayDisplay("Starting the test")
# Change the layout to one that has a chart. This created the ChartView
ln = slicer.mrmlScene.GetFirstNodeByClass('vtkMRMLLayoutNode')
ln.SetViewArrangement(24)
# Get the first ChartView node
cvn = slicer.mrmlScene.GetFirstNodeByClass('vtkMRMLChartViewNode')
# Create arrays of data
dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn.GetArray()
a.SetNumberOfTuples(600)
x = range(0, 600)
for i in range(len(x)):
a.SetComponent(i, 0, x[i] / 50.0)
a.SetComponent(i, 1, math.sin(x[i] / 50.0))
a.SetComponent(i, 2, 0)
dn2 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn2.GetArray()
a.SetNumberOfTuples(600)
x = range(0, 600)
for i in range(len(x)):
a.SetComponent(i, 0, x[i] / 50.0)
a.SetComponent(i, 1, math.cos(x[i] / 50.0))
a.SetComponent(i, 2, 0)
# Create the ChartNode,
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the Chart
cn.AddArray('A double array', dn.GetID())
cn.AddArray('Another double array', dn2.GetID())
# Configure properties of the Chart
cn.SetProperty('default', 'title', 'A simple chart with 2 curves')
cn.SetProperty('default', 'xAxisLabel', 'Something in x')
cn.SetProperty('default', 'yAxisLabel', 'Something in y')
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A simple chart with 2 curves')
# Create another ChartNode
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the Chart
cn.AddArray('Just one array', dn.GetID())
# Configure properties of the chart
cn.SetProperty('default', 'title', 'A simple chart with 1 curve')
cn.SetProperty('default', 'xAxisLabel', 'Just x')
cn.SetProperty('default', 'yAxisLabel', 'Just y')
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A simple chart with 1 curve')
# Create another ChartNode
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the Chart
cn.AddArray('The other array', dn2.GetID())
# Set properties on the chart
cn.SetProperty('default', 'title', 'A simple chart with another curve')
cn.SetProperty('default', 'xAxisLabel', 'time')
cn.SetProperty('default', 'yAxisLabel', 'velocity')
cn.SetProperty('The other array', 'showLines', 'on')
cn.SetProperty('The other array', 'showMarkers', 'off')
cn.SetProperty('The other array', 'color', '#fe7d20')
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A simple chart with another curve')
# Create another data array
dn3 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn3.GetArray()
a.SetNumberOfTuples(12)
x = range(0, 12)
for i in range(len(x)):
a.SetComponent(i, 0, x[i] / 4.0)
a.SetComponent(i, 1, math.sin(x[i] / 4.0))
a.SetComponent(i, 2, 0)
# Create another ChartNode
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the chart
cn.AddArray('Periodic', dn3.GetID())
# Configure properties of the Chart
cn.SetProperty('default', 'title', 'A bar chart')
cn.SetProperty('default', 'xAxisLabel', 'time')
cn.SetProperty('default', 'yAxisLabel', 'velocity')
cn.SetProperty('default', 'type', 'Bar')
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A bar chart')
# Test using a date axis
#
# Create another data array
dn4 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn4.GetArray()
# ugh, python uses localtime
dates = [
"3/27/2010", "6/15/2010", "12/14/2010", "3/8/2011", "9/5/2011",
"12/20/2011", "3/17/2012", "6/12/2012", "9/22/2012", "12/14/2012",
"3/23/2012"
]
#dates = ["3/27/2010","6/15/2010","9/21/2010","12/14/2010","3/8/2011","5/31/2011","9/5/2011","12/20/2011","3/17/2012","6/12/2012","9/22/2012","12/14/2012","3/23/2012"]
times = []
for i in range(len(dates)):
times.append(
time.mktime(
datetime.datetime.strptime(dates[i],
"%m/%d/%Y").timetuple()))
a.SetNumberOfTuples(len(times))
for i in range(len(times)):
a.SetComponent(i, 0, times[i])
a.SetComponent(i, 1, math.sin(x[i] / 4.0) + 4)
a.SetComponent(i, 2, 0)
# Create another ChartNode
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the chart
cn.AddArray('Lesion #1', dn4.GetID())
# Configure properties of the Chart
cn.SetProperty('default', 'title', 'A chart with dates')
cn.SetProperty('default', 'xAxisLabel', 'date')
cn.SetProperty('default', 'xAxisType', 'date')
cn.SetProperty('default', 'yAxisLabel', 'size (cm)')
cn.SetProperty('default', 'type', 'Bar')
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A chart with dates')
# Test using a color table to look up label names
#
#
# Create another data array
dn5 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn5.GetArray()
a.SetNumberOfTuples(4)
a.SetComponent(0, 0, 6)
a.SetComponent(0, 1, 32)
a.SetComponent(1, 0, 3)
a.SetComponent(1, 1, 12)
a.SetComponent(2, 0, 4)
a.SetComponent(2, 1, 20)
a.SetComponent(3, 0, 5)
a.SetComponent(3, 1, 6)
# Create another ChartNode
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the chart
cn.AddArray('Volumes', dn5.GetID())
# Configure properties of the Chart
cn.SetProperty('default', 'title', 'A chart with labels')
cn.SetProperty('default', 'xAxisLabel', 'structure')
cn.SetProperty('default', 'xAxisType', 'categorical')
cn.SetProperty('default', 'yAxisLabel', 'size (cm)')
cn.SetProperty('default', 'type', 'Bar')
cn.SetProperty('Volumes', 'lookupTable',
slicer.util.getNode('GenericAnatomyColors').GetID())
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A chart with labels')
# Test box plots
#
#
# Create another data array
dn6 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn6.GetArray()
a.SetNumberOfTuples(40)
for i in range(a.GetNumberOfTuples()):
a.SetComponent(i, 0, 1)
a.SetComponent(i, 1, (2.0 * random.random() - 0.5) + 20.0)
# Create another data array
dn7 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn7.GetArray()
a.SetNumberOfTuples(25)
for i in range(20):
a.SetComponent(i, 0, 2)
a.SetComponent(i, 1, 2.0 * (2.0 * random.random() - 1.0) + 27.0)
for i in range(5):
a.SetComponent(20 + i, 0, 2)
a.SetComponent(20 + i, 1,
10.0 * (2.0 * random.random() - 1.0) + 27.0)
# Create another data array
dn8 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn8.GetArray()
a.SetNumberOfTuples(25)
for i in range(20):
a.SetComponent(i, 0, 3)
a.SetComponent(i, 1, 3.0 * (2.0 * random.random() - 1.0) + 24.0)
for i in range(5):
a.SetComponent(20 + i, 0, 2)
a.SetComponent(20 + i, 1,
10.0 * (2.0 * random.random() - 1.0) + 24.0)
# Create another ChartNode
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the chart
cn.AddArray('Controls', dn6.GetID())
cn.AddArray('Group A', dn7.GetID())
cn.AddArray('Group B', dn8.GetID())
# Configure properties of the Chart
cn.SetProperty('default', 'title', 'A box chart')
cn.SetProperty('default', 'xAxisLabel', 'population')
cn.SetProperty('default', 'xAxisType', 'categorical')
cn.SetProperty('default', 'yAxisLabel', 'size (ml)')
cn.SetProperty('default', 'type', 'Box')
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A box chart')
#
self.delayDisplay('Test passed!')
