def test_pixel_cleaner_remove_all(self):
"""Test the pixel cleaner to ensure it appropriately clears all pixels."""
from deid.dicom import DicomCleaner
dicom_file = get_file(self.dataset)
deid = os.path.join(self.deidpath, "remove_all.dicom")
client = DicomCleaner(output_folder=self.tmpdir, deid=deid)
out = client.detect(dicom_file)
self.assertTrue(out["flagged"])
client.clean()
cleanedfile = client.save_dicom()
outputfile = read_file(cleanedfile)
outputpixels = outputfile.pixel_array
inputfile = read_file(dicom_file)
inputpixels = inputfile.pixel_array
compare = inputpixels == outputpixels
self.assertFalse(compare.all())
inputpixels[:, :] = 0
compare = inputpixels == outputpixels
self.assertTrue(compare.all())
def test_pixel_cleaner_remove_multiple_filters(self):
"""Test the pixel cleaner to ensure that multiple remove coordinates in different filters remove the appropriate pixels."""
from deid.dicom import DicomCleaner
dicom_file = get_file(self.dataset)
deid = os.path.join(self.deidpath,
"remove_coordinates_multiple_filters.dicom")
client = DicomCleaner(output_folder=self.tmpdir, deid=deid)
out = client.detect(dicom_file)
self.assertTrue(out["flagged"])
client.clean()
cleanedfile = client.save_dicom()
outputfile = read_file(cleanedfile)
outputpixels = outputfile.pixel_array
inputfile = read_file(dicom_file)
inputpixels = inputfile.pixel_array
compare = inputpixels == outputpixels
self.assertFalse(compare.all())
inputpixels[0:10, 0:10] = 0
inputpixels[10:20, 10:20] = 0
compare = inputpixels == outputpixels
self.assertTrue(compare.all())
def test_pixel_cleaner_keepcoordinates_from(self):
"""Test the pixel cleaner to ensure that multiple keep coordinates retrieved from a dicom field are appropriately retained."""
from deid.dicom import DicomCleaner
dicom_file = get_file(self.dataset)
deid = os.path.join(self.deidpath, "keepcoordinates_from.dicom")
client = DicomCleaner(output_folder=self.tmpdir, deid=deid)
out = client.detect(dicom_file)
self.assertTrue(out["flagged"])
client.clean()
cleanedfile = client.save_dicom()
outputfile = read_file(cleanedfile)
outputpixels = outputfile.pixel_array
inputfile = read_file(dicom_file)
inputpixels = inputfile.pixel_array
compare = inputpixels == outputpixels
self.assertFalse(compare.all())
inputpixels[1000:2000, 0:1000] = 0
inputpixels[0:1000, 1000:2000] = 0
compare = inputpixels[0:2000, 0:2000] == outputpixels[0:2000, 0:2000]
self.assertTrue(compare.all())
def test_3d_Greyscale_cine_clip(self):
"""
Test the pixel cleaner to ensure pixels are appropriately deidentified
on "3D" images - greyscale cine clips. Pixel data will have the shape (frames, X, Y)
"""
from deid.dicom import DicomCleaner
dicom_file = get_file(self.dataset, "GREYSCALE_CINE.zip", self.tmpdir)
deid = os.path.join(self.deidpath, "remove_coordinates_us.dicom")
client = DicomCleaner(output_folder=self.tmpdir, deid=deid)
out = client.detect(dicom_file)
self.assertTrue(out["flagged"])
client.clean()
cleanedfile = client.save_dicom()
outputfile = read_file(cleanedfile)
outputpixels = outputfile.pixel_array
inputfile = read_file(dicom_file)
inputpixels = inputfile.pixel_array
compare = inputpixels == outputpixels
self.assertFalse(compare.all())
inputpixels[:, 0:500, 0:500] = 0
compare = inputpixels == outputpixels
self.assertTrue(compare.all())
def test_2d_Greyscale_image_all(self):
"""
Test the pixel cleaner to ensure pixels are appropriately deidentified - all keyword -
on "2D" images - Greyscale images. Pixel data will have the shape (X, Y)
"""
from deid.dicom import DicomCleaner
dicom_file = get_file(self.dataset, "GREYSCALE_IMAGE.dcm")
deid = os.path.join(self.deidpath, "remove_coordinates_us_all.dicom")
client = DicomCleaner(output_folder=self.tmpdir, deid=deid)
out = client.detect(dicom_file)
self.assertTrue(out["flagged"])
client.clean()
cleanedfile = client.save_dicom()
outputfile = read_file(cleanedfile)
outputpixels = outputfile.pixel_array
inputfile = read_file(dicom_file)
inputpixels = inputfile.pixel_array
compare = inputpixels == outputpixels
self.assertFalse(compare.all())
inputpixels[:, :] = 0
compare = inputpixels == outputpixels
