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EAMapReader.py
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EAMapReader.py
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import unittest
import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import logging
import os
import ntpath
import xml.etree.ElementTree as ET
import re
import zipfile
import shutil
import struct
import numpy as np
import math
################################################################################
# EAMapReader
#
class EAMapReader(ScriptedLoadableModule):
def __init__(self, parent):
ScriptedLoadableModule.__init__(self, parent)
self.parent.title = "EA Map Reader"
self.parent.categories = ["Cardiac Electrophysiology"]
self.parent.dependencies = []
self.parent.contributors = ["Stephan Hohmann (Hannover Medical School)"]
self.parent.helpText = """
This extension reads electroanatomic maps exported from various systems into 3D Slicer.
Currently supported are Ensite NavX (Abbott, St. Paul, MN), CARTO 3 (Biosense Webster, Diamond Bar, CA), and RHYTHMIA (Boston Scientific, Marlborough, MA).
For research use only. The manufacturers of the respective mapping systems are not affiliated with the development of this extension.
This software has not been approved for clinical use, and imported maps should be cross-checked with their representation on the original mapping system.
See documentation for detailed export instructions.
"""
self.parent.helpText += self.getDefaultModuleDocumentationLink()
self.parent.acknowledgementText = """
This extension was developed by Stephan Hohmann, Hannover Medical School.
This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - project no. 380200397.
If you use EAMapReader in your own research please cite the following publication: Hohmann S, Henkenberens C, Zormpas C, Christiansen H, Bauersachs J, Duncker D, Veltmann C. A novel open-source software based high-precision workflow for target definition in cardiac radioablation. J Cardiovasc Electrophysiol 2020. doi:10.1111/jce.14660
"""
################################################################################
# EAMapReaderWidget
#
class EAMapReaderWidget(ScriptedLoadableModuleWidget):
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.logic = EAMapReaderLogic()
self.logic.logCallback = self.addLog
self.logic.progressCallback = self.updateProgress
self.loadingInProgress = False
# Instantiate and connect widgets ...
self.buttonEnsite = qt.QPushButton("Ensite")
self.buttonEnsite.toolTip = "Import Ensite map."
self.buttonEnsite.enabled = True
self.layout.addWidget(self.buttonEnsite)
self.buttonCarto = qt.QPushButton("CARTO 3")
self.buttonCarto.toolTip = "Import CARTO 3 map."
self.buttonCarto.enabled = True
self.layout.addWidget(self.buttonCarto)
self.buttonRhythmia = qt.QPushButton("RHYTHMIA")
self.buttonRhythmia.toolTip = "Import RHYTHMIA Map."
self.buttonRhythmia.enabled = True
self.layout.addWidget(self.buttonRhythmia)
self.statusLabel = qt.QPlainTextEdit()
self.statusLabel.setTextInteractionFlags(qt.Qt.TextSelectableByMouse)
self.statusLabel.setCenterOnScroll(True)
self.layout.addWidget(self.statusLabel)
self.progressBar=qt.QProgressBar()
self.progressBar.setRange(0, 100)
self.progressBar.setValue(0)
self.layout.addWidget(self.progressBar)
# connections
self.buttonEnsite.connect('clicked(bool)', self.onButtonEnsite)
self.buttonCarto.connect('clicked(bool)', self.onButtonCarto)
self.buttonRhythmia.connect('clicked(bool)', self.onButtonRhythmia)
def cleanup(self):
pass
def reenableButtons(self):
self.buttonEnsite.text = "Ensite"
self.buttonEnsite.enabled = True
self.buttonCarto.text = "CARTO 3"
self.buttonCarto.enabled = True
self.buttonRhythmia.text = "RHYTHMIA"
self.buttonRhythmia.enabled = True
def onButtonEnsite(self):
if self.loadingInProgress:
self.loadingInProgress = False
self.logic.abortRequested = True
self.buttonEnsite.text = "Cancelling..."
self.buttonEnsite.enabled = False
return
self.clearLog()
self.filename = qt.QFileDialog.getOpenFileName(self.parent, "Open Ensite file", "", "XML files (*.xml);;All files (*.*)", qt.QFileDialog.ExistingFile)
if len(self.filename) > 0:
self.loadingInProgress = True
self.buttonEnsite.text = "Cancel Ensite import."
if not self.logic.readEnsite(self.filename):
self.addLog("Import failed.")
self.loadingInProgress = False
self.logic.abortRequested = False
self.reenableButtons()
def onButtonCarto(self):
if self.loadingInProgress:
self.loadingInProgress = False
self.logic.abortRequested = True
self.buttonCarto.text = "Cancelling..."
