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MAINT: revise style of all files (except for workflows) #839

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merged 1 commit into from Apr 5, 2020
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MAINT: revise style of all files (except for workflows) #839

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21 changes: 8 additions & 13 deletions mriqc/__about__.py
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Expand Up @@ -3,18 +3,13 @@
"""MRIQC."""

from ._version import get_versions
__version__ = get_versions()['version']
del get_versions

__copyright__ = ('Copyright 2009, Center for Reproducible Neuroscience, '
'Stanford University')
__credits__ = 'Oscar Esteban'
__download__ = ('https://github.com/poldracklab/mriqc/archive/'
'{}.tar.gz'.format(__version__))
__version__ = get_versions()["version"]
del get_versions

__all__ = [
'__version__',
'__copyright__',
'__credits__',
'__download__'
]
__copyright__ = (
"Copyright 2020, Center for Reproducible Neuroscience, Stanford University"
)
__credits__ = "Oscar Esteban"
__download__ = f"https://github.com/poldracklab/mriqc/archive/{__version__}.tar.gz"
__all__ = ["__version__", "__copyright__", "__credits__", "__download__"]
6 changes: 3 additions & 3 deletions mriqc/__init__.py
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Expand Up @@ -14,7 +14,7 @@


__all__ = [
'__copyright__',
'__credits__',
'__version__',
"__copyright__",
"__credits__",
"__version__",
]
4 changes: 1 addition & 3 deletions mriqc/_warnings.py
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Expand Up @@ -12,9 +12,7 @@ def _warn(message, category=None, stacklevel=1, source=None):
category = type(category).__name__
category = category.replace("type", "WARNING")

logging.getLogger("py.warnings").warning(
f"{category or 'WARNING'}: {message}"
)
logging.getLogger("py.warnings").warning(f"{category or 'WARNING'}: {message}")


def _showwarning(message, category, filename, lineno, file=None, line=None):
Expand Down
95 changes: 50 additions & 45 deletions mriqc/bin/abide2bids.py
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Expand Up @@ -25,30 +25,34 @@

def main():
"""Entry point"""
parser = ArgumentParser(description='ABIDE2BIDS downloader',
formatter_class=RawTextHelpFormatter)
g_input = parser.add_argument_group('Inputs')
g_input.add_argument('-i', '--input-abide-catalog', action='store',
required=True)
g_input.add_argument('-n', '--dataset-name', action='store',
default='ABIDE Dataset')
g_input.add_argument('-u', '--nitrc-user', action='store',
default=os.getenv('NITRC_USER'))
g_input.add_argument('-p', '--nitrc-password', action='store',
default=os.getenv('NITRC_PASSWORD'))

g_outputs = parser.add_argument_group('Outputs')
g_outputs.add_argument('-o', '--output-dir', action='store',
default='ABIDE-BIDS')
parser = ArgumentParser(
description="ABIDE2BIDS downloader", formatter_class=RawTextHelpFormatter
)
g_input = parser.add_argument_group("Inputs")
g_input.add_argument("-i", "--input-abide-catalog", action="store", required=True)
g_input.add_argument(
"-n", "--dataset-name", action="store", default="ABIDE Dataset"
)
g_input.add_argument(
"-u", "--nitrc-user", action="store", default=os.getenv("NITRC_USER")
)
g_input.add_argument(
"-p", "--nitrc-password", action="store", default=os.getenv("NITRC_PASSWORD")
)

g_outputs = parser.add_argument_group("Outputs")
g_outputs.add_argument("-o", "--output-dir", action="store", default="ABIDE-BIDS")

opts = parser.parse_args()

if opts.nitrc_user is None or opts.nitrc_password is None:
raise RuntimeError('NITRC user and password are required')
raise RuntimeError("NITRC user and password are required")

dataset_desc = {'BIDSVersion': '1.0.0rc3',
'License': 'CC Attribution-NonCommercial-ShareAlike 3.0 Unported',
'Name': opts.dataset_name}
dataset_desc = {
"BIDSVersion": "1.0.0rc3",
"License": "CC Attribution-NonCommercial-ShareAlike 3.0 Unported",
"Name": opts.dataset_name,
}

out_dir = op.abspath(opts.output_dir)
try:
Expand All @@ -57,19 +61,18 @@ def main():
if exc.errno != errno.EEXIST:
raise exc

