def updateTable(self):
self.itemsLoc = []
self.itemsLD = []
self.itemsAng = []
# self.itemsDia = []
self.screwList = slicer.modules.PedicleScrewPlannerWidget.measurementsStep.screwList
self.screwNumber = len(self.screwList)
self.screwTable.setRowCount(self.screwNumber)
for i in range(self.screwNumber):
currentScrew = self.screwList[i]
self.screwLoc = str(currentScrew[0])
screwLD = str(currentScrew[3]) + " x " + str(currentScrew[4])
screwAng = str(currentScrew[1]) + " / " + str(currentScrew[2])
qtscrewLoc = qt.QTableWidgetItem(self.screwLoc)
qtscrewLD = qt.QTableWidgetItem(screwLD)
qtscrewAng = qt.QTableWidgetItem(screwAng)
#qtscrewDia = qt.QTableWidgetItem(screwDia)
self.itemsLoc.append(qtscrewLoc)
self.itemsLD.append(qtscrewLD)
self.itemsAng.append(qtscrewAng)
#self.itemsDia.append(qtscrewDia)
self.screwName.append("Isthmus_Screw_{}".format(self.screwLoc))
# logging.debug(self.screwName)
logging.debug("self.screwName:{}".format(self.screwName))
self.screwTable.setItem(i, 0, qtscrewLoc)
self.screwTable.setItem(i, 1, qtscrewLD)
self.screwTable.setItem(i, 2, qtscrewAng)
def setLoadables(self,loadablesByPlugin):
"""Load the table widget with a list
of volume options (of class DICOMVolume)
"""
loadableCount = 0
for plugin in loadablesByPlugin:
for loadable in loadablesByPlugin[plugin]:
loadableCount += 1
self.widget.clearContents()
self.widget.setColumnCount(2)
self.widget.setHorizontalHeaderLabels(['DICOM Data','Warnings'])
self.widget.setColumnWidth(0,int(self.width * 0.4))
self.widget.setColumnWidth(1,int(self.width * 0.6))
self.widget.setRowCount(loadableCount)
row = 0
for plugin in loadablesByPlugin:
for selectState in (True,False):
for loadable in loadablesByPlugin[plugin]:
if loadable.selected == selectState:
# name and check state
self.loadables[row] = loadable
item = qt.QTableWidgetItem(loadable.name)
item.setCheckState(loadable.selected * 2)
self.items.append(item)
self.widget.setItem(row,0,item)
item.setToolTip(loadable.tooltip)
# warning
if loadable.warning:
warnItem = qt.QTableWidgetItem(loadable.warning)
self.items.append(warnItem)
self.widget.setItem(row,1,warnItem)
item.setToolTip(item.toolTip() + "\n" + loadable.warning)
warnItem.setToolTip(item.toolTip())
row += 1
self.widget.setVerticalHeaderLabels(row * [""])
def updateTable(self):
#print pNode.GetParameter('vertebrae')
self.fiducial = slicer.mrmlScene.GetNodeByID(
'vtkMRMLMarkupsFiducialNode1')
self.fidNumber = self.fiducial.GetNumberOfFiducials()
self.fidLabels = []
self.fidLevels = []
self.fidSides = []
self.itemsLabels = []
self.itemsLevels = []
self.itemsSides = []
self.rulerList = []
self.lengthCombo = []
self.widthCombo = []
self.angleTable.setRowCount(self.fidNumber)
for i in range(0, self.fidNumber):
self.fidLabels.append(
slicer.modules.PedicleScrewSimulator_v3Widget.landmarksStep.
table2.item(i, 0).text())
self.fidLevels.append(
slicer.modules.PedicleScrewSimulator_v3Widget.landmarksStep.
table2.cellWidget(i, 1).currentText)
self.fidSides.append(
slicer.modules.PedicleScrewSimulator_v3Widget.landmarksStep.
table2.cellWidget(i, 2).currentText)
for i in range(0, self.fidNumber):
Label = str(self.fidLabels[i])
Level = str(self.fidLevels[i])
Side = str(self.fidSides[i])
#print Label
#print Level
#print Side
#print self.levelselection[i] + "loop"
qtLabel = qt.QTableWidgetItem(Label)
qtLevel = qt.QTableWidgetItem(Level)
qtSide = qt.QTableWidgetItem(Side)
self.itemsLabels.append(qtLabel)
self.itemsLevels.append(qtLevel)
self.itemsSides.append(qtSide)
#print self.items
self.angleTable.setItem(i, 0, qtLabel)
self.angleTable.setItem(i, 1, qtLevel)
self.angleTable.setItem(i, 2, qtSide)
self.lengthCombo.insert(i, qt.QComboBox())
self.widthCombo.insert(i, qt.QComboBox())
self.lengthCombo[i].addItem(" ")
self.widthCombo[i].addItem(" ")
#self.rulerMeasures()
#self.measuresLength = qt.QComboBox()
#self.measuresLength.addItems(self.rulerList)
#self.measuresWidth = qt.QComboBox()
#self.measuresWidth.addItems(self.rulerList)
if self.entryCount == 0:
self.angleTable.setCellWidget(i, 3, self.lengthCombo[i])
self.angleTable.setCellWidget(i, 4, self.widthCombo[i])
self.entryCount = 1
def addFiducialToTable(self, observer, event):
logging.debug("Modified - {0}".format(event))
self.fiducial = self.fiducialNode()
self.fidNumber = self.fiducial.GetNumberOfFiducials()
slicer.modules.markups.logic().SetAllMarkupsVisibility(self.fiducial,1)
logging.debug(self.fidNumber)
self.fidLabels = []
self.items = []
self.Label = qt.QTableWidgetItem()
self.table2.setRowCount(self.fidNumber)
for i in range(0,self.fidNumber):
self.Label = qt.QTableWidgetItem(self.fiducial.GetNthFiducialLabel(i))
self.items.append(self.Label)
self.table2.setItem(i, 0, self.Label)
self.comboLevel = qt.QComboBox()
self.comboLevel.addItems(self.levelselection)
self.comboSide = qt.QComboBox()
self.comboSide.addItems(["Left","Right"])
self.table2.setCellWidget(i,1, self.comboLevel)
self.table2.setCellWidget(i,2, self.comboSide)
if i == 0 or i == 1:
self.table2.cellWidget(i,1).setCurrentIndex(0)
if i == 1:
self.table2.cellWidget(i,2).setCurrentIndex(1)
elif i == 2 or i == 3:
self.table2.cellWidget(i,1).setCurrentIndex(1)
if i == 3:
self.table2.cellWidget(i,2).setCurrentIndex(1)
elif i == 4 or i == 5:
self.table2.cellWidget(i,1).setCurrentIndex(2)
if i == 5:
self.table2.cellWidget(i,2).setCurrentIndex(1)
def updateFiducialsTable(self):
if not self.logic.SourceNode or self.logic.SourceNode == None:
self.FiducialTable.clear()
self.FiducialTable.setHorizontalHeaderLabels(
self.FiducialTableHeaders)
else:
self.FiducialTableData = []
numControlPoints = self.logic.SourceNode.GetNumberOfFiducials()
self.FiducialTable.setRowCount(numControlPoints)
for i in range(numControlPoints):
name = self.logic.SourceNode.GetNthFiducialLabel(i)
pos = [0, 0, 0]
self.logic.SourceNode.GetNthFiducialPosition(i, pos)
cellName = qt.QTableWidgetItem(name)
cellX = qt.QTableWidgetItem('%.3f' % pos[0])
cellY = qt.QTableWidgetItem('%.3f' % pos[1])
cellZ = qt.QTableWidgetItem('%.3f' % pos[2])
row = [cellName, cellX, cellY, cellZ]
self.FiducialTable.setItem(i, 0, row[0])
self.FiducialTable.setItem(i, 1, row[1])
self.FiducialTable.setItem(i, 2, row[2])
self.FiducialTable.setItem(i, 3, row[3])