def test_MichaelReid1(self):
import numpy
import slicer
import math
# Switch to a layout (24) that contains a Chart View to initiate the construction of the widget and Chart View Node
lns = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
lns.InitTraversal()
ln = lns.GetNextItemAsObject()
ln.SetViewArrangement(24)
# Get the Chart View Node
cvns = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
cvns.InitTraversal()
cvn = cvns.GetNextItemAsObject()
referenceToRas = slicer.vtkMRMLLinearTransformNode()
referenceToRas.SetName('referenceToRas')
slicer.mrmlScene.AddNode(referenceToRas)
TREdata = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
TREarray = TREdata.GetArray()
TREarray.SetNumberOfTuples(9)
for i in range(1,10):
TREarray.SetComponent(i, 0, i*10)
# Experiment parameters (start from here if you have alphaToBeta already)
for N in range(1,10): # Number of fiducials
average,referenceToRasMatrix=self.distance(N,referenceToRas)
createModelsLogic = slicer.modules.createmodels.logic()
referenceModelNode = createModelsLogic.CreateCoordinate(20, 2)
referenceModelNode.SetName('referenceCoordinateModel')
postModelNode = createModelsLogic.CreateCoordinate(20, 2)
postModelNode.SetName('RasCoordinateModel')
referenceModelNode.GetDisplayNode().SetColor(1, 0, 0)
postModelNode.GetDisplayNode().SetColor(0, 1, 0)
postModelNode.SetAndObserveTransformNodeID(referenceToRas.GetID())
targetPoint_Reference = numpy.array([0, 0, 0, 1])
targetPoint_Ras = referenceToRasMatrix.MultiplyFloatPoint(targetPoint_Reference)
distance = numpy.linalg.norm(targetPoint_Reference - targetPoint_Ras)
print "Average distance after registration: " + str(average)
print 'Target Registration Error: ' + str(distance)
TREarray.SetComponent(N, 1, distance)
#plotting TRE as function of num points
# Create a Chart Node.
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add the Array Nodes to the Chart. The first argument is a string used for the legend and to refer to the Array when setting properties.
cn.AddArray('A double array', TREdata.GetID())
# Set a few properties on the Chart. The first argument is a string identifying which Array to assign the property.
# 'default' is used to assign a property to the Chart itself (as opposed to an Array Node).
cn.SetProperty('default', 'title', 'TRE as a function of number of points')
cn.SetProperty('default', 'xAxisLabel', 'Number of points')
cn.SetProperty('default', 'yAxisLabel', 'TRE')
# Tell the Chart View which Chart to display
cvn.SetChartNodeID(cn.GetID())
def chartTest(self):
import math, random
lns = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
lns.InitTraversal()
ln = lns.GetNextItemAsObject()
ln.SetViewArrangement(24)
chartView = findChildren(className='qMRMLChartView')[0]
print(
chartView.connect("dataMouseOver(const char *,int,double,double)",
self.chartMouseOverCallback))
print(
chartView.connect(
"dataPointClicked(const char *,int,double,double)",
self.chartCallback))
cvns = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
cvns.InitTraversal()
cvn = cvns.GetNextItemAsObject()
dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn.GetArray()
a.SetNumberOfTuples(600)
x = range(0, 600)
phase = random.random()
for i in range(len(x)):
a.SetComponent(i, 0, x[i] / 50.0)
a.SetComponent(i, 1, math.sin(phase + x[i] / 50.0))
a.SetComponent(i, 2, 0)
dn2 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn2.GetArray()
a.SetNumberOfTuples(600)
x = range(0, 600)
for i in range(len(x)):
a.SetComponent(i, 0, x[i] / 50.0)
a.SetComponent(i, 1, math.cos(phase + x[i] / 50.0))
a.SetComponent(i, 2, 0)
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
cn.AddArray('A double array', dn.GetID())
cn.AddArray('Another double array', dn2.GetID())
cvn.SetChartNodeID(cn.GetID())
cn.SetProperty('default', 'title', 'A simple chart with 2 curves')
cn.SetProperty('default', 'xAxisLabel', 'Something in x')
cn.SetProperty('default', 'yAxisLabel', 'Something in y')
cvn.SetChartNodeID(cn.GetID())
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
print cn.GetID()
cn.AddArray('Just one array', dn.GetID())
cn.SetProperty('default', 'title', 'A simple chart with 1 curve')
cn.SetProperty('default', 'xAxisLabel', 'Just x')
cn.SetProperty('default', 'yAxisLabel', 'Just y')
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
print cn.GetID()
cn.AddArray('The other array', dn2.GetID())
cn.SetProperty('default', 'title', 'A simple chart with another curve')
cn.SetProperty('default', 'xAxisLabel', 'time')
cn.SetProperty('default', 'yAxisLabel', 'velocity')
cn.SetProperty('The other array', 'showLines', 'on')
cn.SetProperty('The other array', 'showMarkers', 'off')
cn.SetProperty('The other array', 'color', '#fe7d20')
dn3 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
print dn3.GetID()
a = dn3.GetArray()
a.SetNumberOfTuples(12)
x = range(0, 12)
for i in range(len(x)):
a.SetComponent(i, 0, x[i] / 4.0)
a.SetComponent(i, 1, math.sin(x[i] / 4.0))
a.SetComponent(i, 2, 0)
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
print cn.GetID()
cn.AddArray('Periodic', dn3.GetID())
cn.SetProperty('default', 'title', 'A bar chart')
cn.SetProperty('default', 'xAxisLabel', 'time')
cn.SetProperty('default', 'yAxisLabel', 'velocity')
cn.SetProperty('default', 'type', 'Bar')
def test_Charting1(self):
""" Testing charting
"""
self.delayDisplay("Starting the test")
#
# first, get some data
#
#import urllib
#downloads = (
# ('http://slicer.kitware.com/midas3/download?items=5767', 'FA.nrrd', slicer.util.loadVolume),
# )
#
#for url,name,loader in downloads:
# filePath = slicer.app.temporaryPath + '/' + name
# if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
# print('Requesting download %s from %s...\n' % (name, url))
# urllib.urlretrieve(url, filePath)
# if loader:
# print('Loading %s...\n' % (name,))
# loader(filePath)
#self.delayDisplay('Finished with download and loading\n')
#volumeNode = slicer.util.getNode(pattern="FA")
#logic = ChartingLogic()
#self.assertIsNotNone( logic.hasImageData(volumeNode) )
# Change the layout to one that has a chart. This created the ChartView
ln = slicer.mrmlScene.GetFirstNodeByClass('vtkMRMLLayoutNode')
ln.SetViewArrangement(24)
# Get the first ChartView node
cvn = slicer.mrmlScene.GetFirstNodeByClass('vtkMRMLChartViewNode')
# Create arrays of data
dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn.GetArray()
