def test_write_read_files(self):
'''test_write_read_files will test the functions
write_file and read_file
'''
print("Testing utils.write_file...")
from deid.utils import write_file
tmpfile = tempfile.mkstemp()[1]
os.remove(tmpfile)
write_file(tmpfile, "blaaahumbug")
self.assertTrue(os.path.exists(tmpfile))
print("Testing utils.read_file...")
from deid.utils import read_file
content = read_file(tmpfile)[0]
self.assertEqual("blaaahumbug", content)
from deid.utils import write_json
print("Testing utils.write_json...")
print("Case 1: Providing bad json")
bad_json = {"Wakkawakkawakka'}": [{True}, "2", 3]}
tmpfile = tempfile.mkstemp()[1]
os.remove(tmpfile)
with self.assertRaises(TypeError) as cm:
write_json(bad_json, tmpfile)
print("Case 2: Providing good json")
good_json = {"Wakkawakkawakka": [True, "2", 3]}
tmpfile = tempfile.mkstemp()[1]
os.remove(tmpfile)
write_json(good_json, tmpfile)
content = json.load(open(tmpfile, 'r'))
self.assertTrue(isinstance(content, dict))
self.assertTrue("Wakkawakkawakka" in content)
def main():
parser = get_parser()
try:
args = parser.parse_args()
except:
sys.exit(0)
from deid.dicom import (get_files, DicomCleaner)
from logger import bot
if args.folder is None:
bot.error("Please provide a folder with dicom files with --input.")
sys.exit(1)
# This is an iterator, so must convert to list to get length
dicom_files = get_files(args.folder)
# Create a Dicom Cleaner client
number_files = len(list(get_files(args.folder)))
client = DicomCleaner(output_folder=args.outfolder, deid=args.deid)
bot.info('Processing [images]%s [output-folder]%s' %
(number_files, client.output_folder))
outcomes = {True: 'flagged', False: ' clean'}
# Keep a list of flagged and clean
flagged = []
clean = []
summary = dict()
# We will move images into respective folders
if args.save is "pdf":
pdf_report = '%s/deid-clean-%s.pdf' % (args.outfolder, number_files)
pp = PdfPages(pdf_report)
# Perform detection one at a time
for dicom_file in dicom_files:
dicom_name = os.path.basename(dicom_file)
# detect --> clean
result = client.detect(dicom_file)
client.clean()
summary[dicom_name] = result
# Generate title/description for result
title = '%s: %s' % (outcomes[result['flagged']], dicom_name)
bot.info(title)
# How does the user want to save data?
if args.save == "dicom":
outfile = client.save_dicom()
elif args.save == "png":
outfile = client.save_png(title=title)
# pdf (default)
else:
plt = client.get_figure(title=title)
fig = plt.gcf()
pp.savefig(fig)
plt.close(fig)
# Whether dicom or png, append to respective list
if args.save is not "pdf":
if result['flagged']:
flagged.append(outfile)
else:
clean.append(outfile)
# Save summary json file
summary_json = '%s/deid-clean-%s.json' % (args.outfolder, number_files)
write_json(summary, summary_json)
bot.info('json data written to %s' % summary_json)
# When we get here, if saving pdf, close it.
if args.save == "pdf":
bot.info('pdf report written to %s' % pdf_report)
pp.close()
# Otherwise, move files into respective folders
else:
move_files(files=flagged, dest='%s/flagged' % args.outfolder)
move_files(files=cleaned, dest='%s/clean' % args.outfolder)