self.FiducialTableData.append(row)
self.FiducialTable.show()
def addLoadableRow(self,loadable,row,reader):
"""Add a row to the loadable table
"""
# name and check state
qt_ItemIsEditable = 2 # not in PythonQt
self.loadables[row] = loadable
item = qt.QTableWidgetItem(loadable.name)
item.setCheckState(loadable.selected * 2)
self.items.append(item)
self.widget.setItem(row,0,item)
item.setToolTip(loadable.tooltip)
# reader
if reader:
readerItem = qt.QTableWidgetItem(reader)
readerItem.setFlags(readerItem.flags() ^ qt_ItemIsEditable)
self.items.append(readerItem)
self.widget.setItem(row,1,readerItem)
readerItem.setToolTip(item.toolTip())
# warning
if loadable.warning:
warnItem = qt.QTableWidgetItem(loadable.warning)
warnItem.setFlags(warnItem.flags() ^ qt_ItemIsEditable)
self.items.append(warnItem)
self.widget.setItem(row,2,warnItem)
item.setToolTip(item.toolTip() + "\n" + loadable.warning)
warnItem.setToolTip(item.toolTip())
def updateTable(self):
self.itemsLoc = []
self.itemsLen = []
self.itemsDia = []
self.screwList = slicer.modules.PedicleScrewSimulator_v3Widget.screwStep.screwList
self.screwNumber = len(self.screwList)
self.screwTable.setRowCount(self.screwNumber)
for i in range(0,self.fidNumber):
currentScrew = self.screwList[i]
screwLoc = str(currentScrew[0])
screwLen = str(currentScrew[1]) + " x " + str(currentScrew[2])
qtscrewLoc = qt.QTableWidgetItem(screwLoc)
qtscrewLen = qt.QTableWidgetItem(screwLen)
#qtscrewDia = qt.QTableWidgetItem(screwDia)
self.itemsLoc.append(qtscrewLoc)
self.itemsLen.append(qtscrewLen)
#self.itemsDia.append(qtscrewDia)
self.screwTable.setItem(i, 0, qtscrewLoc)
self.screwTable.setItem(i, 1, qtscrewLen)
def setHeader(self, file):
"""Load the table widget with header values for the file
"""
self.widget.clearContents()
self.widget.setColumnCount(2)
self.widget.setHorizontalHeaderLabels(['Tag', 'Value'])
self.widget.setColumnWidth(0, 100)
self.widget.setColumnWidth(1, 200)
if not file:
return
slicer.dicomDatabase.loadFileHeader(file)
keys = slicer.dicomDatabase.headerKeys()
self.widget.setRowCount(len(keys))
row = 0
for key in keys:
item = qt.QTableWidgetItem(key)
self.widget.setItem(row, 0, item)
self.items.append(item)
dump = slicer.dicomDatabase.headerValue(key)
try:
value = dump[dump.index('[') + 1:dump.index(']')]
except ValueError:
value = "Unknown"
item = qt.QTableWidgetItem(value)
self.widget.setItem(row, 1, item)
self.items.append(item)
row += 1
def setHeader(self,reportNode):
"""Load the table widget with annotations for the report
"""
Helper.Debug('setHeader() called')
self.widget.clearContents()
self.widget.setColumnCount(2)
self.widget.setHorizontalHeaderLabels(['Markup','Visibility'])
self.widget.horizontalHeader().setResizeMode(0, qt.QHeaderView.Stretch)
self.widget.horizontalHeader().setResizeMode(1, qt.QHeaderView.Fixed)
self.widget.setEditTriggers(qt.QAbstractItemView.NoEditTriggers)
if not reportNode:
return
# get the volume node associated with this report
volumeID = reportNode.GetVolumeNodeID()
Helper.Debug('volumeID = '+volumeID)
if volumeID == "":
return
volumeNode = slicer.mrmlScene.GetNodeByID(volumeID)
if not volumeNode:
return
# get the annotations associated with this report
# find displayble nodes that are associated with this volume
numDisplayableNodes = slicer.mrmlScene.GetNumberOfNodesByClass("vtkMRMLDisplayableNode")
nodeIDList = [volumeID]
for n in range(numDisplayableNodes):
displayableNode = slicer.mrmlScene.GetNthNodeByClass(n, "vtkMRMLDisplayableNode")
# how best to get at module widget logic?
Helper.Debug('Will check if in report here for '+displayableNode.GetID())
inReport = slicer.modules.reporting.logic().IsInReport(displayableNode)
Helper.Debug('Checked for report')
if inReport:
Helper.Debug('Found node associated with the report node: ' + displayableNode.GetName())
nodeIDList.append(displayableNode.GetID())
else:
Helper.Debug('Failed to found associated node')
self.widget.setRowCount(len(nodeIDList))
row = 0
for nodeID in nodeIDList:
node = Helper.getNodeByID(nodeID)
item = qt.QTableWidgetItem(node.GetName())
self.widget.setItem(row,0,item)
self.items.append(item)
if node.IsA("vtkMRMLAnnotationNode"):
item = qt.QTableWidgetItem()
# save the id for toggling visibility on the node
# TODO: make this more elegant instead of overloading the what's this role with the id
item.setData(qt.Qt.WhatsThisRole, node.GetID())
if node.GetDisplayVisibility() == 1:
item.setData(qt.Qt.DecorationRole,qt.QPixmap(":/Icons/Small/SlicerVisible.png"))
else:
item.setData(qt.Qt.DecorationRole,qt.QPixmap(":/Icons/Small/SlicerInvisible.png"))
self.widget.setItem(row,1,item)
self.items.append(item)
row += 1
def saveApi(self):
table = self.apiTable
apiNameTableItem = qt.QTableWidgetItem(str(self.apiNameLineEdit.text))
apiKeyTableItem = qt.QTableWidgetItem(str(self.apiKeyLineEdit.text))
self.apiKeyTableItems.append(apiKeyTableItem)
self.apiNameTableItems.append(apiNameTableItem)
if self.dialogRole == 'Add':
self.numberOfRows += 1
table.setRowCount(self.numberOfRows)
table.setItem(self.numberOfRows -1, 0, apiNameTableItem)
table.setItem(self.numberOfRows -1, 1, apiKeyTableItem)
elif self.dialogRole == 'Edit':
table.setItem(self.currentAPIRow, 0, apiNameTableItem)
table.setItem(self.currentAPIRow, 1, apiKeyTableItem)
self.restartLabel.setVisible(True)
def addNewEmptyRow(self, rowIndex):
item = qt.QTableWidgetItem("dummy")
self.fiducialsWidget.fiducialsList.setItem(rowIndex,0,item.clone())
self.fiducialsWidget.fiducialsList.setItem(rowIndex,1,item.clone())
self.fiducialsWidget.fiducialsList.setItem(rowIndex,2,item.clone())
self.fiducialsWidget.fiducialsList.setItem(rowIndex,3,item.clone())
self.fiducialsWidget.fiducialsList.setItem(rowIndex,4,item.clone())
def initializeTable(self):
print("initialize table")
self.table.setRowCount(len(self.landmarks))
i = 0
for landmark in self.landmarks:
landmarkName = qt.QTableWidgetItem(landmark.name)
landmarkPlaced = qt.QTableWidgetItem(str(landmark.placed))
self.landmarkNamesInTable.append(landmark.name)
self.table.setItem(i, 0, landmarkName)
self.table.setItem(i, 2, 0)
self.table.setItem(i, 3, 0)
self.table.setItem(i, 4, 0)
i += 1
self.table.selectRow(self.selectedTableRow)
def updateTargetFiducialsTable(self):