with open(op.join(out_dir, 'dataset_description.json'), 'w') as dfile:
with open(op.join(out_dir, "dataset_description.json"), "w") as dfile:
json.dump(dataset_desc, dfile)

catalog = et.parse(opts.input_abide_catalog).getroot()
urls = [el.get('URI') for el in catalog.iter() if el.get('URI') is not None]
urls = [el.get("URI") for el in catalog.iter() if el.get("URI") is not None]

pool = Pool()
args_list = [(url, opts.nitrc_user, opts.nitrc_password, out_dir)
for url in urls]
args_list = [(url, opts.nitrc_user, opts.nitrc_password, out_dir) for url in urls]
res = pool.map(fetch, args_list)

tsv_data = np.array([('subject_id', 'site_name')] + res)
np.savetxt(op.join(out_dir, 'participants.tsv'), tsv_data, fmt='%s', delimiter='\t')
tsv_data = np.array([("subject_id", "site_name")] + res)
np.savetxt(op.join(out_dir, "participants.tsv"), tsv_data, fmt="%s", delimiter="\t")


def fetch(args):
Expand All @@ -86,55 +89,57 @@ def fetch(args):
else:
out_dir = op.abspath(out_dir)

pkg_id = [u[9:] for u in url.split('/') if u.startswith('NITRC_IR_')][0]
sub_file = op.join(tmpdir, '%s.zip' % pkg_id)
pkg_id = [u[9:] for u in url.split("/") if u.startswith("NITRC_IR_")][0]
sub_file = op.join(tmpdir, "%s.zip" % pkg_id)

cmd = ['curl', '-s', '-u', '%s:%s' % (user, password), '-o', sub_file, url]
cmd = ["curl", "-s", "-u", "%s:%s" % (user, password), "-o", sub_file, url]
sp.check_call(cmd)
sp.check_call(['unzip', '-qq', '-d', tmpdir, '-u', sub_file])
sp.check_call(["unzip", "-qq", "-d", tmpdir, "-u", sub_file])

abide_root = op.join(tmpdir, 'ABIDE')
abide_root = op.join(tmpdir, "ABIDE")
files = []
for root, path, fname in os.walk(abide_root):
if fname and (fname[0].endswith('nii') or fname[0].endswith('nii.gz')):
if fname and (fname[0].endswith("nii") or fname[0].endswith("nii.gz")):
if path:
root = op.join(root, path[0])
files.append(op.join(root, fname[0]))

site_name, sub_str = files[0][len(abide_root) + 1:].split('/')[0].split('_')
subject_id = 'sub-' + sub_str
site_name, sub_str = files[0][len(abide_root) + 1:].split("/")[0].split("_")
subject_id = "sub-" + sub_str

for i in files:
ext = '.nii.gz'
if i.endswith('.nii'):
ext = '.nii'
if 'mprage' in i:
bids_dir = op.join(out_dir, subject_id, 'anat')
ext = ".nii.gz"
if i.endswith(".nii"):
ext = ".nii"
if "mprage" in i:
bids_dir = op.join(out_dir, subject_id, "anat")
try:
os.makedirs(bids_dir)
except OSError as exc:
if exc.errno != errno.EEXIST:
raise exc
shutil.copy(i, op.join(bids_dir, subject_id + '_T1w' + ext))
shutil.copy(i, op.join(bids_dir, subject_id + "_T1w" + ext))

if 'rest' in i:
bids_dir = op.join(out_dir, subject_id, 'func')
if "rest" in i:
bids_dir = op.join(out_dir, subject_id, "func")
try:
os.makedirs(bids_dir)
except OSError as exc:
if exc.errno != errno.EEXIST:
raise exc
shutil.copy(i, op.join(bids_dir, subject_id + '_rest_bold' + ext))
shutil.copy(i, op.join(bids_dir, subject_id + "_rest_bold" + ext))

shutil.rmtree(tmpdir, ignore_errors=True, onerror=_myerror)

print('Successfully processed subject %s from site %s' % (subject_id[4:], site_name))
print(
"Successfully processed subject %s from site %s" % (subject_id[4:], site_name)
)
return subject_id[4:], site_name


def _myerror(msg):
print('WARNING: Error deleting temporal files: %s' % msg)
print("WARNING: Error deleting temporal files: %s" % msg)