self.buttonCarto.enabled = False
return
self.clearLog()
self.filename = qt.QFileDialog.getOpenFileName(self.parent, "Open CARTO 3 file", "", "ZIP archives (*.zip);;All files (*.*)", qt.QFileDialog.ExistingFile)
if len(self.filename) > 0:
self.loadingInProgress = True
self.buttonCarto.text = "Cancel CARTO 3 import."
if not self.logic.readCarto(self.filename):
self.addLog("Import failed.")
self.loadingInProgress = False
self.logic.abortRequested = False
self.reenableButtons()
def onButtonRhythmia(self):
if self.loadingInProgress:
self.loadingInProgress = False
self.logic.abortRequested = True
self.buttonRhythmia.text = "Cancelling..."
self.buttonRhythmia.enabled = False
return
self.clearLog()
self.filename = qt.QFileDialog.getOpenFileName(self.parent, "Open RHYTHMIA file", "", "RHYTHMIA exported archive (*.000);;All files (*.*)", qt.QFileDialog.ExistingFile)
if len(self.filename) > 0:
self.loadingInProgress = True
self.buttonRhythmia.text = "Cancel RHYTHMIA import."
if not self.logic.readRhythmia(self.filename):
self.addLog("Import failed.")
self.loadingInProgress = False
self.logic.abortRequested = False
self.reenableButtons()
def clearLog(self):
# Clear text in log window
self.statusLabel.plainText = ''
self.progressBar.setValue(0)
slicer.app.processEvents() # force update
def addLog(self, text):
# Append text to log window
self.statusLabel.appendPlainText(text)
slicer.app.processEvents() # force update
def updateProgress(self, percent):
# Update progress bar
self.progressBar.setValue(percent)
slicer.app.processEvents() # force update
################################################################################
# EAMapReaderLogic
#
class EAMapReaderLogic(ScriptedLoadableModuleLogic):
""" Uses ScriptedLoadableModuleLogic base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
"""
def __init__(self):
ScriptedLoadableModuleLogic.__init__(self)
self.logCallback = None
self.progressCallback = None
self.abortRequested = False
self.progress = 0
def addLog(self, text):
logging.info(text)
if self.logCallback:
self.logCallback(text)
def updateProgress(self):
if self.progressCallback:
self.progressCallback(self.progress)
def getTempDirectoryBase(self):
tempDir = qt.QDir(slicer.app.temporaryPath)
fileInfo = qt.QFileInfo(qt.QDir(tempDir), "EAMapReader")
dirPath = fileInfo.absoluteFilePath()
qt.QDir().mkpath(dirPath)
return dirPath
def createTempDirectory(self):
tempDir = qt.QDir(self.getTempDirectoryBase())
tempDirName = qt.QDateTime().currentDateTime().toString("yyyyMMdd_hhmmss_zzz")
fileInfo = qt.QFileInfo(qt.QDir(tempDir), tempDirName)
dirPath = fileInfo.absoluteFilePath()
qt.QDir().mkpath(dirPath)
return dirPath
################################################################################
# Model creation
#
def mkVtkIdList(self, it):
vil = vtk.vtkIdList()
for i in it:
vil.InsertNextId(int(i))
return vil
def CreateMesh(self, modelNode, arrayVertices, arrayVertexNormals, arrayTriangles, labelsScalars, arrayScalars):
# based on https://vtk.org/Wiki/VTK/Examples/Python/DataManipulation/Cube.py
# modelNode : a vtkMRMLModelNode in the Slicer scene which will hold the mesh
# arrayVertices : list of triples [[x1,y1,z2], [x2,y2,z2], ... ,[xn,yn,zn]] of vertex coordinates
# arrayVertexNormals : list of triples [[nx1,ny1,nz2], [nx2,ny2,nz2], ... ] of vertex normals
# arrayTriangles : list of triples of 0-based indices defining triangles
# labelsScalars : list of strings such as ["bipolar", "unipolar"] to label the individual scalars data sets
# arrayScalars : list of n m-tuples for n vertices and m individual scalar sets
# create the building blocks of polydata including data attributes.
mesh = vtk.vtkPolyData()
points = vtk.vtkPoints()
normals = vtk.vtkFloatArray()
polys = vtk.vtkCellArray()
# load the array data into the respective VTK data structures
#self.addLog(" Initializing vertices.")
for i in range(len(arrayVertices)):
points.InsertPoint(i, arrayVertices[i])
if self.abortRequested:
return False
#self.addLog(" Initializing triangles.")