a.SetNumberOfTuples(600)
x = range(0, 600)
for i in range(len(x)):
a.SetComponent(i, 0, x[i]/50.0)
a.SetComponent(i, 1, math.sin(x[i]/50.0))
a.SetComponent(i, 2, 0)
dn2 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn2.GetArray()
a.SetNumberOfTuples(600)
x = range(0, 600)
for i in range(len(x)):
a.SetComponent(i, 0, x[i]/50.0)
a.SetComponent(i, 1, math.cos(x[i]/50.0))
a.SetComponent(i, 2, 0)
# Create the ChartNode,
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the Chart
cn.AddArray('A double array', dn.GetID())
cn.AddArray('Another double array', dn2.GetID())
# Configure properties of the Chart
cn.SetProperty('default', 'title', 'A simple chart with 2 curves')
cn.SetProperty('default', 'xAxisLabel', 'Something in x')
cn.SetProperty('default', 'yAxisLabel', 'Something in y')
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A simple chart with 2 curves')
# Create another ChartNode
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the Chart
cn.AddArray('Just one array', dn.GetID())
# Configure properties of the chart
cn.SetProperty('default', 'title', 'A simple chart with 1 curve')
cn.SetProperty('default', 'xAxisLabel', 'Just x')
cn.SetProperty('default', 'yAxisLabel', 'Just y')
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A simple chart with 1 curve')
# Create another ChartNode
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the Chart
cn.AddArray('The other array', dn2.GetID())
# Set properties on the chart
cn.SetProperty('default', 'title', 'A simple chart with another curve')
cn.SetProperty('default', 'xAxisLabel', 'time')
cn.SetProperty('default', 'yAxisLabel', 'velocity')
cn.SetProperty('The other array', 'showLines', 'on')
cn.SetProperty('The other array', 'showMarkers', 'off')
cn.SetProperty('The other array', 'color', '#fe7d20')
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A simple chart with another curve')
# Create another data array
dn3 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn3.GetArray()
a.SetNumberOfTuples(12)
x = range(0, 12)
for i in range(len(x)):
a.SetComponent(i, 0, x[i]/4.0)
a.SetComponent(i, 1, math.sin(x[i]/4.0))
a.SetComponent(i, 2, 0)
# Create another ChartNode
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the chart
cn.AddArray('Periodic', dn3.GetID())
# Configure properties of the Chart
cn.SetProperty('default', 'title', 'A bar chart')
cn.SetProperty('default', 'xAxisLabel', 'time')
cn.SetProperty('default', 'yAxisLabel', 'velocity')
cn.SetProperty('default', 'type', 'Bar');
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A bar chart')
# Test using a date axis
#
# Create another data array
dn4 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn4.GetArray()
# ugh, python uses localtime
dates = ["3/27/2010","6/15/2010","12/14/2010","3/8/2011","9/5/2011","12/20/2011","3/17/2012","6/12/2012","9/22/2012","12/14/2012","3/23/2012"]
#dates = ["3/27/2010","6/15/2010","9/21/2010","12/14/2010","3/8/2011","5/31/2011","9/5/2011","12/20/2011","3/17/2012","6/12/2012","9/22/2012","12/14/2012","3/23/2012"]
times = []
for i in range(len(dates)):
times.append(time.mktime(datetime.datetime.strptime(dates[i], "%m/%d/%Y").timetuple()))
a.SetNumberOfTuples(len(times))
for i in range(len(times)):
a.SetComponent(i, 0, times[i])
a.SetComponent(i, 1, math.sin(x[i]/4.0) + 4)
a.SetComponent(i, 2, 0)
# Create another ChartNode
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the chart
cn.AddArray('Lesion #1', dn4.GetID())
# Configure properties of the Chart
cn.SetProperty('default', 'title', 'A chart with dates')
cn.SetProperty('default', 'xAxisLabel', 'date')
cn.SetProperty('default', 'xAxisType', 'date')
cn.SetProperty('default', 'yAxisLabel', 'size (cm)')
cn.SetProperty('default', 'type', 'Bar');
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A chart with dates')
# Test using a color table to look up label names
#
#
# Create another data array
dn5 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn5.GetArray()
a.SetNumberOfTuples(4)
a.SetComponent(0, 0, 6)
a.SetComponent(0, 1, 32)
a.SetComponent(1, 0, 3)
a.SetComponent(1, 1, 12)
a.SetComponent(2, 0, 4)
a.SetComponent(2, 1, 20)
a.SetComponent(3, 0, 5)
a.SetComponent(3, 1, 6)
# Create another ChartNode
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the chart
cn.AddArray('Volumes', dn5.GetID())
# Configure properties of the Chart
cn.SetProperty('default', 'title', 'A chart with labels')
cn.SetProperty('default', 'xAxisLabel', 'structure')
cn.SetProperty('default', 'xAxisType', 'categorical')
cn.SetProperty('default', 'yAxisLabel', 'size (cm)')
cn.SetProperty('default', 'type', 'Bar');
cn.SetProperty('Volumes', 'lookupTable', slicer.util.getNode('GenericAnatomyColors').GetID() )
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A chart with labels')
# Test box plots
#
#
# Create another data array
dn6 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn6.GetArray()
a.SetNumberOfTuples(40)
for i in range(a.GetNumberOfTuples()):
a.SetComponent(i, 0, 1)
a.SetComponent(i, 1, (2.0*random.random() - 0.5) + 20.0)
# Create another data array
dn7 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn7.GetArray()
a.SetNumberOfTuples(25)
for i in range(20):
a.SetComponent(i, 0, 2)
a.SetComponent(i, 1, 2.0*(2.0*random.random()-1.0) + 27.0)
for i in range(5):
a.SetComponent(20+i, 0, 2)
a.SetComponent(20+i, 1, 10.0*(2.0*random.random()-1.0) + 27.0)
# Create another data array
dn8 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn8.GetArray()
a.SetNumberOfTuples(25)
for i in range(20):
a.SetComponent(i, 0, 3)
a.SetComponent(i, 1, 3.0*(2.0*random.random()-1.0) + 24.0)
for i in range(5):
a.SetComponent(20+i, 0, 2)
a.SetComponent(20+i, 1, 10.0*(2.0*random.random()-1.0) + 24.0)
# Create another ChartNode
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the chart
cn.AddArray('Controls', dn6.GetID())
cn.AddArray('Group A', dn7.GetID())
cn.AddArray('Group B', dn8.GetID())
# Configure properties of the Chart
cn.SetProperty('default', 'title', 'A box chart')
cn.SetProperty('default', 'xAxisLabel', 'population')
cn.SetProperty('default', 'xAxisType', 'categorical')
cn.SetProperty('default', 'yAxisLabel', 'size (ml)')
cn.SetProperty('default', 'type', 'Box');
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A box chart')
#
self.delayDisplay('Test passed!')
