def restoreStateBeforeExitingModule(self):
"""Load the last state of the module when the user exited (labelmap, opacity, contrast window, etc.)
"""
try:
if self.savedVolumeID:
# There is a previously saved valid state.
SlicerUtil.setActiveVolumeIds(self.savedVolumeID)
SlicerUtil.changeContrastWindow(self.savedContrastLevel[0],
self.savedContrastLevel[1])
# if self.savedLabelmapID:
# print "Restoring active labelmap: " + self.savedLabelmapID
# # There was a valid labelmap. Restore it
# SlicerUtil.displayLabelmapVolume(self.savedLabelmapID)
# # Restore previous opacity
# SlicerUtil.changeLabelmapOpacity(self.savedLabelmapOpacity)
# else:
# # Hide labelmap
# print "No labelmap saved. Hide all"
# SlicerUtil.displayLabelmapVolume(None)
# else:
# # Hide labelmap
# print "No volume saved. Hide labelmap"
# SlicerUtil.displayLabelmapVolume(None)
# Restore layout
SlicerUtil.changeLayout(self.savedLayout)
except:
Util.print_last_exception()
pass
def loadFiducials(self, volumeNode, fileName):
""" Load from disk a list of fiducials for a particular volume node
:param volumeNode: Volume (scalar node)
:param fileName: full path of the file to load the fiducials where
"""
with open(fileName, "r") as f:
xml = f.read()
geom = GTD.GeometryTopologyData.from_xml(xml)
for point in geom.points:
subtype = point.chest_type
if subtype in self.params.mainTypes.keys():
# Main type. The subtype will be "Any"
mainType = subtype
subtype = 0
else:
mainType = self.params.getMainTypeForSubtype(subtype)
# Activate the current fiducials list based on the main type
fidList = self.setActiveFiducialsListNode(volumeNode, mainType, subtype, point.feature_type)
# Check if the coordinate system is RAS (and make the corresponding transform otherwise)
if geom.coordinate_system == geom.LPS:
coord = Util.lps_to_ras(point.coordinate)
elif geom.coordinate_system == geom.IJK:
coord = Util.ijk_to_ras(volumeNode, point.coordinate)
else:
# Try default mode (RAS)
coord = point.coordinate
# Add the fiducial
fidList.AddFiducial(coord[0], coord[1], coord[2], self.getMarkupLabel(mainType, subtype, point.feature_type))
def saveResults(self):
try:
if SlicerUtil.isSlicerACILLoaded():
saveResultsRemotely = qt.QMessageBox.question(
slicer.util.mainWindow(), "Save volume remotely?",
"Do you want to save the results remotely?",
qt.QMessageBox.Yes
| qt.QMessageBox.No) == qt.QMessageBox.Yes
else:
saveResultsRemotely = False
# First, save locally to the results directory (as a backup)
labelmap = self.getCurrentLabelMapNode()
localPath = os.path.join(self.saveResultsDirectoryButton.directory,
labelmap.GetName() + ".nrrd")
if saveResultsRemotely:
self.caseNavigatorWidget.uploadVolume(
labelmap,
callbackFunction=self._uploadFileCallback_,
localPath=localPath)
else:
slicer.util.saveNode(labelmap, localPath)
slicer.util.infoDisplay(
"Results saved to '{}'".format(localPath))
except Exception as ex:
Util.print_last_exception()
slicer.util.errorDisplay(ex.message)
def loadFiducialsXml(self, volumeNode, fileName):
""" Load from disk a list of fiducials for a particular volume node
:param volumeNode: Volume (scalar node)
:param fileName: full path of the file to load the fiducials where
"""
with open(fileName, "r") as f:
xml = f.read()
self.currentGeometryTopologyData = gtd.GeometryTopologyData.from_xml(
xml)
for point in self.currentGeometryTopologyData.points:
# Activate the current fiducials list based on the type list
typesList = self.getTypesListFromXmlPoint(point)
fidListNode = self.setActiveFiducialsListNode(
volumeNode, typesList)