for i in range(len(arrayTriangles)):
polys.InsertNextCell(self.mkVtkIdList(arrayTriangles[i]))
if self.abortRequested:
return False
# Normals: http://vtk.1045678.n5.nabble.com/Set-vertex-normals-td5734525.html
# First pre-allocating memory for the vtkDataArray using vtkDataArray::SetNumberOfComponents() and vtkDataArray::SetNumberOfTuples()
# and then setting the actual values through SetTuple() is orders of magnitude faster than inserting them one-by-one (and allocating memory dynamically)
# with InsertTuple()
normals.SetNumberOfComponents(3)
normals.SetNumberOfTuples(len(arrayVertexNormals))
#self.addLog(" Initializing normals.")
for i in range(len(arrayVertexNormals)):
normals.SetTuple3(i, arrayVertexNormals[i][0], arrayVertexNormals[i][1], arrayVertexNormals[i][2])
if self.abortRequested:
return False
# put together the mesh object
# self.addLog(" Building mesh.")
mesh.SetPoints(points)
mesh.SetPolys(polys)
if(len(arrayVertexNormals) == len(arrayVertices)):
mesh.GetPointData().SetNormals(normals)
if self.abortRequested:
return False
# self.addLog(" Adding scalar data.")
# Add scalars
scalars = []
for j in range(len(labelsScalars)):
scalars.append(vtk.vtkFloatArray())
scalars[j].SetNumberOfComponents(1)
scalars[j].SetNumberOfTuples(len(arrayScalars))
for i in range(len(arrayScalars)):
scalars[j].SetTuple1(i,arrayScalars[i][j])
if self.abortRequested:
return False
scalars[j].SetName(labelsScalars[j])
mesh.GetPointData().AddArray(scalars[j])
if self.abortRequested:
return False
modelNode.SetAndObservePolyData(mesh)
self.addLog("Model created.")
return True
def transformNode(self, node, matrix):
transform = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLinearTransformNode')
transformMatrix = vtk.vtkMatrix4x4()
transformMatrix.Zero()
for row in range(4):
for col in range(4):
transformMatrix.SetElement(row, col, matrix[row][col])
transform.SetMatrixTransformToParent(transformMatrix)
# Apply transform to node...
node.SetAndObserveTransformNodeID(transform.GetID())
# ... and harden it
transformLogic = slicer.vtkSlicerTransformLogic()
transformLogic.hardenTransform(node)
# delete transform node
slicer.mrmlScene.RemoveNode(transform)
################################################################################
# XML parsing helper functions
#
def findallRecursive(self, node, element):
for item in node.findall(element):
yield item
for child in node:
for item in self.findallRecursive(child, element):
yield item
def TextToFloat(self, text):
# First remove any leading and trailing spaces and newlines
leadingNonDigits = "^[^0-9.-]*"
trailingNonDigits = "[^0-9.-]*$"
text = re.sub(leadingNonDigits, "",text)
text = re.sub(trailingNonDigits, "",text)
lines = re.split("\n",text)
numbers = []
for i in range(len(lines)):
lines[i] = re.sub(leadingNonDigits, "",lines[i])
lines[i] = re.sub(trailingNonDigits, "",lines[i])
lineSplit = re.split("\s+", lines[i])
#print(lines[i])
#print(lineSplit)
thisNumbers = []
for j in range(len(lineSplit)):
thisNumbers.append(float(lineSplit[j]))
numbers.append(thisNumbers)
return numbers
################################################################################
# Ensite import
#
def readEnsite(self, filename):
self.progress = 0
self.updateProgress()
if self.abortRequested:
return False
self.addLog("Importing Ensite map:")
self.addLog(" Parsing file "+filename)
tree = ET.parse(filename)
root = tree.getroot()
self.progress = 5
self.updateProgress()
if self.abortRequested:
return False
volumes = list(self.findallRecursive(root, "Volume"))
self.addLog(" Found "+str(len(volumes))+" volumes(s) in file.")
self.progress = 10
self.updateProgress()
if self.abortRequested:
return False
progressSteps = 6
progressEnd = 100
progressIncrement = ((progressEnd - self.progress)/progressSteps)/len(volumes)
volumeCounter = 0
for volume in volumes:
try:
plaintext = volume.find("Vertices").text
vertices = self.TextToFloat(plaintext)
self.addLog(" Reading volume "+str(volumeCounter)+".")
self.addLog(" Read "+str(len(vertices))+" vertices.")
self.progress = self.progress + progressIncrement
self.updateProgress()
except AttributeError:
self.addLog(" ERROR: No vertices found in volume "+str(volumeCounter)+".")
