junifer 0.0.6.dev252__tar.gz → 0.0.6.dev266__tar.gz

{junifer-0.0.6.dev252 → junifer-0.0.6.dev266}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev252
+Version: 0.0.6.dev266
 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-0.0.6.dev266/docs/changes/newsfragments/388.bugfix

@@ -0,0 +1 @@
+Fix coordinates space transformation using ANTs by `Synchon Mandal`_

junifer-0.0.6.dev266/docs/changes/newsfragments/398.bugfix

@@ -0,0 +1 @@
+Fix metadata update for :class:`.MultipleDataGrabber` and adjust :meth:`.PatternDataGrabber.get_elements` to check ``list``-like data type values by `Fede Raimondo`_ and `Synchon Mandal`_

{junifer-0.0.6.dev252 → junifer-0.0.6.dev266}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev252'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev252')
+__version__ = version = '0.0.6.dev266'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev266')

{junifer-0.0.6.dev252 → junifer-0.0.6.dev266}/junifer/data/coordinates/_ants_coordinates_warper.py

@@ -55,19 +55,24 @@ class ANTsCoordinatesWarper:
 
         # Save existing coordinates to a tempfile
         pretransform_coordinates_path = (
-            element_tempdir / "pretransform_coordinates.txt"
+            element_tempdir / "pretransform_coordinates.csv"
         )
+        # Convert LPS to RAS
+        seeds[:, 0] *= -1
+        seeds[:, 1] *= -1
         np.savetxt(
             pretransform_coordinates_path,
             seeds,
             delimiter=",",
             # Add header while saving to make ANTs work
             header="x,y,z",
+            # Remove comment tag for header
+            comments="",
         )
 
         # Create a tempfile for transformed coordinates output
         transformed_coords_path = (
-            element_tempdir / "coordinates_transformed.txt"
+            element_tempdir / "coordinates_transformed.csv"
         )
         # Set antsApplyTransformsToPoints command
         apply_transforms_to_points_cmd = [
@@ -86,9 +91,14 @@ class ANTsCoordinatesWarper:
         )
 
         # Load coordinates
-        return np.loadtxt(
+        transformed_seeds = np.loadtxt(
             # Skip header when reading
             transformed_coords_path,
             delimiter=",",
             skiprows=1,
         )
+        # Convert RAS to LPS
+        transformed_seeds[:, 0] *= -1
+        transformed_seeds[:, 1] *= -1
+
+        return transformed_seeds

{junifer-0.0.6.dev252 → junifer-0.0.6.dev266}/junifer/data/coordinates/_coordinates.py

@@ -362,7 +362,7 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                 seeds = ANTsCoordinatesWarper().warp(
                     seeds=seeds,
                     target_data=target_data,
-                    warp_data=warper_spec,
+                    warp_data=inverse_warper_spec,
                 )
 
         return seeds, labels

{junifer-0.0.6.dev252 → junifer-0.0.6.dev266}/junifer/datagrabber/multiple.py

@@ -111,8 +111,12 @@ class MultipleDataGrabber(BaseDataGrabber):
 
         # Update all the metas again
         for kind in out:
-            self.update_meta(out[kind], "datagrabber")
-            out[kind]["meta"]["datagrabber"]["datagrabbers"] = metas
+            to_update = out[kind]
+            if not isinstance(to_update, list):
+                to_update = [to_update]
+            for t_kind in to_update:
+                self.update_meta(t_kind, "datagrabber")
+                t_kind["meta"]["datagrabber"]["datagrabbers"] = metas
         return out
 
     def __enter__(self) -> "MultipleDataGrabber":

{junifer-0.0.6.dev252 → junifer-0.0.6.dev266}/junifer/datagrabber/pattern.py

@@ -13,6 +13,7 @@ from typing import Optional, Union
 import numpy as np
 
 from ..api.decorators import register_datagrabber
+from ..typing import DataGrabberPatterns
 from ..utils import logger, raise_error
 from .base import BaseDataGrabber
 from .pattern_validation_mixin import PatternValidationMixin
@@ -171,7 +172,7 @@ class PatternDataGrabber(BaseDataGrabber, PatternValidationMixin):
     def __init__(
         self,
         types: list[str],
-        patterns: dict[str, dict[str, str]],
+        patterns: DataGrabberPatterns,
         replacements: Union[list[str], str],
         datadir: Union[str, Path],
         confounds_format: Optional[str] = None,
@@ -478,58 +479,63 @@ class PatternDataGrabber(BaseDataGrabber, PatternValidationMixin):
             t_type = self.types[t_idx]
             types_element = set()
 
