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SmartTemplate.py
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SmartTemplate.py
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import os
import unittest
import csv
import numpy
import math
from decimal import *
from __main__ import vtk, qt, ctk, slicer
#from slicer.ScriptedLoadableModule import *
#
# SmartTemplate
#
class SmartTemplate():
#class SmartTemplate(ScriptedLoadableModule):
def __init__(self, parent = None):
#ScriptedLoadableModule.__init__(self, parent)
parent.title = "Smart Template"
parent.categories = ["IGT"]
parent.dependencies = []
parent.contributors = ["Yuting Zhao, INP Toulouse-ENSEEIHT"] # replace with "Firstname Lastname (Org)"
parent.helpText = """
This module is to establish the communication connection with the Smart Template Robot device produced by Physical Sciences Inc. and Surgical Planning Laboratory at Brigham and Women's Hospital. This module aslo determines the angulated needle path.
"""
parent.acknowledgementText = """
This module was developed by Yuting Zhao(INP Toulouse - ENSEEIHT, yuting.zhao@outlook.com). The research is funded by NIH(R41CA192446)
""" # replace with organization, grant and thanks.
self.parent = parent
#
# SmartTemplateWidget
#
class SmartTemplateWidget():
#class SmartTemplateWidget(ScriptedLoadableModuleWidget):
def __init__(self, parent = None):
#def __init__(self, parent):
#ScriptedLoadableModuleWidget.setup(self)
self.tnode = None
self.strHostname = None
self.times0 = 0
self.chooseCell = False
self.connectTag = False
self.registTag = False
self.receiveCurrentNode = None
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
self.logic = SmartTemplateLogic(None)
self.generateTag = False
def setup(self):
#
# Collapsible button - Restart 3D Slicer
#
restartCollapsibleButton = ctk.ctkCollapsibleButton()
restartCollapsibleButton.text = "Restart"
self.layout.addWidget(restartCollapsibleButton)
restartCollapsibleButton.collapsed = True
buttonRestart = qt.QPushButton("Restart 3D Slicer")
buttonRestart.connect('clicked(bool)', self.onButtonRestartClicked)
restartLayout = qt.QVBoxLayout(restartCollapsibleButton)
restartLayout.addWidget(buttonRestart)
#
# Collapsible button - Configuration
#
setCollapsibleButton = ctk.ctkCollapsibleButton()
setCollapsibleButton.text = "Configuration"
self.layout.addWidget(setCollapsibleButton)
configLayout = qt.QVBoxLayout(setCollapsibleButton)
configFormFrame = qt.QFrame()
configFormLayout = qt.QFormLayout(configFormFrame)
configLayout.addWidget(configFormFrame)
gridLayout = qt.QGridLayout(setCollapsibleButton)
gridLayout.setSpacing(10)
labelHostname = qt.QLabel("Hostname: ")
self.lineEditHostname = qt.QLineEdit()
self.lineEditHostname.setPlaceholderText("localhost")
self.lineEditHostname.setText("localhost")
self.lineEditHostname.setFixedWidth(150)
labelPort = qt.QLabel("Port Number: ")
self.lineEditPort = qt.QLineEdit()
self.lineEditPort.setPlaceholderText("18944")
self.lineEditPort.setText("10000")
self.lineEditPort.setFixedWidth(150)
#TODO: better to change checkbox to radiobutton
oldTemplateLabel = qt.QLabel("14*7 Old template")
self.oldTemplateCheckBox = qt.QCheckBox()
self.oldTemplateCheckBox.connect('toggled(bool)', self.onOldTemplateChecked)
newTemplateLabel = qt.QLabel("9*7 New template")
self.newTemplateCheckBox = qt.QCheckBox()
self.newTemplateCheckBox.connect('toggled(bool)', self.onNewTemplateChecked)
gridLayout.addWidget(labelHostname, 1, 0)
gridLayout.addWidget(self.lineEditHostname, 1, 1)
gridLayout.addWidget(labelPort, 1, 2)
gridLayout.addWidget(self.lineEditPort, 1, 3)
gridLayout.addWidget(oldTemplateLabel, 2, 0)
gridLayout.addWidget(self.oldTemplateCheckBox, 2, 1)
gridLayout.addWidget(newTemplateLabel, 2, 2)
gridLayout.addWidget(self.newTemplateCheckBox, 2, 3)
configFormLayout.addRow(gridLayout)
templateConfigPathLayout = qt.QHBoxLayout()
templateConfigPathLayout.setSpacing(10)
self.templateConfigPathEdit = qt.QLineEdit()
# settings = qt.QSettings()
# templateConfigPath = settings.value("SmartTemplateModule/templateConfigFile")
# if os.path.exists(templateConfigPath):
# self.logic.loadTemplateConfigFile(templateConfigPath)
# self.templateConfigPathEdit.text = templateConfigPath
# self.templateConfigPathEdit.readOnly = False
self.templateConfigPathEdit.frame = True
self.templateConfigPathEdit.styleSheet = "QLineEdit { background:transparent; }"
self.templateConfigPathEdit.cursor = qt.QCursor(qt.Qt.IBeamCursor)
templateConfigPathLayout.addWidget(self.templateConfigPathEdit)
self.templateConfigButton = qt.QPushButton("...")
