def setUp(self):
self.pwd = get_installdir()
self.deid = os.path.abspath("%s/../examples/deid/deid.dicom" %
self.pwd)
self.dataset = get_dataset("dicom-cookies")
self.tmpdir = tempfile.mkdtemp()
print("\n######################START######################")
def setUp(self):
self.pwd = get_installdir()
self.deid = os.path.abspath("%s/../examples/deid/deid.dicom" %
self.pwd)
self.dataset = get_dataset("animals") # includes private tags
self.tmpdir = tempfile.mkdtemp()
print("\n######################START######################")
def test_get_installdir(self):
'''get install directory should return the base of where singularity
is installed
'''
print("Testing finding the installation directory.")
from deid.utils import get_installdir
whereami = get_installdir()
self.assertTrue(whereami.endswith('deid'))
def get_dataset(dataset=None):
'''get_dataset will return some data provided by the application,
based on a user-provided label. In the future, we can add https endpoints
to retrieve online datasets.
'''
data_base = get_installdir()
valid_datasets = {'dicom-cookies': '%s/data/dicom-cookies' % data_base}
if dataset is not None:
# In case the user gave an extension
dataset = os.path.splitext(dataset)[0].lower()
if dataset in valid_datasets:
return valid_datasets[dataset]
bot.info("Valid datasets include: %s" %
(','.join(list(valid_datasets.keys()))))
def get_dataset(dataset=None):
"""get_dataset will return some data provided by the application,
based on a user-provided label. In the future, we can add https endpoints
to retrieve online datasets.
"""
data_base = get_installdir()
valid_datasets = {
"dicom-cookies": os.path.join(data_base, "data", "dicom-cookies"),
"animals": os.path.join(data_base, "data", "animals"),
"humans": os.path.join(data_base, "data", "humans"),
}
if dataset is not None:
# In case the user gave an extension
dataset = os.path.splitext(dataset)[0].lower()
if dataset in valid_datasets:
return valid_datasets[dataset]
bot.info("Valid datasets include: %s" %
(",".join(list(valid_datasets.keys()))))
def find_deid(path=None):
"""find_deid is a helper function to load_deid to find a deid file in
a folder, or return the path provided if it is the file.
Parameters
==========
path: a path on the filesystem. If not provided, will assume PWD.
"""
# A default deid will be loaded if all else fails
default_deid = os.path.join(get_installdir(), "data", "deid.dicom")
if path is None:
path = os.getcwd()
# The user has provided a directory
if os.path.isdir(path):
contenders = [
"%s/%s" % (path, x) for x in os.listdir(path)
if x.startswith("deid")
]
if len(contenders) == 0:
bot.warning(
"No deid settings files found in %s, will use default dicom.deid."
% path)
contenders.append(default_deid)
elif len(contenders) > 1:
bot.warning("Multiple deid files found in %s, will use first." %
(path))
path = contenders[0]
# We have a file path at this point
if not os.path.exists(path):
bot.exit("Cannot find deid file %s, exiting." % (path))
return path
# Create a DeidRecipe
from deid.config import DeidRecipe
recipe = DeidRecipe()
# Since we didn't load a custom deid recipe text file, we get a default
# WARNING No specification, loading default base deid.dicom
# You can add custom deid files with .load().
# We can look at the criteria loaded:
recipe.deid
# You can also provide your own deid recipe file, and in doing so, you
# won't load a default
path = os.path.abspath("%s/../examples/deid/" % get_installdir())
recipe = DeidRecipe(deid=path)
# You can also choose to load the default base with your own recipe
recipe = DeidRecipe(deid=path, base=True)
# Or specify a different base entirely. The base is the deid.<tag> in the
# deid.data folder. So for example, under deid/data/deid.dicom.chest.xray we would
# do:
recipe = DeidRecipe(deid=path, base=True, default_base='dicom.xray.chest')
# We can also specify one of the deid recipes provided by the library as our
# only to use.
recipe = DeidRecipe(deid='dicom.xray.chest')
# This is to encourage sharing! If you have a general recipe that others might
def setUp(self):
self.pwd = get_installdir()
self.tmpdir = tempfile.mkdtemp()
print("\n######################START######################")
def setUp(self):
self.pwd = get_installdir()
self.deidpath = os.path.abspath("%s/tests/resources/" % self.pwd)
self.dataset = get_dataset("animals")
self.tmpdir = tempfile.mkdtemp()
print("\n######################START######################")