-            # Get the pattern dict
-            t_pattern = self.patterns[t_type]
-            # Conditional fetch of base pattern for getting elements
-            pattern = None
-            # Try for data type pattern
-            pattern = t_pattern.get("pattern")
-            # Try for nested data type pattern
-            if pattern is None and self.partial_pattern_ok:
-                for v in t_pattern.values():
-                    if isinstance(v, dict) and "pattern" in v:
-                        pattern = v["pattern"]
-                        break
-
-            # Replace the pattern
-            (
-                re_pattern,
-                glob_pattern,
-                t_replacements,
-            ) = self._replace_patterns_regex(pattern)
-            for fname in self.datadir.glob(glob_pattern):
-                suffix = fname.relative_to(self.datadir).as_posix()
-                m = re.match(re_pattern, suffix)
-                if m is not None:
-                    # Find the groups of replacements present in the pattern
-                    # If one replacement is not present, set it to None.
-                    # We will take care of this in the intersection
-                    t_element = tuple([m.group(k) for k in t_replacements])
-                    if len(self.replacements) == 1:
-                        t_element = t_element[0]
-                    types_element.add(t_element)
-            # TODO: does this make sense as elements is always None
-            if elements is None:
-                elements = types_element
-            else:
-                # Do the intersection by filtering out elements in which
-                # the replacements are not None
-                if t_replacements == self.replacements:
-                    elements.intersection(types_element)
+            # Data type dictionary
+            patterns = self.patterns[t_type]
+            # Conditional for list dtype vals like Warp
+            if not isinstance(patterns, list):
+                patterns = [patterns]
+            for t_pattern in patterns:
+                # Conditional fetch of base pattern for getting elements
+                pattern = None
+                # Try for data type pattern
+                pattern = t_pattern.get("pattern")
+                # Try for nested data type pattern
+                if pattern is None and self.partial_pattern_ok:
+                    for v in t_pattern.values():
+                        if isinstance(v, dict) and "pattern" in v:
+                            pattern = v["pattern"]
+                            break
+
+                # Replace the pattern
+                (
+                    re_pattern,
+                    glob_pattern,
+                    t_replacements,
+                ) = self._replace_patterns_regex(pattern)
+                for fname in self.datadir.glob(glob_pattern):
+                    suffix = fname.relative_to(self.datadir).as_posix()
+                    m = re.match(re_pattern, suffix)
+                    if m is not None:
+                        # Find the groups of replacements present in the
+                        # pattern. If one replacement is not present, set it
+                        # to None. We will take care of this in the
+                        # intersection.
+                        t_element = tuple([m.group(k) for k in t_replacements])
+                        if len(self.replacements) == 1:
+                            t_element = t_element[0]
+                        types_element.add(t_element)
+                # TODO: does this make sense as elements is always None
+                if elements is None:
+                    elements = types_element
                 else:
-                    t_repl_idx = [
-                        i
-                        for i, v in enumerate(self.replacements)
-                        if v in t_replacements
-                    ]
-                    new_elements = set()
-                    for t_element in elements:
-                        if (
-                            tuple(np.array(t_element)[t_repl_idx])
-                            in types_element
-                        ):
-                            new_elements.add(t_element)
-                    elements = new_elements
+                    # Do the intersection by filtering out elements in which
+                    # the replacements are not None
+                    if t_replacements == self.replacements:
+                        elements.intersection(types_element)
+                    else:
+                        t_repl_idx = [
+                            i
+                            for i, v in enumerate(self.replacements)
+                            if v in t_replacements
+                        ]
+                        new_elements = set()
+                        for t_element in elements:
+                            if (
+                                tuple(np.array(t_element)[t_repl_idx])
+                                in types_element
+                            ):
+                                new_elements.add(t_element)
+                        elements = new_elements
         if elements is None:
             elements = set()
         return list(elements)

{junifer-0.0.6.dev252 → junifer-0.0.6.dev266}/junifer/datagrabber/pattern_validation_mixin.py