# Check if the coordinate system is RAS (and make the corresponding transform otherwise)
if self.currentGeometryTopologyData.coordinate_system == self.currentGeometryTopologyData.LPS:
coord = Util.lps_to_ras(point.coordinate)
elif self.currentGeometryTopologyData.coordinate_system == self.currentGeometryTopologyData.IJK:
coord = Util.ijk_to_ras(volumeNode, point.coordinate)
else:
# Try default mode (RAS)
coord = point.coordinate
# Add the fiducial
fidListNode.AddFiducial(coord[0], coord[1], coord[2],
self.getMarkupLabel(typesList))
def loadFiducialsXml(self, volumeNode, fileName):
""" Load from disk a list of fiducials for a particular volume node
:param volumeNode: Volume (scalar node)
:param fileName: full path of the file to load the fiducials where
"""
with open(fileName, "r") as f:
xml = f.read()
self.currentGeometryTopologyData = GTD.GeometryTopologyData.from_xml(
xml)
for point in self.currentGeometryTopologyData.points:
subtype = point.chest_type
if subtype in self.params.mainTypes.keys():
# Main type. The subtype will be "Any"
mainType = subtype
subtype = 0
else:
mainType = self.params.getMainTypeForSubtype(subtype)
# Activate the current fiducials list based on the main type
fidListNode = self.setActiveFiducialsListNode(
volumeNode, mainType, subtype, point.feature_type)
# Check if the coordinate system is RAS (and make the corresponding transform otherwise)
if self.currentGeometryTopologyData.coordinate_system == self.currentGeometryTopologyData.LPS:
coord = Util.lps_to_ras(point.coordinate)
elif self.currentGeometryTopologyData.coordinate_system == self.currentGeometryTopologyData.IJK:
coord = Util.ijk_to_ras(volumeNode, point.coordinate)
else:
# Try default mode (RAS)
coord = point.coordinate
# Add the fiducial
fidListNode.AddFiducial(
coord[0], coord[1], coord[2],
self.getMarkupLabel(mainType, subtype, point.feature_type))
def saveResultsCurrentNode(self):
""" Get current active node and save the xml fiducials file
"""
try:
d = self.saveResultsDirectoryButton.directory
if not os.path.isdir(d):
# Ask the user if he wants to create the folder
if qt.QMessageBox.question(
slicer.util.mainWindow(), "Create directory?",
"The directory '{0}' does not exist. Do you want to create it?"
.format(d), qt.QMessageBox.Yes
| qt.QMessageBox.No) == qt.QMessageBox.Yes:
try:
os.makedirs(d)
# Make sure that everybody has write permissions (sometimes there are problems because of umask)
os.chmod(d, 0o777)
except:
qt.QMessageBox.warning(
slicer.util.mainWindow(), 'Directory incorrect',
'The folder "{0}" could not be created. Please select a valid directory'
.format(d))
return
else:
# Abort process
SlicerUtil.logDevelop("Saving results process aborted",
includePythonConsole=True)
return
# self.logic.saveCurrentFiducials(d, self.caseNavigatorWidget, self.uploadFileResult)
# qt.QMessageBox.information(slicer.util.mainWindow(), 'Results saved',
# "The results have been saved succesfully")
# else:
if SlicerUtil.isSlicerACILLoaded():
question = qt.QMessageBox.question(
slicer.util.mainWindow(), "Save results remotely?",
"Your results will be saved locally. Do you also want to save your results in your remote server? (MAD, etc.)",
qt.QMessageBox.Yes | qt.QMessageBox.No
| qt.QMessageBox.Cancel)
if question == qt.QMessageBox.Cancel:
return
saveInRemoteRepo = question == qt.QMessageBox.Yes
else:
saveInRemoteRepo = False
self.logic.saveCurrentFiducials(
d,
caseNavigatorWidget=self.caseNavigatorWidget,
callbackFunction=self.uploadFileResult,
saveInRemoteRepo=saveInRemoteRepo)
qt.QMessageBox.information(