return False
if self.abortRequested:
return False
try:
plaintext = volume.find("Map_data").text
map_data = self.TextToFloat(plaintext)
self.addLog(" Read "+str(len(map_data))+" map data points.")
no_scalars = False
self.progress = self.progress + progressIncrement
self.updateProgress()
except AttributeError:
self.addLog(" No map data points (scalars) found in volume "+str(volumeCounter)+".")
no_scalars = True
if self.abortRequested:
return False
try:
plaintext = volume.find("Normals").text
vertexnormals = self.TextToFloat(plaintext)
self.addLog(" Read "+str(len(vertexnormals))+" vertex normals.")
self.progress = self.progress + progressIncrement
self.updateProgress()
except AttributeError:
self.addLog(" ERROR: No vertex normals found in volume "+str(volumeCounter)+".")
return False
if self.abortRequested:
return False
try:
plaintext = volume.find("Polygons").text
triangles_all = self.TextToFloat(plaintext)
# Change base from 1 to 0
for i in range(len(triangles_all)):
for j in range(3):
triangles_all[i][j] = int(triangles_all[i][j]-1)
except AttributeError:
self.addLog(" ERROR: No polygon information found in volume "+str(volumeCounter)+".")
return False
# Triangles are binned into different "Surfaces of origin" (i.e. models in the file),
# according to the separate table Surface_of_origin
try:
plaintext = volume.find("Surface_of_origin").text
surface_of_origin_1tuple = self.TextToFloat(plaintext) # TextToFloat returns a list of "1-tuples" (lists of length 1): [[1.0], [2.0], [1.0], [0.0], ...]
surface_of_origin = []
for i in range(len(surface_of_origin_1tuple)): # Convert this into a list of lists into a list of integers: [1, 2, 1, 0, ...]
surface_of_origin.append(surface_of_origin_1tuple[i][0])
# Initialize triangles as list of n empty lists, with n being the maximum surface number in surface_of_origin
triangles = [ [] for _ in range(int(max(surface_of_origin)+1))]
for i in range(len(surface_of_origin)):
triangles[int(surface_of_origin[i])].append(triangles_all[i])
self.addLog(" Read "+str(len(triangles_all))+" triangles in "+str(len(triangles))+" separate meshes.")
except:
self.addLog(" NOTE: No \"Surface of Origin\" information in file.")
triangles = [[]]
triangles[0]=triangles_all
self.progress = self.progress + progressIncrement
self.updateProgress()
if self.abortRequested:
return False
for i in range(len(triangles)):
meshName = "Ensite_"+str(volumeCounter)+"-"+str(i)
self.addLog("Creating model "+meshName+":")
modelNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLModelNode')
if not no_scalars:
names = ["Map data"]
scalars = map_data
else:
names = []
scalars = []
if not self.CreateMesh(modelNode, vertices, vertexnormals, triangles[i], names, scalars):
slicer.mrmlScene.RemoveNode(modelNode)
return False
self.progress = self.progress + (2*progressIncrement)/len(triangles)
self.updateProgress()
if self.abortRequested:
return False
# Ensite mesh coordinates are LPS, Slicer is RAS
matrixLPStoRAS = [[-1, 0, 0, 0],
[ 0,-1, 0, 0],
[ 0, 0, 1, 0],
[ 0, 0, 0, 1]]
self.transformNode(modelNode, matrixLPStoRAS)
modelNode.SetName(meshName)
modelNode.CreateDefaultDisplayNodes()
self.addLog("Done.")
self.progress = 100
self.updateProgress()
return True
################################################################################
# CARTO 3 import
#
def readCarto(self, filename):
self.progress = 0
self.updateProgress()
if not zipfile.is_zipfile(filename):
self.addLog("File is not a valid zip archive: "+filename)
return False
if self.abortRequested:
return False
self.addLog("Importing CARTO 3 map:")
tempDir = self.createTempDirectory()
self.addLog(" Extracting archive "+filename+" to "+tempDir)
with zipfile.ZipFile(filename, "r") as cartoArchive:
fileList = cartoArchive.namelist()
for singleFile in fileList:
if singleFile.endswith(".mesh") or singleFile.endswith("_car.txt") or singleFile == "VisiTagExport/Sites.txt":
cartoArchive.extract(singleFile, tempDir)
if self.abortRequested:
shutil.rmtree(tempDir)
return False
self.progress = 10
self.updateProgress()
progressSteps = len(os.listdir(tempDir))
progressEnd = 100
progressIncrement = ((progressEnd - self.progress)/progressSteps)
for filename in os.listdir(tempDir):
if filename.endswith(".mesh"):
if not self.readCartoMesh(os.path.join(tempDir, filename)):
shutil.rmtree(tempDir)
return False
if filename.endswith("_car.txt"):
if not self.readCartoPoints(os.path.join(tempDir, filename)):
shutil.rmtree(tempDir)
return False
self.progress = self.progress + progressIncrement
self.updateProgress()
if self.abortRequested:
shutil.rmtree(tempDir)
return False
if os.path.exists(os.path.join(tempDir, "VisiTagExport/Sites.txt")):
if not self.readCartoAblationSites(os.path.join(tempDir, "VisiTagExport/Sites.txt")):
shutil.rmtree(tempDir)
#Delete temp dir
self.addLog("Cleaning up temporary files.")
