# Copyright 2017, Wenjia Bai. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the 'License');
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an 'AS IS' BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# ==============================================================================
"""
Parser for cvi42 exported xml files.
This parser searches for dicom UIDs in the xml file, extract the contour
point coordinates and save them in a pickle file for each image slice.
"""
import os
import sys
import pickle
import numpy as np
from xml.dom import minidom
def keepElementNodes(nodes):
""" Get the element nodes """
nodes2 = []
for node in nodes:
if node.nodeType == node.ELEMENT_NODE:
nodes2 += [node]
return nodes2
def parseContours(node):
"""
Parse a Contours object. Each Contours object may contain several contours.
We first parse the contour name, then parse the points and pixel size.
"""
contours = {}
for child in keepElementNodes(node.childNodes):
contour_name = child.getAttribute('Hash:key')
sup = 1
for child2 in keepElementNodes(child.childNodes):
if child2.getAttribute('Hash:key') == 'Points':
points = []
for child3 in keepElementNodes(child2.childNodes):
x = float(child3.getElementsByTagName('Point:x')[0].firstChild.data)
y = float(child3.getElementsByTagName('Point:y')[0].firstChild.data)
points += [[x, y]]
if child2.getAttribute('Hash:key') == 'SubpixelResolution':
sub = int(child2.firstChild.data)
points = np.array(points)
points /= sub
contours[contour_name] = points
return contours
def traverseNode(node, uid_contours):
""" Traverse the nodes """
child = node.firstChild
while child:
if child.nodeType == child.ELEMENT_NODE:
# This is where the information for each dicom file starts
if child.getAttribute('Hash:key') == 'ImageStates':
for child2 in keepElementNodes(child.childNodes):
# UID for the dicom file
uid = child2.getAttribute('Hash:key')
for child3 in keepElementNodes(child2.childNodes):
if child3.getAttribute('Hash:key') == 'Contours':
contours = parseContours(child3)
if contours:
uid_contours[uid] = contours
traverseNode(child, uid_contours)
child = child.nextSibling
def parseFile(xml_name, output_dir):
""" Parse a cvi42 xml file """
dom = minidom.parse(xml_name)
uid_contours = {}
traverseNode(dom, uid_contours)
# Save the contours for each dicom file
for uid, contours in uid_contours.items():
with open(os.path.join(output_dir, '{0}.pickle'.format(uid)), 'wb') as f:
pickle.dump(contours, f)
if __name__ == '__main__':
if len(sys.argv) < 3:
print('Usage: {0} cvi_xml output_dir'.format(sys.argv[0]))
exit(0)
parseFile(sys.argv[1], sys.argv[2])
