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RF: Anatomical processing #286

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Merged
merged 13 commits into from
May 11, 2023
Merged

RF: Anatomical processing #286

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45a63a6
ENH: Add helper method to fetch resource files
mgxd May 9, 2023
792a293
RF: Converge anatomical template workflow to mimic smriprep's
mgxd May 9, 2023
0581d4f
RF: Change module name to reflect lack of preprocessing
mgxd May 9, 2023
b1ec6e1
RF: Reflect changes on import/initialization
mgxd May 9, 2023
fe0769b
ENH: Extract shared anat preprocessing step into standalone workflow
mgxd May 9, 2023
f5ab000
RF/ENH: Clean up template handling, use cleaned T2w instead of raw
mgxd May 9, 2023
7e80006
ENH: Conform precomputed mask/aseg if available (only for single runs)
mgxd May 9, 2023
4dc12c5
RF: Clean up segmentation workflow
mgxd May 10, 2023
adb5c57
RF: Incorporate precomputed mask into coregistration workflow
mgxd May 10, 2023
ce1ab4a
ENH: Reflect downstream changes in anatomical preprocessing workflow
mgxd May 10, 2023
993f44c
FIX: Syntax & connections
mgxd May 10, 2023
5475910
RF: Remove alternate precomputed mask workflow
mgxd May 11, 2023
57f3ca6
STY: Annotate infant anat workflow
mgxd May 11, 2023
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24 changes: 23 additions & 1 deletion nibabies/utils/misc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,9 @@
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Miscellaneous utilities."""

from pathlib import Path
from typing import Union

from .. import __version__


Expand All @@ -14,7 +17,6 @@ def fix_multi_source_name(in_files):
'/path/to/sub-045_T1w.nii.gz'
"""
import re
from pathlib import Path

from nipype.utils.filemanip import filename_to_list

Expand Down Expand Up @@ -113,3 +115,23 @@ def combine_meepi_source(in_files):
entities = [ent for ent in in_file.split("_") if not ent.startswith("echo-")]
basename = "_".join(entities)
return os.path.join(base, basename)


def get_file(pkg: str, src_path: Union[str, Path]) -> str:
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I like this. But I would consider using a module-local ExitStack and cached responses to avoid unnecessary duplicates.

Example:

import atexit
from contextlib import ExitStack
from functools import cache
try:
    from importlib.resources import as_file, files
except ImportError:
    from importlib_resources import as_file, files

# Module-scoped
exit_stack = ExitStack()
atexit.register(exit_stack.close)

@cache
def get_file(pkg: str, src_path: Union[str, Path]) -> str:
    file_ref = files(pkg) / src_path
    pathlike = exit_stack.enter_context(as_file(file_ref))
    return str(pathlike)

"""
Get or extract a source file.
Assures the file will be available until the lifetime of the current Python process.
"""
import atexit
from contextlib import ExitStack

try:
from importlib.resources import as_file, files
except ImportError:
from importlib_resources import as_file, files

file_manager = ExitStack()
atexit.register(file_manager.close)
ref = files(pkg) / str(src_path)
fl = file_manager.enter_context(as_file(ref))
return str(fl)
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