shutil.rmtree(tempDir)
self.progress = 100
self.updateProgress()
self.addLog("Done.")
return True
def readCartoMesh(self, filename):
meshName = ntpath.basename(filename)
self.addLog("Reading "+meshName+":")
section = "none"
verticesText = ""
trianglesText = ""
scalarsText = ""
attributesText = ""
scalarLabels = ""
with open(filename, "r", encoding="latin-1") as filehandle:
for line in filehandle:
if self.abortRequested:
return False
# Remove trailing newline and trailing and leading spaces
line = re.sub("[\n]$", "", line)
line = re.sub("[ ]*$", "", line)
line = re.sub("^[ ]*", "", line)
if len(line) == 0: # empty line
continue
if line[0] == ";": # comment line
continue
if line.find("[GeneralAttributes]") > -1:
section = "general"
continue
if line.find("[VerticesSection]") > -1:
section = "vertices"
continue
if line.find("[TrianglesSection]") > -1:
section = "triangles"
continue
if line.find("[VerticesColorsSection]") > -1:
section = "scalars"
continue
if line.find("[VerticesAttributesSection]") > -1:
section = "attributes"
continue
if section == "general":
# Look for scalar labels
if line.find("ColorsNames") > -1:
line = re.sub("^ColorsNames[ ]*=[ ]*", "", line)
scalarLabels = re.split("\s+",line)
if section == "vertices":
# remove line number ("0 =")
line = re.sub("[0-9]*[ ]*=[ ]*", "", line)
# add "clean" line to string
verticesText = verticesText+line+'\n'
if section == "triangles":
line = re.sub("[0-9]*[ ]*=[ ]*", "", line)
trianglesText = trianglesText+line+'\n'
if section == "scalars":
line = re.sub("[0-9]*[ ]*=[ ]*", "", line)
scalarsText = scalarsText+line+'\n'
if section == "attributes":
line = re.sub("[0-9]*[ ]*=[ ]*", "", line)
attributesText = attributesText+line+'\n'
verticesLong = self.TextToFloat(verticesText)
vertices = []
vertexnormals = []
for i in range(len(verticesLong)):
vertices.append([verticesLong[i][0], verticesLong[i][1], verticesLong[i][2]])
vertexnormals.append([verticesLong[i][3], verticesLong[i][4], verticesLong[i][5]])
if self.abortRequested:
return False
trianglesLong = self.TextToFloat(trianglesText)
triangles = []
for i in range(len(trianglesLong)):
triangles.append([trianglesLong[i][0], trianglesLong[i][1], trianglesLong[i][2]])
if self.abortRequested:
return False
if len(scalarsText) > 0:
scalars = self.TextToFloat(scalarsText)
else:
scalars = []
if len(attributesText) > 0:
attributes = self.TextToFloat(attributesText) # currently not used
else:
attributes = []
self.addLog(" Read "+str(len(vertices))+" vertices, "+str(len(vertexnormals))+" vertex normals, and "+str(len(triangles))+" triangles.")
self.addLog(" Read "+str(len(scalarLabels))+" sets of scalars: "+str(scalarLabels)+".")
