def chartContact(self, screwCount):
# Get the Chart View Node
cvns = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
cvns.InitTraversal()
cvn = cvns.GetNextItemAsObject()
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
arrayNodes = []
for i in range(0,screwCount):
# Create an Array Node and add some data
dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
arrayNodes.insert(i,dn)
a = dn.GetArray()
a.SetNumberOfTuples(10)
x = range(0, 10)
screwValues = self.screwContact[i]
for j in range(len(x)):
a.SetComponent(j, 0, (j * 10) + 5)
a.SetComponent(j, 1, screwValues[j])
a.SetComponent(j, 2, 0)
print j
print screwValues[j]
cn.AddArray('Screw %s' % i, dn.GetID())
dnCort = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
dnCanc = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a1 = dnCort.GetArray()
a2 = dnCanc.GetArray()
a1.SetNumberOfTuples(2)
a2.SetNumberOfTuples(2)
a1.SetComponent(0, 0, 0)
a1.SetComponent(0, 1, 250)
a1.SetComponent(0, 2, 0)
a1.SetComponent(1, 0, 100)
a1.SetComponent(1, 1, 250)
a1.SetComponent(1, 2, 0)
a2.SetComponent(0, 0, 0)
a2.SetComponent(0, 1, 130)
a2.SetComponent(0, 2, 0)
a2.SetComponent(1, 0, 100)
a2.SetComponent(1, 1, 130)
a2.SetComponent(1, 2, 0)
cn.AddArray('Cortical Bone', dnCort.GetID())
cn.AddArray('Cancellous Bone', dnCanc.GetID())
#cn.SetProperty('default', 'title', 'Information for Screw at point %s' % fidName)
cn.SetProperty('default', 'title', 'Screw - Bone Contact')
cn.SetProperty('default', 'xAxisLabel', 'Screw Percentile (Head - Tip)')
#cn.SetProperty('default', 'xAxisType', 'categorical')
cn.SetProperty('default', 'yAxisLabel', 'Average HU Contact')
cn.SetProperty('default', 'showLegend', 'on')
cn.SetProperty('default', 'type', 'Line')
cn.SetProperty('default', 'xAxisPad', '0')
#cn.SetProperty('default', 'xAxisPad', '0')
cvn.SetChartNodeID(cn.GetID())
def chartContact(self, screwCount):
# Get the Chart View Node
cvns = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
cvns.InitTraversal()
cvn = cvns.GetNextItemAsObject()
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
arrayNodes = []
for i in range(0,screwCount):
# Create an Array Node and add some data
dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
arrayNodes.insert(i,dn)
a = dn.GetArray()
a.SetNumberOfTuples(10)
x = range(0, 10)
screwValues = self.screwContact[i]
for j in range(len(x)):
a.SetComponent(j, 0, (j * 10) + 5)
a.SetComponent(j, 1, screwValues[j])
a.SetComponent(j, 2, 0)
print j
print screwValues[j]
cn.AddArray('Screw %s' % i, dn.GetID())
dnCort = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
dnCanc = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
a1 = dnCort.GetArray()
a2 = dnCanc.GetArray()
a1.SetNumberOfTuples(2)
a2.SetNumberOfTuples(2)
a1.SetComponent(0, 0, 0)
a1.SetComponent(0, 1, 250)
a1.SetComponent(0, 2, 0)
a1.SetComponent(1, 0, 100)
a1.SetComponent(1, 1, 250)
a1.SetComponent(1, 2, 0)
a2.SetComponent(0, 0, 0)
a2.SetComponent(0, 1, 130)
a2.SetComponent(0, 2, 0)
a2.SetComponent(1, 0, 100)
a2.SetComponent(1, 1, 130)
a2.SetComponent(1, 2, 0)
cn.AddArray('Cortical Bone', dnCort.GetID())
cn.AddArray('Cancellous Bone', dnCanc.GetID())
#cn.SetProperty('default', 'title', 'Information for Screw at point %s' % fidName)
cn.SetProperty('default', 'title', 'Screw - Bone Contact')
cn.SetProperty('default', 'xAxisLabel', 'Screw Percentile (Head - Tip)')
#cn.SetProperty('default', 'xAxisType', 'categorical')
cn.SetProperty('default', 'yAxisLabel', 'Average HU Contact')
cn.SetProperty('default', 'showLegend', 'on')
cn.SetProperty('default', 'type', 'Line')
cn.SetProperty('default', 'xAxisPad', '0')
#cn.SetProperty('default', 'xAxisPad', '0')
cvn.SetChartNodeID(cn.GetID())
def chartRatios(self):
ratiosAr = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
ratiosArinv = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
firstName=self.firstSelector.currentNode().GetName()
secondName=self.secondSelector.currentNode().GetName()
ratiosAr.SetName(firstName+"-"+secondName+"-ratios")
ratiosArinv.SetName(firstName+"-"+secondName+"-inverse-ratios")
arrayD = ratiosAr.GetArray()
arrayDinv = ratiosArinv.GetArray()
arrayD.SetNumberOfTuples(self.table.rowCount)
arrayDinv.SetNumberOfTuples(self.table.rowCount)
for n in range(self.table.rowCount):
if self.table.item(n,3):
arrayD.SetComponent(n, 0, n)
arrayDinv.SetComponent(n, 0, n)
arrayD.SetComponent(n, 1, float(self.table.item(n,3).text()))
arrayDinv.SetComponent(n, 1, float(self.table.item(self.table.rowCount-1-n,3).text()))
layoutNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
layoutNodes.SetReferenceCount(layoutNodes.GetReferenceCount()-1)
layoutNodes.InitTraversal()
layoutNode = layoutNodes.GetNextItemAsObject()
layoutNode.SetViewArrangement(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpQuantitativeView)
chartViewNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
chartViewNodes.SetReferenceCount(chartViewNodes.GetReferenceCount()-1)
chartViewNodes.InitTraversal()
chartViewNode = chartViewNodes.GetNextItemAsObject()
chartNode = slicer.mrmlScene.GetNodesByClassByName("vtkMRMLChartNode","Ratios").GetItemAsObject(0)
if not chartNode:
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
chartNode.SetName("Ratios")
print("set properties")
chartNode.SetProperty('default', 'title', 'Ratios')
chartNode.SetProperty('default', 'xAxisLabel', 'slice')
chartNode.SetProperty('default', 'yAxisLabel', 'Ratio')
chartNode.SetProperty('default', 'type', 'Line')
chartNode.SetProperty('default', 'showLegend', 'on')
chartNode.SetProperty('default', 'Markers', 'on')
chartViewNode.SetChartNodeID(chartNode.GetID())
chartNode.AddArray("Ratio", ratiosAr.GetID())
chartNode.AddArray("Ratioinv", ratiosArinv.GetID())
def showChart(self, samples, names):
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)
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
cvNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
cvNodes.SetReferenceCount(cvNodes.GetReferenceCount()-1)
cvNodes.InitTraversal()
cvNode = cvNodes.GetNextItemAsObject()
for pairs in zip(names,doubleArrays):
chartNode.AddArray(pairs[0],pairs[1].GetID())
cvNode.SetChartNodeID(chartNode.GetID())
return
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 + 1)
array.SetComponent(tuple, 1, self.labelStats[index,
valueToPlot])
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', 'Label Statistics')
chartNode.SetProperty('default', 'xAxisLabel', 'Label')
chartNode.SetProperty('default', 'yAxisLabel', valueToPlot)
chartNode.SetProperty('default', 'type', 'Line')
chartNode.SetProperty('default', 'xAxisType', 'categorical')
chartNode.SetProperty('default', 'showLegend', 'off')
# series level properties
if labelNode.IsA("vtkMRMLSequenceNode"):
if labelNode.GetNthDataNode(
0).GetDisplayNode() != None and labelNode.GetNthDataNode(
