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singlespsinglesp
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Merge branch 'main' into docstrings-parker
2 parents e9ca76a + 3b8bca0 commit c684155

24 files changed

+427
-7421
lines changed

‎cubids/cli.py‎

Lines changed: 19 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -105,9 +105,13 @@ def _path_exists(path, parser):
105105
argparse.ArgumentError
106106
If the path does not exist or is None.
107107
"""
108-
if path is None or not Path(path).exists():
109-
raise parser.error(f"Path does not exist: <{path}>.")
110-
return Path(path).absolute()
108+
if path is not None:
109+
path = Path(path)
110+
111+
if path is None or not path.exists():
112+
raise parser.error(f"Path does not exist: <{path.absolute()}>.")
113+
return path.absolute()
114+
111115

112116

113117
def _is_file(path, parser):
@@ -132,12 +136,14 @@ def _is_file(path, parser):
132136
"""
133137
path = _path_exists(path, parser)
134138
if not path.is_file():
135-
raise parser.error(f"Path should point to a file (or symlink of file): <{path}>.")
139+
raise parser.error(
140+
f"Path should point to a file (or symlink of file): <{path.absolute()}>."
141+
)
136142
return path
137143

138144

139145
def _parse_validate():
140-
"""Create and configure the argument parser for the CuBIDS validation CLI.
146+
"""Create and configure the argument parser for the "cubids validate" command.
141147
142148
This function sets up an argument parser with various options for running
143149
the BIDS validator, including specifying the BIDS dataset directory, output
@@ -146,7 +152,7 @@ def _parse_validate():
146152
Returns
147153
-------
148154
argparse.ArgumentParser
149-
Configured argument parser for the CuBIDS validation CLI.
155+
Configured argument parser for the "cubids validate" command.
150156
151157
Parameters
152158
----------
@@ -227,6 +233,13 @@ def _parse_validate():
227233
nargs="+",
228234
required=False,
229235
)
236+
parser.add_argument(
237+
"--local-validator",
238+
action="store_true",
239+
default=False,
240+
help="Lets user run a locally installed BIDS validator. Default is set to False ",
241+
required=False,
242+
)
230243
return parser
231244

232245

‎cubids/config.py‎

Lines changed: 12 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,18 @@
55
import yaml
66

77
def load_config(config_file):
8-
"""Load a YAML file containing a configuration for param groups."""
8+
"""Load a YAML file containing a configuration for param groups.
9+
10+
Parameters
11+
----------
12+
config_file : str or pathlib.Path, optional
13+
The path to the configuration file. If None, the default configuration file is used.
14+
15+
Returns
16+
-------
17+
dict
18+
The configuration loaded from the YAML file.
19+
"""
920
if config_file is None:
1021
config_file = Path(importlib.resources.files("cubids") / "data/config.yml")
1122

‎cubids/cubids.py‎

Lines changed: 173 additions & 45 deletions
Original file line numberDiff line numberDiff line change
@@ -469,55 +469,19 @@ def change_filename(self, filepath, entities):
469469
-----
470470
This is the function I need to spend the most time on, since it has entities hardcoded.
471471
"""
472+
new_path = build_path(
473+
filepath=filepath,
474+
entities=entities,
475+
out_dir=str(self.path),
476+
)
477+
472478
exts = Path(filepath).suffixes
473479
old_ext = "".join(exts)
474480

475481
suffix = entities["suffix"]
476-
entity_file_keys = []
477-
478-
# Entities that may be in the filename?
479-
file_keys = ["task", "acquisition", "direction", "reconstruction", "run"]
480-
481-
for key in file_keys:
482-
if key in list(entities.keys()):
483-
entity_file_keys.append(key)
484482

485-
sub = get_key_name(filepath, "sub")
486-
ses = get_key_name(filepath, "ses")
487-
sub_ses = sub + "_" + ses
488-
489-
if "run" in list(entities.keys()) and "run-0" in filepath:
490-
# XXX: This adds an extra leading zero to run.
491-
entities["run"] = "0" + str(entities["run"])
492-
493-
filename = "_".join([f"{key}-{entities[key]}" for key in entity_file_keys])
494-
filename = (
495-
filename.replace("acquisition", "acq")
496-
.replace("direction", "dir")
497-
.replace("reconstruction", "rec")
498-
)
499-
if len(filename) > 0:
500-
filename = sub_ses + "_" + filename + "_" + suffix + old_ext
501-
else:
502-
raise ValueError(f"Could not construct new filename for {filepath}")
503-
504-
# CHECK TO SEE IF DATATYPE CHANGED
505-
# datatype may be overridden/changed if the original file is located in the wrong folder.
506-
dtypes = ["anat", "func", "perf", "fmap", "dwi"]
507-
dtype_orig = ""
508-
for dtype in dtypes:
509-
if dtype in filepath:
510-
dtype_orig = dtype
511-
512-
if "datatype" in entities.keys():
513-
dtype_new = entities["datatype"]
514-
if entities["datatype"] != dtype_orig:
515-
print("WARNING: DATATYPE CHANGE DETECETD")
516-
else:
517-
dtype_new = dtype_orig
518-
519-
# Construct the new filename
520-
new_path = str(self.path) + "/" + sub + "/" + ses + "/" + dtype_new + "/" + filename
483+
sub = get_entity_value(filepath, "sub")
484+
ses = get_entity_value(filepath, "ses")
521485

522486
# Add the scan path + new path to the lists of old, new filenames
523487
self.old_filenames.append(filepath)
@@ -1762,9 +1726,173 @@ def img_to_new_ext(img_path, new_ext):
17621726
return img_path.replace(".nii.gz", "").replace(".nii", "") + new_ext
17631727