if not self.targetFiducialsNode:
self.fiducialsTable.clear()
self.fiducialsTable.setHorizontalHeaderLabels(
self.fiducialsTableHeaders)
else:
extrapolate = self.extrapolateCheckBox.isChecked()
showErrorVec = self.showErrorVectorCheckBox.isChecked()
self.fiducialsTableData = []
nOfControlPoints = self.targetFiducialsNode.GetNumberOfFiducials()
if self.fiducialsTable.rowCount != nOfControlPoints:
self.fiducialsTable.setRowCount(nOfControlPoints)
dist = ''
for i in range(nOfControlPoints):
label = self.targetFiducialsNode.GetNthFiducialLabel(i)
pos = [0.0, 0.0, 0.0]
self.targetFiducialsNode.GetNthFiducialPosition(i, pos)
(err, evec) = self.logic.distanceToPoint(pos, extrapolate)
posstr = '(%.3f, %.3f, %.3f)' % (pos[0], pos[1], pos[2])
if showErrorVec:
dist = '%.3f (%.3f, %.3f, %.3f)' % (err, evec[0], evec[1],
evec[2])
else:
dist = '%.3f' % err
cellLabel = qt.QTableWidgetItem(label)
cellPosition = qt.QTableWidgetItem(posstr)
cellDistance = qt.QTableWidgetItem(dist)
row = [cellLabel, cellPosition, cellDistance]
self.fiducialsTable.setItem(i, 0, row[0])
self.fiducialsTable.setItem(i, 1, row[1])
self.fiducialsTable.setItem(i, 2, row[2])
self.fiducialsTableData.append(row)
self.fiducialsTable.show()
def setupManualSampleTable( self, mrmlNode ):
'''
'''
vtkId = self.mrmlManager().MapMRMLNodeIDToVTKNodeID( mrmlNode.GetID() )
# number of volumes
numberOfVolumes = self.mrmlManager().GetTargetNumberOfSelectedVolumes()
numberOfSamples = self.mrmlManager().GetTreeNodeDistributionNumberOfSamples( vtkId )
# empty all old items, we need a class variable here to store the references
# if not, the items will be all lost!!
self.__items = []
# erase all items in the manual sampling table
for r in range( self.__manualSampleTable.rowCount ):
self.__manualSampleTable.removeRow( r )
for c in range( self.__manualSampleTable.columnCount ):
self.__manualSampleTable.removeColumn( c )
self.__manualSampleTable.rowCount = 0
self.__manualSampleTable.columnCount = 0
# configure the rows and columns of the table
volumes = []
for n in range( numberOfVolumes ):
# save the columns
volumeId = self.mrmlManager().GetTargetSelectedVolumeNthID( n )
volumeName = self.mrmlManager().GetVolumeName( volumeId )
volumes.append( volumeName )
# create new column
self.__manualSampleTable.insertColumn( self.__manualSampleTable.columnCount )
self.__manualSampleTable.setHorizontalHeaderLabels( volumes )
# add the manual sample intensity values to the table
for m in range( numberOfSamples ):
# create new row
self.__manualSampleTable.insertRow( self.__manualSampleTable.rowCount )
for n in range( numberOfVolumes ):
# fill the new row
volumeId = self.mrmlManager().GetTargetSelectedVolumeNthID( n )
intensity = self.mrmlManager().GetTreeNodeDistributionSampleIntensityValue( vtkId, m, volumeId )
self.__items.append( qt.QTableWidgetItem( str( intensity ) ) )
self.__manualSampleTable.setItem( m, n, self.__items[-1] )
self.mrmlManager().ResetTreeNodeDistributionLogMeanCorrection( vtkId );
self.mrmlManager().ResetTreeNodeDistributionLogCovarianceCorrection( vtkId );
self.__vtkId = vtkId
self.__manualSampling = True
def populateAPITable(self):
settings = qt.QSettings()
table = self.apiTable
settings.beginGroup("TCIABrowser/API-Keys")
userApiNames = settings.childKeys()
self.numberOfRows = len(userApiNames)
table.setRowCount(self.numberOfRows)
row = 0
for api in userApiNames:
apiNameTableItem = qt.QTableWidgetItem(str(api))
apiKeyTableItem = qt.QTableWidgetItem(str(settings.value(api)))
table.setItem( row, 0, apiNameTableItem)
self.apiNameTableItems.append(apiNameTableItem)
table.setItem( row, 1, apiKeyTableItem)
self.apiKeyTableItems.append(apiKeyTableItem)
row += 1
settings.endGroup()
def updateTable(self):
print "updateTable() is called"
if not self.targetFiducialsNode:
self.table.clear()
self.table.setHorizontalHeaderLabels(self.headers)
else:
self.tableData = []
nOfControlPoints = self.targetFiducialsNode.GetNumberOfFiducials()
if self.table.rowCount != nOfControlPoints:
self.table.setRowCount(nOfControlPoints)
for i in range(nOfControlPoints):
label = self.targetFiducialsNode.GetNthFiducialLabel(i)
pos = [0.0, 0.0, 0.0]
self.targetFiducialsNode.GetNthFiducialPosition(i, pos)
(indexX, indexY, depth,
inRange) = self.logic.computeNearestPath(pos)
posstr = '(%.3f, %.3f, %.3f)' % (pos[0], pos[1], pos[2])
cellLabel = qt.QTableWidgetItem(label)
cellIndex = qt.QTableWidgetItem('(%s, %s)' % (indexX, indexY))
cellDepth = None
if inRange:
cellDepth = qt.QTableWidgetItem('%.3f' % depth)
else:
cellDepth = qt.QTableWidgetItem('(%.3f)' % depth)
cellPosition = qt.QTableWidgetItem(posstr)
row = [cellLabel, cellIndex, cellDepth, cellPosition]
self.table.setItem(i, 0, row[0])
self.table.setItem(i, 1, row[1])
self.table.setItem(i, 2, row[2])
self.table.setItem(i, 3, row[3])
self.tableData.append(row)
self.table.show()
def addFiducialToTable(self, observer, event):
logging.debug("Modified - {0}".format(event))
self.fidNumber = self.fidNode.GetNumberOfFiducials()
slicer.modules.markups.logic().SetAllMarkupsVisibility(self.fidNode, 1)
logging.debug(self.fidNumber)
self.fidLabels = []
self.items = []
self.Label = qt.QTableWidgetItem()
self.table2.setRowCount(self.fidNumber)
for i in range(0, self.fidNumber):
self.Label = qt.QTableWidgetItem(
self.fidNode.GetNthFiducialLabel(i))
self.items.append(self.Label)
self.table2.setItem(i, 0, self.Label)
self.combofidlist = qt.QComboBox()
self.combofidlist.addItems(self.fiduciallist)
self.table2.setCellWidget(i, 1, self.combofidlist)
def updateTable(self):
# logging.debug(pNode.GetParameter('vertebrae'))
self.fiducial = self.fiducialNode()
self.fidNumber = self.fiducial.GetNumberOfFiducials()
logging.debug(self.fidNumber)
self.fidLabels = []
self.items = []
self.Label = qt.QTableWidgetItem()
self.table2.setRowCount(self.fidNumber)
logging.debug(self.fiduciallist)
for i in range(0, self.fidNumber):
self.Label = qt.QTableWidgetItem(
self.fiducial.GetNthFiducialLabel(i))
self.items.append(self.Label)
self.table2.setItem(i, 0, self.Label)
self.combofidlist = qt.QComboBox()
self.combofidlist.addItems(self.fiduciallist)
self.table2.setCellWidget(i, 1, self.combofidlist)
logging.debug(self.fiduciallist)