slicer.util.mainWindow(), 'Results saved',
"The results have been saved succesfully")
except:
Util.print_last_exception()
qt.QMessageBox.critical(
slicer.util.mainWindow(), "Error when saving the results",
"Error when saving the results. Please review the console for additional info"
)
def refreshTextboxes(self, reset=False):
""" Update the information of the textboxes that give information about the measurements
"""
self.aortaTextBox.setText("0")
self.paTextBox.setText("0")
self.ratioTextBox.setText("0")
self.ratioTextBox.setStyleSheet(
" QLineEdit { background-color: white; color: black}")
volumeId = self.volumeSelector.currentNodeID
# if volumeId not in self.logic.currentVolumesLoaded:
# return
if volumeId:
self.logic.changeActiveRulersColor(volumeId,
self.logic.defaultColor)
aorta = None
pa = None
if not reset:
rulerAorta, newAorta = self.logic.getRulerNodeForVolumeAndStructure(
self.volumeSelector.currentNodeID,
self.logic.AORTA,
createIfNotExist=False)
rulerPA, newPA = self.logic.getRulerNodeForVolumeAndStructure(
self.volumeSelector.currentNodeID,
self.logic.PA,
createIfNotExist=False)
if rulerAorta:
aorta = rulerAorta.GetDistanceMeasurement()
self.aortaTextBox.setText(str(aorta))
if rulerPA:
pa = rulerPA.GetDistanceMeasurement()
self.paTextBox.setText(str(pa))
if pa is not None and aorta is not None and aorta != 0:
try:
ratio = pa / aorta
self.ratioTextBox.setText(str(ratio))
if ratio > 1.0:
# Switch colors ("alarm")
st = " QLineEdit {{ background-color: rgb({0}, {1}, {2}); color: white }}". \
format(int(self.logic.defaultWarningColor[0]*255),
int(self.logic.defaultWarningColor[1]*255),
int(self.logic.defaultWarningColor[2]*255))
self.ratioTextBox.setStyleSheet(st)
self.logic.changeActiveRulersColor(
volumeId, self.logic.defaultWarningColor)
except Exception:
Util.print_last_exception()
def refreshTextboxes(self, reset=False):
""" Update the information of the textboxes that give information about the measurements
"""
self.rvTextBox.setText("0")
self.lvTextBox.setText("0")
self.ratioTextBox.setText("0")
self.ratioTextBox.setStyleSheet(
" QLineEdit { background-color: white; color: black}")
volumeId = self.volumeSelector.currentNodeID
# if volumeId not in self.logic.currentVolumesLoaded:
# return
rv = None
lv = None
if not reset:
rulerRV, newRV = self.logic.getRulerNodeForVolumeAndStructure(
self.volumeSelector.currentNodeID,
self.logic.RV,
createIfNotExist=False)
rulerLV, newLV = self.logic.getRulerNodeForVolumeAndStructure(
self.volumeSelector.currentNodeID,
self.logic.LV,
createIfNotExist=False)
if rulerRV:
rv = rulerRV.GetDistanceMeasurement()
self.rvTextBox.setText(str(rv))
if rulerLV:
lv = rulerLV.GetDistanceMeasurement()
self.lvTextBox.setText(str(lv))
if lv is not None and rv is not None and rv != 0:
try:
ratio = lv / rv
self.ratioTextBox.setText(str(ratio))
if ratio > 1.0:
# Switch colors ("alarm")
st = " QLineEdit {{ background-color: rgb({0}, {1}, {2}); color: white }}". \
format(int(self.logic.defaultWarningColor[0]*255),
int(self.logic.defaultWarningColor[1]*255),
int(self.logic.defaultWarningColor[2]*255))
self.ratioTextBox.setStyleSheet(st)
except Exception:
Util.print_last_exception()
def saveResultsCurrentNode(self):
""" Get current active node and save the xml fiducials file
"""
try:
d = self.saveResultsDirectoryButton.directory
if not os.path.isdir(d):
# Ask the user if he wants to create the folder
if qt.QMessageBox.question(
slicer.util.mainWindow(), "Create directory?",
"The directory '{0}' does not exist. Do you want to create it?"