0).GetDisplayNode().GetColorNode() != None:
chartNode.SetProperty(
valueToPlot, 'lookupTable',
labelNode.GetNthDataNode(
0).GetDisplayNode().GetColorNodeID())
else:
chartNode.SetProperty(
valueToPlot, 'lookupTable',
slicer.mrmlScene.GetNodeByID('vtkMRMLColorTableNodeRed'))
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)
try:
v = float(self.labelStats[index,valueToPlot])
except (KeyError, TypeError):
v = float(0)
array.SetComponent(tuple, 1, v)
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 Chart(self,dists):
"""Make a MRML chart of the current stats
"""
if dists:
layoutNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
layoutNodes.SetReferenceCount(layoutNodes.GetReferenceCount()-1)
layoutNodes.InitTraversal()
layoutNode = layoutNodes.GetNextItemAsObject()
layoutNode.SetViewArrangement(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpQuantitativeView)
chartViewNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
chartViewNodes.SetReferenceCount(chartViewNodes.GetReferenceCount()-1)
chartViewNodes.InitTraversal()
chartViewNode = chartViewNodes.GetNextItemAsObject()
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
#dists=self.sides + self.diagonals
# samples=len(dists)
minimum=min(dists)
maximum=max(dists)
nbins=10.0
binsize=(maximum-minimum)/nbins
hist=self.createHst(binsize,dists)
samples=len(hist['bin'])
print("samples: " + str(samples))
array.SetNumberOfTuples(samples)
# for n in range(samples):
# array.SetComponent(n, 0, n)
# array.SetComponent(n, 1, dists[n])
for n in range(samples):
array.SetComponent(n, 0, hist['bin'][n])
array.SetComponent(n, 1, hist['freq'][n])
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
chartNode.SetName("Freq")
chartNode.AddArray("Distances", arrayNode.GetID())
chartViewNode.SetChartNodeID(chartNode.GetID())
print("set properties")
chartNode.SetProperty('default', 'title', 'Measured Distances')
chartNode.SetProperty('default', 'xAxisLabel', 'Distance')
chartNode.SetProperty('default', 'yAxisLabel', 'N')
#chartNode.SetProperty('default', 'type', 'Bar');
chartNode.SetProperty('default', 'type', 'Scatter');
#chartNode.SetProperty('default', 'xAxisType', 'categorical')
chartNode.SetProperty('default', 'showLegend', 'off')
def setSlicerDoubleArray(self):
if self.dn is not None:
return
from __main__ import slicer
self.dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
array = self.dn.GetArray()
#Trim zeroes
x = np.trim_zeros(self.x,'b')
array.SetNumberOfTuples(len(x))
for i in range(len(x)):
array.SetComponent(i, 0, x[i])
array.SetComponent(i, 1, self.y[i])
array.SetComponent(i, 2, self.err[i])
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 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.regionTags)
tuples = samples
array.SetNumberOfTuples(tuples)
tuple = 0
cycle = 'insp'
for i in xrange(samples):
index = self.regionTags[i]
array.SetComponent(tuple, 0, i)
array.SetComponent(tuple, 1, self.labelStats[cycle, 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:
chartNode.SetProperty(valueToPlot, 'lookupTable',
labelNode.GetDisplayNode().GetColorNodeID())
def CreateAndFillArray(self,hist,name):
arrayNode = slicer.mrmlScene.GetNodesByClassByName("vtkMRMLDoubleArrayNode",name).GetItemAsObject(0)
if not arrayNode:
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
arrayNode.SetName(name)
arrayD = arrayNode.GetArray()
arrayD.SetNumberOfTuples(len(hist[0]))
for n in range(len(hist[0])):
arrayD.SetComponent(n, 0, hist[0][n])
arrayD.SetComponent(n, 1, hist[1][n])
return arrayNode
def initializeCharting(self):
# Enable iCharting Settings
self.iCharting.setChecked(True)
self.iCharting.enabled = True
self.iChartingCollapsibleButton.collapsed = False
# Initialize image data (pre-contrast node at index '0')
self.nComponents = len(self.volumeNodes)
self.nodeImageData = []
for node in xrange(self.nComponents):
self.nodeImageData.append(self.volumeNodes[node].GetImageData())
self.extent = self.nodeImageData[0].GetExtent()
# Change active volume nodes in scene
appLogic = slicer.app.applicationLogic()
selectionNode = appLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(self.nodePre.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(
self.nodeSegmentCAD.GetID())
selectionNode.SetReferenceSecondaryVolumeID(self.node1.GetID())
appLogic.PropagateVolumeSelection()
# Change scene layout to conventional quantitative view
layoutNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
layoutNodes.InitTraversal()
layoutNode = layoutNodes.GetNextItemAsObject()
layoutNode.SetViewArrangement(
slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalQuantitativeView)
# Set up chart within the scene
self.chartViewNodes = slicer.mrmlScene.GetNodesByClass(
'vtkMRMLChartViewNode')
self.chartViewNodes.InitTraversal()
self.chartViewNode = self.chartViewNodes.GetNextItemAsObject()
self.arrayNode = slicer.mrmlScene.AddNode(
slicer.vtkMRMLDoubleArrayNode())
self.chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
self.chartNode.AddArray('voxelijk', self.arrayNode.GetID())
self.chartNode.SetProperty('default', 'title', 'Interactive Charting')
self.chartNode.SetProperty('default', 'xAxisLabel', 'DCE-MRI Volumes')
self.chartNode.SetProperty('default', 'yAxisLabel',
'Percentage Increase from Baseline')
self.chartNode.SetProperty('default', 'type', 'Line')
self.chartNode.SetProperty('default', 'xAxisType', 'quantitative')
self.chartNode.SetProperty('default', 'showGrid', 'on')
self.chartNode.SetProperty('default', 'showLegend', 'on')
self.chartNode.SetProperty('default', 'showMarkers', 'on')
self.chartNode.SetProperty('default', 'xAxisPad', '1')
self.chartViewNode.SetChartNodeID(self.chartNode.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.regionTags)
tuples = samples
array.SetNumberOfTuples(tuples)
tuple = 0
cycle = 'insp'
for i in xrange(samples):
index = self.regionTags[i]
array.SetComponent(tuple, 0, i)
array.SetComponent(tuple, 1, self.labelStats[cycle,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:
chartNode.SetProperty(valueToPlot, 'lookupTable', labelNode.GetDisplayNode().GetColorNodeID());
def initializeCharting(self):
# Enable iCharting Settings
self.iCharting.setChecked(True)
self.iCharting.enabled = True
self.iChartingCollapsibleButton.collapsed = False
# Initialize image data (pre-contrast node at index '0')
self.nComponents = len(self.volumeNodes)
self.nodeImageData = []
for node in xrange (self.nComponents):
self.nodeImageData.append(self.volumeNodes[node].GetImageData())
self.extent = self.nodeImageData[0].GetExtent()
# Change active volume nodes in scene
appLogic = slicer.app.applicationLogic()
selectionNode = appLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(self.nodePre.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(self.nodeSegmentCAD.GetID())