self.templateConfigButton.toolTip = "Choose a template configuration file"
self.templateConfigButton.enabled = True
self.templateConfigButton.connect('clicked(bool)', self.onTemplateConfigButton)
templateConfigPathLayout.addWidget(self.templateConfigButton)
configFormLayout.addRow("Template Config File: ", templateConfigPathLayout)
#
# Collapsible button - Robot status
#
statusCollapsibleButton = ctk.ctkCollapsibleButton()
statusCollapsibleButton.text = "SNRMRRobot status"
self.layout.addWidget(statusCollapsibleButton)
statusLayout = qt.QHBoxLayout(statusCollapsibleButton)
statusFormFrame = qt.QFrame()
statusFormLayout = qt.QFormLayout(statusFormFrame)
statusLayout.addWidget(statusFormFrame)
statusGridLayout = qt.QGridLayout(statusCollapsibleButton)
statusGridLayout.setSpacing(10)
labelStatus = qt.QLabel("Connection status: ")
self.lineEditStatus = qt.QLineEdit()
self.lineEditStatus.setFixedWidth(150)
labelRegistTime = qt.QLabel("Registration Time: ")
self.lineEditRegistTime = qt.QLineEdit()
self.lineEditRegistTime.setFixedWidth(150)
labelCurrent = qt.QLabel("Current: ")
self.lineEditCurrent = qt.QLineEdit()
statusGridLayout.addWidget(labelStatus, 1, 0)
statusGridLayout.addWidget(self.lineEditStatus, 1, 1)
statusGridLayout.addWidget(labelRegistTime, 1, 2)
statusGridLayout.addWidget(self.lineEditRegistTime, 1, 3)
statusGridLayout.addWidget(labelCurrent, 2, 0)
statusGridLayout.addWidget(self.lineEditCurrent, 2, 1)
statusFormLayout.addRow(statusGridLayout)
#
# Collapsible button - Controller
#
controlCollapsibleButton = ctk.ctkCollapsibleButton()
controlCollapsibleButton.text = "SNRMRRobot Controller"
self.layout.addWidget(controlCollapsibleButton)
mainLayout = qt.QVBoxLayout(controlCollapsibleButton)
controllerFormFrame = qt.QFrame()
controllerFormLayout = qt.QFormLayout(controllerFormFrame)
mainLayout.addWidget(controllerFormFrame)
controllerGridLayout = qt.QGridLayout(controlCollapsibleButton)
controllerGridLayout.setSpacing(10)
lengthButton = 160
heightButton = 65
self.buttonConnect = qt.QPushButton("Connect")
self.buttonConnect.setFixedSize(lengthButton, heightButton)
self.buttonConnect.toolTip = "Make connection to the Robot Controller"
self.buttonRegistration = qt.QPushButton("Registration")
self.buttonRegistration.setFixedSize(lengthButton, heightButton)
self.buttonSendTarget = qt.QPushButton("Send\n Target")
self.buttonSendTarget.setFixedSize(lengthButton, heightButton)
#self.buttonSendTarget.setEnabled(False)
self.buttonGeneratePath = qt.QPushButton("Generate\n Path")
self.buttonGeneratePath.setFixedSize(lengthButton, heightButton)
self.buttonCurrent = qt.QPushButton("Current")
#self.buttonCurrent.setEnabled(False)
self.buttonDisconnect = qt.QPushButton("Disconnect")
self.buttonDisconnect.setFixedSize(lengthButton, heightButton)
#self.buttonDisconnect.setEnabled(False)
self.buttonReconnect = qt.QPushButton("Reconnect")
#self.buttonReconnect.setEnabled(False)
controllerGridLayout.addWidget(self.buttonConnect, 1, 0)
controllerGridLayout.addWidget(self.buttonRegistration, 1, 1)
controllerGridLayout.addWidget(self.buttonGeneratePath, 1, 2)
controllerGridLayout.addWidget(self.buttonSendTarget, 1, 3)
controllerGridLayout.addWidget(self.buttonDisconnect, 1, 4)
controllerFormLayout.addRow(controllerGridLayout)
# connect of the buttons
self.buttonConnect.connect('clicked(bool)', self.onButtonConnectClicked)
self.buttonRegistration.connect('clicked(bool)', self.onButtonRegistrationClicked)
self.buttonGeneratePath.connect('clicked(bool)', self.onButtonGeneratePathClicked)
self.buttonSendTarget.connect('clicked(bool)', self.onButtonSendTargetClicked)
self.buttonCurrent.connect('clicked(bool)', self.onButtonCurrentClicked)
self.buttonDisconnect.connect('clicked(bool)', self.onButtonDisconnectClicked)
self.buttonReconnect.connect('clicked(bool)', self.onButtonReconnectClicked)
generatePathLayout = qt.QHBoxLayout()
