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
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:
print("B:replace ", point.coordinate)
# Switch to LPS (RAS will be assumed)
point.coordinate = Util.ras_to_lps(point.coordinate)
print("To: ", point.coordinate)
points.append(point)
# Replace the points
geom.points = points
geom.coordinate_system = geom.LPS
# Save file
xml = geom.to_xml()
p = path.join(results_dir, file_name)
with open(p, "w") as f:
f.write(xml)
import os
from CIP.logic import Util
from os import path
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:
print("B:replace ", point.coordinate)
# Switch to LPS (RAS will be assumed)
point.coordinate = Util.ras_to_lps(point.coordinate)
print("To: ", point.coordinate)
points.append(point)
# Replace the points
geom.points = points
geom.coordinate_system = geom.LPS
# Save file
xml = geom.to_xml()
p = path.join(results_dir, file_name)
with open(p, "w") as f:
f.write(xml)
import os
from CIP.logic import Util
from os import path
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
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