def getPositionsOfFiducials(self):
print ("get fiducial positions")
fidNode = slicer.mrmlScene.GetNodeByID('vtkMRMLMarkupsFiducialNode1')
numFids = fidNode.GetNumberOfFiducials()
for i in range(0, numFids):
position = [0, 0, 0]
fidNode.GetNthFiducialPosition(i, position)
print(position)
self.landmarks[i].x = position[0]
self.landmarks[i].y = position[1]
self.landmarks[i].z = position[2]
x = qt.QTableWidgetItem(str(position[0]))
y = qt.QTableWidgetItem(str(position[1]))
z = qt.QTableWidgetItem(str(position[2]))
self.table.setItem(i, 2, x)
self.table.setItem(i, 3, y)
self.table.setItem(i, 4, z)
def updateTable(self):
#logging.debug(pNode.GetParameter('vertebrae'))
self.fiducial = self.fiducialNode()
self.fidNumber = self.fiducial.GetNumberOfFiducials()
logging.debug(self.fidNumber)
self.fidLabels = []
self.items = []
self.Label = qt.QTableWidgetItem()
self.table2.setRowCount(self.fidNumber)
for i in range(0,self.fidNumber):
self.Label = qt.QTableWidgetItem(self.fiducial.GetNthFiducialLabel(i))
self.items.append(self.Label)
self.table2.setItem(i, 0, self.Label)
self.comboLevel = qt.QComboBox()
self.comboLevel.addItems(self.levelselection)
self.comboSide = qt.QComboBox()
self.comboSide.addItems(["Left","Right"])
self.table2.setCellWidget(i,1, self.comboLevel)
self.table2.setCellWidget(i,2, self.comboSide)
logging.debug(self.Label.text())
def addLoadableRow(self, loadable, row, reader):
"""Add a row to the loadable table
"""
# set checked state to unckecked if there is a loadable with the
# same file list in the table already
if len(self.loadables) > 0:
for addedRow in self.loadables.keys():
if len(self.loadables[addedRow].files) == 1 and len(
loadable.files) == 1:
# needed because of the tuple-sequence comparison does not work,
# and sometimes tuples are created by some reason
if self.loadables[addedRow].files[0] == loadable.files[0]:
loadable.selected = False
break
elif self.loadables[addedRow].files == loadable.files:
loadable.selected = False
break
# name and check state
self.loadables[row] = loadable
item = qt.QTableWidgetItem(loadable.name)
item.setCheckState(loadable.selected * 2)
self.items.append(item)
self.widget.setItem(row, 0, item)
item.setToolTip(loadable.tooltip)
# reader
if reader:
readerItem = qt.QTableWidgetItem(reader)
self.items.append(readerItem)
self.widget.setItem(row, 1, readerItem)
readerItem.setToolTip(item.toolTip())
# warning
if loadable.warning:
warnItem = qt.QTableWidgetItem(loadable.warning)
self.items.append(warnItem)
self.widget.setItem(row, 2, warnItem)
item.setToolTip(item.toolTip() + "\n" + loadable.warning)
warnItem.setToolTip(item.toolTip())
def updateStatsTable(self, release_downloads):
self.statsTable.setRowCount(len(release_downloads))
self.statsTable.setColumnCount(len(self.statsTableHeader))
self.statsTable.setHorizontalHeaderLabels(self.statsTableHeader)
self.items = []
row = 0
for release, downloads in release_downloads.items():
item = qt.QTableWidgetItem(release)
self.items.append(
item) # required, otherwise the item does not appear
item.setFlags(item.flags()
^ qt.Qt.ItemIsEditable) # make the item read-only
self.statsTable.setItem(row, 0, item)
item = qt.QTableWidgetItem(str(downloads))
self.items.append(
item) # required, otherwise the item does not appear
item.setFlags(item.flags()
^ qt.Qt.ItemIsEditable) # make the item read-only
self.statsTable.setItem(row, 1, item)
row = row + 1
self.statsTable.horizontalHeader().setResizeMode(
qt.QHeaderView.Stretch)
def onApply(self):
self.applyButton.text = "Working..."
self.applyButton.repaint()
slicer.app.processEvents()
self.logic = MarginCalculatorLogic()
self.logic.run(self.inputDoseVolumeSelector.currentNode(), self.referenceDoseVolumeSelector.currentNode(), self.inputContourSelector.currentNode(), self.numberOfSimulations, self.numberOfFractions, self.systematicErrorRange, self.randomErrorRange, self.doseGrowRange, self.ROIRadiusX, self.ROIRadiusY, self.ROIRadiusZ, self.doseGrowingOption)
self.applyButton.text = "Calculate"
marginResult = self.logic.getMarginResult()
print marginResult
if marginResult:
self.saveButton.enabled = True
numberOfRows = len(marginResult)
self.tableWidget.clearContents()
self.tableWidget.setRowCount(numberOfRows)
for i in range(numberOfRows):
item = qt.QTableWidgetItem()
item.setText(str(marginResult[i][0]))
self.items.append(item)
self.tableWidget.setItem(i, 0, item )
item2 = qt.QTableWidgetItem()
item2.setText(str(marginResult[i][1]))
self.items.append(item2)
self.tableWidget.setItem(i, 1, item2 )
item3 = qt.QTableWidgetItem()
item3.setText(str(marginResult[i][2]))
self.items.append(item3)
self.tableWidget.setItem(i, 2, item3 )
item4 = qt.QTableWidgetItem()
item4.setText(str(marginResult[i][3]))
self.items.append(item4)
self.tableWidget.setItem(i, 3, item4 )
item5 = qt.QTableWidgetItem()
item5.setText(str(marginResult[i][4]))
self.items.append(item5)
self.tableWidget.setItem(i, 4, item5 )
def addContentItemRow(self, stringCont, row):
"""Add a row to the loadable table
"""
colStrs = string.split(stringCont, ',')
col = 0
for colStr in colStrs:
# name and check state
self.strings.append(colStr)
item = qt.QTableWidgetItem(colStr[1:-1])
item.setCheckState(0)
#if not self.multiSelect:
# item.setFlags(33)
#else:
# # allow checkboxes interaction
# item.setFlags(49)
self.items.append(item)
self.widget.setItem(row, col, item)
col += 1
def placeFiducialAsLandmark(self, observer, event):
print(event)
fiducial = slicer.mrmlScene.GetNodeByID('vtkMRMLMarkupsFiducialNode1')
fidNumber = fiducial.GetNumberOfFiducials()
if (fidNumber > self.curNumberOfFids):
print ("Fiducial added")
slicer.modules.markups.logic().SetAllMarkupsVisibility(fiducial, 1)
print (fidNumber)
fiducialID = qt.QTableWidgetItem(fiducial.GetNthFiducialLabel(fidNumber - 1))
self.table.setItem(self.selectedTableRow, 1, fiducialID)
self.table.selectRow(self.selectedTableRow + 1)
self.selectedTableRow += 1
self.curNumberOfFids += 1
if (self.selectedTableRow >= len(self.landmarks)):
self.stop()
self.btnBeginPlacingLandmarks.hide()
def addNameAndUrl(self, name, url):
"""
Adds a name and url to the table by adding a
new row.
@param name: The name of the host to add.
@type name: str
@param url: The url of the host to add.