self.lineEditNumOfOptionalPath = qt.QLineEdit()
self.lineEditNumOfOptionalPath.setText("1")
self.lineEditNumOfOptionalPath.setFixedWidth(30)
#self.buttonGeneratePath = qt.QPushButton("Generate Path")
#controllerFormLayout.addWidget(self.buttonGeneratePath)
#self.buttonGeneratePath.connect('clicked(bool)', self.onButtonGeneratePathClicked)
generatePathLayout.addWidget(self.lineEditNumOfOptionalPath)
#generatePathLayout.addWidget(self.buttonGeneratePath)
controllerFormLayout.addRow("Number of Optional Path: ", generatePathLayout)
self.showTemplateCheckBox = qt.QCheckBox()
self.showTemplateCheckBox.checked = 0
self.showTemplateCheckBox.setToolTip("Show 3D model of the template")
self.showTemplateCheckBox.connect('toggled(bool)', self.onShowTemplate)
controllerFormLayout.addRow("Show Template:", self.showTemplateCheckBox)
self.showOptionalCheckBox = qt.QCheckBox()
self.showOptionalCheckBox.checked = 0
self.showOptionalCheckBox.setToolTip("Show 3D model of the needle path")
self.showOptionalCheckBox.connect('toggled(bool)', self.onShowOptionalPath)
controllerFormLayout.addRow("Show Optional Path:", self.showOptionalCheckBox)
#
# input markup fiducials node
#
self.targetFiducialsSelector = slicer.qMRMLNodeComboBox()
self.targetFiducialsSelector.nodeTypes = (("vtkMRMLMarkupsFiducialNode"), "")
self.targetFiducialsSelector.addEnabled = True
self.targetFiducialsSelector.removeEnabled = True
self.targetFiducialsSelector.selectNodeUponCreation = True
self.targetFiducialsSelector.noneEnabled = False
self.targetFiducialsSelector.showHidden = False
self.targetFiducialsSelector.showChildNodeTypes = False
self.targetFiducialsSelector.setMRMLScene(slicer.mrmlScene)
controllerFormLayout.addRow("Target: ", self.targetFiducialsSelector)
self.targetFiducialsNode = None
self.targetFiducialsSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onFiducialsSelected)
#
# target list table
#
self.table = qt.QTableWidget(1, 4)
self.table.setSelectionBehavior(qt.QAbstractItemView.SelectRows)
self.table.setSelectionMode(qt.QAbstractItemView.SingleSelection)
self.headers = ["Name", "Hole", "Depth(mm)", "Position(RAS)"]
self.table.setHorizontalHeaderLabels(self.headers)
self.table.horizontalHeader().setStretchLastSection(True)
mainLayout.addWidget(self.table)
self.table.connect('cellClicked(int, int)', self.onTableSelected)
self.onFiducialsSelected()
# Add vertical spacer
self.layout.addStretch(1)
#
# path list table
#
self.pathTable = qt.QTableWidget(1, 4)
self.pathTable.setSelectionBehavior(qt.QAbstractItemView.SelectRows)
self.pathTable.setSelectionMode(qt.QAbstractItemView.SingleSelection)
self.pathTable.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
self.headersPathTable = ["Name", "Hole", "Depth(mm)", "Degree"]
self.pathTable.setHorizontalHeaderLabels(self.headersPathTable)
self.pathTable.horizontalHeader().setStretchLastSection(True)
mainLayout.addWidget(self.pathTable)
self.pathTable.connect('cellClicked(int, int)', self.onPathTableSelected)
def onOldTemplateChecked(self):
if self.newTemplateCheckBox.checked == 1:
self.newTemplateCheckBox.checked = 0
self.rowDict = {'A':1, 'B':2, 'C':3, 'D':4, 'E':5, 'F':6, 'G':7, 'H':8, 'I':9, 'J':10, 'K':11, 'L':12, 'M':13, 'N':14}
self.colDict = {' "-7"':-7, ' "-6"':-6, ' "-5"':-5, ' "-4"':-4, ' "-3"':-3, ' "-2"':-2, ' "-1"':-1, ' "0"':0, ' "1"':1, ' "2"':2, ' "3"':3, ' "4"':4, ' "5"':5, ' "6"':6, ' "7"':7}
print "onOldTemplateChecked"
def onNewTemplateChecked(self):
if self.oldTemplateCheckBox.checked == 1:
self.oldTemplateCheckBox.checked = 0
self.rowDict = {'A':1, 'B':2, 'C':3, 'D':4, 'E':5, 'F':6, 'G':7, 'H':8, 'I':9}
self.colDict = {' "-3"':1, ' "-2"':2, ' "-1"':3, ' "0"':4, ' "1"':5, ' "2"':6, ' "3"':7}
print "onNewTemplateChecked"
def onButtonRestartClicked(self):
slicer.app.restart()
def onButtonConnectClicked(self):
if self.connectTag: # check already has a connect node
print "Olalalalala!!!"