.format(d), qt.QMessageBox.Yes
| qt.QMessageBox.No) == qt.QMessageBox.Yes:
try:
os.makedirs(d)
# Make sure that everybody has write permissions (sometimes there are problems because of umask)
os.chmod(d, 0777)
except:
qt.QMessageBox.warning(
slicer.util.mainWindow(), 'Directory incorrect',
'The folder "{0}" could not be created. Please select a valid directory'
.format(d))
return
self.logic.saveCurrentFiducials(d,
self.caseNavigatorWidget,
self.uploadFileResult)
qt.QMessageBox.information(
slicer.util.mainWindow(), 'Results saved',
"The results have been saved succesfully")
else:
self.logic.saveCurrentFiducials(d, self.caseNavigatorWidget,
self.uploadFileResult)
qt.QMessageBox.information(
slicer.util.mainWindow(), 'Results saved',
"The results have been saved succesfully")
except:
Util.print_last_exception()
qt.QMessageBox.critical(
slicer.util.mainWindow(), "Error when saving the results",
"Error when saving the results. Please review the console for additional info"
)
def saveCurrentFiducials(self, directory):
""" Save all the fiducials for the current volume.
The name of the file will be VolumeName_parenchymaTraining.xml"
:param volume: scalar node
:param directory: destiny directory
:return:
"""
volume = slicer.util.getNode(self.currentVolumeId)
print("DEBUG: saving the fidcuals for volume " + volume.GetName())
# Iterate over all the fiducials list nodes
pos = [0,0,0]
topology = GTD.GeometryTopologyData()
topology.coordinate_system = topology.LPS
# Get the transformation matrix LPS-->IJK
matrix = Util.get_lps_to_ijk_transformation_matrix(volume)
topology.lps_to_ijk_transformation_matrix = Util.convert_vtk_matrix_to_list(matrix)
for fidListNode in slicer.util.getNodes("{0}_fiducials_*".format(volume.GetID())).itervalues():
# Get all the markups
for i in range(fidListNode.GetNumberOfMarkups()):
fidListNode.GetNthFiducialPosition(i, pos)
# Get the type from the description (region will always be 0)
desc = fidListNode.GetNthMarkupDescription(i)
typeId = int(desc.split("_")[0])
artifactId = int(desc.split("_")[1])
# Switch coordinates from RAS to LPS
lps_coords = Util.ras_to_lps(list(pos))
p = GTD.Point(0, typeId, artifactId, lps_coords)
topology.add_point(p)
# Get the xml content file
xml = topology.to_xml()
# Save the file
fileName = os.path.join(directory, "{0}_parenchymaTraining.xml".format(volume.GetName()))
with open(fileName, 'w') as f:
f.write(xml)
# Mark the current volume as saved
#self.savedVolumes.add(volume.GetID())
self.savedVolumes[volume.GetID()] = True
def saveStateBeforeEnteringModule(self):
"""Save the state of the module regarding labelmap, etc. This state will be saved/loaded when
exiting/entering the module
"""
if self.preventSavingState:
# Avoid that the first time that the module loads, the state is saved twice
self.preventSavingState = False
return
# Save existing layout
self.savedLayout = None
if slicer.app.layoutManager() is not None:
self.savedLayout = slicer.app.layoutManager().layout
# Get the active volume (it it exists)
activeVolumeId = SlicerUtil.getFirstActiveVolumeId()
if activeVolumeId is None:
# Reset state
self.resetModuleState()
else:
# There is a Volume loaded. Save state
try:
self.savedVolumeID = activeVolumeId
displayNode = SlicerUtil.getNode(
activeVolumeId).GetDisplayNode()
self.savedContrastLevel = (displayNode.GetWindow(),
displayNode.GetLevel())
# activeLabelmapId = SlicerUtil.getFirstActiveLabelmapId()
# self.savedLabelmapID = activeLabelmapId
# if activeLabelmapId is None:
# self.savedLabelmapOpacity = None
# else:
# self.savedLabelmapOpacity = SlicerUtil.getLabelmapOpacity()
# # Hide any labelmap
# SlicerUtil.displayLabelmapVolume(None)
except:
Util.print_last_exception()
# Not action really needed
pass
def refreshTextboxes(self, reset=False):
""" Update the information of the textboxes that give information about the measurements
"""
self.aortaTextBox.setText("0")
self.paTextBox.setText("0")
self.ratioTextBox.setText("0")
self.ratioTextBox.setStyleSheet(" QLineEdit { background-color: white; color: black}")
volumeId = self.volumeSelector.currentNodeId
if volumeId not in self.logic.currentVolumesLoaded:
return
if volumeId:
self.logic.changeColor(volumeId, self.logic.defaultColor)
aorta = None
pa = None
if not reset:
rulerAorta, newAorta = self.logic.getRulerNodeForVolumeAndStructure(
self.volumeSelector.currentNodeId, self.logic.AORTA, createIfNotExist=False
)
rulerPA, newPA = self.logic.getRulerNodeForVolumeAndStructure(
self.volumeSelector.currentNodeId, self.logic.PA, createIfNotExist=False
)
if rulerAorta:
aorta = rulerAorta.GetDistanceMeasurement()
self.aortaTextBox.setText(str(aorta))
if rulerPA:
pa = rulerPA.GetDistanceMeasurement()
self.paTextBox.setText(str(pa))
if aorta is not None and aorta != 0:
try:
ratio = pa / aorta
self.ratioTextBox.setText(str(ratio))
if ratio > 1:
# Switch colors ("alarm")
self.ratioTextBox.setStyleSheet(" QLineEdit { background-color: rgb(255, 0, 0); color: white}")
self.logic.changeColor(volumeId, self.logic.defaultWarningColor)
except Exception:
Util.print_last_exception()
if not path.isdir(results_dir):
# Create the results folder if it doesn't exist
os.makedirs(results_dir)
files = os.listdir(files_dir)
types_delete = [97, 98, 99, 100]
types_replace = {
94: 84,
96: 85,
101: 34,
102: 86,
103: 88
}
for file_name in files:
if Util.get_file_extension(file_name) != ".xml":
continue
p = path.join(files_dir, file_name)
print ("Processing {0}...".format(file_name))
with open(p, "r+b") as f:
xml = f.read()
geom = gtd.GeometryTopologyData.from_xml(xml)
geom.num_dimensions = 3
points = []
change_coords = geom.coordinate_system != geom.LPS
for point in geom.points:
if point.chest_type not in types_delete:
if types_replace.has_key(point.chest_type):
# Replace type
point.chest_type = types_replace[point.chest_type]
if change_coords:
sys.path.append("/Users/jonieva/Projects/SlicerCIP/Scripted/CIP_Common/")
from CIP.logic import geometry_topology_data as gtd
from CIP.logic import Util
import os
import os.path
import re
wrong_cases_path = "/Volumes/Mac500/Dropbox/rola-jorge/LH ROI failure/"
xmls_path = "/Volumes/Mac500/Dropbox/ACIL-Biomarkers/parenchyma training 2015-10-02/"
results_path = "/Volumes/Mac500/Data/tempdata/parenchyma training 2015-10-02/Removed Points/LH ROI failure"
current_case = ""
caseIds = dict()
for file_name in os.listdir(wrong_cases_path):
if Util.get_file_extension(file_name) != ".png":
continue
expr = "(?P<caseid>(^(.*?)_(.*?)_(.*?)_(.*?)_(.*?)))_(.*?)_p(?P<point>(.*?))_(.*)"
r = re.match(expr, file_name)
caseId = r.group("caseid")
point = int(r.group("point"))
if not caseIds.has_key(caseId):
caseIds[caseId] = []
caseIds[caseId].append(point)
for caseId, excludedPoints in caseIds.iteritems():
# Load the Geometry object
geom = gtd.GeometryTopologyData.from_xml_file(os.path.join(xmls_path, caseId + "_parenchymaTraining.xml"))
newPoints=[]
for i in range(len(geom.points)):
if i not in excludedPoints:
def saveCurrentFiducials(self,
localFilePath,
caseNavigatorWidget=None,
callbackFunction=None,
saveInRemoteRepo=False):
""" Save all the fiducials for the current volume.