@type url: str
"""
#--------------------
# Add the hostName and hostUrl items
# accordingly.
#--------------------
hostNameItem = qt.QTableWidgetItem(name)
hostUrlItem = qt.QTableWidgetItem(url)
#--------------------
# Add the username item.
#--------------------
usernameItem = qt.QTableWidgetItem('No username stored.')
#--------------------
# Turn sorting off.
#--------------------
self.setSortingEnabled(False)
#--------------------
# NOTE: QTableWiget quirk: we have to
# set the rowcount of the table beforehand.
#--------------------
self.setRowCount(self.rowCount + 1)
#--------------------
# Add the new items to the 'trackedItems'
# variable otherwise the table will destroy them
# and the items will disappear immediately on
# add.
#--------------------
self.trackedItems[self.rowCount - 1] = {}
self.trackedItems[self.rowCount - 1]['name'] = hostNameItem
self.trackedItems[self.rowCount - 1]['url'] = hostUrlItem
self.trackedItems[self.rowCount - 1]['stored login'] = usernameItem
#--------------------
# Set the added items' aeshetics.
#--------------------
for key, item in self.trackedItems[self.rowCount - 1].iteritems():
item.setFont(Settings_Hosts.FONT)
#--------------------
# Call on the QTableWidget 'setItem' function.
#--------------------
self.setItem(self.rowCount - 1, self.getColumn('name'), hostNameItem)
self.setItem(self.rowCount - 1, self.getColumn('url'), hostUrlItem)
self.setItem(self.rowCount-1, self.getColumn('stored login'), \
usernameItem)
#--------------------
# Again, turn sorting off.
#--------------------
self.setSortingEnabled(False)
def contact(self, input, screwModel, fidName, screwIndex):
#Get points in shaft of screw
insidePoints = self.cropPoints(screwModel)
#Get scalars to array
scalarsArray = input.GetPolyData().GetPointData().GetScalars('NRRDImage')
self.pointsArray = screwModel.GetPolyData()
#Get total number of tuples/points
value = scalarsArray.GetNumberOfTuples()
#Reset variables
point = [0]
point2 = [0,0,0]
corticalCount = 0
cancellousCount = 0
totalCount = 0
bounds = [0]
shaftBounds = 0
count00 = 0
points00 = 0
avg00 = 0.0
count10 = 0
points10 = 0
avg10 = 0.0
count20 = 0
points20 = 0
avg20 = 0.0
count30 = 0
points30 = 0
avg30 = 0.0
count40 = 0
points40 = 0
avg40 = 0.0
count50 = 0
points50 = 0
avg50 = 0.0
count60 = 0
points60 = 0
avg60 = 0.0
count70 = 0
points70 = 0
avg70 = 0.0
count80 = 0
points80 = 0
avg80 = 0.0
count90 = 0
points90 = 0
avg90 = 0.0
avgTotal = []
avgQuad1 = []
avgQuad2 = []
avgQuad3 = []
avgQuad4 = []
countQ1_00 = 0
pointsQ1_00 = 0
countQ2_00 = 0
pointsQ2_00 = 0
countQ3_00 = 0
pointsQ3_00 = 0
countQ4_00 = 0
pointsQ4_00 = 0
countQ1_10 = 0
pointsQ1_10 = 0
countQ2_10 = 0
pointsQ2_10 = 0
countQ3_10 = 0
pointsQ3_10 = 0
countQ4_10 = 0
pointsQ4_10 = 0
countQ1_20 = 0
pointsQ1_20 = 0
countQ2_20 = 0
pointsQ2_20 = 0
countQ3_20 = 0
pointsQ3_20 = 0
countQ4_20 = 0
pointsQ4_20 = 0
countQ1_30 = 0
pointsQ1_30 = 0
countQ2_30 = 0
pointsQ2_30 = 0
countQ3_30 = 0
pointsQ3_30 = 0
countQ4_30 = 0
pointsQ4_30 = 0
countQ1_40 = 0
pointsQ1_40 = 0
countQ2_40 = 0
pointsQ2_40 = 0
countQ3_40 = 0
pointsQ3_40 = 0
countQ4_40 = 0
pointsQ4_40 = 0
countQ1_50 = 0
pointsQ1_50 = 0
countQ2_50 = 0
pointsQ2_50 = 0
countQ3_50 = 0
pointsQ3_50 = 0
countQ4_50 = 0
pointsQ4_50 = 0
countQ1_60 = 0
pointsQ1_60 = 0
countQ2_60 = 0
pointsQ2_60 = 0
countQ3_60 = 0
pointsQ3_60 = 0
countQ4_60 = 0
pointsQ4_60 = 0
countQ1_70 = 0
pointsQ1_70 = 0
countQ2_70 = 0
pointsQ2_70 = 0
countQ3_70 = 0
pointsQ3_70 = 0
countQ4_70 = 0
pointsQ4_70 = 0
countQ1_80 = 0
pointsQ1_80 = 0
countQ2_80 = 0
pointsQ2_80 = 0
countQ3_80 = 0
pointsQ3_80 = 0
countQ4_80 = 0
pointsQ4_80 = 0
countQ1_90 = 0
pointsQ1_90 = 0
countQ2_90 = 0
pointsQ2_90 = 0
countQ3_90 = 0
pointsQ3_90 = 0
countQ4_90 = 0
pointsQ4_90 = 0
xCenter = 0
zCenter = 0
bounds = self.pointsArray.GetPoints().GetBounds()
lowerBound = bounds[2] #+ 17
shaftBounds = 30 # FOR NOW
print bounds
xCenter = (bounds[0] + bounds[1])/2
zCenter = (bounds[4] + bounds[5])/2
#For each point in the screw model...
for i in range(0, value):
#If the point is in the shaft of the screw...