selectionNode.SetReferenceSecondaryVolumeID(self.node1.GetID())
appLogic.PropagateVolumeSelection()
# Change scene layout to conventional quantitative view
layoutNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
layoutNodes.InitTraversal()
layoutNode = layoutNodes.GetNextItemAsObject()
layoutNode.SetViewArrangement(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalQuantitativeView)
# Set up chart within the scene
self.chartViewNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
self.chartViewNodes.InitTraversal()
self.chartViewNode = self.chartViewNodes.GetNextItemAsObject()
self.arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
self.chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
self.chartNode.AddArray('voxelijk', self.arrayNode.GetID())
self.chartNode.SetProperty('default', 'title', 'Interactive Charting')
self.chartNode.SetProperty('default', 'xAxisLabel', 'DCE-MRI Volumes')
self.chartNode.SetProperty('default', 'yAxisLabel', 'Percentage Increase from Baseline')
self.chartNode.SetProperty('default', 'type', 'Line')
self.chartNode.SetProperty('default', 'xAxisType', 'quantitative')
self.chartNode.SetProperty('default', 'showGrid', 'on')
self.chartNode.SetProperty('default', 'showLegend', 'on')
self.chartNode.SetProperty('default', 'showMarkers', 'on')
self.chartNode.SetProperty('default', 'xAxisPad', '1')
self.chartViewNode.SetChartNodeID(self.chartNode.GetID())
def showChart(self, samples, names):
print("Logic showing chart")
print 'samples: ', samples
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:
print sample
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
nDataPoints = sample.GetNumberOfTuples()
array.SetNumberOfTuples(nDataPoints)
array.SetNumberOfComponents(3)
#print 'sample.GetTuple(0): ', sample.GetTuple(0)
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)
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# get 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 calculateLabeledVoxelsMeanAndInitiateChartArray(self):
# calculate the mean in each frame for each label and add to the chart array
nComponents = self.multiVolumeNode.GetNumberOfFrames()
self.dataNodes = {}
for k in self.labeledVoxels.keys():
self.dataNodes[k] = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
self.dataNodes[k].GetArray().SetNumberOfTuples(nComponents)
mvImage = self.multiVolumeNode.GetImageData()
for c in range(nComponents):
for k in self.labeledVoxels.keys():
arr = self.dataNodes[k].GetArray()
mean = 0.
cnt = 0.
for v in self.labeledVoxels[k]:
val = mvImage.GetScalarComponentAsFloat(v[0], v[1], v[2], c)
if math.isnan(val):
val = 0
mean = mean + val
cnt += 1
arr.SetComponent(c, 0, self.multiVolumeLabels[c])
arr.SetComponent(c, 1, mean / cnt)
arr.SetComponent(c, 2, 0)
def calculateLabeledVoxelsMeanAndInitiateChartArray(self):
# calculate the mean in each frame for each label and add to the chart array
nComponents = self.multiVolumeNode.GetNumberOfFrames()
self.dataNodes = {}
for k in self.labeledVoxels.keys():
self.dataNodes[k] = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
self.dataNodes[k].GetArray().SetNumberOfTuples(nComponents)
mvImage = self.multiVolumeNode.GetImageData()
for c in range(nComponents):
for k in self.labeledVoxels.keys():
arr = self.dataNodes[k].GetArray()
mean = 0.
cnt = 0.
for v in self.labeledVoxels[k]:
val = mvImage.GetScalarComponentAsFloat(v[0], v[1], v[2], c)
if math.isnan(val):
val = 0
mean = mean + val
cnt += 1
arr.SetComponent(c, 0, self.multiVolumeLabels[c])
arr.SetComponent(c, 1, mean / cnt)
arr.SetComponent(c, 2, 0)
def showChart(self, samples, names, distanceArrays, chartNode):
print("Logic showing chart")
# Switch to a layut 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 zip(distanceArrays, samples):
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
nDataPoints = len(sample[0])
array.SetNumberOfTuples(nDataPoints)
array.SetNumberOfComponents(3)
for i in range(nDataPoints):
array.SetComponent(i, 0, sample[0][i])
array.SetComponent(i, 1, sample[1].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()
# ChartNode is passed from the widget
chartNode.ClearArrays()
colorScheme = ["#FF0000","#7CFC00"] # "#FF0000" is red, "#7CFC00" is green, by default is green
for pairs in zip(names, doubleArrays, colorScheme):
chartNode.AddArray(pairs[0], pairs[1].GetID())
chartNode.SetProperty(pairs[0], "color", pairs[2])
cvNode.SetChartNodeID(chartNode.GetID())
return
def initializeChart(self, data, dataName):
# set the layout that includes a chart viewer
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpQuantitativeView)
#
chartViewNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
chartViewNodes.SetReferenceCount(chartViewNodes.GetReferenceCount()-1)
chartViewNodes.InitTraversal()
chartViewNode = chartViewNodes.GetNextItemAsObject()
# populate DoubleArrayNode with the result of the probing
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
samples = data.GetNumberOfTuples()
array.SetNumberOfTuples(samples)
tuple = 0
for i in xrange(samples):
array.SetComponent(tuple, 0, i)
array.SetComponent(tuple, 1, data.GetTuple1(i))
array.SetComponent(tuple, 2, 0)
tuple += 1
# create a new ChartNode
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
state = chartNode.StartModify()
chartNode.AddArray(dataName, arrayNode.GetID())
chartViewNode.SetChartNodeID(chartNode.GetID())
chartNode.SetProperty('default', 'title', 'Image line probe')
chartNode.SetProperty('default', 'xAxisLabel', 'Sample point')
chartNode.SetProperty('default', 'yAxisLabel', 'Intensity')
chartNode.SetProperty('default', 'type', 'Line');
chartNode.SetProperty('default', 'showLegend', 'on')
chartNode.EndModify(state)
def onLabelVolumeChanged(self):
# iterate over the label image and collect the IJK for each label element
labelNode = self.__fSelector.currentNode()
mvNode = self.__mvSelector.currentNode()
if labelNode != None and mvNode != None:
labelID = labelNode.GetID()
img = labelNode.GetImageData()
extent = img.GetWholeExtent()
labeledVoxels = {}
for i in range(extent[1]):
for j in range(extent[3]):
for k in range(extent[5]):
labelValue = img.GetScalarComponentAsFloat(i, j, k, 0)
if labelValue:
if labelValue in labeledVoxels.keys():
labeledVoxels[labelValue].append([i, j, k])
else:
labeledVoxels[labelValue] = []
labeledVoxels[labelValue].append([i, j, k])
# go over all elements, calculate the mean in each frame for each label
# and add to the chart array
nComponents = self.__mvNode.GetNumberOfFrames()
dataNodes = {}
for k in labeledVoxels.keys():
dataNodes[k] = slicer.mrmlScene.AddNode(
slicer.vtkMRMLDoubleArrayNode())
dataNodes[k].GetArray().SetNumberOfTuples(nComponents)
mvImage = self.__mvNode.GetImageData()
for c in range(nComponents):
for k in labeledVoxels.keys():
arr = dataNodes[k].GetArray()
mean = 0.
cnt = 0.
for v in labeledVoxels[k]:
mean = mean + mvImage.GetScalarComponentAsFloat(
v[0], v[1], v[2], c)
cnt = cnt + 1
arr.SetComponent(c, 0, self.__mvLabels[c])
arr.SetComponent(c, 1, mean / cnt)
arr.SetComponent(c, 2, 0)
# setup color node
colorNodeID = labelNode.GetDisplayNode().GetColorNodeID()
colorNode = labelNode.GetDisplayNode().GetColorNode()
lut = colorNode.GetLookupTable()
# add initialized data nodes to the chart
self.__cn.ClearArrays()
for k in labeledVoxels.keys():
name = colorNode.GetColorName(k)
self.__cn.AddArray(name, dataNodes[k].GetID())
#self.__cn.SetProperty(name, "lookupTable", colorNodeID)
rgb = lut.GetTableValue(int(k))
colorStr = self.RGBtoHex(rgb[0] * 255, rgb[1] * 255,
rgb[2] * 255)
self.__cn.SetProperty(name, "color", colorStr)
self.__cvn.Modified()
tag = str(
self.__mvNode.GetAttribute(
'MultiVolume.FrameIdentifyingDICOMTagName'))
units = str(
self.__mvNode.GetAttribute(
'MultiVolume.FrameIdentifyingDICOMTagUnits'))
xTitle = tag + ', ' + units
self.__cn.SetProperty('default', 'xAxisLabel', xTitle)
self.__cn.SetProperty('default', 'yAxisLabel',
'mean signal intensity')
self.__cvn.SetChartNodeID(self.__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 getSliceThk(self,meanProfile=False):
profiles=self.getProfile(self.direction)
self.spacing=self.input.GetSpacing()[self.direction] #todo: adjust
if not meanProfile:
profile=profiles[int(len(profiles)/2)]
X=range(len(profile))
else:
[X,profile]=self.meanTprofiles(profiles)
if self.type==0:
ramp=list(numpy.diff(profile)/numpy.diff(X))
else:
ramp=profile
FWHMres=self.getFWHM(ramp,X)
self.FWHM=FWHMres[0]
FWHMcurve=[[FWHMres[1],FWHMres[1],FWHMres[2],FWHMres[2]],[0,FWHMres[3],FWHMres[3],0]]
layoutNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
layoutNodes.SetReferenceCount(layoutNodes.GetReferenceCount()-1)
layoutNodes.InitTraversal()
layoutNode = layoutNodes.GetNextItemAsObject()
layoutNode.SetViewArrangement(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpQuantitativeView)
chartViewNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
chartViewNodes.SetReferenceCount(chartViewNodes.GetReferenceCount()-1)
chartViewNodes.InitTraversal()
chartViewNode = chartViewNodes.GetNextItemAsObject()
ProfileNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
ProfileNode.SetName("Profile-"+self.input.GetName()+"-"+self.ROI.GetName()+"-array")
self.arrayName=ProfileNode.GetName()
Profile = ProfileNode.GetArray()
Profile.SetNumberOfTuples(len(ramp))
for n in range(len(ramp)):
Profile.SetComponent(n, 0, self.spacing*X[n])
Profile.SetComponent(n, 1, ramp[n])
FWHMNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
FWHMNode.SetName("FWHM-"+self.input.GetName()+"-"+self.ROI.GetName()+"-array")
FWHMarray = FWHMNode.GetArray()
FWHMarray.SetNumberOfTuples(len(FWHMcurve[0]))
for n in range(len(FWHMcurve[0])):
FWHMarray.SetComponent(n, 0, FWHMcurve[0][n])
FWHMarray.SetComponent(n, 1, FWHMcurve[1][n])
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
chartNode.SetName("Profile")
chartNode.AddArray("Profile", ProfileNode.GetID())
chartNode.AddArray("FWHM", FWHMNode.GetID())
chartViewNode.SetChartNodeID(chartNode.GetID())
print("set properties")
chartNode.SetProperty('default', 'title', 'Profile')
chartNode.SetProperty('default', 'xAxisLabel', 'Distance(mm)')
chartNode.SetProperty('default', 'yAxisLabel', 'Profile')
chartNode.SetProperty('default', 'type', 'Line')
chartNode.SetProperty('default', 'showLegend', 'on')
chartNode.SetProperty('default', 'Markers', 'on')
def onCalculateLength(self):
self.inputPolyData = self.vtkNode.GetPolyData()
points = self.inputPolyData.GetPoints()
lines = self.inputPolyData.GetLines()
lines.InitTraversal()
self.distanceTable = list()
for i in range(self.inputPolyData.GetNumberOfCells()):
fiberLength = 0
ids = vtk.vtkIdList()
lines.GetNextCell(ids)
#print(ids.GetNumberOfIds())
for j in range(ids.GetNumberOfIds() - 1):
point1 = [0, 0, 0]
point2 = [0, 0, 0]
points.GetPoint(ids.GetId(j), point1)
points.GetPoint(ids.GetId(j + 1), point2)
x = point2[0] - point1[0]
y = point2[1] - point1[1]
z = point2[2] - point1[2]
step = (x * x + y * y + z * z)**.5
fiberLength += step
self.distanceTable.append(fiberLength)
min, max = self.getDistanceBound()
self.thresholdMin.setValue(min)
self.thresholdMin.enabled = True
self.thresholdMax.setValue(max + 1)
self.thresholdMax.enabled = True
self.applyThresholdButton.enabled = True
layoutNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
layoutNodes.InitTraversal()
layoutNode = layoutNodes.GetNextItemAsObject()
layoutNode.SetViewArrangement(
slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalQuantitativeView)
chartViewNodes = slicer.mrmlScene.GetNodesByClass(
'vtkMRMLChartViewNode')
chartViewNodes.InitTraversal()
chartViewNode = chartViewNodes.GetNextItemAsObject()
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
array.SetNumberOfTuples(10)
step = (max - min) / 10
interMin = min
interMax = min + step
for i in range(10):
numberOfFibers = 0
for length in self.distanceTable:
if length <= interMax and length >= interMin and length <= self.thresholdMax.value and length >= self.thresholdMin.value:
numberOfFibers += 1
array.SetComponent(i, 0, (interMin + interMax) / 2)
array.SetComponent(i, 1, numberOfFibers)
array.SetComponent(i, 2, 0)
interMin += step
interMax += step
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
chartNode.AddArray("Fiber Length", arrayNode.GetID())
chartViewNode.SetChartNodeID(chartNode.GetID())
chartNode.SetProperty('default', 'title', 'Length Distribution')
chartNode.SetProperty('default', 'xAxisLabel', 'Length')
chartNode.SetProperty('default', 'yAxisLabel', 'Distribution')
chartNode.SetProperty('default', 'type', 'Bar')
def onChartRequested(self):
# iterate over the label image and collect the IJK for each label element
labelNode = self.__fSelector.currentNode()
mvNode = self.__mvSelector.currentNode()
if labelNode == None or mvNode == None:
return
labelID = labelNode.GetID()
img = labelNode.GetImageData()
extent = img.GetWholeExtent()
labeledVoxels = {}
for i in range(extent[1]):
for j in range(extent[3]):
for k in range(extent[5]):
labelValue = img.GetScalarComponentAsFloat(i, j, k, 0)
if labelValue:
if labelValue in labeledVoxels.keys():
labeledVoxels[labelValue].append([i, j, k])
else:
labeledVoxels[labelValue] = []
labeledVoxels[labelValue].append([i, j, k])
# go over all elements, calculate the mean in each frame for each label
# and add to the chart array
nComponents = self.__mvNode.GetNumberOfFrames()
dataNodes = {}
for k in labeledVoxels.keys():
dataNodes[k] = slicer.mrmlScene.AddNode(
slicer.vtkMRMLDoubleArrayNode())
dataNodes[k].GetArray().SetNumberOfTuples(nComponents)
mvImage = self.__mvNode.GetImageData()
for c in range(nComponents):
for k in labeledVoxels.keys():
arr = dataNodes[k].GetArray()
mean = 0.
cnt = 0.
for v in labeledVoxels[k]:
mean = mean + mvImage.GetScalarComponentAsFloat(
v[0], v[1], v[2], c)
cnt = cnt + 1
arr.SetComponent(c, 0, self.__mvLabels[c])
arr.SetComponent(c, 1, mean / cnt)
arr.SetComponent(c, 2, 0)
if self.iChartingPercent.checked:
nBaselines = min(self.baselineFrames.value, nComponents)
for k in labeledVoxels.keys():
arr = dataNodes[k].GetArray()
baseline = 0
for bc in range(nBaselines):
baseline += arr.GetComponent(bc, 1)
baseline /= nBaselines
if baseline != 0:
for ic in range(nComponents):
intensity = arr.GetComponent(ic, 1)
percentChange = (intensity / baseline - 1) * 100.
arr.SetComponent(ic, 1, percentChange)
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())
# setup color node
colorNodeID = labelNode.GetDisplayNode().GetColorNodeID()
colorNode = labelNode.GetDisplayNode().GetColorNode()
lut = colorNode.GetLookupTable()
# add initialized data nodes to the chart
chartNode.ClearArrays()
for k in labeledVoxels.keys():
name = colorNode.GetColorName(k)
chartNode.AddArray(name, dataNodes[k].GetID())
rgb = lut.GetTableValue(int(k))
colorStr = self.RGBtoHex(rgb[0] * 255, rgb[1] * 255, rgb[2] * 255)
chartNode.SetProperty(name, "color", colorStr)
tag = str(
self.__mvNode.GetAttribute(
'MultiVolume.FrameIdentifyingDICOMTagName'))
units = str(
self.__mvNode.GetAttribute(
'MultiVolume.FrameIdentifyingDICOMTagUnits'))
xTitle = tag + ', ' + units
chartNode.SetProperty('default', 'xAxisLabel', xTitle)
if self.iChartingPercent.checked:
chartNode.SetProperty('default', 'yAxisLabel',
'change relative to baseline, %')
else:
chartNode.SetProperty('default', 'yAxisLabel',
'mean signal intensity')
chartViewNode.SetChartNodeID(chartNode.GetID())
def onCalculateLength(self):
self.inputPolyData = self.vtkNode.GetPolyData()
points = self.inputPolyData.GetPoints()
lines = self.inputPolyData.GetLines()
lines.InitTraversal()
self.distanceTable = list()
for i in range(self.inputPolyData.GetNumberOfCells()):
fiberLength = 0
ids = vtk.vtkIdList()
lines.GetNextCell(ids)
#print(ids.GetNumberOfIds())
for j in range(ids.GetNumberOfIds() - 1):
point1 = [0,0,0]
point2 = [0,0,0]
points.GetPoint(ids.GetId(j), point1)
points.GetPoint(ids.GetId(j+1), point2)
x = point2[0] - point1[0]
y = point2[1] - point1[1]
z = point2[2] - point1[2]
step = (x*x + y*y + z*z)**.5
fiberLength += step
self.distanceTable.append(fiberLength)
min,max=self.getDistanceBound()
self.thresholdMin.setValue(min)
self.thresholdMin.enabled = True
self.thresholdMax.setValue(max+1)
self.thresholdMax.enabled = True
self.applyThresholdButton.enabled = True
layoutNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
layoutNodes.InitTraversal()
layoutNode = layoutNodes.GetNextItemAsObject()
layoutNode.SetViewArrangement(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalQuantitativeView)
chartViewNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
chartViewNodes.InitTraversal()
chartViewNode = chartViewNodes.GetNextItemAsObject()
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
array.SetNumberOfTuples(10)
step = (max-min)/10
interMin = min
interMax = min+step
for i in range(10):
numberOfFibers = 0
for length in self.distanceTable:
if length<=interMax and length>=interMin and length<=self.thresholdMax.value and length>=self.thresholdMin.value:
numberOfFibers += 1
array.SetComponent(i,0,(interMin+interMax)/2)
array.SetComponent(i,1,numberOfFibers)
array.SetComponent(i,2,0)
interMin += step
interMax += step
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
chartNode.AddArray("Fiber Length",arrayNode.GetID())
chartViewNode.SetChartNodeID(chartNode.GetID())
chartNode.SetProperty('default', 'title', 'Length Distribution')
chartNode.SetProperty('default', 'xAxisLabel', 'Length')
chartNode.SetProperty('default', 'yAxisLabel', 'Distribution')
chartNode.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.assertTrue( logic.hasImageData(volumeNode) )
# Change the layout to one that has a chart. This created the ChartView
ln = slicer.util.getNode(pattern='vtkMRMLLayoutNode*')
ln.SetViewArrangement(24)
# Get the first ChartView node
cvn = slicer.util.getNode(pattern='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')
#
self.delayDisplay('Test passed!')
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 computeDPH(self, inputDoseVolumeNode, referenceDoseVolumeNode, inputContourNode, numberOfSimulations, numberOfFractions, systemError, randomError, doseGrowSizeX, doseGrowSizeY, doseGrowSizeZ, doseGrowOption):
# Step 1: morph dose
outputDoseVolumeNode = slicer.vtkMRMLScalarVolumeNode()
slicer.mrmlScene.AddNode(outputDoseVolumeNode)
from vtkSlicerDoseMorphologyModuleLogic import vtkMRMLDoseMorphologyNode
doseMorphologyNode = vtkMRMLDoseMorphologyNode()
slicer.mrmlScene.AddNode(doseMorphologyNode)
doseMorphologyNode.SetAndObserveInputDoseVolumeNode(inputDoseVolumeNode)
doseMorphologyNode.SetAndObserveReferenceDoseVolumeNode(referenceDoseVolumeNode)
doseMorphologyNode.SetAndObserveOutputDoseVolumeNode(outputDoseVolumeNode)
if doseGrowOption == "Dilation":
doseMorphologyNode.SetOperationToExpandByDilation()
elif doseGrowOption == "Scaling":
doseMorphologyNode.SetOperationToExpandByScaling()
doseMorphologyNode.SetXSize(doseGrowSizeX)
doseMorphologyNode.SetYSize(doseGrowSizeY)
doseMorphologyNode.SetZSize(doseGrowSizeZ)
doseMorphologyLogic = slicer.modules.dosemorphology.logic()
doseMorphologyLogic.SetAndObserveDoseMorphologyNode(doseMorphologyNode)
doseMorphologyLogic.MorphDose()
# print "finished step1"
# Step 2: simulate patient motion
# #first convert ribbon model to labelmap
# inputContourNode.SetAndObserveRasterizationReferenceVolumeNodeId(referenceDoseVolumeNode.GetID())
# inputContourNode.SetRasterizationOversamplingFactor(1.0)
# tempLabelmapNode = inputContourNode.GetIndexedLabelmapVolumeNode()
from vtkSlicerMotionSimulatorDoubleArrayModuleMRML import vtkMRMLMotionSimulatorDoubleArrayNode
motionSimulatorDoubleArrayNode = vtkMRMLMotionSimulatorDoubleArrayNode()
slicer.mrmlScene.AddNode(motionSimulatorDoubleArrayNode)
from vtkSlicerMotionSimulatorModuleLogic import vtkMRMLMotionSimulatorNode
motionSimulatorNode = vtkMRMLMotionSimulatorNode()
slicer.mrmlScene.AddNode(motionSimulatorNode)
motionSimulatorNode.SetAndObserveInputDoseVolumeNode(outputDoseVolumeNode)
motionSimulatorNode.SetAndObserveInputContourNode(inputContourNode)
motionSimulatorNode.SetAndObserveOutputDoubleArrayNode(motionSimulatorDoubleArrayNode)
motionSimulatorNode.SetNumberOfSimulation(numberOfSimulations)
motionSimulatorNode.SetNumberOfFraction(numberOfFractions)
motionSimulatorNode.SetXSysSD(systemError)
motionSimulatorNode.SetYSysSD(systemError)
motionSimulatorNode.SetZSysSD(systemError)
motionSimulatorNode.SetXRdmSD(randomError)
motionSimulatorNode.SetYRdmSD(randomError)
motionSimulatorNode.SetZRdmSD(randomError)
motionSimualtorLogic = slicer.modules.motionsimulator.logic()
motionSimualtorLogic.SetAndObserveMotionSimulatorNode(motionSimulatorNode)
motionSimualtorLogic.RunSimulation()
# print "finished step2"
# Step 3: dose population histogram
from vtkSlicerDosePopulationHistogramModuleLogic import vtkMRMLDosePopulationHistogramNode
dosePopulationHistogramNode = vtkMRMLDosePopulationHistogramNode()
slicer.mrmlScene.AddNode(dosePopulationHistogramNode)
outputDoubleArrayNode = slicer.vtkMRMLDoubleArrayNode()
slicer.mrmlScene.AddNode(outputDoubleArrayNode)
dosePopulationHistogramNode.SetAndObserveDoubleArrayNode(motionSimulatorDoubleArrayNode)
dosePopulationHistogramNode.SetAndObserveDoseVolumeNode(inputDoseVolumeNode)
dosePopulationHistogramNode.SetAndObserveContourNode(inputContourNode)
dosePopulationHistogramNode.SetAndObserveOutputDoubleArrayNode(outputDoubleArrayNode)
dosePopulationHistogramNode.SetUseDoseOptionToD98()
dosePopulationHistogramLogic = slicer.modules.dosepopulationhistogram.logic()
dosePopulationHistogramLogic.SetAndObserveDosePopulationHistogramNode(dosePopulationHistogramNode)
dosePopulationHistogramLogic.ComputeDPH()
# print "finished step3"
arrayNode = outputDoubleArrayNode
doubleArray = arrayNode.GetArray()
numberOfTuples = doubleArray.GetNumberOfTuples()
value = doubleArray.GetComponent(97, 1)
# remove all the nodes
slicer.mrmlScene.RemoveNode(outputDoseVolumeNode)
del outputDoseVolumeNode
slicer.mrmlScene.RemoveNode(doseMorphologyNode)
del doseMorphologyNode
slicer.mrmlScene.RemoveNode(motionSimulatorDoubleArrayNode)
del motionSimulatorDoubleArrayNode
slicer.mrmlScene.RemoveNode(motionSimulatorNode)
del motionSimulatorNode
slicer.mrmlScene.RemoveNode(dosePopulationHistogramNode)
del dosePopulationHistogramNode
slicer.mrmlScene.RemoveNode(outputDoubleArrayNode)
del outputDoubleArrayNode
return value/100.0
"""
def onLabelVolumeChanged(self):
# iterate over the label image and collect the IJK for each label element
labelNode = self.__fSelector.currentNode()
mvNode = self.__mvSelector.currentNode()
if labelNode != None and mvNode != None:
labelID = labelNode.GetID()
img = labelNode.GetImageData()
extent = img.GetWholeExtent()
labeledVoxels = {}
for i in range(extent[1]):
for j in range(extent[3]):
for k in range(extent[5]):
labelValue = img.GetScalarComponentAsFloat(i,j,k,0)
if labelValue:
if labelValue in labeledVoxels.keys():
labeledVoxels[labelValue].append([i,j,k])
else:
labeledVoxels[labelValue] = []
labeledVoxels[labelValue].append([i,j,k])
# go over all elements, calculate the mean in each frame for each label
# and add to the chart array
nComponents = self.__mvNode.GetNumberOfFrames()
dataNodes = {}
for k in labeledVoxels.keys():
dataNodes[k] = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
dataNodes[k].GetArray().SetNumberOfTuples(nComponents)
mvImage = self.__mvNode.GetImageData()
for c in range(nComponents):
for k in labeledVoxels.keys():
arr = dataNodes[k].GetArray()
mean = 0.