self.assertTrue(compare.all())
def test_4d_RGB_cine_clip_all(self):
"""
Test the pixel cleaner to ensure pixels are appropriately deidentified - all keyword -
on "4D" images - RGB cine clips. Pixel data will have the shape (frames, X, Y, channel)
"""
from deid.dicom import DicomCleaner
dicom_file = get_file(self.dataset, "RGB_CINE.zip", self.tmpdir)
deid = os.path.join(self.deidpath, "remove_coordinates_us_all.dicom")
client = DicomCleaner(output_folder=self.tmpdir, deid=deid)
out = client.detect(dicom_file)
self.assertTrue(out["flagged"])
client.clean()
cleanedfile = client.save_dicom()
outputfile = read_file(cleanedfile)
outputpixels = outputfile.pixel_array
inputfile = read_file(dicom_file)
inputpixels = inputfile.pixel_array
compare = inputpixels == outputpixels
self.assertFalse(compare.all())
inputpixels[:, :, :, :] = 0
compare = inputpixels == outputpixels
self.assertTrue(compare.all())
def test_3d_RGB_image(self):
"""
Test the pixel cleaner to ensure pixels are appropriately deidentified
on "3D" images - RGB images. Pixel data will have the shape (X, Y, channel)
"""
from deid.dicom import DicomCleaner
dicom_file = get_file(self.dataset, "RGB_IMAGE.dcm")
deid = os.path.join(self.deidpath, "remove_coordinates_us.dicom")
client = DicomCleaner(output_folder=self.tmpdir, deid=deid)
out = client.detect(dicom_file)
self.assertTrue(out["flagged"])
client.clean()
cleanedfile = client.save_dicom()
outputfile = read_file(cleanedfile)
outputpixels = outputfile.pixel_array
inputfile = read_file(dicom_file)
inputpixels = inputfile.pixel_array
compare = inputpixels == outputpixels
self.assertFalse(compare.all())
inputpixels[0:500, 0:500, :] = 0
compare = inputpixels == outputpixels
self.assertTrue(compare.all())
def test_pixel_cleaner_keepcoordinates_noaction(self):
"""Test the pixel cleaner to ensure that a keepcoordinates with no removecoordinates has no impact on the pixels."""
from deid.dicom import DicomCleaner
dicom_file = get_file(self.dataset)
deid = os.path.join(self.deidpath, "keepcoordinates_noaction.dicom")
client = DicomCleaner(output_folder=self.tmpdir, deid=deid)
out = client.detect(dicom_file)
self.assertTrue(out["flagged"])
client.clean()
cleanedfile = client.save_dicom()
outputfile = read_file(cleanedfile)
outputpixels = outputfile.pixel_array
inputfile = read_file(dicom_file)
inputpixels = inputfile.pixel_array
compare = inputpixels == outputpixels
self.assertTrue(compare.all())
def test_pixel_cleaner_keepcoordinates(self):
"""Test the pixel cleaner to ensure that a keepcoordinates retains appropriate pixels."""
from deid.dicom import DicomCleaner
dicom_file = get_file(self.dataset)
deid = os.path.join(self.deidpath, "keepcoordinates.dicom")
client = DicomCleaner(output_folder=self.tmpdir, deid=deid)
out = client.detect(dicom_file)
self.assertTrue(out["flagged"])
client.clean()
cleanedfile = client.save_dicom()
outputfile = read_file(cleanedfile)
outputpixels = outputfile.pixel_array
inputfile = read_file(dicom_file)
inputpixels = inputfile.pixel_array
compare = inputpixels == outputpixels
self.assertFalse(compare.all())
compare = inputpixels[0:1024, 0:1024] == outputpixels[0:1024, 0:1024]
self.assertTrue(compare.all())
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)
#########################################
# 3. Detect
#########################################
# Detect means using the deid recipe to parse headers
# If we try to clean before we detect, we can't
# client.clean()
# WARNING Use <deid.dicom.pixels.clean.DicomCleaner object at 0x7fafb70b9cf8>.detect() to find coordinates first.
client.detect(dicom_file)
# {'flagged': True,
# 'results': [{'coordinates': [],
# 'group': 'blacklist',
# 'reason': ' ImageType missing or ImageType empty '}]}
#########################################
# 4. Clean and save
#########################################
client.clean()
# If there are coordinates, they are blanked. Otherwise, no change.
# Blanking 0 coordinate results
# Default output folder is temporary, unless specified at client onset
# or directly to saving functions
client.save_png()
client.save_dicom()