if insidePoints.IsInside(i) == 1:
totalCount += 1
#Read scalar value at point to "point" array
scalarsArray.GetTupleValue(i, point)
print point
self.pointsArray.GetPoints().GetPoint(i,point2)
print point2
if point2[1] >= lowerBound and point2[1] < (lowerBound + (shaftBounds*0.1)):
print "00%"
count00 = count00 + point[0]
points00 += 1
print xCenter
print point2[0]
print zCenter
print point2[2]
if point2[0] < xCenter and point2[2] >= zCenter:
print "Quadrant 1"
countQ1_00 = countQ1_00 + point[0]
pointsQ1_00 += 1
elif point2[0] >= xCenter and point2[2] >= zCenter:
print "Quadrant 2"
countQ2_00 = countQ2_00 + point[0]
pointsQ2_00 += 1
elif point2[0] < xCenter and point2[2] < zCenter:
print "Quadrant 3"
countQ3_00 = countQ3_00 + point[0]
pointsQ3_00 += 1
else:
print "Quadrant 4"
countQ4_00 = countQ4_00 + point[0]
pointsQ4_00 += 1
elif point2[1] >= (lowerBound + (shaftBounds*0.1)) and point2[1] < (lowerBound + (shaftBounds*0.2)):
print "10%"
count10 = count10 + point[0]
points10 += 1
print xCenter
print point2[0]
print zCenter
print point2[2]
if point2[0] < xCenter and point2[2] >= zCenter:
print "Quadrant 1"
countQ1_10 = countQ1_10 + point[0]
pointsQ1_10 += 1
elif point2[0] >= xCenter and point2[2] >= zCenter:
print "Quadrant 2"
countQ2_10 = countQ2_10 + point[0]
pointsQ2_10 += 1
elif point2[0] < xCenter and point2[2] < zCenter:
print "Quadrant 3"
countQ3_10 = countQ3_10 + point[0]
pointsQ3_10 += 1
else:
print "Quadrant 4"
countQ4_10 = countQ4_10 + point[0]
pointsQ4_10 += 1
elif point2[1] >= (lowerBound + (shaftBounds*0.2)) and point2[1] < (lowerBound + (shaftBounds*0.3)):
print "20%"
count20 = count20 + point[0]
points20 += 1
if point2[0] < xCenter and point2[2] >= zCenter:
print "Quadrant 1"
countQ1_20 = countQ1_20 + point[0]
pointsQ1_20 += 1
elif point2[0] >= xCenter and point2[2] >= zCenter:
print "Quadrant 2"
countQ2_20 = countQ2_20 + point[0]
pointsQ2_20 += 1
elif point2[0] < xCenter and point2[2] < zCenter:
print "Quadrant 3"
countQ3_20 = countQ3_20 + point[0]
pointsQ3_20 += 1
else:
print "Quadrant 4"
countQ4_20 = countQ4_20 + point[0]
pointsQ4_20 += 1
elif point2[1] >= (lowerBound + (shaftBounds*0.3)) and point2[1] < (lowerBound + (shaftBounds*0.4)):
print "30%"
count30 = count30 + point[0]
points30 += 1
if point2[0] < xCenter and point2[2] >= zCenter:
print "Quadrant 1"
countQ1_30 = countQ1_30 + point[0]
pointsQ1_30 += 1
elif point2[0] >= xCenter and point2[2] >= zCenter:
print "Quadrant 2"
countQ2_30 = countQ2_30 + point[0]
pointsQ2_30 += 1
elif point2[0] < xCenter and point2[2] < zCenter:
print "Quadrant 3"
countQ3_30 = countQ3_30 + point[0]
pointsQ3_30 += 1
else:
print "Quadrant 4"
countQ4_30 = countQ4_30 + point[0]
pointsQ4_30 += 1
elif point2[1] >= (lowerBound + (shaftBounds*0.4)) and point2[1] < (lowerBound + (shaftBounds*0.5)):
print "40%"
count40 = count40 + point[0]
points40 += 1
if point2[0] < xCenter and point2[2] >= zCenter:
print "Quadrant 1"
countQ1_40 = countQ1_40 + point[0]
pointsQ1_40 += 1
elif point2[0] >= xCenter and point2[2] >= zCenter:
print "Quadrant 2"
countQ2_40 = countQ2_40 + point[0]
pointsQ2_40 += 1
elif point2[0] < xCenter and point2[2] < zCenter:
print "Quadrant 3"
countQ3_40 = countQ3_40 + point[0]
pointsQ3_40 += 1
else:
print "Quadrant 4"
countQ4_40 = countQ4_40 + point[0]
pointsQ4_40 += 1
elif point2[1] >= (lowerBound + (shaftBounds*0.5)) and point2[1] < (lowerBound + (shaftBounds*0.6)):
print "50%"
count50 = count50 + point[0]
points50 += 1
if point2[0] < xCenter and point2[2] >= zCenter:
print "Quadrant 1"
countQ1_50 = countQ1_50 + point[0]
pointsQ1_50 += 1
elif point2[0] >= xCenter and point2[2] >= zCenter:
print "Quadrant 2"
countQ2_50 = countQ2_50 + point[0]
pointsQ2_50 += 1
elif point2[0] < xCenter and point2[2] < zCenter:
print "Quadrant 3"
countQ3_50 = countQ3_50 + point[0]
pointsQ3_50 += 1
else:
print "Quadrant 4"
countQ4_50 = countQ4_50 + point[0]
pointsQ4_50 += 1
elif point2[1] >= (lowerBound + (shaftBounds*0.6)) and point2[1] < (lowerBound + (shaftBounds*0.7)):
print "60%"
count60 = count60 + point[0]
points60 += 1
if point2[0] < xCenter and point2[2] >= zCenter:
print "Quadrant 1"
countQ1_60 = countQ1_60 + point[0]
pointsQ1_60 += 1
elif point2[0] >= xCenter and point2[2] >= zCenter:
print "Quadrant 2"
countQ2_60 = countQ2_60 + point[0]
pointsQ2_60 += 1
elif point2[0] < xCenter and point2[2] < zCenter:
print "Quadrant 3"
countQ3_60 = countQ3_60 + point[0]
pointsQ3_60 += 1
else:
print "Quadrant 4"
countQ4_60 = countQ4_60 + point[0]
pointsQ4_60 += 1
elif point2[1] >= (lowerBound + (shaftBounds*0.7)) and point2[1] < (lowerBound + (shaftBounds*0.8)):
print "70%"
count70 = count70 + point[0]
points70 += 1
if point2[0] < xCenter and point2[2] >= zCenter:
print "Quadrant 1"
countQ1_70 = countQ1_70 + point[0]
pointsQ1_70 += 1
elif point2[0] >= xCenter and point2[2] >= zCenter:
print "Quadrant 2"
countQ2_70 = countQ2_70 + point[0]
pointsQ2_70 += 1
elif point2[0] < xCenter and point2[2] < zCenter:
print "Quadrant 3"
countQ3_70 = countQ3_70 + point[0]
pointsQ3_70 += 1
else:
print "Quadrant 4"
countQ4_70 = countQ4_70 + point[0]
pointsQ4_70 += 1
elif point2[1] >= (lowerBound + (shaftBounds*0.8)) and point2[1] < (lowerBound + (shaftBounds*0.9)):
print "80%"
count80 = count80 + point[0]
points80 += 1
if point2[0] < xCenter and point2[2] >= zCenter:
print "Quadrant 1"
countQ1_80 = countQ1_80 + point[0]
pointsQ1_80 += 1
elif point2[0] >= xCenter and point2[2] >= zCenter:
print "Quadrant 2"
countQ2_80 = countQ2_80 + point[0]
pointsQ2_80 += 1
elif point2[0] < xCenter and point2[2] < zCenter:
print "Quadrant 3"
countQ3_80 = countQ3_80 + point[0]
pointsQ3_80 += 1
else:
print "Quadrant 4"
countQ4_80 = countQ4_80 + point[0]
pointsQ4_80 += 1
elif point2[1] >= (lowerBound + (shaftBounds*0.9)) and point2[1] < (lowerBound + (shaftBounds*1)):
print "90%"
count90 = count90 + point[0]
points90 += 1
if point2[0] < xCenter and point2[2] >= zCenter:
print "Quadrant 1"
countQ1_90 = countQ1_90 + point[0]
pointsQ1_90 += 1
elif point2[0] >= xCenter and point2[2] >= zCenter:
print "Quadrant 2"
countQ2_90 = countQ2_90 + point[0]
pointsQ2_90 += 1
elif point2[0] < xCenter and point2[2] < zCenter:
print "Quadrant 3"
countQ3_90 = countQ3_90 + point[0]
pointsQ3_90 += 1
else:
print "Quadrant 4"
countQ4_90 = countQ4_90 + point[0]
pointsQ4_90 += 1
else:
print "no"
#print totalCount
#Keep track of number of points that fall into cortical threshold and cancellous threshold respectively
if point[0] >= self.__corticalMin:
corticalCount += 1
elif point[0] < self.__corticalMin and point[0] >= self.__cancellousMin:
cancellousCount += 1
#Calculate averages
avgQuad1.extend([float(countQ1_00 / pointsQ1_00), float(countQ1_10 / pointsQ1_10), float(countQ1_20 / pointsQ1_20), float(countQ1_30 / pointsQ1_30), float(countQ1_40 / pointsQ1_40), float(countQ1_50 / pointsQ1_50), float(countQ1_60 / pointsQ1_60), float(countQ1_70 / pointsQ1_70), float(countQ1_80 / pointsQ1_80), float(countQ1_90 / pointsQ1_90)])
avgQuad2.extend([float(countQ2_00 / pointsQ2_00), float(countQ2_10 / pointsQ2_10), float(countQ2_20 / pointsQ2_20), float(countQ2_30 / pointsQ2_30), float(countQ2_40 / pointsQ2_40), float(countQ2_50 / pointsQ2_50), float(countQ2_60 / pointsQ2_60), float(countQ2_70 / pointsQ2_70), float(countQ2_80 / pointsQ2_80), float(countQ2_90 / pointsQ2_90)])
