def applyTransformations(data):
for d in data:
success, transform = slicer.util.loadTransform(d['transform'],
returnNode=True)
success, preopLandmarks = slicer.util.loadMarkupsFiducialList(
d['landmarks'], returnNode=True)
ModuleLogicMixin.applyTransform(transform, preopLandmarks)
print "saving to : %s" % os.path.dirname(d['landmarks'])
ModuleLogicMixin.saveNodeData(
preopLandmarks,
os.path.dirname(d['landmarks']),
FileExtension.FCSV,
name="{}-PreopLandmarks-transformed".format(d['case']))
def main(argv):
try:
parser = argparse.ArgumentParser(
description="Slicetracker Transform Applicator")
parser.add_argument(
"-ld",
"--landmark-root-directory",
dest="landmarkRootDir",
metavar="PATH",
default="-",
required=True,
help=
"Root directory that lists all cases holding information for landmarks"
)
parser.add_argument(
"-st",
"--segmentation-type",
dest="segmentationType",
metavar="NAME",
default="-",
choices=['Manual', 'Automatic'],
required=True,
help="Expected transform name will be "
"{casenumber}-TRANSFORM-{transformType}-{segmentationType}.h5")
parser.add_argument(
"-tt",
"--transform-type",
dest="transformType",
metavar="NAME",
default="-",
choices=['rigid', 'affine', 'bSpline'],
required=True,
help=
"%(choices). expected transform name: {casenumber}-TRANSFORM-{transformType}-{segmentationType}.h5"
)
parser.add_argument(
"-ft",
"--fiducial-type",
dest="fiducialType",
metavar="NAME",
default="-",
choices=['Targets', 'Landmarks'],
required=True,
help='list servers, storage, or both (default: %(default)s)')
args = parser.parse_args(argv)
segmentationType = args.segmentationType
transformType = args.transformType
fiducialType = args.fiducialType
for root, dirs, _ in os.walk(args.landmarkRootDir):
for case in dirs:
landmarks = os.path.join(
root, case, "{}-Preop{}.fcsv".format(case, fiducialType))
transform = os.path.join(
root, case,
"{}-TRANSFORM-{}-{}.h5".format(case, transformType,
segmentationType))
# check if exists and if is identity
volume = os.path.join(
root, case,
"{}-VOLUME-{}-{}.nrrd".format(case, transformType,
segmentationType))
if not os.path.exists(volume):
logging.info(
"Case {}: No valid {} transform found.Falling back to affine"
.format(case, transformType))
# volume = os.path.join(root, case, "{}-VOLUME-affine-{}.nrrd".format(case, segmentationType))
transform = os.path.join(
root, case, "{}-TRANSFORM-affine-{}.h5".format(
case, segmentationType))
if all(os.path.exists(f) for f in [landmarks, transform]):
success, landmarksNode = slicer.util.loadMarkupsFiducialList(
landmarks, returnNode=True)
success, transformNode = slicer.util.loadTransform(
transform, returnNode=True)
ModuleLogicMixin.applyTransform(transformNode,
landmarksNode)
fileName = "{}-Preop{}-transformed-{}-{}".format(
case, fiducialType, transformType, segmentationType)
print "saving to : {}/{}{}".format(
os.path.dirname(landmarks), fileName,
FileExtension.FCSV)
ModuleLogicMixin.saveNodeData(landmarksNode,
os.path.dirname(landmarks),
FileExtension.FCSV,
name=fileName)
else:
logging.warn(
"Did not find landmarks/transforms for case %s" % case)
except Exception, e:
print e