def get_files(contenders, check=True, pattern=None, force=False):
'''get_dcm_files will take a list of single dicom files or directories,
and return a generator that yields complete paths to all files
:param pattern: A pattern to use with fnmatch. If None, * is used
:param force: force reading of the files, if some headers invalid.
Not recommended, as many non-dicom will come through
'''
if not isinstance(contenders, list):
contenders = [contenders]
for contender in contenders:
if os.path.isdir(contender):
dicom_files = recursive_find(contender, pattern=pattern)
else:
dicom_files = [contender]
for dicom_file in dicom_files:
if dicom_file is not None:
if check:
validated_files = validate_dicoms(dicom_file, force=force)
else:
validated_files = [dicom_file]
for validated_file in validated_files:
bot.debug("Found contender file %s" % (validated_file))
yield validated_file
def test_recursive_find(self):
'''test_recursive_find should detect 7 dicoms
'''
print("Testing recursive find.")
from deid.utils import recursive_find
files = recursive_find(self.pwd, pattern='*.dcm')
print("Found %s files" % (len(files)))
self.assertTrue(len(files) == 7)
def test_recursive_find_as_list(self):
'''test_recursive_find_as_list should detect 7 dicoms
'''
print("Testing recursive find as lit.")
from deid.utils import recursive_find
expected = 7
files = list(recursive_find(self.pwd, pattern='*.dcm'))
found = len(files)
print("Found %s files" % (len(files)))
self.assertTrue(found == expected)
def test_recursive_find(self):
'''test_recursive_find should detect 7 dicoms
'''
print("Testing recursive find.")
from deid.utils import recursive_find
found = 0
expected = 7
for file in recursive_find(self.pwd, pattern='*.dcm'):
found += 1
print("Found %s files" % (found))
self.assertTrue(found == expected)
def get_files(contenders, check=True, pattern=None, force=False, tempdir=None):
"""get_files will take a list of single dicom files or directories,
and return a generator that yields complete paths to all files
Parameters
==========
contenders: a list of files or directories (contenders!)
check: boolean to indicate if we should validate dicoms (default True)
pattern: A pattern to use with fnmatch. If None, * is used
force: force reading of the files, if some headers invalid.
Not recommended, as many non-dicom will come through
"""
if not isinstance(contenders, list):
contenders = [contenders]
for contender in contenders:
if os.path.isdir(contender):
dicom_files = recursive_find(contender, pattern=pattern)
else:
dicom_files = [contender]
for dicom_file in dicom_files:
dfile, dextension = os.path.splitext(dicom_file)
# The code currently only assumes a single-file per zip. This could be
# expanded to allow for multiple test files within an archive.
if dextension == ".zip":
with zipfile.ZipFile(dicom_file, "r") as compressedFile:
compressedFile.extractall(tempdir)
dicom_file = next(
os.path.join(tempdir, f) for f in os.listdir(tempdir)
if os.path.isfile(os.path.join(tempdir, f)))
if dicom_file is not None:
if check:
validated_files = validate_dicoms(dicom_file, force=force)
else:
validated_files = [dicom_file]
for validated_file in validated_files:
bot.debug("Found contender file %s" % (validated_file))
yield validated_file
def get_files(contenders, check=True, pattern=None, force=False):
'''get_dcm_files will take a list of single dicom files or directories,
and return a single list of complete paths to all files
:param pattern: A pattern to use with fnmatch. If None, * is used
:param force: force reading of the files, if some headers invalid.
Not recommended, as many non-dicom will come through
'''
if not isinstance(contenders, list):
contenders = [contenders]
dcm_files = []
for contender in contenders:
if os.path.isdir(contender):
dicom_dir = recursive_find(contender, pattern=pattern)
bot.debug("Found %s contender files in %s" %
(len(dicom_dir), os.path.basename(contender)))
dcm_files.extend(dicom_dir)
else:
bot.debug("Adding single contender file %s" % (contender))
dcm_files.append(contender)
if check:
dcm_files = validate_dicoms(dcm_files, force=force)
return dcm_files