17641728

1765-
def get_key_name(path, key):
1729+
def get_entity_value(path, key):
17661730
"""Given a filepath and BIDS key name, return value."""
17671731
parts = Path(path).parts
17681732
for part in parts:
17691733
if part.startswith(key + "-"):
17701734
return part
1735+
1736+
1737+
def build_path(filepath, entities, out_dir):
1738+
"""Build a new path for a file based on its BIDS entities.
1739+
1740+
Parameters
1741+
----------
1742+
filepath : str
1743+
The original file path.
1744+
entities : dict
1745+
A dictionary of BIDS entities.
1746+
This should include all of the entities in the filename *except* for subject and session.
1747+
out_dir : str
1748+
The output directory for the new file.
1749+
1750+
Returns
1751+
-------
1752+
new_path : str
1753+
The new file path.
1754+
1755+
Examples
1756+
--------
1757+
>>> build_path(
1758+
... "/input/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz",
1759+
... {"acquisition": "VAR", "suffix": "T2w"},
1760+
... "/output",
1761+
... )
1762+
'/output/sub-01/ses-01/anat/sub-01_ses-01_acq-VAR_T2w.nii.gz'
1763+
1764+
The function does not add an extra leading zero to the run entity when it's a string.
1765+
>>> build_path(
1766+
... "/input/sub-01/ses-01/func/sub-01_ses-01_task-rest_run-01_bold.nii.gz",
1767+
... {"task": "rest", "run": "2", "acquisition": "VAR", "suffix": "bold"},
1768+
... "/output",
1769+
... )
1770+
'/output/sub-01/ses-01/func/sub-01_ses-01_task-rest_acq-VAR_run-2_bold.nii.gz'
1771+
1772+
The function adds an extra leading zero to the run entity when it's an integer
1773+
and the original filename has a leading zero.
1774+
>>> build_path(
1775+
... "/input/sub-01/ses-01/func/sub-01_ses-01_task-rest_run-00001_bold.nii.gz",
1776+
... {"task": "rest", "run": 2, "acquisition": "VAR", "suffix": "bold"},
1777+
... "/output",
1778+
... )
1779+
'/output/sub-01/ses-01/func/sub-01_ses-01_task-rest_acq-VAR_run-00002_bold.nii.gz'
1780+
1781+
The function does not add an extra leading zero to the run entity when it's an integer
1782+
and the original filename doesn't have a leading zero.
1783+
>>> build_path(
1784+
... "/input/sub-01/ses-01/func/sub-01_ses-01_task-rest_run-1_bold.nii.gz",
1785+
... {"task": "rest", "run": 2, "acquisition": "VAR", "suffix": "bold"},
1786+
... "/output",
1787+
... )
1788+
'/output/sub-01/ses-01/func/sub-01_ses-01_task-rest_acq-VAR_run-2_bold.nii.gz'
1789+
1790+
The function doesn't add an extra leading zero to the run entity when there isn't a zero.
1791+
>>> build_path(
1792+
... "/input/sub-01/ses-01/func/sub-01_ses-01_task-rest_run-1_bold.nii.gz",
1793+
... {"task": "rest", "run": "2", "acquisition": "VAR", "suffix": "bold"},
1794+
... "/output",
1795+
... )
1796+
'/output/sub-01/ses-01/func/sub-01_ses-01_task-rest_acq-VAR_run-2_bold.nii.gz'
1797+
1798+
Entities in the original path, but not the entity dictionary, are not included,
1799+
like run in this case.
1800+
>>> build_path(
1801+
... "/input/sub-01/ses-01/func/sub-01_ses-01_task-rest_run-01_bold.nii.gz",
1802+
... {"task": "rest", "acquisition": "VAR", "suffix": "bold"},
1803+
... "/output",
1804+
... )
1805+
'/output/sub-01/ses-01/func/sub-01_ses-01_task-rest_acq-VAR_bold.nii.gz'
1806+
1807+
Entities outside of the prescribed list are ignored, such as "subject"...
1808+
>>> build_path(
1809+
... "/input/sub-01/ses-01/func/sub-01_ses-01_task-rest_run-01_bold.nii.gz",
1810+
... {"subject": "02", "task": "rest", "acquisition": "VAR", "suffix": "bold"},
1811+
... "/output",
1812+
... )
1813+
'/output/sub-01/ses-01/func/sub-01_ses-01_task-rest_acq-VAR_bold.nii.gz'
1814+
1815+
or "echo".
1816+
>>> build_path(
1817+
... "/input/sub-01/ses-01/func/sub-01_ses-01_task-rest_run-01_bold.nii.gz",
1818+
... {"task": "rest", "acquisition": "VAR", "echo": 1, "suffix": "bold"},
1819+
... "/output",
1820+
... )
1821+
'/output/sub-01/ses-01/func/sub-01_ses-01_task-rest_acq-VAR_bold.nii.gz'
1822+
1823+
It can change the datatype, but will warn the user.
1824+
>>> build_path(
1825+
... "/input/sub-01/ses-01/anat/sub-01_ses-01_asl.nii.gz",
1826+
... {"datatype": "perf", "acquisition": "VAR", "suffix": "asl"},
1827+
... "/output",
1828+
... )
1829+
WARNING: DATATYPE CHANGE DETECTED
1830+
'/output/sub-01/ses-01/perf/sub-01_ses-01_acq-VAR_asl.nii.gz'
1831+
1832+
It expects a longitudinal structure, so providing a cross-sectional filename won't work.
1833+
XXX: This is a bug.
1834+
>>> build_path(
1835+
... "/input/sub-01/func/sub-01_task-rest_run-01_bold.nii.gz",
1836+
... {"task": "rest", "acquisition": "VAR", "echo": 1, "suffix": "bold"},
1837+
... "/output",
1838+
... )
1839+
Traceback (most recent call last):
1840+
ValueError: Could not extract subject or session from ...
1841+
"""
1842+
exts = Path(filepath).suffixes
1843+
old_ext = "".join(exts)
1844+
1845+
suffix = entities["suffix"]
1846+
entity_file_keys = []
1847+
1848+
# Entities that may be in the filename?
1849+
file_keys = ["task", "acquisition", "direction", "reconstruction", "run"]
1850+
1851+
for key in file_keys:
1852+
if key in list(entities.keys()):
1853+
entity_file_keys.append(key)
1854+
1855+
sub = get_entity_value(filepath, "sub")
1856+
ses = get_entity_value(filepath, "ses")
1857+
if sub is None or ses is None:
1858+
raise ValueError(f"Could not extract subject or session from {filepath}")
1859+
1860+
# Add leading zeros to run entity if it's an integer.
1861+
# If it's a string, respect the value provided.
1862+
if "run" in entities.keys() and isinstance(entities["run"], int):
1863+
# Infer the number of leading zeros needed from the original filename
1864+
n_leading = 2 # default to 1 leading zero
1865+
if "_run-" in filepath:
1866+
run_str = filepath.split("_run-")[1].split("_")[0]
1867+
n_leading = len(run_str)
1868+
entities["run"] = str(entities["run"]).zfill(n_leading)
1869+
1870+
filename = "_".join([f"{key}-{entities[key]}" for key in entity_file_keys])
1871+
filename = (
1872+
filename.replace("acquisition", "acq")
1873+
.replace("direction", "dir")
1874+
.replace("reconstruction", "rec")
1875+
)
1876+
if len(filename) > 0:
1877+
filename = f"{sub}_{ses}_{filename}_{suffix}{old_ext}"
1878+
else:
1879+
raise ValueError(f"Could not construct new filename for {filepath}")
1880+
1881+
# CHECK TO SEE IF DATATYPE CHANGED
1882+
# datatype may be overridden/changed if the original file is located in the wrong folder.
1883+
dtypes = ["anat", "func", "perf", "fmap", "dwi"]
1884+
dtype_orig = ""
1885+
for dtype in dtypes:
1886+
if dtype in filepath:
1887+
dtype_orig = dtype
1888+
1889+
if "datatype" in entities.keys():
1890+
dtype_new = entities["datatype"]
1891+
if entities["datatype"] != dtype_orig:
1892+
print("WARNING: DATATYPE CHANGE DETECTED")
1893+
else:
1894+
dtype_new = dtype_orig
1895+
1896+
# Construct the new filename
1897+
new_path = str(Path(out_dir) / sub / ses / dtype_new / filename)
1898+
return new_path