meshName = "CARTOmesh_"+re.sub(".mesh$", "", meshName)
self.addLog("Creating model "+meshName+":")
modelNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLModelNode')
if not self.CreateMesh(modelNode, vertices, vertexnormals, triangles, scalarLabels, scalars):
slicer.mrmlScene.RemoveNode(modelNode)
return False
self.transformCarto(modelNode)
modelNode.SetName(meshName)
modelNode.CreateDefaultDisplayNodes()
return True
def readCartoPoints(self, filename):
pointsName = ntpath.basename(filename)
self.addLog("Reading "+pointsName+":")
fiducialsNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLMarkupsFiducialNode')
fiducialsNode.GetMarkupsDisplayNode().SetVisibility(0)
with open(filename, "r") as filehandle:
for line in filehandle:
if self.abortRequested:
return False
# Remove trailing newline and trailing and leading spaces
line = re.sub("[\n]$", "", line)
line = re.sub("[ ]*$", "", line)
line = re.sub("^[ ]*", "", line)
if len(line) == 0: # empty line
continue
lineElements = re.split("[ \t]*", line)
if lineElements[0] == "VERSION_5_0" or lineElements[0] == "VERSION_4_0":
pointsName = lineElements[1]
if lineElements[0] == "P":
pointNr = int(lineElements[2])
pointX = float(lineElements[4])
pointY = float(lineElements[5])
pointZ = float(lineElements[6])
unipolar = float(lineElements[10])
bipolar = float(lineElements[11])
lat = float(lineElements[12])
n = fiducialsNode.AddFiducial(pointX, pointY, pointZ)
fiducialsNode.SetNthControlPointLabel(n, "Point # "+str(pointNr)+" in "+pointsName)
fiducialsNode.SetNthControlPointDescription(n, "Bipolar "+str(bipolar)+" / Unipolar "+str(unipolar)+" / LAT "+str(lat))
fiducialsNode.SetNthControlPointLocked(n, 1)
self.transformCarto(fiducialsNode)
pointsName = "CARTOpoints_"+re.sub("_car.txt$", "", pointsName)
fiducialsNode.SetName(pointsName)
fiducialsNode.GetMarkupsDisplayNode().SetTextScale(0)
fiducialsNode.GetMarkupsDisplayNode().SetVisibility(1)
self.addLog("Created markup fiducials "+pointsName+".")
fiducialsNode.CreateDefaultDisplayNodes()
return True
def readCartoAblationSites(self, filename):
pointsName = ntpath.basename(filename)
self.addLog("Reading "+pointsName+":")
fiducialsNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLMarkupsFiducialNode')
fiducialsNode.GetMarkupsDisplayNode().SetVisibility(0)
with open(filename, "r") as filehandle:
for line in filehandle:
if self.abortRequested:
return False
# Remove trailing newline and trailing and leading spaces
line = re.sub("[\n]$", "", line)
line = re.sub("[ ]*$", "", line)
line = re.sub("^[ ]*", "", line)
if len(line) == 0: # empty line
continue
lineElements = re.split("\s+", line)
if lineElements[0] == "Session" or lineElements[0] == "VERSION_4_0":
continue
pointNr = int(lineElements[2])
pointX = float(lineElements[3])
pointY = float(lineElements[4])
pointZ = float(lineElements[5])
duration = float(lineElements[6])
avgForce = float(lineElements[7])
power = float(lineElements[8])
fti = float(lineElements[9])
n = fiducialsNode.AddFiducial(pointX, pointY, pointZ)
fiducialsNode.SetNthControlPointLabel(n, "Ablation site # "+str(pointNr))
fiducialsNode.SetNthControlPointDescription(n, "FTI "+str(fti)+" ("+str(duration)+" sec, "+str(power)+" W, "+str(avgForce)+" g")
fiducialsNode.SetNthControlPointLocked(n, 1)
self.transformCarto(fiducialsNode)
pointsName = "CARTOablationsites"
fiducialsNode.SetName(pointsName)
fiducialsNode.GetMarkupsDisplayNode().SetTextScale(0)
fiducialsNode.GetMarkupsDisplayNode().SetUseGlyphScale(False)
fiducialsNode.GetMarkupsDisplayNode().SetGlyphSize(6)
fiducialsNode.GetMarkupsDisplayNode().SetSelectedColor(1,0,0)
fiducialsNode.GetMarkupsDisplayNode().SetVisibility(1)
self.addLog("Created markup fiducials "+pointsName+".")
fiducialsNode.CreateDefaultDisplayNodes()
return True
def transformCarto(self, node):
# CARTO mesh is in LPS and seems to be additionally rotated 90 deg around the LR axis
# Transform matrix from CARTO to Slicer is
# -1.0 0.0 0.0 0.0
# 0.0 0.0 1.0 0.0
# 0.0 1.0 0.0 0.0
# 0.0 0.0 0.0 1.0
matrix = [[-1, 0, 0, 0],
[0, 0, 1, 0],
[0, 1, 0, 0],
[0, 0, 0, 1]]
self.transformNode(node, matrix)
################################################################################
# RHYTHMIA import
#
def readRhythmia(self, filename):
self.progress = 0
self.updateProgress()
tempDir = self.createTempDirectory()
filenameStem = os.path.splitext(os.path.basename(filename))[0]
archiveConcatenated = os.path.join(tempDir, filenameStem+".ALL")
print(archiveConcatenated)
if not self.concatenateRhythmiaFiles(filename, archiveConcatenated):
shutil.rmtree(tempDir)
return False
if not self.expandBinaryPayloadFromRhythmiaArchive(archiveConcatenated , os.path.join(tempDir, "archive.xml"), tempDir):
shutil.rmtree(tempDir)
return False
if not self.processRhythmiaXML(os.path.join(tempDir, "archive.xml"), tempDir):
shutil.rmtree(tempDir)
return False
self.progress = 100
self.updateProgress()
# Delete temp dir
self.addLog("Cleaning up temporary files.")