avgQuad3.extend([float(countQ3_00 / pointsQ3_00), float(countQ3_10 / pointsQ3_10), float(countQ3_20 / pointsQ3_20), float(countQ3_30 / pointsQ3_30), float(countQ3_40 / pointsQ3_40), float(countQ3_50 / pointsQ3_50), float(countQ3_60 / pointsQ3_60), float(countQ3_70 / pointsQ3_70), float(countQ3_80 / pointsQ3_80), float(countQ3_90 / pointsQ3_90)])
avgQuad4.extend([float(countQ4_00 / pointsQ4_00), float(countQ4_10 / pointsQ4_10), float(countQ4_20 / pointsQ4_20), float(countQ4_30 / pointsQ4_30), float(countQ4_40 / pointsQ4_40), float(countQ4_50 / pointsQ4_50), float(countQ4_60 / pointsQ4_60), float(countQ4_70 / pointsQ4_70), float(countQ4_80 / pointsQ4_80), float(countQ4_90 / pointsQ4_90)])
print avgQuad1
print avgQuad2
print avgQuad3
print avgQuad4
if points00 != 0:
avg00 = count00 / points00
avgTotal.append(avg00)
if points10 != 0:
avg10 = count10 / points10
avgTotal.append(avg10)
if points20 != 0:
avg20 = count20 / points20
avgTotal.append(avg20)
if points30 != 0:
avg30 = count30 / points30
avgTotal.append(avg30)
if points40 != 0:
avg40 = count40 / points40
avgTotal.append(avg40)
if points50 != 0:
avg50 = count50 / points50
avgTotal.append(avg50)
if points60 != 0:
avg60 = count60 / points60
avgTotal.append(avg60)
if points70 != 0:
avg70 = count70 / points70
avgTotal.append(avg70)
if points80 != 0:
avg80 = count80 / points80
avgTotal.append(avg80)
if points90 != 0:
avg90 = count90 / points90
avgTotal.append(avg90)
print avg00
print points00
print avg10
print points10
print avg20
print points20
print avg30
print points30
print avg40
print points40
print avg50
print points50
print avg60
print points60
print avg70
print points70
print avg80
print points80
print avg90
print points90
self.screwContact.insert(screwIndex, avgTotal)
'''
'''
#Calculate percentages
corticalPercent = float(corticalCount) / float(totalCount) *100
cancellousPercent = float(cancellousCount) / float(totalCount) *100
otherPercent = 100 - corticalPercent - cancellousPercent
print corticalPercent
print cancellousPercent
coP = str("%.0f" % corticalPercent)
caP = str("%.0f" % cancellousPercent)
otP = str("%.0f" % otherPercent)
qtcoP = qt.QTableWidgetItem(coP)
qtcap = qt.QTableWidgetItem(caP)
qtotP = qt.QTableWidgetItem(otP)
self.itemsqtcoP.append(qtcoP)
self.itemsqtcaP.append(qtcap)
self.itemsqtotP.append(qtotP)
print screwIndex
self.screwTable.setItem(screwIndex, 4, qtcoP)
self.screwTable.setItem(screwIndex, 3, qtcap)
self.screwTable.setItem(screwIndex, 2, qtotP)
def contact(self, input, screwModel, fidName, screwIndex):
#Get points in shaft of screw
insidePoints = self.cropPoints(screwModel)
#Get scalars to array
scalarsArray = input.GetPolyData().GetPointData().GetScalars(
'NRRDImage')
self.pointsArray = screwModel.GetPolyData()
#Get total number of tuples/points
value = scalarsArray.GetNumberOfTuples()
#Reset variables
bounds = [0]
shaftBounds = 0
corticalCount = 0
cancellousCount = 0
totalCount = 0
count = [0] * 10 # sum of values along the screw
points = [0] * 10 # number of points along the screw
countQ = [
[0] * 10
] * 4 # sum of values in countQ[quadrant][longitudinalSection]
pointsQ = [
[0] * 10
] * 4 # number of points in pointQ[quadrant][longitudinalSection]
xCenter = 0
zCenter = 0
bounds = self.pointsArray.GetPoints().GetBounds()
lowerBound = bounds[2] #+ 17
shaftBounds = 30 # FOR NOW
logging.debug(bounds)
xCenter = (bounds[0] + bounds[1]) / 2
zCenter = (bounds[4] + bounds[5]) / 2
#For each point in the screw model...
point = [0]
point2 = [0, 0, 0]
for i in range(0, value):
#If the point is in the shaft of the screw...
if insidePoints.IsInside(i) != 1:
continue
totalCount += 1
#Read scalar value at point to "point" array
scalarsArray.GetTypedTuple(i, point)
#logging.debug(point)
self.pointsArray.GetPoints().GetPoint(i, point2)
#logging.debug(point2)
longitudinalIndex = int(
math.floor((point2[1] - lowerBound) / shaftBounds * 10.0))
if longitudinalIndex < 0 or longitudinalIndex >= 10:
continue
if point2[0] < xCenter and point2[2] >= zCenter:
quadrantIndex = 0
elif point2[0] >= xCenter and point2[2] >= zCenter:
quadrantIndex = 1
elif point2[0] < xCenter and point2[2] < zCenter:
quadrantIndex = 2
else:
quadrantIndex = 3
count[longitudinalIndex] += point[0]
points[longitudinalIndex] += 1
countQ[quadrantIndex][longitudinalIndex] += point[0]
pointsQ[quadrantIndex][longitudinalIndex] += 1
#logging.debug(totalCount)
#Keep track of number of points that fall into cortical threshold and cancellous threshold respectively
if point[0] >= self.__corticalMin:
corticalCount += 1
elif point[0] < self.__corticalMin and point[
0] >= self.__cancellousMin:
cancellousCount += 1
#Calculate averages
avgQuad = [[0] * 10] * 4 # average in quadrants
for quadrantIndex in range(4):
for longitudinalIndex in range(10):
numSamples = pointsQ[quadrantIndex][longitudinalIndex]
if numSamples == 0:
continue
avgQuad[quadrantIndex][longitudinalIndex] = float(
countQ[quadrantIndex][longitudinalIndex] / numSamples)
avg = [0.0] * 10 # average along the screw
for longitudinalIndex in range(10):
if points[longitudinalIndex] > 0:
avg[longitudinalIndex] = count[longitudinalIndex] / points[
longitudinalIndex]
self.screwContact.insert(screwIndex, avg)
'''
'''
#Calculate percentages
corticalPercent = float(corticalCount) / float(totalCount) * 100
cancellousPercent = float(cancellousCount) / float(totalCount) * 100
otherPercent = 100 - corticalPercent - cancellousPercent
coP = str("%.0f" % corticalPercent)
caP = str("%.0f" % cancellousPercent)
otP = str("%.0f" % otherPercent)
qtcoP = qt.QTableWidgetItem(coP)
qtcap = qt.QTableWidgetItem(caP)
qtotP = qt.QTableWidgetItem(otP)
self.itemsqtcoP.append(qtcoP)
self.itemsqtcaP.append(qtcap)
self.itemsqtotP.append(qtotP)
logging.debug(screwIndex)
self.screwTable.setItem(screwIndex, 4, qtcoP)
self.screwTable.setItem(screwIndex, 3, qtcap)
self.screwTable.setItem(screwIndex, 2, qtotP)
def setup(self):
for cervicalVertebrae in range(
1, self.CONST_NUMBER_OF_CERVICAL_VERTERBRAE + 1):
self.verterbraeNames.append("C" + str(cervicalVertebrae))
for thoracicVertebrae in range(
1, self.CONST_NUMBER_OF_THORACIC_VERTERBRAE + 1):
self.verterbraeNames.append("T" + str(thoracicVertebrae))
for lumbarVertebrae in range(
1, self.CONST_NUMBER_OF_LUMBAR_VERTERBRAE + 1):
self.verterbraeNames.append("L" + str(lumbarVertebrae))
self.superiorAnglesList = [
None
] * self.CONST_NUMBER_OF_CERVICAL_VERTERBRAE * self.CONST_NUMBER_OF_THORACIC_VERTERBRAE * self.CONST_NUMBER_OF_LUMBAR_VERTERBRAE
self.inferiorAnglesList = [
None
] * self.CONST_NUMBER_OF_CERVICAL_VERTERBRAE * self.CONST_NUMBER_OF_THORACIC_VERTERBRAE * self.CONST_NUMBER_OF_LUMBAR_VERTERBRAE
# Instantiate and connect widgets
#
# Brief Explanation Text
instructionsCollapsibleButton = ctk.ctkCollapsibleButton()
instructionsCollapsibleButton.text = "Instructions"
self.layout.addWidget(instructionsCollapsibleButton)
instructionsLayout = qt.QVBoxLayout(instructionsCollapsibleButton)
self.namingInstructions = ctk.ctkFittedTextBrowser()
self.namingInstructions.setReadOnly(True)
self.namingInstructions.setPlainText(
"C - Cervical, T - Thoracic, L - Lumbar\ns - Superior, i - Inferior\nName ruler annotations like so: T1-s, T1-i, T2-s, etc."
)
instructionsLayout.addWidget(self.namingInstructions)
# Input Area
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Input"
self.layout.addWidget(parametersCollapsibleButton)
# Layout
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
# Input Selector
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = (("vtkMRMLAnnotationHierarchyNode"), "")
self.inputSelector.selectNodeUponCreation = True
self.inputSelector.addEnabled = True
self.inputSelector.removeEnabled = True
self.inputSelector.noneEnabled = False
self.inputSelector.showHidden = False
self.inputSelector.showChildNodeTypes = False
self.inputSelector.setMRMLScene(slicer.mrmlScene)
self.inputSelector.setToolTip("Pick the input to the algorithm.")
parametersFormLayout.addRow("Input Rulers: ", self.inputSelector)
self.projectionPlaneBox = qt.QComboBox()
self.projectionPlaneBox.addItems(["Coronal", "Axial", "Sagittal"])
parametersFormLayout.addRow("Projection Plane: ",
self.projectionPlaneBox)
#
# Output Area
#
outputCollapsibleButton = ctk.ctkCollapsibleButton()
outputCollapsibleButton.text = "Output"
self.layout.addWidget(outputCollapsibleButton)
# Layout
outputVerticalLayout = qt.QGridLayout(outputCollapsibleButton)
# Calculate Button
self.calculateButton = qt.QPushButton("Start Calculating")
outputVerticalLayout.addWidget(self.calculateButton, 0, 0, 1, 5)
# Save Button
self.saveButton = qt.QPushButton("Save as CSV")
outputVerticalLayout.addWidget(self.saveButton, 1, 0, 1, 5)
# Angle Table
horizontalHeaders = [
"Vertebrae", "Superior Angles (degrees)",
"Inferior Angles (degrees)"
]
self.angleTable = qt.QTableWidget(
self.CONST_NUMBER_OF_CERVICAL_VERTERBRAE +
self.CONST_NUMBER_OF_THORACIC_VERTERBRAE +
self.CONST_NUMBER_OF_LUMBAR_VERTERBRAE, 3)
self.angleTable.sortingEnabled = False
self.angleTable.setEditTriggers(0)
self.angleTable.setMinimumHeight(
self.angleTable.verticalHeader().length() + 25)
self.angleTable.horizontalHeader().setResizeMode(
qt.QHeaderView.Stretch)
self.angleTable.setSizePolicy(qt.QSizePolicy.MinimumExpanding,
qt.QSizePolicy.Preferred)
outputVerticalLayout.addWidget(self.angleTable, 2, 0, 1, 5)
self.angleTable.setHorizontalHeaderLabels(horizontalHeaders)
self.labelReferences = []
self.superiorAngleReferences = []
self.inferiorAngleReferences = []
for verterbraeIndex, verterbraeName in enumerate(self.verterbraeNames):
vertebraeLabel = qt.QTableWidgetItem(verterbraeName)
self.labelReferences.append(vertebraeLabel)
self.angleTable.setItem(verterbraeIndex, 0, vertebraeLabel)
superiorAngleItem = qt.QTableWidgetItem("")
self.superiorAngleReferences.append(superiorAngleItem)
self.angleTable.setItem(verterbraeIndex, 1, superiorAngleItem)
inferiorAngleItem = qt.QTableWidgetItem("")
self.inferiorAngleReferences.append(inferiorAngleItem)
self.angleTable.setItem(verterbraeIndex, 2, inferiorAngleItem)
# connections
self.calculateButton.connect('clicked(bool)', self.onCalculateButton)
self.saveButton.connect('clicked(bool)', self.onSaveButton)
self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
self.layout.addStretch(1)
def addNameAndUrl(self, name, url, setModfiable = [True, True]):
""" Adds a name and url to the table by adding a
new row.
"""
#--------------------
# Create the modifiable flags corresponding with
# the 'setModifiable' argument for
# feeding into the XnatSettingsFile.
#--------------------
flags = []
for state in setModfiable:
if state:
flags.append(None)
else:
flags.append(1)
#--------------------
# Add the hostName and hostUrl items
# accordingly.
#--------------------
hostNameItem = qt.QTableWidgetItem(name)
if flags[0]:
hostNameItem.setFlags(flags[0])
hostUrlItem = qt.QTableWidgetItem(url)
if flags[1]:
hostUrlItem.setFlags(flags[1])
#--------------------
# Add the username item.
#--------------------
usernameItem = qt.QTableWidgetItem('No username stored.')
#--------------------
# Turn sorting off.
#--------------------
self.setSortingEnabled(False)
#--------------------
# NOTE: QTableWiget quirk: we have to
# set the rowcount of the table beforehand.
#--------------------
self.setRowCount(self.rowCount + 1)
#--------------------
# Add the new items to the 'trackedItems'
# variable otherwise the table will destroy them
# and the items will disappear immediately on
# add.
#--------------------
self.trackedItems[self.rowCount-1] = {}
self.trackedItems[self.rowCount-1]['name'] = hostNameItem
self.trackedItems[self.rowCount-1]['url'] = hostUrlItem
self.trackedItems[self.rowCount-1]['stored login'] = usernameItem
#--------------------
# Set the added items' aeshetics.
#--------------------
for key, item in self.trackedItems[self.rowCount-1].iteritems():
item.setFont(self.MODULE.GLOBALS.LABEL_FONT)
#--------------------
# Call on the QTableWidget 'setItem' function.
#--------------------
self.setItem(self.rowCount-1, self.getColumn('name'), hostNameItem)
self.setItem(self.rowCount-1, self.getColumn('url'), hostUrlItem)
self.setItem(self.rowCount-1, self.getColumn('stored login'), usernameItem)
#--------------------
# Again, turn sorting off.
#--------------------
self.setSortingEnabled(False)
