junifer 0.0.5.dev93__py3-none-any.whl → 0.0.5.dev98__py3-none-any.whl

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/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/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.dist-info → junifer-0.0.5.dev98.dist-info}/METADATA

@@ -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.dist-info → junifer-0.0.5.dev98.dist-info}/RECORD

@@ -1,5 +1,5 @@
 junifer/__init__.py,sha256=x1UR2jUcrUdm2HNl-3Qvyi4UUrU6ms5qm2qcmNY7zZk,391
-junifer/_version.py,sha256=OuEXOAHKhbHnm8jc8By5AoScd2qmQjT4HRDoRe1JlYM,426
+junifer/_version.py,sha256=41cHsK1eRPpQ9ajnDhEe8UsfX7jGdL3It4yHcQyql1w,426
 junifer/stats.py,sha256=jN22_qFvWYBU9ZIMnCSzN4iOscWnWrcrUPIdLeDkV64,6163
 junifer/api/__init__.py,sha256=pSj8V8tmwOAQ3sshWJfRfB-n3z5bcJj3pHOBX4-8ONc,251
 junifer/api/cli.py,sha256=53pews3mXkJ7DUDSkV51PbitYnuVAdQRkWG-gjO08Uw,16142
@@ -94,7 +94,7 @@ junifer/datagrabber/base.py,sha256=KgMSKfkwd4yLW4PhoJDoWMgcDkGmDoIs6jkgKyOJd9A,6
 junifer/datagrabber/datalad_base.py,sha256=gP-DsyCd2F8W-aF2PXOg99Ntp2bj8QEtb535y06q39o,11009
 junifer/datagrabber/dmcc13_benchmark.py,sha256=se9F6QVw9WX22MNld33OQv_BtdW-yPvXXu6kYykxLNw,12225
 junifer/datagrabber/multiple.py,sha256=eXQIsvSNvD8GuEITjMaMoi1GwoeyWXXbQMRi-f2qgc4,4923
-junifer/datagrabber/pattern.py,sha256=w1aTL5xZRH9vq3-RofdmW-d_1t2OrAKRL0McCQErHGE,15273
+junifer/datagrabber/pattern.py,sha256=4OcGSCwBpeQOj6_YZohJjRFC_L69y7MAKsoE4-XO2So,15949
 junifer/datagrabber/pattern_datalad.py,sha256=R3LMeknT7tAXs2AN0XVPRf6tGkCMPgDfkNT2bfi7UNc,4526
 junifer/datagrabber/utils.py,sha256=s0Ife1qKEwXP47GfoxQ0qGqSP8L8ZNAms3HAvrSFoGI,9406
 junifer/datagrabber/aomic/__init__.py,sha256=R7yrRVBWsBW25CH0fw-KHpFwb_EC-MlPKDzssGfj5A0,281
@@ -113,7 +113,7 @@ junifer/datagrabber/tests/test_datagrabber_utils.py,sha256=x1nqFiHI9xHBQFwXji0DP
 junifer/datagrabber/tests/test_datalad_base.py,sha256=SYxUB9_4YPMfrb7iJM-aJCWbGa3EJfYz31wAUCNa03s,16285
 junifer/datagrabber/tests/test_dmcc13_benchmark.py,sha256=DcqkDXXBoabHFVbxekGR2NZyGeugGlxpOwXIwy38Ofg,9109
 junifer/datagrabber/tests/test_multiple.py,sha256=Mx3xfDrQiWG2W5MW24P5L2XiSeALpJ2-jFlzWkKtu9w,5659
-junifer/datagrabber/tests/test_pattern.py,sha256=Zmwg79f-qs6AEPVoFpooOquK7rm1hsmgkzuo11BG5PE,8019
+junifer/datagrabber/tests/test_pattern.py,sha256=H55jYRPfT3rMsoIQOAnWJgw3nGrkU7m2xFa3-ed6NQE,9527
 junifer/datagrabber/tests/test_pattern_datalad.py,sha256=hxw_aXBwHjUo-aUrHescBA2dn1bSJxh-0oV8495iIEA,6483
 junifer/datareader/__init__.py,sha256=_vtrLX_vxlHFD90gPa3gWnhTuvfWM7Uzyj6y8ZPaWm8,259
 junifer/datareader/default.py,sha256=_ntvkcF0H089bHwj0VOLTKWp8RvP7qy2HyieWHuRp2c,6680
@@ -253,10 +253,10 @@ junifer/utils/logging.py,sha256=furcU3XIUpUvnpe4PEwzWWIWgmH4j2ZA4MQdvSGWjj0,9216
 junifer/utils/tests/test_fs.py,sha256=WQS7cKlKEZ742CIuiOYYpueeAhY9PqlastfDVpVVtvE,923
 junifer/utils/tests/test_helpers.py,sha256=k5qqfxK8dFyuewTJyR1Qn6-nFaYNuVr0ysc18bfPjyU,929
 junifer/utils/tests/test_logging.py,sha256=l8oo-AiBV7H6_IzlsNcj__cLeZBUvgIGoaMszD9VaJg,7754
-junifer-0.0.5.dev93.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.5.dev93.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.5.dev93.dist-info/METADATA,sha256=GPQBJL5Fvtivl1q6VYeAV6eoIDVCjubyMZCizh3mn9k,8234
-junifer-0.0.5.dev93.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-junifer-0.0.5.dev93.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
-junifer-0.0.5.dev93.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.5.dev93.dist-info/RECORD,,
+junifer-0.0.5.dev98.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.5.dev98.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.5.dev98.dist-info/METADATA,sha256=bhP82n2v_xWS0SXTrwNePMWFS8onrdxujcj-0DGXtIk,8234
+junifer-0.0.5.dev98.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+junifer-0.0.5.dev98.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
+junifer-0.0.5.dev98.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.5.dev98.dist-info/RECORD,,