shutil.rmtree(tempDir)
self.progress = 100
self.updateProgress()
self.addLog("Done.")
return True
def concatenateRhythmiaFiles(self, startfilename, targetfilename):
# Get all files startfilename.000 , .001, .002, ...
filePathStem = os.path.splitext(startfilename)[0]
filesToAdd = []
i=0
while(os.path.isfile(filePathStem+"."+str(i).zfill(3))):
filesToAdd.append(filePathStem+"."+str(i).zfill(3))
i += 1
progressIncrement = (20-self.progress) / len(filesToAdd)
# Merge all these files into one (in the temp dir)
with open(targetfilename, "wb", 0) as targetfile:
for fileToAdd in filesToAdd:
with open(fileToAdd, "rb") as fid:
self.addLog("Reading file "+fileToAdd+" ...")
targetfile.write(fid.read())
self.progress += progressIncrement
self.updateProgress()
if self.abortRequested:
return False
targetfile.flush()
os.fsync(targetfile.fileno())
self.progress = 20
self.updateProgress()
return True
def expandBinaryPayloadFromRhythmiaArchive(self, archiveFilename, xmlFilename, folder):
# Parse the (completed, concatenated) Rhythmia archive archiveFilename and extract the binary chunks
# into separate files in the directory folder
# Also, write the remaining XML (stripped from binary data) into xmlFilename
tagBinaryStart = re.compile(b"<inlinedbin .* BIN=[0-9]*>")
tagBinaryEnd = re.compile(b"</inlinedbin>")
pointer = 0
xmlBuffer = ""
binaryFilenamePattern = "binary"
# We are using a rather rough method here by loading the entire (multi-GB) archive into
# (virtual) memory as one chunk. If this should cause problems with even larger archives in
# the future, chunk-wise processing might be an option (caution: expressions spanning chunk boundaries)
# See e.g. https://stackoverflow.com/questions/29052510/search-string-with-regex-in-large-binary-file-2-gb-or-more
# and https://stackoverflow.com/questions/14289421/how-to-use-mmap-in-python-when-the-whole-file-is-too-big
readChunkSize = 500 * 1024 * 1024 # 500 MB, arbitrary
archiveBuffer = bytes("", 'ASCII') # explicite bytes() type cast necessary for Python3 compatability, see https://stackoverflow.com/questions/21689365/python-3-typeerror-must-be-str-not-bytes-with-sys-stdout-write/21689447
readChunk = ""
archiveFileSize = os.stat(archiveFilename).st_size
progressStart = self.progress
progressEnd = 50
self.addLog("Unpacking archive ... (This can take several minutes and Slicer might appear unresponsive)")
with open(archiveFilename, "rb") as archiveFile:
while True:
readChunk = archiveFile.read(readChunkSize) # Read in chunks of 500 MB to allow processing of cancel requests between chunks
if len(readChunk) == 0: # End of file
break
archiveBuffer += readChunk
self.progress = progressStart + ((progressEnd-progressStart)*(len(archiveBuffer)/archiveFileSize))
self.updateProgress()
if self.abortRequested:
return False
self.progress = progressEnd
self.updateProgress()
progressStart = self.progress
progressEnd = 80
binaryFileCounter = 0
while pointer < len(archiveBuffer):
# locate beginning and end of next opening <inlinedbin> tag
nextInlinedbinOpening = tagBinaryStart.search(archiveBuffer, pointer)
# next <inlinedbin> tag found
if nextInlinedbinOpening:
openingTagStart = nextInlinedbinOpening.start()
openingTagEnd = nextInlinedbinOpening.end()
# copy everything from current seek pointer till the end of the opening tag
# to the "clean" XML
# Note: In Python3, the archiveBuffer is (binary) bytes, but the xmlBuffer is a string --> explicite decoding necessary
xmlBuffer += archiveBuffer[pointer:openingTagEnd].decode('ASCII')
# locate beginning and end of next closing <inlinedbin> tag, start search at
# end of opening tag
nextInlinedbinClosing = tagBinaryEnd.search(archiveBuffer, openingTagEnd)
if nextInlinedbinClosing:
closingTagStart = nextInlinedbinClosing.start()
closingTagEnd = nextInlinedbinClosing.end()
# write out binary payload
binaryFileName = binaryFilenamePattern+str(binaryFileCounter).zfill(8)+".dat"
binaryFileCounter += 1
with open(os.path.join(folder, binaryFileName), "wb", 0) as binaryFile:
binaryFile.write(archiveBuffer[openingTagEnd:closingTagStart])
binaryFile.flush()
os.fsync(binaryFile.fileno())
# write filename into clean XML
xmlBuffer += binaryFileName
# set pointer to beginning of closing tag (next search from here)
pointer = closingTagStart
else:
self.addLog("Premature end of archive file (closing </inlinedbin> tag not found)")
xmlBuffer += archiveBuffer[pointer:].decode('ASCII')
pointer = pointer = len(archiveBuffer)
return False
else: # no opening <inlinedbin> found
# copy everything from current pointer location till end of buffer into clean XML
xmlBuffer += archiveBuffer[pointer:].decode('ASCII')
pointer = len(archiveBuffer)
self.progress = progressStart+((progressEnd-progressStart)*(pointer/len(archiveBuffer)))
self.updateProgress()
if self.abortRequested:
return False
# Correct one remaining non-XML-conformant statement:
# the <inlinedbin> tags contain an attribute declaration like BIN=580 (the number of bytes)
# However, this should read BIN="580" in order to be standard-conformant
xmlBuffer = re.sub(r'BIN=([0-9]*)', r'BIN="\1"', xmlBuffer)
with open(xmlFilename, "w") as xmlFile:
xmlFile.write(xmlBuffer)
return True
# convert voltage values from log(uV) to mV
def calculateRhythmiaVoltage(self, x):
return math.exp(x) / 1000
def processRhythmiaXML(self, xmlFilename, folder):
calculateRhythmiaVoltageVectorized = np.vectorize(self.calculateRhythmiaVoltage)
matrixRhythmiaToSlicer = [[ 1, 0, 0, 0],
[ 0, 0,-1, 0],
[ 0, 1, 0, 0],
[ 1, 0, 0, 1]]
tree = ET.parse(xmlFilename)
root = tree.getroot()
patientsList = []
patients = list(self.findallRecursive(root, "Patient"))
for patient in patients:
patProperties = patient.find("PatientInfo").find("Properties")
if patProperties is not None:
patID = patProperties.find("PatientID").text
patName = patProperties.find("NameLast").text+", "+patProperties.find("NameFirst").text
patientsList.append([patID, patName])
# Create patient in subject hierarchy
subjectHierarchyNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
sceneRoot = subjectHierarchyNode.GetSceneItemID()
subjectHierarchyNode.CreateSubjectItem(sceneRoot, patID+" ("+patName+")")
currentSubjectHierarchyPatientID = subjectHierarchyNode.GetItemChildWithName(sceneRoot, patID+" ("+patName+")")
studies = list(self.findallRecursive(patient, "Study"))
for study in studies:
studyName = study.find("Properties").find("Label").text
# Create study in subject hierarchy
subjectHierarchyNode.CreateStudyItem(currentSubjectHierarchyPatientID, studyName)
currentSubjectHierarchyStudyID = subjectHierarchyNode.GetItemChildWithName(currentSubjectHierarchyPatientID, studyName)
self.addLog("Processing study \""+studyName+"\" of patient ID "+patID+" ("+patName+")...")
anatomies = list(self.findallRecursive(study, "Anatomy"))
for anatomyNumber, anatomy in enumerate(anatomies):
anatomyName = anatomy.find("Properties").find("Label").text
if anatomyName == None:
anatomyName = "unnamed"+str(anatomyNumber)
anatomyTransformString = anatomy.find("Transform").text
anatomyTransformMatrix = [[1, 0, 0, 0],
[0, 1, 0, 0],
[0, 0, 1, 0],
[0, 0, 0, 1]]
if anatomyTransformString != None:
anatomyTransformNumbers = re.split("\s+", anatomyTransformString)
i = 0
for row in range(4):
for col in range(4):
anatomyTransformMatrix[col][row] = float(anatomyTransformNumbers[i])
i += 1
scalarLabels = []
scalarValues = []
meshes = list(self.findallRecursive(anatomy, "Mesh"))
for mesh in meshes: