import os.path as op
import logging
from AFQ.utils.path import drop_extension
logger = logging.getLogger('AFQ')
__all__ = ["Definition", "find_file", "name_from_path"]
[docs]class Definition(object):
'''
All Definitions should inherit this.
For a given subject and session within the API, the definition is used
to create a given image or map.
Definitions have an init function which the users uses to specify
how they want the definition to behave.
The find_path function is called by the AFQ API.
The api calls find_path to let the definition find relevant files
for the given subject and session.
'''
def __init__(self):
raise NotImplementedError("Please implement an __init__ method")
[docs] def find_path(self, bids_layout, from_path,
subject, session, required=True):
pass
[docs] def str_for_toml(self):
"""
Uses __init__ in str_for_toml to make string that will instantiate
itself. Assumes object will have attributes of same name as
__init__ args. This is important for reading/writing definitions
as arguments to config files.
"""
return type(self).__name__\
+ "("\
+ _arglist_to_string(
self.__init__.__code__.co_varnames,
get_attr=self)\
+ ')'
def _arglist_to_string(args, get_attr=None):
'''
Helper function
Takes a list of arguments and unfolds them into a string.
If get_attr is not None, it will be used to get the attribute
corresponding to each argument instead.
'''
to_string = ""
for arg in args:
if arg == "self":
continue
if get_attr is not None:
arg = getattr(get_attr, arg)
if isinstance(arg, Definition):
arg = arg.str_for_toml()
elif isinstance(arg, str):
arg = f"\"{arg}\""
elif isinstance(arg, list):
arg = f"[{_arglist_to_string(arg)}]"
to_string = to_string + str(arg) + ', '
if to_string[-2:] == ', ':
to_string = to_string[:-2]
return to_string
[docs]def name_from_path(path):
file_name = op.basename(path) # get file name
file_name = drop_extension(file_name) # remove extension
if "-" in file_name:
file_name = file_name.split("-")[-1] # get suffix if exists
return file_name
def _ff_helper(required, err_msg):
if required:
raise ValueError(err_msg)
else:
logger.warning(err_msg)
return None
[docs]def find_file(bids_layout, path, filters, suffix, session, subject,
extension=".nii.gz", required=True):
"""
Helper function
Generic calls to get_nearest to find a file
"""
if "extension" not in filters:
filters["extension"] = extension
if "suffix" not in filters:
filters["suffix"] = suffix
# First, try to match the session.
nearest = bids_layout.get_nearest(
path,
**filters,
session=session,
subject=subject,
full_search=True,
strict=False,
)
# If that fails, loosen session restriction
# in order to find scans that are not session specific
if nearest is None:
nearest = bids_layout.get_nearest(
path,
**filters,
subject=subject,
full_search=True,
strict=False,
)
# Nothing is found
if nearest is None:
return _ff_helper(required, (
"No file found with these parameters:\n"
f"suffix: {suffix},\n"
f"session (searched with and without): {session},\n"
f"subject: {subject},\n"
f"filters: {filters},\n"
f"near path: {path},\n"))
path_subject = bids_layout.parse_file_entities(path).get(
"subject", None
)
file_subject = bids_layout.parse_file_entities(nearest).get(
"subject", None
)
path_session = bids_layout.parse_file_entities(path).get(
"session", None
)
file_session = bids_layout.parse_file_entities(nearest).get(
"session", None
)
# found file is wrong subject
if path_subject != file_subject:
return _ff_helper(required, (
f"Expected subject IDs to match for the retrieved image file "
f"and the supplied `from_path` file. Got sub-{file_subject} "
f"from image file {nearest} and sub-{path_subject} "
f"from `from_path` file {path}."))
# found file is wrong session
if (file_session is not None) and (path_session != file_session):
return _ff_helper(required, (
f"Expected session IDs to match for the retrieved image file "
f"and the supplied `from_path` file. Got ses-{file_session} "
f"from image file {nearest} and ses-{path_session} "
f"from `from_path` file {path}."))
return nearest
