From fc2ccabfdb387c9300aee8315b96e9d1fc4faae9 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 23 Feb 2021 17:36:58 +0000
Subject: [PATCH] RF: Require at least one entity in a BIDS file name. Do not
use realpath on metadata file name, as files within a BIDS data set may be
sym-linked from another file/directory structure (e.g. datalad/git-annex)
---
fsl/utils/bids.py | 30 +++++++++++++++++-------------
1 file changed, 17 insertions(+), 13 deletions(-)
diff --git a/fsl/utils/bids.py b/fsl/utils/bids.py
index cae75cb4f..317aa5688 100644
--- a/fsl/utils/bids.py
+++ b/fsl/utils/bids.py
@@ -18,6 +18,7 @@
All of the other functions in this module should not be considered part of the
public API.
+.. see:: https://bids-specification.readthedocs.io/en/stable/
.. note:: The `pybids <https://bids-standard.github.io/pybids/>`_ library is
a more suitable choice if you are after a more robust and featured
@@ -36,8 +37,8 @@ import fsl.utils.path as fslpath
class BIDSFile(object):
- """The ``BIDSFile`` class parses and stores the entities and suffix contained
- in a BIDS file. See the :func:`parseFilename` function.
+ """The ``BIDSFile`` class parses and stores the entities and suffix
+ contained in a BIDS file. See the :func:`parseFilename` function.
The :meth:`match` method can be used to compare two ``BIDSFile`` instances.
@@ -91,15 +92,9 @@ class BIDSFile(object):
def parseFilename(filename):
- """Parses a BIDS-like file name. The file name must consist of zero or more
- "entities" (alpha-numeric ``name-value`` pairs), a "suffix", all separated
- by underscores, and a regular file extension. For example, the following
- file::
-
- sub-01_ses-01_task-stim_bold.nii.gz
-
- has suffix ``bold``, entities ``sub=01``, ``ses=01`` and ``task=stim``, and
- extension ``.nii.gz``.
+ """Parses a BIDS-like file name, returning the entities and suffix encoded
+ in the name. See the :func:`isBIDSFile` function for an explanation of
+ what is considered to be a valid BIDS file name.
.. note:: This function assumes that no period (``.``) characters occur in
the body of a BIDS filename.
@@ -161,13 +156,22 @@ def inBIDSDir(filename):
def isBIDSFile(filename, strict=True):
"""Returns ``True`` if ``filename`` looks like a BIDS image or JSON file.
+ A BIDS file name must consist of one or more "entities" (alpha-numeric
+ ``name-value`` pairs), a "suffix", all separated by underscores, and a
+ regular file extension. For example, the following file::
+
+ sub-01_ses-01_task-stim_bold.nii.gz
+
+ has suffix ``bold``, entities ``sub=01``, ``ses=01`` and ``task=stim``, and
+ extension ``.nii.gz``.
+
:arg filename: Name of file to check
:arg strict: If ``True`` (the default), the file must be within a BIDS
dataset directory, as defined by :func:`inBIDSDir`.
"""
name = op.basename(filename)
- pattern = r'([a-z0-9]+-[a-z0-9]+_)*([a-z0-9])+\.(.+)'
+ pattern = r'([a-z0-9]+-[a-z0-9]+_)+([a-z0-9])+\.(.+)'
flags = re.ASCII | re.IGNORECASE
match = re.fullmatch(pattern, name, flags) is not None
@@ -189,7 +193,7 @@ def loadMetadata(filename):
``filename``
"""
- filename = op.realpath(op.abspath(filename))
+ filename = op.abspath(filename)
bfile = BIDSFile(filename)
dirname = op.dirname(filename)
prevdir = filename
--
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