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made / separator compatible across OS's in cubids.py
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@gabridele
gabridele committed Jan 17, 2025
1 parent f61e1ef commit 5870dc2
Showing 1 changed file with 36 additions and 32 deletions.
68 changes: 36 additions & 32 deletions cubids/cubids.py
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Original file line number Diff line number Diff line change
Expand Up @@ -107,7 +107,7 @@ def __init__(
self.acq_group_level = acq_group_level
self.scans_txt = None # txt file of scans to purge (for purge only)
self.force_unlock = force_unlock # force unlock for add-nifti-info
self.cubids_code_dir = Path(self.path + "/code/CuBIDS").is_dir()
self.cubids_code_dir = (Path(self.path) / "code" / "CuBIDS").is_dir()
self.data_dict = {} # data dictionary for TSV outputs
self.use_datalad = use_datalad # True if flag set, False if flag unset
if self.use_datalad:
Expand Down Expand Up @@ -169,8 +169,8 @@ def create_cubids_code_dir(self):
"""
# check if BIDS_ROOT/code/CuBIDS exists
if not self.cubids_code_dir:
subprocess.run(["mkdir", self.path + "/code"])
subprocess.run(["mkdir", self.path + "/code/CuBIDS/"])
subprocess.run(["mkdir", os.path.join(self.path, "code")])
subprocess.run(["mkdir", os.path.join(self.path, "code", "CuBIDS")])
self.cubids_code_dir = True
return self.cubids_code_dir

Expand Down Expand Up @@ -251,7 +251,7 @@ def add_nifti_info(self):
# loop through all niftis in the bids dir
for path in Path(self.path).rglob("sub-*/**/*.*"):
# ignore all dot directories
if "/." in str(path):
if any(part.startswith('.') for part in path.parts):
continue

if str(path).endswith(".nii") or str(path).endswith(".nii.gz"):
Expand Down Expand Up @@ -328,15 +328,15 @@ def apply_tsv_changes(self, summary_tsv, files_tsv, new_prefix, raise_on_error=T
self.old_filenames = []
self.new_filenames = []

if "/" not in str(summary_tsv):
if os.sep not in str(summary_tsv):
if not self.cubids_code_dir:
self.create_cubids_code_dir()
summary_tsv = self.path + "/code/CuBIDS/" + summary_tsv
summary_tsv = Path(self.path) / "code" / "CuBIDS" / summary_tsv

if "/" not in str(files_tsv):
if os.sep not in str(files_tsv):
if not self.cubids_code_dir:
self.create_cubids_code_dir()
files_tsv = self.path + "/code/CuBIDS/" + files_tsv
files_tsv = Path(self.path) / "code" / "CuBIDS" / files_tsv

summary_df = pd.read_table(summary_tsv)
files_df = pd.read_table(files_tsv)
Expand Down Expand Up @@ -392,7 +392,7 @@ def apply_tsv_changes(self, summary_tsv, files_tsv, new_prefix, raise_on_error=T

for row in range(len(files_df)):
file_path = self.path + files_df.loc[row, "FilePath"]
if Path(file_path).exists() and "/fmap/" not in file_path:
if Path(file_path).exists() and Path("fmap") not in Path(file_path).parts:
key_param_group = files_df.loc[row, "KeyParamGroup"]

if key_param_group in to_change:
Expand Down Expand Up @@ -505,7 +505,7 @@ def change_filename(self, filepath, entities):

# MAKE SURE THESE AREN'T COVERED BY get_associations!!!
# Update DWI-specific files
if "/dwi/" in filepath:
if "dwi" in Path(filepath).parts:
# add the bval and bvec if there
bval_old = img_to_new_ext(filepath, ".bval")
bval_new = img_to_new_ext(new_path, ".bval")
Expand All @@ -524,7 +524,7 @@ def change_filename(self, filepath, entities):
old_suffix = parse_file_entities(filepath)["suffix"]
scan_end = "_" + old_suffix + old_ext

if "_task-" in filepath:
if "_task-" in Path(filepath).parts:
old_events = filepath.replace(scan_end, "_events.tsv")
if Path(old_events).exists():
self.old_filenames.append(old_events)
Expand All @@ -547,7 +547,7 @@ def change_filename(self, filepath, entities):
self.new_filenames.append(new_physio)

# Update ASL-specific files
if "/perf/" in filepath:
if "perf" in Path(filepath).parts:
old_context = filepath.replace(scan_end, "_aslcontext.tsv")
if Path(old_context).exists():
self.old_filenames.append(old_context)
Expand Down Expand Up @@ -577,7 +577,7 @@ def change_filename(self, filepath, entities):
self.new_filenames.append(new_labeling)

# RENAME INTENDED FORS!
ses_path = self.path + "/" + sub + "/" + ses
ses_path = Path(self.path) / sub / ses
files_with_if = []
files_with_if += Path(ses_path).rglob("fmap/*.json")
files_with_if += Path(ses_path).rglob("perf/*_m0scan.json")
Expand Down Expand Up @@ -655,7 +655,7 @@ def copy_exemplars(self, exemplars_dir, exemplars_tsv, min_group_size):
if os.sep not in str(exemplars_tsv):
if not self.cubids_code_dir:
self.create_cubids_code_dir()
exemplars_tsv = self.path + "/code/CuBIDS/" + exemplars_tsv
exemplars_tsv = Path(self.path) / "code" / "CuBIDS" / exemplars_tsv

# load the exemplars tsv
subs = pd.read_table(exemplars_tsv)
Expand All @@ -674,15 +674,15 @@ def copy_exemplars(self, exemplars_dir, exemplars_tsv, min_group_size):
# cast list to a set to drop duplicates, then convert back to list
unique_subs = list(set(unique["subject"].tolist()))
for subid in unique_subs:
source = str(self.path) + "/" + subid
dest = exemplars_dir + "/" + subid
source = Path(self.path) / subid
dest = Path(exemplars_dir) / subid
# Copy the content of source to destination
copytree(source, dest)

# Copy the dataset_description.json
copyfile(
str(self.path) + "/" + "dataset_description.json",
exemplars_dir + "/" + "dataset_description.json",
source = os.path.join(self.path, "dataset_description.json"),
destination = os.path.join(exemplars_dir, "dataset_description.json"),
)

s1 = "Copied one subject from each Acquisition Group "
Expand All @@ -708,7 +708,7 @@ def purge(self, scans_txt):
with open(scans_txt, "r") as fd:
reader = csv.reader(fd)
for row in reader:
scans.append(self.path + "/" + str(row[0]))
scans.append(os.path.join(self.path, str(row[0])))

# check to ensure scans are all real files in the ds!

Expand Down Expand Up @@ -772,14 +772,14 @@ def _purge_associations(self, scans):

# ensure association is not an IntendedFor reference!
if ".nii" not in str(path):
if "/dwi/" in str(path):
if "dwi" in Path(path).parts:
# add the bval and bvec if there
if Path(img_to_new_ext(str(path), ".bval")).exists():
to_remove.append(img_to_new_ext(str(path), ".bval"))
if Path(img_to_new_ext(str(path), ".bvec")).exists():
to_remove.append(img_to_new_ext(str(path), ".bvec"))

if "/func/" in str(path):
if "func" in Path(path).parts:
# add tsvs
tsv = img_to_new_ext(str(path), ".tsv").replace("_bold", "_events")
if Path(tsv).exists():
Expand All @@ -804,7 +804,7 @@ def _purge_associations(self, scans):

path_prefix = str(Path(self.path).parent)

with open(path_prefix + "/" + "_full_cmd.sh", "w") as fo:
with open(os.path.join(path_prefix, "_full_cmd.sh"), "w") as fo:
fo.write("#!/bin/bash\n")
fo.write(full_cmd)

Expand All @@ -813,12 +813,12 @@ def _purge_associations(self, scans):
else:
cmt = "Purged Parameter Groups marked for removal"

purge_file = path_prefix + "/" + "_full_cmd.sh"
purge_file = os.path.join(path_prefix, "_full_cmd.sh")
if self.use_datalad:
self.datalad_handle.run(cmd=["bash", purge_file], message=cmt)
else:
subprocess.run(
["bash", path_prefix + "/" + "_full_cmd.sh"],
["bash", purge_file],
stdout=subprocess.PIPE,
cwd=path_prefix,
)
Expand All @@ -835,7 +835,11 @@ def get_nifti_associations(self, nifti):
but with a different extension.
"""
# get all assocation files of a nifti image
no_ext_file = str(nifti).split("/")[-1].split(".")[0]
filename = os.path.basename(nifti)

# Remove the file extension to get the base name without extension
no_ext_file = os.path.splitext(filename)[0]

associations = []
for path in Path(self.path).rglob(f"sub-*/**/{no_ext_file}.*"):
if ".nii.gz" not in str(path):
Expand Down Expand Up @@ -913,11 +917,11 @@ def get_param_groups_from_entity_set(self, entity_set):
to_include.append(filepath)

# get the modality associated with the entity set
modalities = ["/dwi/", "/anat/", "/func/", "/perf/", "/fmap/"]
modalities = ["dwi", "anat", "func", "perf", "fmap"]
modality = ""
for mod in modalities:
if mod in filepath:
modality = mod.replace("/", "").replace("/", "")
modality = mod

if modality == "":
print("Unusual Modality Detected")
Expand Down Expand Up @@ -1216,13 +1220,13 @@ def get_tsvs(self, path_prefix):

# check if path_prefix is absolute or relative
# if relative, put output in BIDS_ROOT/code/CuBIDS/ dir
if "/" not in path_prefix:
if os.sep not in path_prefix:
# path is relative
# first check if code/CuBIDS dir exits
# first check if code/CuBIDS dir exists
# if not, create it
self.create_cubids_code_dir()
# send outputs to code/CuBIDS in BIDS tree
path_prefix = self.path + "/code/CuBIDS/" + path_prefix
path_prefix = str(Path(self.path) / "code" / "CuBIDS" / path_prefix)

big_df, summary = self.get_param_groups_dataframes()

Expand Down Expand Up @@ -1259,7 +1263,7 @@ def get_entity_sets(self):

for path in Path(self.path).rglob("sub-*/**/*.*"):
# ignore all dot directories
if "/." in str(path):
if any(part.startswith('.') for part in path.parts):
continue

if str(path).endswith(".nii") or str(path).endswith(".nii.gz"):
Expand Down Expand Up @@ -1403,7 +1407,7 @@ def _get_participant_relative_path(scan):
This is what will appear in the IntendedFor field of any association.
"""
return "/".join(Path(scan).parts[-3:])
return Path(scan).parts[-3:]


def _get_bidsuri(filename, dataset_root):
Expand Down

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