junifer 0.0.5.dev93__tar.gz → 0.0.5.dev98__tar.gz

{junifer-0.0.5.dev93 → junifer-0.0.5.dev98}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev93
+Version: 0.0.5.dev98
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

junifer-0.0.5.dev98/docs/changes/newsfragments/345.feature

@@ -0,0 +1 @@
+Allow Unix path expansion directives to be used in :class:`.PatternDataGrabber` ``patterns`` by `Synchon Mandal`_

{junifer-0.0.5.dev93 → junifer-0.0.5.dev98}/docs/extending/datagrabber.rst

@@ -314,6 +314,53 @@ This approach can be used directly from the YAML, like so:
      uri: "https://gin.g-node.org/juaml/datalad-example-bids"
      rootdir: example_bids_ses
 
+Advanced: Using Unix-like path expansion directives
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+It is also possible to use some advanced Unix-like path expansion tricks to
+define our patterns.
+
+A very common thing would be to use ``*`` to match any number of
+characters but we cannot use it right after a replacement like:
+
+.. code-block:: python
+
+    "derivatives/freesurfer/{subject}*"
+
+or if there are multiple files or no files which can be globbed.
+
+We can also use ``[]`` and ``[!]`` to glob certain tricky files like with the
+case of FreeSurfer derivatives. The file structure seen in a typical
+FreeSurfer derivative of a dataset (like ``AOMIC`` ones) is like so:
+
+.. code-block::
+
+      .
+      └── derivatives
+          └── freesurfer
+             ├── fsaverage
+             │   ├── mri
+             │   |   ├── T1.mgz
+             │   |   └── ...
+             │   └── ...
+             ├── sub-01
+             │   ├── mri
+             │   |   ├── T1.mgz
+             │   |   └── ...
+             │   |   └── ...
+             │   └── ...
+             ...
+
+With a structure like this, it would be cumbersome to write custom methods
+for the class and thus we could use a pattern like this:
+
+.. code-block:: python
+
+    "derivatives/freesurfer/[!f]{subject}/mri/T1.mg[z]"
+
+This would ignore the ``fsaverage`` directory as a subject and let ``T1.mgz`` be
+fetched as there can be many files with the same prefix.
+
 .. _extending_datagrabbers_base:
 
 Option B: Extending from BaseDataGrabber

{junifer-0.0.5.dev93 → junifer-0.0.5.dev98}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.5.dev93'
-__version_tuple__ = version_tuple = (0, 0, 5, 'dev93')
+__version__ = version = '0.0.5.dev98'
+__version_tuple__ = version_tuple = (0, 0, 5, 'dev98')

{junifer-0.0.5.dev93 → junifer-0.0.5.dev98}/junifer/datagrabber/pattern.py

@@ -214,18 +214,25 @@ class PatternDataGrabber(BaseDataGrabber):
         t_replacements = [
             x for x in self.replacements if f"{{{x}}}" in pattern
         ]
-
+        # Ops on re_pattern
+        # Remove negated unix glob pattern i.e., [!...] for re_pattern
+        re_pattern = re.sub(r"\[!.?\]", "", re_pattern)
+        # Remove enclosing square brackets from unix glob pattern i.e., [...]
+        # for re_pattern
+        re_pattern = re.sub(r"\[|\]", "", re_pattern)
+        # Iteratively replace the first of each with a named group definition
         for t_r in t_replacements:
-            # Replace the first of each with a named group definition
             re_pattern = re_pattern.replace(f"{{{t_r}}}", f"(?P<{t_r}>.*)", 1)
-
+        # Iteratively replace the second appearance of each with the named
+        # group back reference
         for t_r in t_replacements:
-            # Replace the second appearance of each with the named group
-            # back reference
             re_pattern = re_pattern.replace(f"{{{t_r}}}", f"(?P={t_r})")
-
+        # Ops on glob_pattern
+        # Iteratively replace replacements with wildcard i.e., *
+        # for glob_pattern
         for t_r in t_replacements:
             glob_pattern = glob_pattern.replace(f"{{{t_r}}}", "*")
+
         return re_pattern, glob_pattern, t_replacements
 
     def _replace_patterns_glob(self, element: Dict, pattern: str) -> str:
@@ -254,6 +261,10 @@ class PatternDataGrabber(BaseDataGrabber):
                 f"The element keys must be {self.replacements}, "
                 f"element has {list(element.keys())}."
             )
+        # Remove negated unix glob pattern i.e., [!...]
+        pattern = re.sub(r"\[!.?\]", "", pattern)
+        # Remove enclosing square brackets from unix glob pattern i.e., [...]
+        pattern = re.sub(r"\[|\]", "", pattern)
         return pattern.format(**element)
 
     def _get_path_from_patterns(

{junifer-0.0.5.dev93 → junifer-0.0.5.dev98}/junifer/datagrabber/tests/test_pattern.py

@@ -236,6 +236,51 @@ def test_PatternDataGrabber(tmp_path: Path) -> None:
     assert out1["VBM_GM"]["path"] != out2["VBM_GM"]["path"]
 
 
+def test_PatternDataGrabber_unix_path_expansion(tmp_path: Path) -> None:
+    """Test PatterDataGrabber for patterns with unix path expansion.
+
+    Parameters
+    ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
+
+    """
+    # Create test data root dir
+    freesurfer_dir = tmp_path / "derivatives" / "freesurfer"
+    freesurfer_dir.mkdir(parents=True, exist_ok=True)
+    # Create test data sub dirs and files
+    for dir_name in ["fsaverage", "sub-0001"]:
+        mri_dir = freesurfer_dir / dir_name / "mri"
+        mri_dir.mkdir(parents=True, exist_ok=True)
+        # Create files
+        (mri_dir / "T1.mgz").touch(exist_ok=True)
+        (mri_dir / "aseg.mgz").touch(exist_ok=True)
+    # Create datagrabber
+    dg = PatternDataGrabber(
+        datadir=tmp_path,
+        types=["FreeSurfer"],
+        patterns={
+            "FreeSurfer": {
+                "pattern": "derivatives/freesurfer/[!f]{subject}/mri/T1.mg[z]",
+                "aseg": {
+                    "pattern": (
+                        "derivatives/freesurfer/[!f]{subject}/mri/aseg.mg[z]"
+                    )
+                },
+            },
+        },
+        replacements=["subject"],
+    )
+    # Check that "fsaverage" is filtered
+    elements = dg.get_elements()
+    assert elements == ["sub-0001"]
+    # Fetch data
+    out = dg["sub-0001"]
+    # Check paths are found
+    assert set(out["FreeSurfer"].keys()) == {"path", "aseg", "meta"}
+    assert list(out["FreeSurfer"]["aseg"].keys()) == ["path"]
+
+
 def test_PatternDataGrabber_confounds_format_error_on_init() -> None:
     """Test PatterDataGrabber confounds format error on initialisation."""
     with pytest.raises(

{junifer-0.0.5.dev93 → junifer-0.0.5.dev98}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev93
+Version: 0.0.5.dev98
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

{junifer-0.0.5.dev93 → junifer-0.0.5.dev98}/junifer.egg-info/SOURCES.txt

@@ -71,6 +71,7 @@ docs/changes/newsfragments/340.bugfix
 docs/changes/newsfragments/341.enh
 docs/changes/newsfragments/342.misc
 docs/changes/newsfragments/343.feature
+docs/changes/newsfragments/345.feature
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/dependencies.rst