def updateChart(self, outputArray, name, lineResolution):
# 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*')
# If we already created a chart node and it is still exists then reuse that
cn = None
if self.chartNodeID:
cn = slicer.mrmlScene.GetNodeByID(cvn.GetChartNodeID())
if not cn:
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
self.chartNodeID = cn.GetID()
# Configure properties of the Chart
cn.SetProperty('default', 'title', 'Line profile')
cn.SetProperty('default', 'xAxisLabel', 'Distance (mm)')
cn.SetProperty('default', 'yAxisLabel', 'Intensity')
cn.AddArray(name, outputArray.GetID())
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
cvn.Modified()
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 __init__( self, parent=None ):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout( qt.QVBoxLayout() )
else:
self.parent = parent
self.layout = self.parent.layout()
# this flag is 1 if there is an update in progress
self.__updating = 1
self.__mvNode = None
self.extractFrame = False
# chart view node
self.__cvn = None
# data node
#slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
# chart node
self.__cn = slicer.vtkMRMLChartNode()
self.__cn.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(self.__cn)
# image play setup
self.timer = qt.QTimer()
self.timer.setInterval(50)
self.timer.connect('timeout()', self.goToNext)
def __init__(self, parent=None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
else:
self.parent = parent
self.layout = self.parent.layout()
# this flag is 1 if there is an update in progress
self.__updating = 1
self.__mvNode = None
self.extractFrame = False
# chart view node
self.__cvn = None
# data node
#slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
# chart node
self.__cn = slicer.vtkMRMLChartNode()
self.__cn.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(self.__cn)
# image play setup
self.timer = qt.QTimer()
self.timer.setInterval(50)
self.timer.connect('timeout()', self.goToNext)
def updateChart(self,outputArray,name,lineResolution):
# 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*')
# If we already created a chart node and it is still exists then reuse that
cn = None
if self.chartNodeID:
cn = slicer.mrmlScene.GetNodeByID(cvn.GetChartNodeID())
if not cn:
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
self.chartNodeID = cn.GetID()
# Configure properties of the Chart
cn.SetProperty('default', 'title', 'Line profile')
cn.SetProperty('default', 'xAxisLabel', 'Distance (mm)')
cn.SetProperty('default', 'yAxisLabel', 'Intensity')
cn.AddArray(name, outputArray.GetID())
# Set the chart to display
cvn.SetChartNodeID(cn.GetID())
cvn.Modified()
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 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 prepareCharts(self):
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","OTF").GetItemAsObject(0)
if not chartNode:
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
chartNode.SetName("OTF")
print("set properties")
chartNode.SetProperty('default', 'title', 'OTF')
chartNode.SetProperty('default', 'xAxisLabel', 'lp/mm')
chartNode.SetProperty('default', 'yAxisLabel', 'Signal')
chartNode.SetProperty('default', 'type', 'Line')
chartNode.SetProperty('default', 'showLegend', 'on')
chartNode.SetProperty('default', 'Markers', 'on')
chartViewNode.SetChartNodeID(chartNode.GetID())
SFchartNode = None
if self.intermSave:
SFchartNode = slicer.mrmlScene.GetNodesByClassByName("vtkMRMLChartNode","SF").GetItemAsObject(0)
if not SFchartNode:
SFchartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
SFchartNode.SetName("SF")
print("set properties")
SFchartNode.SetProperty('default', 'title', 'SF')
SFchartNode.SetProperty('default', 'xAxisLabel', 'mm')
SFchartNode.SetProperty('default', 'yAxisLabel', 'Signal')
SFchartNode.SetProperty('default', 'type', 'Line')
SFchartNode.SetProperty('default', 'showLegend', 'on')
SFchartNode.SetProperty('default', 'Markers', 'on')
return [chartNode,SFchartNode]
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 section_PluginAutoSearch(self):
self.delayDisplay("Plugin auto search",self.delayMs)
# Test whether the owner plugin is automatically searched when the associated data node changes
chartNode2 = slicer.vtkMRMLChartNode()
slicer.mrmlScene.AddNode(chartNode2)
chartNode2.SetName(self.sampleChartName + '2')
clonedMarkupShNode = slicer.util.getNode(self.sampleMarkupName + ' Copy_SubjectHierarchy')
clonedMarkupShNode.SetAssociatedNodeID(chartNode2.GetID())
self.assertTrue( clonedMarkupShNode.GetOwnerPluginName() == 'Charts' )
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 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 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 createChartNodeAndInsertData(self):
# setup color node
colorNode = self.labelNode.GetDisplayNode().GetColorNode()
lut = colorNode.GetLookupTable()
# add initialized data nodes to the chart
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