else: # first time to create the connect node
self.connectNode = slicer.vtkMRMLIGTLConnectorNode()
self.connectNode.SetName('testConnectNode')
slicer.mrmlScene.AddNode(self.connectNode)
lenHost = len(self.lineEditHostname.text)
lenPort = len(self.lineEditPort.text)
# check the input
if lenHost == 0 or lenPort == 0:
qt.QMessageBox.information(
slicer.util.mainWindow(),
"Slicer Python", "Hostname/Port invalid!")
else:
self.strHostname = str(self.lineEditHostname.text)
self.intPort = int(self.lineEditPort.text)
self.connectNode.SetTypeClient(self.strHostname, self.intPort)
self.connectNode.Start() # connect
self.activeEvent() # active the monitor
self.buttonDisconnect.setEnabled(True)
self.connectTag = True
def onButtonRegistrationClicked(self):
if self.registTag: # check already has a registration data node
self.connectNode.PushNode(self.dataNodeZFrame)
else: # fist time to creat the registration data node
self.dataNodeZFrame = slicer.vtkMRMLLinearTransformNode()
self.dataNodeZFrame.SetName("ZFrameTransform")
slicer.mrmlScene.AddNode(self.dataNodeZFrame)
self.connectNode.RegisterOutgoingMRMLNode(self.dataNodeZFrame)
self.connectNode.PushNode(self.dataNodeZFrame) # send the ZFrameTransform data to controller
self.registTag = True
def onButtonSendTargetClicked(self):
#temp = self.cellPosTarget + self.sendPathInfoTarget + self.templateNum
#tempStr = "%.3f, %.3f, %.3f, %.3f, %.3f, %d, %d" %(temp[0], temp[1], temp[2], temp[3], temp[4], temp[5], temp[6])
# targetRAS[3], templatePlane[3], holeRAS[3], depth, degree, (x, y)
R = self.sendPathInfo[1][0]
A = self.sendPathInfo[1][1]
S = self.sendPathInfo[1][2]
holeRAS = [R, A, S]
temp = self.cellPosTarget + self.smartTemplatePlane3 + holeRAS + self.sendPathInfoTarget + self.templateNum
tempStr = "%.3f, %.3f, %.3f, %.3f, %.3f, %.3f, %.3f, %.3f, %.3f, %.3f, %.3f, %d, %d" %(temp[0], temp[1], temp[2], temp[3], temp[4], temp[5], temp[6], temp[7], temp[8], temp[9], temp[10], temp[11], temp[12])
if self.chooseCell == True:
confirmBox = qt.QMessageBox()
confirmBox.setText(self.rowStr)
confirmBox.setStandardButtons(qt.QMessageBox.Yes | qt.QMessageBox.Cancel)
confirmBox.setDefaultButton(qt.QMessageBox.Yes)
reply = confirmBox.exec_()
if reply == qt.QMessageBox.Yes:
print "TargetCellPos: ", self.cellPos
self.targetCellNode = slicer.vtkMRMLTextNode()
self.targetCellNode.SetName("TARGETCell")
# self.targetCellNode.SetText(self.cellPos)
self.targetCellNode.SetText(tempStr)
slicer.mrmlScene.AddNode(self.targetCellNode)
# self.sendPathNode = slicer.vtkMRMLTextNode()
# self.sendPathNode.SetName("SelectPath")
# self.sendPathNode.SetText(self.sendPathInfo)
# slicer.mrmlScene.AddNode(self.sendPathNode)
self.connectNode.RegisterOutgoingMRMLNode(self.targetCellNode)
# self.connectNode.RegisterOutgoingMRMLNode(self.sendPathNode)
self.connectNode.PushNode(self.targetCellNode)
# self.connectNode.PushNode(self.sendPathNode)
elif reply == qt.QMessageBox.Cancel:
pass
else:
allTargetBox = qt.QMessageBox()
allTargetBox.setText("Do you want to send <font color='red'><strong>all the target</strong></font> to the robot?")