a.SetComponent(i, 0, x[i]/50.0)
a.SetComponent(i, 1, math.sin(x[i]/50.0))
a.SetComponent(i, 2, 0)
dn2 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
print(dn2.GetID())
a = dn2.GetArray()
a.SetNumberOfTuples(600)
x = range(0, 600)
for i in range(len(x)):
a.SetComponent(i, 0, x[i]/50.0)
a.SetComponent(i, 1, math.cos(x[i]/50.0))
a.SetComponent(i, 2, 0)
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
print(cn.GetID())
cn.AddArray('A double array', dn.GetID())
cn.AddArray('Another double array', dn2.GetID())
cn.SetProperty('default', 'title', 'A simple chart with 2 curves')
cn.SetProperty('default', 'xAxisLabel', 'Something in x')
cn.SetProperty('default', 'yAxisLabel', 'Something in y')
cvn.SetChartNodeID(cn.GetID())
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
print(cn.GetID())
cn.AddArray('Just one array', dn.GetID())
cn.SetProperty('default', 'title', 'A simple chart with 1 curve')
cn.SetProperty('default', 'xAxisLabel', 'Just x')
cn.SetProperty('default', 'yAxisLabel', 'Just y')
def plot(self, args):
if "Title" in args:
self.Title = args["Title"]
if "XLabel" in args:
self.XLabel = args["XLabel"]
if "YLabel" in args:
self.YLabel = args["YLabel"]
if "Data" in args:
self.Data = args["Data"]
if "xAxis" in args:
self.xAxis = args["xAxis"]
if "Name" in args:
self.chartName = args["Name"]
# Get the Chart View Node
chartViewNodes = slicer.mrmlScene.GetNodesByClass(
'vtkMRMLChartViewNode')
chartViewNodes.InitTraversal()
chartViewNode = chartViewNodes.GetNextItemAsObject()
# Create an Array Node and add some data
serieArrayNode = slicer.mrmlScene.AddNode(
slicer.vtkMRMLDoubleArrayNode())
serieArrayNode.SetName(self.doubleArrayNodeFMRSIName)
serieArray = serieArrayNode.GetArray()
lenXAxis = len(self.xAxis)
lenData = len(self.Data)
if lenXAxis == 0:
self.xAxis = range(0, lenData)
if lenData > 0:
serieArray.SetNumberOfTuples(lenData)
for i in range(lenData):
serieArray.SetComponent(i, 0, self.xAxis[i])
serieArray.SetComponent(i, 1, self.Data[i])
serieArray.SetComponent(i, 2, 0)
# Create a Chart Node.
# Delete previous existing node
try:
chartNode = slicer.util.getNode(self.chartName)
except:
chartNode = None
if chartNode is not None:
nod = chartNode.GetArray('Data')
if nod is not None:
slicer.mrmlScene.RemoveNode(slicer.util.getNode(nod))
slicer.mrmlScene.RemoveNode(chartNode)
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Set a few properties on the Chart. The first argument is a string identifying which Array to assign the property.
# 'default' is used to assign a property to the Chart itself (as opposed to an Array Node).
chartNode.SetProperty('default', 'title', self.Title)
chartNode.SetProperty('default', 'xAxisLabel', self.XLabel)
chartNode.SetProperty('default', 'yAxisLabel', self.YLabel)
chartNode.SetProperty('default', 'color', self.Color)
chartNode.SetName(self.chartName)
# Add the Array Nodes to the Chart. The first argument is a string used for the legend and to refer to the Array when setting properties.