‎cubids/tests/test_apply.py‎

Lines changed: 6 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -230,32 +230,28 @@ def summary_data():
230230
(
231231
"relpath_long",
232232
relpath_intendedfor_long,
233-
# XXX: Should not have extra leading zero in run entity, but that's a known bug.
234-
"ses-01/dwi/sub-01_ses-01_acq-VAR_dir-AP_run-001_dwi.nii.gz",
233+
"ses-01/dwi/sub-01_ses-01_acq-VAR_dir-AP_run-01_dwi.nii.gz",
235234
"pass",
236235
),
237236
(
238237
"bidsuri_long",
239238
bidsuri_intendedfor_long,
240-
# XXX: Should not have extra leading zero in run entity, but that's a known bug.
241-
"bids::sub-01/ses-01/dwi/sub-01_ses-01_acq-VAR_dir-AP_run-001_dwi.nii.gz",
239+
"bids::sub-01/ses-01/dwi/sub-01_ses-01_acq-VAR_dir-AP_run-01_dwi.nii.gz",
242240
"pass",
243241
),
244242
(
245243
"relpath_cs",
246244
relpath_intendedfor_cs,
247-
# XXX: Should not have extra leading zero in run entity, but that's a known bug.
248245
# XXX: CuBIDS enforces longitudinal dataset, so this fails.
249-
"dwi/sub-01_acq-VAR_dir-AP_run-001_dwi.nii.gz",
250-
TypeError,
246+
"dwi/sub-01_acq-VAR_dir-AP_run-01_dwi.nii.gz",
247+
ValueError,
251248
),
252249
(
253250
"bidsuri_cs",
254251
bidsuri_intendedfor_cs,
255-
# XXX: Should not have extra leading zero in run entity, but that's a known bug.
256252
# XXX: CuBIDS enforces longitudinal dataset, so this fails.
257-
"bids::sub-01/dwi/sub-01_acq-VAR_dir-AP_run-001_dwi.nii.gz",
258-
TypeError,
253+
"bids::sub-01/dwi/sub-01_acq-VAR_dir-AP_run-01_dwi.nii.gz",
254+
ValueError,
259255
),
260256
],
261257
)

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