allTargetBox.setStandardButtons(qt.QMessageBox.Yes | qt.QMessageBox.Cancel)
allTargetBox.setDefaultButton(qt.QMessageBox.Yes)
replyAll = allTargetBox.exec_()
if replyAll == qt.QMessageBox.Yes:
self.currentTargetNode = self.targetFiducialsSelector.currentNode()
self.connectNode.RegisterOutgoingMRMLNode(self.currentTargetNode)
self.connectNode.PushNode(self.currentTargetNode)
elif replyAll == qt.QMessageBox.Cancel:
pass
def onButtonCurrentClicked(self):
self.dataNodeCurrent = slicer.vtkMRMLLinearTransformNode()
self.dataNodeCurrent.SetName("CURRENT22222")
slicer.mrmlScene.AddNode(self.dataNodeCurrent)
def onButtonDisconnectClicked(self):
self.connectNode.Stop()
self.lineEditStatus.setText("Disconnect")
self.lineEditStatus.setStyleSheet("background-color: red")
self.buttonReconnect.setEnabled(True)
def onButtonReconnectClicked(self):
pass # add function
def activeEvent(self):
print "into activeEvent"
self.tempLinearNode = slicer.vtkMRMLLinearTransformNode()
self.tempLinearNode.SetName('temp')
#self.tagTemp = self.tempLinearNode.AddObserver('ModifiedEvent', self.putInfo)
#self.tagTemp = self.connectNode.AddObserver('ModifiedEvent', self.putInfo)
#self.tagTemp = self.connectNode.AddObserver(slicer.vtkMRMLIGTLConnectorNode.ReceiveEvent, self.putInfo)
#self.tagTemp = self.tempLinearNode.AddObserver(vtk.vtkCommand.ModifiedEvent, self.putInfo)
#self.tagTemp = self.tempLinearNode.AddObserver(self.connectNode.ReceiveEvent, self.putInfo)
self.tagTemp = self.connectNode.AddObserver(self.connectNode.ReceiveEvent, self.putInfo)
#test
self.times1 = 0
def putInfo(self, caller, event): # caller: vtkMRMLIGTLConnectorNode
self.times1 = self.times1+1
#print "********************"
#print ("into caller", self.times1)
if caller.IsA('vtkMRMLIGTLConnectorNode'):
nInNode = caller.GetNumberOfIncomingMRMLNodes()
for i in range(nInNode): # start from 0
node = caller.GetIncomingMRMLNode(i)
if node.IsA("vtkMRMLLinearTransformNode"): # lineartransform node
if node.GetName() == "CURRENT": # node name the same robot controller part
if self.receiveCurrentNode == None:
self.receiveCurrentNode = slicer.vtkMRMLLinearTransformNode()
self.receiveCurrentNode.SetName("receiveCurrent")
slicer.mrmlScene.AddNode(self.receiveCurrentNode)
else:
mat4x4 = self.receiveCurrentNode.GetMatrixTransformToParent()
self.matR = mat4x4.GetElement(0, 3)
self.matA = mat4x4.GetElement(1, 3)
self.matS = mat4x4.GetElement(2, 3)
strCurrent = "(%.3f, %.3f, %.3f)" %(self.matR, self.matA, self.matS)
self.lineEditCurrent.setText(strCurrent)
self.connectNode.UnregisterIncomingMRMLNode(node)
elif node.IsA("vtkMRMLTextNode"): # text node
if node.GetName() == "feedStatus":
self.lineEditStatus.setText(node.GetText())
self.lineEditStatus.setStyleSheet("background-color: green")
self.connectNode.UnregisterIncomingMRMLNode(node)
elif node.GetName() == "feedInfoRegistTime":
self.lineEditRegistTime.setText(node.GetText())
qt.QMessageBox.information(
slicer.util.mainWindow(),
"Slicer Python", "Registration Accepted!")
self.connectNode.UnregisterIncomingMRMLNode(node)
self.buttonSendTarget.setEnabled(True)
elif node.GetName() == "feedTarget":
print node.GetText()
qt.QMessageBox.information(
slicer.util.mainWindow(),
"Slicer Python", "Target Accepted!")
self.connectNode.UnregisterIncomingMRMLNode(node)
self.buttonCurrent.setEnabled(True)
elif node.GetName() == "feedTargetCell":
print node.GetText()
qt.QMessageBox.information(
slicer.util.mainWindow(),
"Slicer Python", "Cell Accepted!")
self.connectNode.UnregisterIncomingMRMLNode(node)
else: # else to node.IsA
print "no feedBack!!!!!"
#print i # start from 0
#print node.GetID() # MRML ID
#print node.GetNodeTagName() # MRML Type
#print node.GetClassName()
#print node.GetName()
#print node.IsA('vtkMRMLLinearTransformNode') # True
def onFiducialsSelected(self):
# Remove observer if previous node exists
if self.targetFiducialsNode and self.tag:
self.targetFiducialsNode.RemoveObserver(self.tag)
# Update selected node, add observer, and update control points
if self.targetFiducialsSelector.currentNode():
self.targetFiducialsNode = self.targetFiducialsSelector.currentNode()
self.tag = self.targetFiducialsNode.AddObserver("ModifiedEvent", self.onFiducialsUpdated)
self.updateTable()
def onFiducialsUpdated(self, caller, event):
if caller.IsA("vtkMRMLMarkupsFiducialNode") and event == "ModifiedEvent":
self.updateTable()
if self.generateTag:
self.logic.hideOptionalPath()
def onTableSelected(self, row, column):
print "onTableSelected(%d, %d)" %(row, column)
self.rowNum = row+1
#self.rowStr = "Do you want to send target: <font color='red'><strong>F-" + str(self.rowNum) + "</strong></font>to the robot?"
pos = [0.0, 0.0, 0.0]
self.selectedTargetLabel = self.targetFiducialsNode.GetNthFiducialLabel(row)
self.targetFiducialsNode.GetNthFiducialPosition(row, pos)
print "onTableSelected: ", pos
(indexX, indexY, depth, inRange) = self.logic.computeNearestPath(pos)
self.cellPos = "%.3f, %.3f, %.3f" %(pos[0], pos[1], pos[2])
self.cellPosTarget = [pos[0], pos[1], pos[2]]
self.chooseCell = True
def onPathTableSelected(self, row, column):
self.pathSelect = self.holeInfoList[row]
print "pathSelect: ", self.pathSelect
if self.angleList[row] > 15.0:
self.rowStr = "Out of range, please choose another needle! :)"
else:
self.rowStr = "Do you want to send target: <font color='red'><strong>F-" + str(self.rowNum) + ", (" + self.pathSelect[0][0] + ", " + self.pathSelect[0][1] + ") , Depth: " + str(self.pathSelect[1]) + " " + "Angle: " + str(self.angleList[row]) + " " + "</strong></font>to the robot?"
# temporary change Sep25 by yz
insertionPointRAS = self.logic.visualNeedlePath(numpy.array(self.cellPosTarget), self.pathSelect[3])
# end tchange
## self.sendPathInfo = (hole, array, depth, degree)
self.sendPathInfo = ((self.pathSelect[0][0], self.pathSelect[0][1]), insertionPointRAS, self.pathSelect[1], self.angleList[row])
#self.sendPathInfo = "%.3f, %.3f" %(self.pathSelect[1], self.angleList[row])
self.sendPathInfoTarget = [self.pathSelect[1], self.angleList[row]]
self.templateNum = self.alpha2num(self.pathSelect[0][0], self.pathSelect[0][1])
print "self.sendPathInfo: ", self.sendPathInfo #(('F', ' "0"'), array([ 0., 0., 30.]), 67.125, 0.886)
def alpha2num(self, x, y):
rowIndex = x
colIndex = y
row = self.rowDict[rowIndex]
col = self.colDict[colIndex]
return [row, col]
def updateTable(self):
self.times0 = self.times0 + 1
print "updateTable: ", self.times0
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)
# end the range
# show the table
self.table.show()
def onTemplateConfigButton(self):
path = self.templateConfigPathEdit.text
path = qt.QFileDialog.getOpenFileName(None, 'Open Template File', path, '*.csv')
self.templateConfigPathEdit.setText(path)
# if path is not None and path != "":
# self.templateConfigPathEdit.setText(path)
# settings = qt.QSettings()
# settings.setValue('SmartTemplateModule/templateConfigFile', path)
self.logic.loadTemplateConfigFile(path)
self.updateTable()
def onShowTemplate(self):
print "onShowTemplate(self)"
self.logic.setTemplateVisibility(self.showTemplateCheckBox.checked)
def onShowOptionalPath(self):
print "onShowOptionalPath()"
self.logic.setOptionalPathVisibility(self.showOptionalCheckBox.checked)
def onButtonGeneratePathClicked(self):
self.smartTemplatePlane4 = self.logic.determineTemplatePlane()
self.smartTemplatePlane3 = [self.smartTemplatePlane4[0], self.smartTemplatePlane4[1], self.smartTemplatePlane4[2]]
self.generateTag = True
intNumOfOptionalPath = int(self.lineEditNumOfOptionalPath.text)
(self.projectPoint, self.depthBase, self.holeInfoList, self.angleList) = self.logic.generatePath(self.cellPosTarget, intNumOfOptionalPath)
self.pathTableData = []
getNumberOfPath = len(self.holeInfoList)
if self.pathTable.rowCount != getNumberOfPath:
self.pathTable.setRowCount(getNumberOfPath)
for i in range(getNumberOfPath):
nthPath = self.holeInfoList[i]
if nthPath[1] > 150.0: # max depth = 150mm
nthPath[1] = Decimal('Infinity')
indexHole = nthPath[0]
cellLabel = qt.QTableWidgetItem(self.selectedTargetLabel)
cellIndex = qt.QTableWidgetItem("(%s, %s)" %(indexHole[0], indexHole[1]))
cellDepth = qt.QTableWidgetItem("(%.3f)" %nthPath[1])
cellDegree = qt.QTableWidgetItem("(%.3f)" %self.angleList[i])
# posRAS = "(%.3f, %.3f, %.3f)" %(round(self.cellPosTarget[0], 3), round(self.cellPosTarget[1], 3), round(self.cellPosTarget[2], 3))
# RAS = qt.QTableWidgetItem(posRAS)
row = [cellLabel, cellIndex, cellDepth, cellDegree]
self.pathTable.setItem(i, 0, row[0])
self.pathTable.setItem(i, 1, row[1])
self.pathTable.setItem(i, 2, row[2])
self.pathTable.setItem(i, 3, row[3])
self.pathTableData.append(row)
self.pathTable.show()
# ----------------------------------------------------------------------------------------------------------------
# SmartTemplateLogic
#
class SmartTemplateLogic():
#class SmartTemplateLogic(ScriptedLoadableModuleLogic):
def __init__(self, parent = None):
#def __init__(self, parent):
#ScriptedLoadableModuleLogic.__init__(self, parent)
self.pathVectors = []
self.pathOrigins = []
self.templateModelNodeID = ''
self.needlePathModelNodeID = ''
self.optionalPathModelNodeID = ''
self.selectNeedleNodeID = ''
self.templateMaxDepth = []
self.templatePathOrigins = [] ## Origins of needle paths
self.templatePathVectors = [] ## Normal vectors of needle paths
self.pathOrigins = [] ## Origins of needle paths (after transformation by parent transform node)
self.pathVectors = [] ## Normal vectors of needle paths (after transformation by parent transform node)
self.generateTag = False
def loadTemplateConfigFile(self, path):
print "loadTemplateConfigFile"
self.templateIndex = []
self.templateConfig = []
self.templateInRAS = []
self.templateOutRAS = []
header = False
reader = csv.reader(open(path, 'rb'))
try:
for column in reader:
if header:
self.templateIndex.append(column[0:2])
self.templateConfig.append([float(column[2]), float(column[3]), float(column[4]),
float(column[5]), float(column[6]), float(column[7]),
float(column[8])])
self.templateInRAS.append([float(column[2]), float(column[3]), float(column[4])])
self.templateOutRAS.append([float(column[5]), float(column[6]), float(column[7])])
else:
self.templateName = column[0]
header = True
except csv.Error as e:
print('file %s, line %d: %s' % (filename, reader.line_num, e))
self.createTemplateModel()
self.setTemplateVisibility(0)
self.updateTemplateVectors()
self.setOptionalPathVisibility(0)
#----------------------------------------------------------------------------------------------------------------
def createTemplateModel(self):
self.templatePathVectors = []
self.templatePathOrigins = []
tempModelNode = slicer.mrmlScene.GetNodeByID(self.templateModelNodeID)
if tempModelNode == None:
tempModelNode = slicer.vtkMRMLModelNode()
tempModelNode.SetName('NeedleGuideTemplate')
slicer.mrmlScene.AddNode(tempModelNode)
self.templateModelNodeID = tempModelNode.GetID()
dnode = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(dnode)
tempModelNode.SetAndObserveDisplayNodeID(dnode.GetID())
self.modelNodetag = tempModelNode.AddObserver(slicer.vtkMRMLTransformableNode.TransformModifiedEvent,
self.onTemplateTransformUpdated)
tempModelAppend = vtk.vtkAppendPolyData()
for row in self.templateConfig:
p1 = numpy.array(row[0:3])
p2 = numpy.array(row[3:6])
tempLineSource = vtk.vtkLineSource()
tempLineSource.SetPoint1(p1)
tempLineSource.SetPoint2(p2)
tempTubeFilter = vtk.vtkTubeFilter()
tempTubeFilter.SetInputConnection(tempLineSource.GetOutputPort())
tempTubeFilter.SetRadius(1.0)
tempTubeFilter.SetNumberOfSides(18)
tempTubeFilter.CappingOn()
tempTubeFilter.Update()
pathLineSource = vtk.vtkLineSource()
v = p2-p1
nl = numpy.linalg.norm(v)
n = v/nl # normal vector
l = row[6]
p3 = p1 + l * n
pathLineSource.SetPoint1(p1)
pathLineSource.SetPoint2(p3)
self.templatePathOrigins.append([row[0], row[1], row[2], 1.0])
self.templatePathVectors.append([n[0], n[1], n[2], 1.0])
self.templateMaxDepth.append(row[6])
pathTubeFilter = vtk.vtkTubeFilter()
pathTubeFilter.SetInputConnection(pathLineSource.GetOutputPort())
pathTubeFilter.SetRadius(0.8)
pathTubeFilter.SetNumberOfSides(18)
pathTubeFilter.CappingOn()
pathTubeFilter.Update()
if vtk.VTK_MAJOR_VERSION <= 5:
tempModelAppend.AddInput(tempTubeFilter.GetOutput())
# pathModelAppend.AddInput(pathTubeFilter.GetOutput())
else:
tempModelAppend.AddInputData(tempTubeFilter.GetOutput())
# pathModelAppend.AddInputData(pathTubeFilter.GetOutput())
tempModelAppend.Update()
tempModelNode.SetAndObservePolyData(tempModelAppend.GetOutput())
# pathModelAppend.Update()
# pathModelNode.SetAndObservePolyData(pathModelAppend.GetOutput())
def setModelVisibilityByID(self, id, visible):
mnode = slicer.mrmlScene.GetNodeByID(id)
if mnode != None:
dnode = mnode.GetDisplayNode()
if dnode != None:
dnode.SetVisibility(visible)
def setModelSliceIntersectionVisibilityByID(self, id, visible):
mnode = slicer.mrmlScene.GetNodeByID(id)
if mnode != None:
dnode = mnode.GetDisplayNode()
if dnode != None:
dnode.SetSliceIntersectionVisibility(visible)
def setTemplateVisibility(self, visibility):
self.setModelVisibilityByID(self.templateModelNodeID, visibility)
def setOptionalPathVisibility(self, visibility):
print "setOptionalPathVisibility: ", visibility
self.setModelVisibilityByID(self.optionalPathModelNodeID, visibility)
self.setModelSliceIntersectionVisibilityByID(self.optionalPathModelNodeID, visibility)
def onTemplateTransformUpdated(self,caller,event):
print 'onTemplateTransformUpdated()'
self.updateTemplateVectors()
def updateTemplateVectors(self):
print 'updateTemplateVectors()'
mnode = slicer.mrmlScene.GetNodeByID(self.templateModelNodeID)
if mnode == None:
return 0
tnode = mnode.GetParentTransformNode()
trans = vtk.vtkMatrix4x4()
if tnode != None:
tnode.GetMatrixTransformToWorld(trans);
else:
trans.Identity()
# Calculate offset
zero = [0.0, 0.0, 0.0, 1.0]
offset = []
offset = trans.MultiplyDoublePoint(zero)
self.pathOrigins = []
self.pathVectors = []
i = 0
for orig in self.templatePathOrigins:
torig = trans.MultiplyDoublePoint(orig)
self.pathOrigins.append(numpy.array(torig[0:3]))
vec = self.templatePathVectors[i]
tvec = trans.MultiplyDoublePoint(vec)
self.pathVectors.append(numpy.array([tvec[0]-offset[0], tvec[1]-offset[1], tvec[2]-offset[2]]))
i = i + 1
def computeNearestPath(self, pos):
p = numpy.array(pos)
minMag2 = numpy.Inf
minDepth = 0.0
minIndex = -1
i = 0
for orig in self.pathOrigins:
vec = self.pathVectors[i]
op = p - orig
aproj = numpy.inner(op, vec)
perp = op-aproj*vec
mag2 = numpy.vdot(perp, perp) # magnitude^2
if mag2 < minMag2:
minMag2 = mag2
minIndex = i
minDepth = aproj
i = i + 1
indexX = "--"
indexY = "--"
inRange = False
if minIndex >= 0:
indexX = self.templateIndex[minIndex][0]
indexY = self.templateIndex[minIndex][1]
if minDepth > 0 and minDepth < self.templateMaxDepth[minIndex]:
inRange = True
return (indexX, indexY, minDepth, inRange)
# ----------------------------------------------------------------------------------------------------------------
def generatePath(self, cellPos, intNumOfOptionalPath):
pos = numpy.array(cellPos)
print "generatePath() called"
print "pos: ", (round(pos[0], 3), round(pos[1], 3), round(pos[2], 3))
# TODO: should randomly choose 3 points on the template (!!! same line situation)
template = self.determineTemplatePlane()
print "template: ", template
pPoint = self.projectPoint(pos, template)
print "projectPoint: ", (round(pPoint[0],3), round(pPoint[1],3), round(pPoint[2],3))
depthBase = self.disPoint2Plane(pos, template)
print "depthBase: ", round(depthBase, 3)
[xDisHList, xDisSList] = self.insertionPathsDistance(intNumOfOptionalPath)
disList = self.disPoint2Holes(pos, self.pathOrigins)
holeInfoList = self.closestPath(pos, xDisSList, disList, self.pathOrigins)
print "holeInfoList: ", holeInfoList #[[['F', ' "-3"'], 61.482, 0.0, 79]]
angleList = self.determineAngle(depthBase, holeInfoList)
self.createOptionalPathModel(pos, holeInfoList, intNumOfOptionalPath)
return (pPoint, depthBase, holeInfoList, angleList)
def determineTemplatePlane(self):
print "determineTemplatePlane()"
point1 = self.pathOrigins[0]
point2 = self.pathOrigins[129]
point3 = self.pathOrigins[200]
point1R = point1[0]
point1A = point1[1]
point1S = point1[2]
point2R = point2[0]
point2A = point2[1]
point2S = point2[2]