if __name__ == '__main__':
if __name__ == "__main__":
main()
79 changes: 54 additions & 25 deletions mriqc/bin/dfcheck.py
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Expand Up @@ -20,15 +20,34 @@
def main():
"""Entry point"""
from ..classifier.data import read_iqms
parser = ArgumentParser(description='compare two pandas dataframes',
formatter_class=RawTextHelpFormatter)
g_input = parser.add_argument_group('Inputs')
g_input.add_argument('-i', '--input-csv', action='store', type=Path,
required=True, help='input data frame')
g_input.add_argument('-r', '--reference-csv', action='store', type=Path,
required=True, help='reference dataframe')
g_input.add_argument('--tolerance', type=float, default=1.e-5,
help='relative tolerance for comparison')

parser = ArgumentParser(
description="compare two pandas dataframes",
formatter_class=RawTextHelpFormatter,
)
g_input = parser.add_argument_group("Inputs")
g_input.add_argument(
"-i",
"--input-csv",
action="store",
type=Path,
required=True,
help="input data frame",
)
g_input.add_argument(
"-r",
"--reference-csv",
action="store",
type=Path,
required=True,
help="reference dataframe",
)
g_input.add_argument(
"--tolerance",
type=float,
default=1.0e-5,
help="relative tolerance for comparison",
)

opts = parser.parse_args()

Expand All @@ -39,17 +58,19 @@ def main():
tst_df.set_index(tst_bids)

if sorted(ref_bids) != sorted(tst_bids):
sys.exit('Dataset has different BIDS bits w.r.t. reference')
sys.exit("Dataset has different BIDS bits w.r.t. reference")

if sorted(ref_names) != sorted(tst_names):
sys.exit('Output CSV file changed number of columns')
sys.exit("Output CSV file changed number of columns")

ref_df = ref_df.sort_values(by=ref_bids)
tst_df = tst_df.sort_values(by=tst_bids)

if len(ref_df) != len(tst_df):
print('Input datases have different lengths (input %d, reference %d).' % (
len(ref_df), len(tst_df)))
print(
"Input datases have different lengths (input %d, reference %d)."
% (len(ref_df), len(tst_df))
)
tst_rows = tst_df[tst_bids]
ref_rows = ref_df[ref_bids]

Expand All @@ -58,7 +79,9 @@ def main():
tst_keep = np.sum(tst_rows.isin(ref_rows).values.ravel().tolist())
print(tst_keep)

diff = ~np.isclose(ref_df[ref_names].values, tst_df[tst_names].values, rtol=opts.tolerance)
diff = ~np.isclose(
ref_df[ref_names].values, tst_df[tst_names].values, rtol=opts.tolerance
)
if np.any(diff):
# ne_stacked = pd.DataFrame(data=diff, columns=ref_names).stack()
# ne_stacked = np.isclose(ref_df[ref_names], tst_df[ref_names]).stack()
Expand All @@ -69,26 +92,32 @@ def main():
changed_to = tst_df[ref_names].values[difference_locations]
cols = [ref_names[v] for v in difference_locations[1]]
bids_df = ref_df.loc[difference_locations[0], ref_bids].reset_index()
chng_df = pd.DataFrame({'iqm': cols, 'from': changed_from, 'to': changed_to})
chng_df = pd.DataFrame({"iqm": cols, "from": changed_from, "to": changed_to})
table = pd.concat([bids_df, chng_df], axis=1)
print(table[ref_bids + ['iqm', 'from', 'to']].to_string(index=False))
print(table[ref_bids + ["iqm", "from", "to"]].to_string(index=False))

corr = pd.DataFrame()
corr['iqms'] = ref_names
corr['cc'] = [float(np.corrcoef(ref_df[[var]].values.ravel(),
tst_df[[var]].values.ravel(),
rowvar=False)[0, 1])
for var in ref_names]
corr["iqms"] = ref_names
corr["cc"] = [
float(
np.corrcoef(
ref_df[[var]].values.ravel(),
tst_df[[var]].values.ravel(),
rowvar=False,
)[0, 1]
)
for var in ref_names
]

if np.any(corr.cc < 0.95):
print('IQMs with Pearson correlation < 0.95:')
print("IQMs with Pearson correlation < 0.95:")
print(corr[corr.cc < 0.95])
sys.exit('Output CSV file changed one or more values')
sys.exit("Output CSV file changed one or more values")
else:
print('All IQMs show a Pearson correlation >= 0.95')
print("All IQMs show a Pearson correlation >= 0.95")

sys.exit(0)


if __name__ == '__main__':
if __name__ == "__main__":
main()