chartNode.ClearArrays()
for k in self.labeledVoxels.keys():
k = int(k)
name = colorNode.GetColorName(k)
chartNode.AddArray(name, self.dataNodes[k].GetID())
rgb = lut.GetTableValue(int(k))
colorStr = Helper.RGBtoHex(rgb[0] * 255, rgb[1] * 255, rgb[2] * 255)
chartNode.SetProperty(name, "color", colorStr)
return chartNode
def createChartNodeAndInsertData(self):
# setup color node
colorNode = self.labelNode.GetDisplayNode().GetColorNode()
lut = colorNode.GetLookupTable()
# add initialized data nodes to the chart
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
chartNode.ClearArrays()
for k in self.labeledVoxels.keys():
k = int(k)
name = colorNode.GetColorName(k)
chartNode.AddArray(name, self.dataNodes[k].GetID())
rgb = lut.GetTableValue(int(k))
colorStr = Helper.RGBtoHex(rgb[0] * 255, rgb[1] * 255, rgb[2] * 255)
chartNode.SetProperty(name, "color", colorStr)
return chartNode
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 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 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 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.assertTrue( subjectHierarchyWidget != None )
self.assertTrue( subjectHierarchyPluginLogic != None )
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 + ' Copy' + slicer.vtkMRMLSubjectHierarchyConstants.GetSubjectHierarchyNodeNamePostfix())
clonedMarkupShNode.SetAssociatedNodeID(chartNode2.GetID())
self.assertTrue( clonedMarkupShNode.GetOwnerPluginName() == 'Charts' )
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 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.assertTrue( subjectHierarchyWidget != None )
self.assertTrue( subjectHierarchyPluginLogic != None )
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 + ' Copy' + slicer.vtkMRMLSubjectHierarchyConstants.GetSubjectHierarchyNodeNamePostfix())
clonedMarkupShNode.SetAssociatedNodeID(chartNode2.GetID())
self.assertTrue( clonedMarkupShNode.GetOwnerPluginName() == 'Charts' )
def addChart(self,patient):
ln = slicer.util.getNode(pattern='vtkMRMLLayoutNode*')
ln.SetViewArrangement(26)
cvn = slicer.util.getNode(pattern='vtkMRMLChartViewNode*')
cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
linePattern = ["solid","dashed","dotted","dashed-dotted"]
planNumber = 0
chartNames = []
if patient.plans == []:
print "No plans."
return
for plan in patient.plans:
for voi in plan.vois:
if voi.voiTableCheckBox.checkState() == 0:
continue
voi.setSlicerDoubleArray() #set double array for chart
newName = voi.name
n = 1
nameBool = True
while nameBool:
nameBool = False
for name in chartNames:
if newName == name:
nameBool = True
newName = voi.name + "_" + str(n)
n += 1
break
cn.AddArray(newName, voi.dn.GetID())
cn.SetProperty(voi.name,'linePattern',linePattern[planNumber])
chartNames.append(newName)
planNumber += 1
if plan.optDose == 100:
cn.SetProperty('default', 'xAxisLabel', 'Dose [%]')
else:
cn.SetProperty('default', 'xAxisLabel', 'Dose [Gy]')
cn.SetProperty('default', 'yAxisLabel', 'Volume [%]')
cvn.SetChartNodeID(cn.GetID())
return
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 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 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 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 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 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 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 setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# First volume selector
#
self.inputSelector1 = slicer.qMRMLNodeComboBox()
self.inputSelector1.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
self.inputSelector1.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", 0 )
self.inputSelector1.selectNodeUponCreation = True
self.inputSelector1.addEnabled = False
self.inputSelector1.removeEnabled = False
self.inputSelector1.noneEnabled = False
self.inputSelector1.showHidden = False
self.inputSelector1.showChildNodeTypes = False
self.inputSelector1.setMRMLScene( slicer.mrmlScene )
self.inputSelector1.setToolTip( "Pick the first input to the algorithm." )
parametersFormLayout.addRow("First Volume: ", self.inputSelector1)
#
# Second volume selector
#
self.inputSelector2 = slicer.qMRMLNodeComboBox()
self.inputSelector2.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
self.inputSelector2.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", 0 )
self.inputSelector2.selectNodeUponCreation = True
self.inputSelector2.addEnabled = False
self.inputSelector2.removeEnabled = False
self.inputSelector2.noneEnabled = False
self.inputSelector2.showHidden = False
self.inputSelector2.showChildNodeTypes = False
self.inputSelector2.setMRMLScene( slicer.mrmlScene )
self.inputSelector2.setToolTip( "Pick the second input to the algorithm." )
parametersFormLayout.addRow("Second Volume: ", self.inputSelector2)
#
# output volume selector
#
self.outputSelector = slicer.qMRMLNodeComboBox()
self.outputSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
self.outputSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", 0 )
self.outputSelector.selectNodeUponCreation = False
self.outputSelector.addEnabled = True
self.outputSelector.removeEnabled = True
self.outputSelector.noneEnabled = False
self.outputSelector.showHidden = False
self.outputSelector.showChildNodeTypes = False
self.outputSelector.setMRMLScene( slicer.mrmlScene )
self.outputSelector.setToolTip( "Pick the output to the algorithm." )
parametersFormLayout.addRow("Output Volume: ", self.outputSelector)
#
# Ruler selector
#
self.rulerSelector = slicer.qMRMLNodeComboBox ()
self.rulerSelector.nodeTypes = ( ("vtkMRMLAnnotationRulerNode"), "" )
self.rulerSelector.selectNodeUponCreation = True
self.rulerSelector.addEnabled = False
self.rulerSelector.removeEnabled = False
self.rulerSelector.noneEnabled = False
self.rulerSelector.showHidden = False
self.rulerSelector.showChildNodeTypes = False
self.rulerSelector.setMRMLScene( slicer.mrmlScene )
self.rulerSelector.setToolTip( "Pick the ruler to sample along." )
parametersFormLayout.addRow("Ruler: ", self.rulerSelector)
#
#Number of sample points parameter
#
self.numOfPointsField = qt.QSpinBox()
self.numOfPointsField.setRange(1, 2000)
self.numOfPointsField.value = 100
self.numOfPointsField.setSingleStep(1)
parametersFormLayout.addRow("Num Of Points: ", self.numOfPointsField)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = True
parametersFormLayout.addRow(self.applyButton)
self.chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
# Add vertical spacer
self.layout.addStretch(1)
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.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_LineIntensityProfile1(self):
""" Ideally you should have several levels of tests. At the lowest level
tests sould exercise the functionality of the logic with different inputs
(both valid and invalid). At higher levels your tests should emulate the
way the user would interact with your code and confirm that it still works
the way you intended.
One of the most important features of the tests is that it should alert other
developers when their changes will have an impact on the behavior of your
module. For example, if a developer removes a feature that you depend on,
your test should break so they know that the feature is needed.
"""
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 = LineIntensityProfileLogic()
self.assertTrue( logic.hasImageData(volumeNode) )
# initialize ruler node in a known location
rulerNode = slicer.vtkMRMLAnnotationRulerNode()
slicer.mrmlScene.AddNode(rulerNode)
rulerNode.SetPosition1(-65,110,60)
rulerNode.SetPosition2(-15,60,60)
rulerNode.SetName('Test')
numOfPointsField = qt.QSpinBox()
numOfPointsField.value = 100
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# initialize input selectors
moduleWidget = slicer.modules.LineIntensityProfileWidget
moduleWidget.rulerSelector.setCurrentNode(rulerNode)
moduleWidget.inputSelector1.setCurrentNode(volumeNode)
moduleWidget.inputSelector2.setCurrentNode(volumeNode)
self.delayDisplay('Inputs initialized!')
# run the logic with the initialized inputs
moduleWidget.onApplyButton()
self.delayDisplay('If you see a ruler and a plot - test passed!')
# here we check the sample is correct or not
GroundTruth = [0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0 \
,0.0499952547252 ,0.132161304355,0.157250195742,0.182541355491 ,0.224097684026,0.307691186666,0.421751081944,0.539702475071,0.566307783127,0.502181112766,0.466381758451 \
,0.454870164394 ,0.451874107122 ,0.45154094696,0.445982009172,0.434947699308,0.422306239605,0.413488268852,0.409934103489,0.414202958345,0.409307956696 \
,0.397122174501,0.397800117731,0.411369532347,0.429417848587,0.439514577389,0.423818171024,0.40110757947,0.386767745018,0.379366248846,0.370953738689,0.36441424489 \
,0.36140397191,0.367857933044,0.38929861784,0.418379157782,0.408268928528,0.379027366638,0.332919150591,0.297374159098,0.296240001917,0.311986237764,0.350458532572 \
,0.370930314064,0.357974469662,0.326200008392,0.316009640694,0.312490910292,0.32052642107,0.316521972418,0.279196560383,0.244257837534,0.238702788949,0.255041092634 \
,0.280225723982,0.320494830608,0.28876376152,0.277780592442,0.253679126501,0.247220918536,0.244660764933]
logic.run(volumeNode, volumeNode, rulerNode, numOfPointsField, chartNode)
sample = logic.getImageSamples()[0]
isTestValid = True
for i in range(numOfPointsField.value):
if abs(sample.GetTuple1(i)-float(GroundTruth[i])) > 0.000001:
isTestValid = False
if isTestValid:
self.delayDisplay('Sample point test passed!')
else:
self.delayDisplay('Sample point test failed!')
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 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.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')
#
self.delayDisplay('Test passed!')
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 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')