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)
# print ("Processing {0}...".format(p))
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)
# print ("Processing {0}...".format(p))
