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 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))
wrong_points = []
wrong_cases = set()
for file_name in xmls:
if Util.get_file_extension(file_name) != ".xml":
continue
# Open volume
volFile = "{0}/{1}.nhdr".format(vols_dir, file_name.replace("_parenchymaTraining.xml", ""))
v = slicer.util.loadVolume(volFile, returnNode=True)[1]
# print(volFile)
dims = v.GetImageData().GetDimensions()
p = path.join(xmls_dir, file_name)
with open(p, "r+b") as f:
xml = f.read()
geom = gtd.GeometryTopologyData.from_xml(xml)
for point in geom.points:
ras = Util.lps_to_ras(point.coordinate)
ijk = Util.ras_to_ijk(v, ras)
for i in range(3):
if ijk[i] < 0 or ijk[i] >= dims[i]:
# Flip just the second coord
# point.coordinate[1] = -point.coordinate[1]
wrong_points.append((file_name, point.coordinate, ijk))
wrong_cases.add(file_name)
# if file_name in wrong_cases:
# print("Added " + file_name)
# ras = point.coordinate
# point.coordinate = Util.ras_to_lps(ras)
## Change sign
# for case in wrong_cases:
# p = path.join(xmls_dir, case)
wrong_points = []
wrong_cases = set()
for file_name in xmls:
if Util.get_file_extension(file_name) != ".xml":
continue
# Open volume
volFile = "{0}/{1}.nhdr".format(vols_dir, file_name.replace("_parenchymaTraining.xml", ""))
v = slicer.util.loadVolume(volFile, returnNode=True)[1]
# print(volFile)
dims = v.GetImageData().GetDimensions()
p = path.join(xmls_dir, file_name)
with open(p, "r+b") as f:
xml = f.read()
geom = gtd.GeometryTopologyData.from_xml(xml)
for point in geom.points:
ras = Util.lps_to_ras(point.coordinate)
ijk = Util.ras_to_ijk(v, ras)
for i in range(3):
if ijk[i] < 0 or ijk[i] >= dims[i]:
# Flip just the second coord
# point.coordinate[1] = -point.coordinate[1]
wrong_points.append((file_name, point.coordinate, ijk))
wrong_cases.add(file_name)
# if file_name in wrong_cases:
# print("Added " + file_name)
# ras = point.coordinate
# point.coordinate = Util.ras_to_lps(ras)
## Change sign
# for case in wrong_cases:
# p = path.join(xmls_dir, case)