The name of the file will be VolumeName_parenchymaTraining.xml"
:param filePath: destination file (local)
:param caseNavigatorWidget: case navigator widget (optional)
:param callbackFunction: function to invoke when the file has been uploaded to the server (optional)
"""
volume = slicer.mrmlScene.GetNodeByID(self.currentVolumeId)
#fileName = volume.GetName() + Util.file_conventions_extensions[self._xmlFileExtensionKey_]
# If there is already a xml file in the results directory, make a copy.
#localFilePath = os.path.join(directory, fileName)
if os.path.isfile(localFilePath):
# Make a copy of the file for history purposes
copyfile(localFilePath,
localFilePath + "." + time.strftime("%Y%m%d.%H%M%S"))
# Iterate over all the fiducials list nodes
pos = [0, 0, 0]
geometryTopologyData = gtd.GeometryTopologyData()
geometryTopologyData.coordinate_system = geometryTopologyData.LPS
# Get the transformation matrix LPS-->IJK
matrix = Util.get_lps_to_ijk_transformation_matrix(volume)
geometryTopologyData.lps_to_ijk_transformation_matrix = Util.convert_vtk_matrix_to_list(
matrix)
# Save spacing and origin of the volume
geometryTopologyData.origin = volume.GetOrigin()
geometryTopologyData.spacing = volume.GetSpacing()
geometryTopologyData.dimensions = volume.GetImageData().GetDimensions()
# Get the hashtable and seed from previously loaded GeometryTopologyData object (if available)
if self.currentGeometryTopologyData is None:
hashTable = {}
else:
hashTable = self.currentGeometryTopologyData.get_hashtable()
geometryTopologyData.seed_id = self.currentGeometryTopologyData.seed_id
# Get a timestamp that will be used for all the points
timestamp = gtd.GeometryTopologyData.get_timestamp()
for fidListNode in slicer.util.getNodes("{0}_fiducials_*".format(
volume.GetName())).itervalues():
# Get all the markups
for i in range(fidListNode.GetNumberOfMarkups()):
fidListNode.GetNthFiducialPosition(i, pos)
# Get the type from the description (region will always be 0)
desc = fidListNode.GetNthMarkupDescription(i)
# Switch coordinates from RAS to LPS
lps_coords = Util.ras_to_lps(list(pos))
pointMetadata = self.getPointMetadataFromFiducialDescription(
desc)
p = gtd.Point(pointMetadata[0],
pointMetadata[1],
pointMetadata[2],
lps_coords,
description=pointMetadata[3])
key = p.get_hash()
if hashTable.has_key(key):
# Add previously existing point
geometryTopologyData.add_point(hashTable[key],
fill_auto_fields=False)
else:
# Add a new point with a precalculated timestamp
geometryTopologyData.add_point(p, fill_auto_fields=True)
p.timestamp = timestamp
# Get the xml content file
xml = geometryTopologyData.to_xml()
# Save the file
with open(localFilePath, 'w') as f:
f.write(xml)
# Use the new object as the current GeometryTopologyData
self.currentGeometryTopologyData = geometryTopologyData
# Upload to MAD if we are using the ACIL case navigator
if saveInRemoteRepo:
caseNavigatorWidget.uploadFile(localFilePath,
callbackFunction=callbackFunction)
# Mark the current volume as saved
self.savedVolumes[volume.GetName()] = True
sys.path.append("/Users/jonieva/Projects/SlicerCIP/Scripted/CIP_Common/")
from CIP.logic import geometry_topology_data as gtd
from CIP.logic import Util
import os
import os.path
import re
wrong_cases_path = "/Volumes/Mac500/Dropbox/rola-jorge/LH ROI failure/"
xmls_path = "/Volumes/Mac500/Dropbox/ACIL-Biomarkers/parenchyma training 2015-10-02/"
results_path = "/Volumes/Mac500/Data/tempdata/parenchyma training 2015-10-02/Removed Points/LH ROI failure"
current_case = ""
caseIds = dict()
for file_name in os.listdir(wrong_cases_path):
if Util.get_file_extension(file_name) != ".png":
continue
expr = "(?P<caseid>(^(.*?)_(.*?)_(.*?)_(.*?)_(.*?)))_(.*?)_p(?P<point>(.*?))_(.*)"
r = re.match(expr, file_name)
caseId = r.group("caseid")
point = int(r.group("point"))
if not caseIds.has_key(caseId):
caseIds[caseId] = []
caseIds[caseId].append(point)
for caseId, excludedPoints in caseIds.iteritems():
# Load the Geometry object
geom = gtd.GeometryTopologyData.from_xml_file(
os.path.join(xmls_path, caseId + "_parenchymaTraining.xml"))
newPoints = []
for i in range(len(geom.points)):
if not path.isdir(results_dir):
# Create the results folder if it doesn't exist
os.makedirs(results_dir)
files = os.listdir(files_dir)
types_delete = [97, 98, 99, 100]
types_replace = {
94: 84,
96: 85,
101: 34,
102: 86,
103: 88
}
for file_name in files:
if Util.get_file_extension(file_name) != ".xml":
continue
p = path.join(files_dir, file_name)
print ("Processing {0}...".format(file_name))
with open(p, "r+b") as f:
xml = f.read()
geom = gtd.GeometryTopologyData.from_xml(xml)
geom.num_dimensions = 3
points = []
change_coords = geom.coordinate_system != geom.LPS
for point[ in geom.points:
if point.chest_type not in types_delete:
if types_replace.has_key(point.chest_type):
# Replace type
point.chest_type = types_replace[point.chest_type]
if change_coords:
def saveCurrentFiducials(self,
directory,
caseNavigatorWidget=None,
callbackFunction=None):
""" Save all the fiducials for the current volume.