chartNode.AddArray('Data', serieArrayNode.GetID())
# chartNode.AddArray('Another double array', serieArrayNode2.GetID())
# Tell the Chart View which Chart to display
chartViewNode.SetChartNodeID(chartNode.GetID())
def chartTest(self):
import math,random
ln = slicer.mrmlScene.GetFirstNodeByClass('vtkMRMLLayoutNode')
ln.SetViewArrangement(24)
chartView = findChildren(className='qMRMLChartView')[0]
print(chartView.connect("dataMouseOver(const char *,int,double,double)", self.chartMouseOverCallback))
print(chartView.connect("dataPointClicked(const char *,int,double,double)", self.chartCallback))
cvn = slicer.mrmlScene.GetFirstNodeByClass('vtkMRMLChartViewNode')
dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn.GetArray()
a.SetNumberOfTuples(600)
x = range(0, 600)
phase = random.random()
for i in range(len(x)):
a.SetComponent(i, 0, x[i]/50.0)
a.SetComponent(i, 1, math.sin(phase+x[i]/50.0))
a.SetComponent(i, 2, 0)
dn2 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn2.GetArray()
a.SetNumberOfTuples(600)
x = range(0, 600)
for i in range(len(x)):
a.SetComponent(i, 0, x[i]/50.0)
a.SetComponent(i, 1, math.cos(phase+x[i]/50.0))
a.SetComponent(i, 2, 0)
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
cn.AddArray('A double array', dn.GetID())
cn.AddArray('Another double array', dn2.GetID())
cvn.SetChartNodeID(cn.GetID())
cn.SetProperty('default', 'title', 'A simple chart with 2 curves')
cn.SetProperty('default', 'xAxisLabel', 'Something in x')
cn.SetProperty('default', 'yAxisLabel', 'Something in y')
cvn.SetChartNodeID(cn.GetID())
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
print(cn.GetID())
cn.AddArray('Just one array', dn.GetID())
cn.SetProperty('default', 'title', 'A simple chart with 1 curve')
cn.SetProperty('default', 'xAxisLabel', 'Just x')
cn.SetProperty('default', 'yAxisLabel', 'Just y')
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
print(cn.GetID())
cn.AddArray('The other array', dn2.GetID())
cn.SetProperty('default', 'title', 'A simple chart with another curve')
cn.SetProperty('default', 'xAxisLabel', 'time')
cn.SetProperty('default', 'yAxisLabel', 'velocity')
cn.SetProperty('The other array', 'showLines', 'on')
cn.SetProperty('The other array', 'showMarkers', 'off')
cn.SetProperty('The other array', 'color', '#fe7d20')
dn3 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
print(dn3.GetID())
a = dn3.GetArray()
a.SetNumberOfTuples(12)
x = range(0, 12)
for i in range(len(x)):
a.SetComponent(i, 0, x[i]/4.0)
a.SetComponent(i, 1, math.sin(x[i]/4.0))
a.SetComponent(i, 2, 0)
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
print(cn.GetID())
cn.AddArray('Periodic', dn3.GetID())
cn.SetProperty('default', 'title', 'A bar chart')
cn.SetProperty('default', 'xAxisLabel', 'time')
cn.SetProperty('default', 'yAxisLabel', 'velocity')
cn.SetProperty('default', 'type', 'Bar');
for i in range(len(x)):
a.SetComponent(i, 0, x[i] / 50.0)
a.SetComponent(i, 1, math.sin(x[i] / 50.0))
a.SetComponent(i, 2, 0)
dn2 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
print(dn2.GetID())
a = dn2.GetArray()
a.SetNumberOfTuples(600)
x = range(0, 600)
for i in range(len(x)):
a.SetComponent(i, 0, x[i] / 50.0)
a.SetComponent(i, 1, math.cos(x[i] / 50.0))
a.SetComponent(i, 2, 0)
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
print(cn.GetID())
cn.AddArray('A double array', dn.GetID())
cn.AddArray('Another double array', dn2.GetID())
cn.SetProperty('default', 'title', 'A simple chart with 2 curves')
cn.SetProperty('default', 'xAxisLabel', 'Something in x')
cn.SetProperty('default', 'yAxisLabel', 'Something in y')
cvn.SetChartNodeID(cn.GetID())
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
print(cn.GetID())
cn.AddArray('Just one array', dn.GetID())
cn.SetProperty('default', 'title', 'A simple chart with 1 curve')
cn.SetProperty('default', 'xAxisLabel', 'Just x')
cn.SetProperty('default', 'yAxisLabel', 'Just y')
def OnCurveButton(self):
if (str(self.inputSmoothSelector.currentNode())
or str(self.imagenMultuply.currentNode())) == "None":
print('ERROR: Select Input Volume Node and Label Mask')
qt.QMessageBox.information(
slicer.util.mainWindow(), 'Slicer Python',
'ERROR: Select Input Volume Node and Label Mask')
return True
else:
mvNode = slicer.vtkMRMLMultiVolumeNode(
) #creación nodo multivolumen
slicer.mrmlScene.AddNode(mvNode) #añadir a la escena el nodo
escena = slicer.mrmlScene
volumen4D = self.inputSmoothSelector.currentNode()
imagenvtk4D = volumen4D.GetImageData()
numero_imagenes = volumen4D.GetNumberOfFrames(
) #numero de frames del MV
#print('imagenes: ' + str(numero_imagenes))
#filtro vtk para descomponer un volumen 4D
extract1 = vtk.vtkImageExtractComponents()
extract1.SetInputData(imagenvtk4D)
#matriz de transformacion
ras2ijk = vtk.vtkMatrix4x4()
ijk2ras = vtk.vtkMatrix4x4()
#le solicitamos al volumen original que nos devuelva sus matrices
volumen4D.GetRASToIJKMatrix(ras2ijk)
volumen4D.GetIJKToRASMatrix(ijk2ras)
#creo un volumen nuevo
#volumenFijo = self.inputVolumeSelector.currentNode();
#le asigno las transformaciones
#le asigno el volumen 3D fijo
extract1.SetComponents(0)
extract1.Update()
volumenFiltro = slicer.vtkMRMLScalarVolumeNode()
volumenFiltro.SetName('Filtro')
volumenFiltro.SetAndObserveImageData(extract1.GetOutput())
volumenFiltro.SetRASToIJKMatrix(ras2ijk)
volumenFiltro.SetIJKToRASMatrix(ijk2ras)
#anado el nuevo volumen a la escena
escena.AddNode(volumenFiltro)
volumenSalida = slicer.vtkMRMLScalarVolumeNode()
#creacion de volumen de salida
slicer.mrmlScene.AddNode(volumenSalida)
j = 1
bandera = 0
frameLabelsAttr = ''
volumeLabels = vtk.vtkDoubleArray()
volumeLabels.SetNumberOfTuples(numero_imagenes)
volumeLabels.SetNumberOfComponents(1)
volumeLabels.Allocate(numero_imagenes)
mvImage = vtk.vtkImageData()
mvImage.SetExtent(volumenFiltro.GetImageData().GetExtent()
) ##Se le asigna la dimension del miltuvolumen
mvImage.AllocateScalars(
volumenFiltro.GetImageData().GetScalarType(), numero_imagenes
) ##Se le asigna el tipo y numero de cortes al multivolumen
mvImageArray = vtk.util.numpy_support.vtk_to_numpy(
mvImage.GetPointData().GetScalars()
) ## Se crea la matriz de datos donde va a ir la imagen
mat = vtk.vtkMatrix4x4()
##Se hace la conversion y se obtiene la matriz de transformacion del nodo
volumenFiltro.GetRASToIJKMatrix(mat)
mvNode.SetRASToIJKMatrix(mat)
volumenFiltro.GetIJKToRASMatrix(mat)
mvNode.SetIJKToRASMatrix(mat)
##
vector_int = []
for i in range(numero_imagenes):
# extraigo la imagen movil
extract1.SetComponents(i) #Seleccionar un volumen lejano
extract1.Update()
#Creo un volumen movil, y realizamos el mismo procedimiento que con el fijo
volumenFiltro.SetAndObserveImageData(extract1.GetOutput())
volumenFiltro.SetName('Filtrado')
escena.AddNode(volumenFiltro)
#parametros para la operacion de registro que seran entregados al modulo cli "brainsfit" segun tipo de registro
parameters = {}
parameters['Conductance'] = 1
parameters['numberOfIterations'] = 5
parameters['timeStep'] = 0.0625
parameters['inputVolume'] = volumenFiltro.GetID()
parameters['outputVolume'] = volumenFiltro.GetID()
cliNode = slicer.cli.run(
slicer.modules.gradientanisotropicdiffusion,
None,
parameters,
wait_for_completion=True)
slicer.util.saveNode(volumenFiltro,
'volumenFilter' + str(i) + '.nrrd')
vol = slicer.vtkMRMLScalarVolumeNode()
escena = slicer.mrmlScene
vol.SetName('salida')
escena.AddNode(vol)
Label = self.imagenMultuply.currentNode()
Label = slicer.util.getNode('vtkMRMLLabelMapVolumeNode1')
#parametros para la operacion de registro
parameters = {}
parameters['inputVolume1'] = escena.GetNodeByID(
'vtkMRMLLabelMapVolumeNode1'
) #dos volumenes de la escena, uno de ellos debe ser la mascara creada en el EDITOR
parameters['inputVolume2'] = volumenFiltro
parameters['outputVolume'] = vol
cliNode = slicer.cli.run(slicer.modules.multiplyscalarvolumes,
None,
parameters,
wait_for_completion=True)
slicer.util.saveNode(vol, 'volumenMulty' + str(i) + '.nrrd')
print(vol)
a = slicer.util.arrayFromVolume(vol)
intensidad = np.mean(a[:])
vector_int.append(intensidad)
# Switch to a layout (24) that contains a Chart View to initiate the construction of the widget and Chart View Node
lns = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
lns.InitTraversal()
ln = lns.GetNextItemAsObject()
ln.SetViewArrangement(24)
# Get the Chart View Node
cvns = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
cvns.InitTraversal()
cvn = cvns.GetNextItemAsObject()
# Create an Array Node and add some data
dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn.GetArray()
a.SetNumberOfTuples(numero_imagenes)
x = range(0, 600)
i = 0
for i in range(numero_imagenes):
a.SetComponent(i, 0, i)
a.SetComponent(i, 1, vector_int[i])
a.SetComponent(i, 2, 0)
# Create a Chart Node.
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add the Array Nodes to the Chart. The first argument is a string used for the legend and to refer to the Array when setting properties.
cn.AddArray('Prostate perfusion', dn.GetID())
# Set a few properties on the Chart. The first argument is a string identifying which Array to assign the property.
# 'default' is used to assign a property to the Chart itself (as opposed to an Array Node).
cn.SetProperty('default', 'title', 'Perfusion curves')
cn.SetProperty('default', 'xAxisLabel', 'Time (s)')
cn.SetProperty('default', 'yAxisLabel', 'Intensity')
# Tell the Chart View which Chart to display
cvn.SetChartNodeID(cn.GetID())
def createStatsChart(self, labelNode, valueToPlot, ignoreZero=False, normalize=False,nbins=-1):
if valueToPlot != "Distribution":
LabelStatisticsLogic.createStatsChart(self, labelNode, valueToPlot, ignoreZero)
else:
layoutNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
layoutNodes.SetReferenceCount(layoutNodes.GetReferenceCount()-1)
layoutNodes.InitTraversal()
layoutNode = layoutNodes.GetNextItemAsObject()
layoutNode.SetViewArrangement(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalQuantitativeView)
chartViewNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
chartViewNodes.SetReferenceCount(chartViewNodes.GetReferenceCount()-1)
chartViewNodes.InitTraversal()
chartViewNode = chartViewNodes.GetNextItemAsObject()
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
displayNode = self.labelNode.GetDisplayNode()
colorNode = displayNode.GetColorNode()
color=numpy.full(4,0)
#arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
#array = arrayNode.GetArray()
samples = len(self.labelStats["Labels"])
qu=QCLib.QCUtil()
rect=qu.minRectangle(labelNode)
ROI=labelNode.GetImageData()
nslices=ROI.GetDimensions()[2] #3D Volumes only
im=self.grayscaleNode.GetImageData()
s=[numpy.Inf,-numpy.Inf]
start=0
if ignoreZero and samples>1:
start=1
for ln in range(start,samples):
l=self.labelStats["Labels"][ln]
min=self.labelStats[l,"Min"]
max=self.labelStats[l,"Max"]
if min<s[0]:
s[0]=min
if max>s[1]:
s[1]=max
sr=range(int(s[0]),int(s[1])+1)
distr={}
cont={}
for sl in range(nslices):
if ignoreZero:
xmin=rect['xmin'][sl]
xmax=rect['xmax'][sl]
ymin=rect['ymin'][sl]
ymax=rect['ymax'][sl]
else:
xmin=0
xmax=ROI.GetDimensions()[0]
ymin=0
ymax=ROI.GetDimensions()[1]
for x in range(xmin,xmax+1):
for y in range(ymin,ymax+1):
label=ROI.GetScalarComponentAsDouble(x,y,sl,0)
if not (ignoreZero and label == 0): #TODO : use numpy.histogram
val=im.GetScalarComponentAsDouble(x,y,sl,0)
try:
dslab=distr[label]
except: #TODO: errorcode
distr[label]=numpy.full(self.labelStats[label,"Count"],0)
dslab=distr[label]
cont[label]=-1
cont[label]=cont[label]+1
dslab[cont[label]]=val
#dx=numpy.diff(sr[0:2])[0]
for n in range(samples):
label=self.labelStats["Labels"][n]
if not (ignoreZero and label == 0):
if nbins=="FB":
#Freedman Diaconis Estimator
IQR=numpy.percentile(distr[label],75)-numpy.percentile(distr[label],25)
bnw=2*IQR/numpy.power(distr[label].size,1.0/3.0)
nb=int((s[1]-s[0])/bnw)
elif nbins=="Rice":
#Rice
nb=int(2*numpy.power(distr[label].size,1.0/3.0))
elif nbins=="Doane":
#Doane
mu=numpy.mean(distr[label])
std=numpy.std(distr[label])
g1=numpy.mean(numpy.power((distr[label]-mu)/float(std),3))
n=distr[label].size
sg1=numpy.sqrt(float(6*(n-2))/float(((n+1)*(n+3))))
nb=int(1+numpy.log2(n)+numpy.log2(1+numpy.abs(g1)/sg1))
elif nbins<=0:
#nb=int(s[1]-s[0]+1) #TODO: if is not integer?
nb=len(numpy.unique(distr[label]))
else:
#Manual
nb=nbins
if nbins>0:
nm="-hist-"+str(nb)
else:
nm=""
name=colorNode.GetColorName(label) + "-" + self.grayscaleNode.GetName() + nm
ntuple=nb
hst,bins=numpy.histogram(distr[label],bins=nb,range=[s[0],s[1]],density=normalize)
arrayNode = slicer.mrmlScene.GetNodesByClassByName("vtkMRMLDoubleArrayNode",name).GetItemAsObject(0)
if not arrayNode:
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
arrayNode.SetName(name)
arrayD = arrayNode.GetArray()
arrayD.SetNumberOfComponents(2)
arrayD.SetNumberOfTuples(ntuple)
for n in range(ntuple):
arrayD.SetComponent(n, 0, bins[n]) #TODO
arrayD.SetComponent(n, 1, hst[n])
state = chartNode.StartModify()
chartNode.AddArray(name, arrayNode.GetID())
chartViewNode.SetChartNodeID(chartNode.GetID())
chartNode.SetProperty('default', 'title', 'Histogram')
chartNode.SetProperty('default', 'xAxisLabel', 'Grey Values')
chartNode.SetProperty('default', 'yAxisLabel', valueToPlot)
chartNode.SetProperty('default', 'type', 'Line');
chartNode.SetProperty('default', 'xAxisType', 'quantitative')
chartNode.SetProperty('default', 'yAxisType', 'quantitative')
chartNode.SetProperty('default', 'showLegend', 'on')
colorNode.GetColor(label,color)
col='#'+str(hex(color[0]*255)[2:4])+str(hex(color[1]*255)[2:4])+str(hex(color[2]*255)[2:4])
chartNode.SetProperty(name,'color',col)
chartNode.EndModify(state)
def grafTiempo(self):
## Se recupera la escena para recuperar el numero de imagenes el el volumen 4D
escena = slicer.mrmlScene
VectorInt = []
volumen4D = self.inputSelector.currentNode()
#Se carga el volumen seleccionado por el usuario
numero_imagenes = volumen4D.GetNumberOfFrames(
) #Numero de volumenes en el volumen 4D cargado
# Switch to a layout (24) that contains a Chart View to initiate the construction of the widget and Chart View Node
lns = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
lns.InitTraversal()
ln = lns.GetNextItemAsObject()
ln.SetViewArrangement(24)
# Get the Chart View Node
cvns = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
cvns.InitTraversal()
cvn = cvns.GetNextItemAsObject()
# Create an Array Node and add some data
dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn.GetArray()
a.SetNumberOfTuples(numero_imagenes - 2)
x = range(3, numero_imagenes)
# se crea el nodo de salida para la multiplicacion de volumenes entre la roi y los volumenes funcionales
#vol = slicer.vtkMRMLScalarVolumeNode();
#vol.SetName('salida')
#escena.AddNode(vol)
## se realiza la multiplicacion con cada volumen del volumen 4D
for i in range(3, numero_imagenes): #numero_imagenes
vol = slicer.vtkMRMLScalarVolumeNode()
vol.SetName('salida' + str(i))
escena.AddNode(vol)
parameters = {} # parametros para la multiplicacion
parameters['inputVolume1'] = self.inputSelectorRoi.currentNode()
#dos volumenes de la escena, uno de ellos debe ser la mascara creada en el EDITOR
parameters['inputVolume2'] = slicer.util.getNode('volumenmovil' +
str(i))
parameters['outputVolume'] = vol.GetID()
# se corre el modulo de multiplicacion
cliNode = slicer.cli.run(slicer.modules.multiplyscalarvolumes,
None,
parameters,
wait_for_completion=True)
VolNP = slicer.util.array(
'salida' + str(i)
) # se recupera el volumen resultante de la multiplicacion como un arreglo
a.SetComponent(i - 2, 0,
i * 0.19) # se agrega el tiempo para graficar
a.SetComponent(i - 2, 1, np.mean(
VolNP)) # se arregla el valor medio de intensidad de la roi
a.SetComponent(i - 2, 2, 0)
# Create a Chart Node.
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add the Array Nodes to the Chart. The first argument is a string used for the legend and to refer to the Array when setting properties.
cn.AddArray('Intensidad', dn.GetID())
# Set a few properties on the Chart. The first argument is a string identifying which Array to assign the property.
# 'default' is used to assign a property to the Chart itself (as opposed to an Array Node).
cn.SetProperty('default', 'title', 'Intensidad vs Tiempo')
cn.SetProperty('default', 'xAxisLabel', 'Time[min]')
cn.SetProperty('default', 'yAxisLabel', 'Intensity ROI mean')
# Tell the Chart View which Chart to display
cvn.SetChartNodeID(cn.GetID())
def test_Charting1(self):
""" Testing charting
"""
self.delayDisplay("Starting the test")
# Change the layout to one that has a chart. This created the ChartView
ln = slicer.mrmlScene.GetFirstNodeByClass('vtkMRMLLayoutNode')
ln.SetViewArrangement(24)
# Get the first ChartView node
cvn = slicer.mrmlScene.GetFirstNodeByClass('vtkMRMLChartViewNode')
# Create arrays of data
dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn.GetArray()
a.SetNumberOfTuples(600)
x = range(0, 600)
for i in range(len(x)):
a.SetComponent(i, 0, x[i]/50.0)
a.SetComponent(i, 1, math.sin(x[i]/50.0))
a.SetComponent(i, 2, 0)
dn2 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn2.GetArray()
a.SetNumberOfTuples(600)
x = range(0, 600)
for i in range(len(x)):
a.SetComponent(i, 0, x[i]/50.0)
a.SetComponent(i, 1, math.cos(x[i]/50.0))
a.SetComponent(i, 2, 0)
# Create the ChartNode,
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the Chart
cn.AddArray('A double array', dn.GetID())
cn.AddArray('Another double array', dn2.GetID())
# Configure properties of the Chart
cn.SetProperty('default', 'title', 'A simple chart with 2 curves')
cn.SetProperty('default', 'xAxisLabel', 'Something in x')
cn.SetProperty('default', 'yAxisLabel', 'Something in y')
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A simple chart with 2 curves')
# Create another ChartNode
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the Chart
cn.AddArray('Just one array', dn.GetID())
# Configure properties of the chart
cn.SetProperty('default', 'title', 'A simple chart with 1 curve')
cn.SetProperty('default', 'xAxisLabel', 'Just x')
cn.SetProperty('default', 'yAxisLabel', 'Just y')
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A simple chart with 1 curve')
# Create another ChartNode
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the Chart
cn.AddArray('The other array', dn2.GetID())
# Set properties on the chart
cn.SetProperty('default', 'title', 'A simple chart with another curve')
cn.SetProperty('default', 'xAxisLabel', 'time')
cn.SetProperty('default', 'yAxisLabel', 'velocity')
cn.SetProperty('The other array', 'showLines', 'on')
cn.SetProperty('The other array', 'showMarkers', 'off')
cn.SetProperty('The other array', 'color', '#fe7d20')
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A simple chart with another curve')
# Create another data array
dn3 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn3.GetArray()
a.SetNumberOfTuples(12)
x = range(0, 12)
for i in range(len(x)):
a.SetComponent(i, 0, x[i]/4.0)
a.SetComponent(i, 1, math.sin(x[i]/4.0))
a.SetComponent(i, 2, 0)
# Create another ChartNode
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the chart
cn.AddArray('Periodic', dn3.GetID())
# Configure properties of the Chart
cn.SetProperty('default', 'title', 'A bar chart')
cn.SetProperty('default', 'xAxisLabel', 'time')
cn.SetProperty('default', 'yAxisLabel', 'velocity')
cn.SetProperty('default', 'type', 'Bar');
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A bar chart')
# Test using a date axis
#
# Create another data array
dn4 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn4.GetArray()
# ugh, python uses localtime
dates = ["3/27/2010","6/15/2010","12/14/2010","3/8/2011","9/5/2011","12/20/2011","3/17/2012","6/12/2012","9/22/2012","12/14/2012","3/23/2012"]
#dates = ["3/27/2010","6/15/2010","9/21/2010","12/14/2010","3/8/2011","5/31/2011","9/5/2011","12/20/2011","3/17/2012","6/12/2012","9/22/2012","12/14/2012","3/23/2012"]
times = []
for i in range(len(dates)):
times.append(time.mktime(datetime.datetime.strptime(dates[i], "%m/%d/%Y").timetuple()))
a.SetNumberOfTuples(len(times))
for i in range(len(times)):
a.SetComponent(i, 0, times[i])
a.SetComponent(i, 1, math.sin(x[i]/4.0) + 4)
a.SetComponent(i, 2, 0)
# Create another ChartNode
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the chart
cn.AddArray('Lesion #1', dn4.GetID())
# Configure properties of the Chart
cn.SetProperty('default', 'title', 'A chart with dates')
cn.SetProperty('default', 'xAxisLabel', 'date')
cn.SetProperty('default', 'xAxisType', 'date')
cn.SetProperty('default', 'yAxisLabel', 'size (cm)')
cn.SetProperty('default', 'type', 'Bar');
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A chart with dates')
# Test using a color table to look up label names
#
#
# Create another data array
dn5 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn5.GetArray()
a.SetNumberOfTuples(4)
a.SetComponent(0, 0, 6)
a.SetComponent(0, 1, 32)
a.SetComponent(1, 0, 3)
a.SetComponent(1, 1, 12)
a.SetComponent(2, 0, 4)
a.SetComponent(2, 1, 20)
a.SetComponent(3, 0, 5)
a.SetComponent(3, 1, 6)
# Create another ChartNode
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the chart
cn.AddArray('Volumes', dn5.GetID())
# Configure properties of the Chart
cn.SetProperty('default', 'title', 'A chart with labels')
cn.SetProperty('default', 'xAxisLabel', 'structure')
cn.SetProperty('default', 'xAxisType', 'categorical')
cn.SetProperty('default', 'yAxisLabel', 'size (cm)')
cn.SetProperty('default', 'type', 'Bar');
cn.SetProperty('Volumes', 'lookupTable', slicer.util.getNode('GenericAnatomyColors').GetID() )
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A chart with labels')
# Test box plots
#
#
# Create another data array
dn6 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn6.GetArray()
a.SetNumberOfTuples(40)
for i in range(a.GetNumberOfTuples()):
a.SetComponent(i, 0, 1)
a.SetComponent(i, 1, (2.0*random.random() - 0.5) + 20.0)
# Create another data array
dn7 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn7.GetArray()
a.SetNumberOfTuples(25)
for i in range(20):
a.SetComponent(i, 0, 2)
a.SetComponent(i, 1, 2.0*(2.0*random.random()-1.0) + 27.0)
for i in range(5):
a.SetComponent(20+i, 0, 2)
a.SetComponent(20+i, 1, 10.0*(2.0*random.random()-1.0) + 27.0)
# Create another data array
dn8 = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a = dn8.GetArray()
a.SetNumberOfTuples(25)
for i in range(20):
a.SetComponent(i, 0, 3)
a.SetComponent(i, 1, 3.0*(2.0*random.random()-1.0) + 24.0)
for i in range(5):
a.SetComponent(20+i, 0, 2)
a.SetComponent(20+i, 1, 10.0*(2.0*random.random()-1.0) + 24.0)
# Create another ChartNode
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# Add data to the chart
cn.AddArray('Controls', dn6.GetID())
cn.AddArray('Group A', dn7.GetID())
cn.AddArray('Group B', dn8.GetID())
# Configure properties of the Chart
cn.SetProperty('default', 'title', 'A box chart')
cn.SetProperty('default', 'xAxisLabel', 'population')
cn.SetProperty('default', 'xAxisType', 'categorical')
cn.SetProperty('default', 'yAxisLabel', 'size (ml)')
cn.SetProperty('default', 'type', 'Box');
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
self.delayDisplay('A box chart')
#
self.delayDisplay('Test passed!')