cnt = 0.
for v in labeledVoxels[k]:
mean = mean+mvImage.GetScalarComponentAsFloat(v[0],v[1],v[2],c)
cnt = cnt+1
arr.SetComponent(c, 0, self.__mvLabels[c])
arr.SetComponent(c, 1, mean/cnt)
arr.SetComponent(c, 2, 0)
# setup color node
colorNodeID = labelNode.GetDisplayNode().GetColorNodeID()
colorNode = labelNode.GetDisplayNode().GetColorNode()
lut = colorNode.GetLookupTable()
# add initialized data nodes to the chart
self.__cn.ClearArrays()
for k in labeledVoxels.keys():
name = colorNode.GetColorName(k)
self.__cn.AddArray(name, dataNodes[k].GetID())
#self.__cn.SetProperty(name, "lookupTable", colorNodeID)
rgb = lut.GetTableValue(int(k))
colorStr = self.RGBtoHex(rgb[0]*255,rgb[1]*255,rgb[2]*255)
self.__cn.SetProperty(name, "color", colorStr)
self.__cvn.Modified()
tag = str(self.__mvNode.GetAttribute('MultiVolume.FrameIdentifyingDICOMTagName'))
units = str(self.__mvNode.GetAttribute('MultiVolume.FrameIdentifyingDICOMTagUnits'))
xTitle = tag+', '+units
self.__cn.SetProperty('default','xAxisLabel',xTitle)
self.__cn.SetProperty('default','yAxisLabel','mean signal intensity')
self.__cvn.SetChartNodeID(self.__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 onApplyThreshold(self):
min,max = self.getDistanceBound()
newPoints = vtk.vtkPoints()
newLines = vtk.vtkCellArray()
newTensors = vtk.vtkFloatArray()
newTensors.SetNumberOfComponents(9)
newScalars = vtk.vtkFloatArray()
points = self.inputPolyData.GetPoints()
lines = self.inputPolyData.GetLines()
tensors = self.inputPolyData.GetPointData().GetTensors()
lines.InitTraversal()
newId = 0
for length in self.distanceTable:
if length<=self.thresholdMax.value and length>=self.thresholdMin.value:
ids = vtk.vtkIdList()
lines.GetNextCell(ids)
newLine = vtk.vtkPolyLine()
#print(ids.GetNumberOfIds())
newLine.GetPointIds().SetNumberOfIds(ids.GetNumberOfIds())
#print(((length-min)/(max-min))*100)
for i in range(ids.GetNumberOfIds()):
newPoints.InsertNextPoint(points.GetPoint(ids.GetId(i)))
newLine.GetPointIds().SetId(i,newId)
newScalars.InsertNextValue(((length-min)/(max-min)))
newId += 1
tensorValue = [0]*9
if(tensors != None):
for j in range(9):
tensorValue[j] = tensors.GetComponent(ids.GetId(i),j)
newTensors.InsertNextTuple(tensorValue)
newLines.InsertNextCell(newLine)
self.outputPolyData = vtk.vtkPolyData()
self.outputPolyData.SetPoints(newPoints)
self.outputPolyData.SetLines(newLines)
self.outputPolyData.GetPointData().SetTensors(newTensors)
newScalars.SetName("Length")
self.outputPolyData.GetPointData().AddArray(newScalars)
self.outputNode.SetAndObservePolyData(self.outputPolyData)
chartViewNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
chartViewNodes.InitTraversal()
chartViewNode = chartViewNodes.GetNextItemAsObject()
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
array.SetNumberOfTuples(10)
step = (max-min)/10
interMin = min
interMax = min+step
for i in range(10):
numberOfFibers = 0
for length in self.distanceTable:
if length<=interMax and length>=interMin and length<=self.thresholdMax.value and length>=self.thresholdMin.value:
numberOfFibers += 1
array.SetComponent(i,0,(interMin+interMax)/2)
array.SetComponent(i,1,numberOfFibers)
array.SetComponent(i,2,0)
interMin += step
interMax += step
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
chartNode.AddArray("Fiber Length",arrayNode.GetID())
chartViewNode.SetChartNodeID(chartNode.GetID())
chartNode.SetProperty('default', 'title', 'Length Distribution')
chartNode.SetProperty('default', 'xAxisLabel', 'Length')
chartNode.SetProperty('default', 'yAxisLabel', 'Distribution')
chartNode.SetProperty('default', 'type', 'Bar')
def onChartRequested(self):
# iterate over the label image and collect the IJK for each label element
labelNode = self.__fSelector.currentNode()
mvNode = self.__mvSelector.currentNode()
if labelNode == None or mvNode == None:
return
labelID = labelNode.GetID()
img = labelNode.GetImageData()
extent = img.GetWholeExtent()
labeledVoxels = {}
for i in range(extent[1]):
for j in range(extent[3]):
for k in range(extent[5]):
labelValue = img.GetScalarComponentAsFloat(i,j,k,0)
if labelValue:
if labelValue in labeledVoxels.keys():
labeledVoxels[labelValue].append([i,j,k])
else:
labeledVoxels[labelValue] = []
labeledVoxels[labelValue].append([i,j,k])
# go over all elements, calculate the mean in each frame for each label
# and add to the chart array
nComponents = self.__mvNode.GetNumberOfFrames()
dataNodes = {}
for k in labeledVoxels.keys():
dataNodes[k] = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
dataNodes[k].GetArray().SetNumberOfTuples(nComponents)
mvImage = self.__mvNode.GetImageData()
for c in range(nComponents):
for k in labeledVoxels.keys():
arr = dataNodes[k].GetArray()
mean = 0.
cnt = 0.
for v in labeledVoxels[k]:
mean = mean+mvImage.GetScalarComponentAsFloat(v[0],v[1],v[2],c)
cnt = cnt+1
arr.SetComponent(c, 0, self.__mvLabels[c])
arr.SetComponent(c, 1, mean/cnt)
arr.SetComponent(c, 2, 0)
if self.iChartingPercent.checked:
nBaselines = min(self.baselineFrames.value,nComponents)
for k in labeledVoxels.keys():
arr = dataNodes[k].GetArray()
baseline = 0
for bc in range(nBaselines):
baseline += arr.GetComponent(bc,1)
baseline /= nBaselines
if baseline != 0:
for ic in range(nComponents):
intensity = arr.GetComponent(ic,1)
percentChange = (intensity/baseline-1)*100.
arr.SetComponent(ic,1,percentChange)
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())
# setup color node
colorNodeID = labelNode.GetDisplayNode().GetColorNodeID()
colorNode = labelNode.GetDisplayNode().GetColorNode()
lut = colorNode.GetLookupTable()
# add initialized data nodes to the chart
chartNode.ClearArrays()
for k in labeledVoxels.keys():
name = colorNode.GetColorName(k)
chartNode.AddArray(name, dataNodes[k].GetID())
rgb = lut.GetTableValue(int(k))
colorStr = self.RGBtoHex(rgb[0]*255,rgb[1]*255,rgb[2]*255)
chartNode.SetProperty(name, "color", colorStr)
tag = str(self.__mvNode.GetAttribute('MultiVolume.FrameIdentifyingDICOMTagName'))
units = str(self.__mvNode.GetAttribute('MultiVolume.FrameIdentifyingDICOMTagUnits'))
xTitle = tag+', '+units
chartNode.SetProperty('default','xAxisLabel',xTitle)
if self.iChartingPercent.checked:
chartNode.SetProperty('default','yAxisLabel','change relative to baseline, %')
else:
chartNode.SetProperty('default','yAxisLabel','mean signal intensity')
chartViewNode.SetChartNodeID(chartNode.GetID())
def grafTiempo(self):
# 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)
vectorintensidad = []
# 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(27)
#Volumen
escena = slicer.mrmlScene
#Se recupera la escena cargada
volumen4D = self.inputSelector5.currentNode()
imagenvtk4D = volumen4D.GetImageData()
numero_imagenes = volumen4D.GetNumberOfFrames()
for i in range(0, numero_imagenes, 1):
extract2 = vtk.vtkImageExtractComponents()
extract2.SetInputData(imagenvtk4D)
imagen_movil = extract2.SetComponents(i)
extract2.Update()
#Matriz de transformacion
ras2ijk = vtk.vtkMatrix4x4()
ijk2ras = vtk.vtkMatrix4x4()
#Se solicita al volumen original que devuelva las matrices
volumen4D.GetRASToIJKMatrix(ras2ijk)
volumen4D.GetIJKToRASMatrix(ijk2ras)
#Se crea un volumen movil, y se realiza el mismo procedimiento que con el fijo
volumenMovil = slicer.vtkMRMLScalarVolumeNode()
volumenMovil.SetRASToIJKMatrix(ras2ijk)
volumenMovil.SetIJKToRASMatrix(ijk2ras)
volumenMovil.SetAndObserveImageData(extract2.GetOutput())
escena.AddNode(volumenMovil)
z = slicer.util.arrayFromVolume(volumenMovil)
m = np.mean(z[:])
vectorintensidad.append((m / 15000) - 1)
for i in range(0, numero_imagenes):
a.SetComponent(i, 0, i * 11.11)
a.SetComponent(i, 1, vectorintensidad[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.
# 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', 'intesidad vs tiempo')
cn.SetProperty('default', 'xAxisLabel', 'Tiempo(s)')
cn.SetProperty('default', 'yAxisLabel', 'Intensidad')
# Tell the Chart View which Chart to display
cvn.SetChartNodeID(cn.GetID())
def onApplyThreshold(self):
min, max = self.getDistanceBound()
newPoints = vtk.vtkPoints()
newLines = vtk.vtkCellArray()
newTensors = vtk.vtkFloatArray()
newTensors.SetNumberOfComponents(9)
newScalars = vtk.vtkFloatArray()
points = self.inputPolyData.GetPoints()
lines = self.inputPolyData.GetLines()
tensors = self.inputPolyData.GetPointData().GetTensors()
lines.InitTraversal()
newId = 0
for length in self.distanceTable:
if length <= self.thresholdMax.value and length >= self.thresholdMin.value:
ids = vtk.vtkIdList()
lines.GetNextCell(ids)
newLine = vtk.vtkPolyLine()
#print(ids.GetNumberOfIds())
newLine.GetPointIds().SetNumberOfIds(ids.GetNumberOfIds())
#print(((length-min)/(max-min))*100)
for i in range(ids.GetNumberOfIds()):
newPoints.InsertNextPoint(points.GetPoint(ids.GetId(i)))
newLine.GetPointIds().SetId(i, newId)
newScalars.InsertNextValue(((length - min) / (max - min)))
newId += 1
tensorValue = [0] * 9
if (tensors != None):
for j in range(9):
tensorValue[j] = tensors.GetComponent(
ids.GetId(i), j)
newTensors.InsertNextTuple(tensorValue)
newLines.InsertNextCell(newLine)
self.outputPolyData = vtk.vtkPolyData()
self.outputPolyData.SetPoints(newPoints)
self.outputPolyData.SetLines(newLines)
self.outputPolyData.GetPointData().SetTensors(newTensors)
newScalars.SetName("Length")
self.outputPolyData.GetPointData().AddArray(newScalars)
self.outputNode.SetAndObservePolyData(self.outputPolyData)
chartViewNodes = slicer.mrmlScene.GetNodesByClass(
'vtkMRMLChartViewNode')
chartViewNodes.InitTraversal()
chartViewNode = chartViewNodes.GetNextItemAsObject()
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
array.SetNumberOfTuples(10)
step = (max - min) / 10
interMin = min
interMax = min + step
for i in range(10):
numberOfFibers = 0
for length in self.distanceTable:
if length <= interMax and length >= interMin and length <= self.thresholdMax.value and length >= self.thresholdMin.value:
numberOfFibers += 1
array.SetComponent(i, 0, (interMin + interMax) / 2)
array.SetComponent(i, 1, numberOfFibers)
array.SetComponent(i, 2, 0)
interMin += step
interMax += step
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
chartNode.AddArray("Fiber Length", arrayNode.GetID())
chartViewNode.SetChartNodeID(chartNode.GetID())
chartNode.SetProperty('default', 'title', 'Length Distribution')
chartNode.SetProperty('default', 'xAxisLabel', 'Length')
chartNode.SetProperty('default', 'yAxisLabel', 'Distribution')
chartNode.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.assertTrue( logic.hasImageData(volumeNode) )
# Change the layout to one that has a chart. This created the ChartView
ln = slicer.util.getNode(pattern='vtkMRMLLayoutNode*')
ln.SetViewArrangement(24)
# Get the first ChartView node
cvn = slicer.util.getNode(pattern='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')
#
self.delayDisplay('Test passed!')
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.assertTrue( logic.hasImageData(volumeNode) )
# Change the layout to one that has a chart. This created the ChartView
ln = slicer.util.getNode(pattern="vtkMRMLLayoutNode*")
ln.SetViewArrangement(24)
# Get the first ChartView node
cvn = slicer.util.getNode(pattern="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_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.assertTrue( logic.hasImageData(volumeNode) )
# Change the layout to one that has a chart. This created the ChartView
ln = slicer.util.getNode(pattern='vtkMRMLLayoutNode*')
ln.SetViewArrangement(24)
# Get the first ChartView node
cvn = slicer.util.getNode(pattern='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!')