The name of the file will be VolumeName_parenchymaTraining.xml"
:param volume: scalar node
:param directory: destination directory
"""
volume = slicer.mrmlScene.GetNodeByID(self.currentVolumeId)
fileName = volume.GetName(
) + Util.file_conventions_extensions["ParenchymaTrainingFiducialsXml"]
# If there is already a xml file in the results directory, make a copy.
fiducialsLocalFilePath = os.path.join(directory, fileName)
if os.path.isfile(fiducialsLocalFilePath):
# Make a copy of the file for history purposes
copyfile(
fiducialsLocalFilePath,
fiducialsLocalFilePath + "." + time.strftime("%Y%m%d.%H%M%S"))
# Iterate over all the fiducials list nodes
pos = [0, 0, 0]
geometryTopologyData = GTD.GeometryTopologyData()
geometryTopologyData.coordinate_system = geometryTopologyData.LPS
# Get the transformation matrix LPS-->IJK
matrix = Util.get_lps_to_ijk_transformation_matrix(volume)
geometryTopologyData.lps_to_ijk_transformation_matrix = Util.convert_vtk_matrix_to_list(
matrix)
# Get the hashtable and seed from previously loaded GeometryTopologyData object (if available)
if self.currentGeometryTopologyData is None:
hashTable = {}
else:
hashTable = self.currentGeometryTopologyData.get_hashtable()
geometryTopologyData.id_seed = self.currentGeometryTopologyData.id_seed
# Get a timestamp that will be used for all the points
timestamp = GTD.GeometryTopologyData.get_timestamp()
for fidListNode in slicer.util.getNodes("{0}_fiducials_*".format(
volume.GetName())).itervalues():
# Get all the markups
for i in range(fidListNode.GetNumberOfMarkups()):
fidListNode.GetNthFiducialPosition(i, pos)
# Get the type from the description (region will always be 0)
desc = fidListNode.GetNthMarkupDescription(i)
typeId = int(desc.split("_")[0])
artifactId = int(desc.split("_")[1])
# Switch coordinates from RAS to LPS
lps_coords = Util.ras_to_lps(list(pos))
p = GTD.Point(0, typeId, artifactId, lps_coords)
key = p.get_hash()
if hashTable.has_key(key):
# Add previously existing point
geometryTopologyData.add_point(hashTable[key],
fill_auto_fields=False)
else:
# Add a new point with a precalculated timestamp
geometryTopologyData.add_point(p, fill_auto_fields=True)
p.timestamp = timestamp
# Get the xml content file
xml = geometryTopologyData.to_xml()
# Save the file
with open(fiducialsLocalFilePath, 'w') as f:
f.write(xml)
# Use the new object as the current GeometryTopologyData
self.currentGeometryTopologyData = geometryTopologyData
# Upload to MAD if we are using the ACIL case navigator
if caseNavigatorWidget is not None:
caseNavigatorWidget.uploadFile(fiducialsLocalFilePath,
callbackFunction=callbackFunction)
# Mark the current volume as saved
self.savedVolumes[volume.GetName()] = True