@@ -3,8 +3,8 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Union
 
+from ..typing import DataGrabberPatterns
 from ..utils import logger, raise_error, warn_with_log
 
 
@@ -96,7 +96,7 @@ class PatternValidationMixin:
     def _validate_replacements(
         self,
         replacements: list[str],
-        patterns: dict[str, Union[dict[str, str], list[dict[str, str]]]],
+        patterns: DataGrabberPatterns,
         partial_pattern_ok: bool,
     ) -> None:
         """Validate the replacements.
@@ -263,7 +263,7 @@ class PatternValidationMixin:
         self,
         types: list[str],
         replacements: list[str],
-        patterns: dict[str, Union[dict[str, str], list[dict[str, str]]]],
+        patterns: DataGrabberPatterns,
         partial_pattern_ok: bool = False,
     ) -> None:
         """Validate the patterns.

{junifer-0.0.6.dev252 → junifer-0.0.6.dev266}/junifer/datagrabber/tests/test_datalad_base.py

@@ -14,8 +14,8 @@ from junifer.datagrabber import DataladDataGrabber
 _testing_dataset = {
     "example_bids": {
         "uri": "https://gin.g-node.org/juaml/datalad-example-bids",
-        "commit": "b87897cbe51bf0ee5514becaa5c7dd76491db5ad",
-        "id": "8fddff30-6993-420a-9d1e-b5b028c59468",
+        "commit": "3f288c8725207ae0c9b3616e093e78cda192b570",
+        "id": "582b9696-f13f-42e4-9587-b4e62aa2a8e7",
     },
     "example_bids_ses": {
         "uri": "https://gin.g-node.org/juaml/datalad-example-bids-ses",

{junifer-0.0.6.dev252 → junifer-0.0.6.dev266}/junifer/datagrabber/tests/test_multiple.py

@@ -29,7 +29,7 @@ def test_MultipleDataGrabber() -> None:
     dg1 = PatternDataladDataGrabber(
         rootdir=rootdir,
         uri=repo_uri,
-        types=["T1w"],
+        types=["T1w", "Warp"],
         patterns={
             "T1w": {
                 "pattern": (
@@ -44,6 +44,28 @@ def test_MultipleDataGrabber() -> None:
                     "space": "native",
                 },
             },
+            "Warp": [
+                {
+                    "pattern": (
+                        "{subject}/{session}/anat/"
+                        "{subject}_{session}_from-MNI152NLin2009cAsym_to-T1w_"
+                        "xfm.h5"
+                    ),
+                    "src": "MNI152NLin2009cAsym",
+                    "dst": "native",
+                    "warper": "ants",
+                },
+                {
+                    "pattern": (
+                        "{subject}/{session}/anat/"
+                        "{subject}_{session}_from-T1w_to-MNI152NLin2009cAsym_"
+                        "xfm.h5"
+                    ),
+                    "src": "native",
+                    "dst": "MNI152NLin2009cAsym",
+                    "warper": "ants",
+                },
+            ],
         },
         replacements=replacements,
     )
@@ -75,6 +97,7 @@ def test_MultipleDataGrabber() -> None:
 
     types = dg.get_types()
     assert "T1w" in types
+    assert "Warp" in types
     assert "BOLD" in types
 
     expected_subs = [
@@ -90,6 +113,7 @@ def test_MultipleDataGrabber() -> None:
         elem = dg[("sub-01", "ses-01")]
         # Check data types
         assert "T1w" in elem
+        assert "Warp" in elem
         assert "BOLD" in elem
         # Check meta
         assert "meta" in elem["BOLD"]
@@ -111,7 +135,7 @@ def test_MultipleDataGrabber_no_intersection() -> None:
     dg1 = PatternDataladDataGrabber(
         rootdir=rootdir,
         uri=_testing_dataset["example_bids"]["uri"],
-        types=["T1w"],
+        types=["T1w", "Warp"],
         patterns={
             "T1w": {
                 "pattern": (
@@ -119,6 +143,28 @@ def test_MultipleDataGrabber_no_intersection() -> None:
                 ),
                 "space": "native",
             },
+            "Warp": [
+                {
+                    "pattern": (
+                        "{subject}/{session}/anat/"
+                        "{subject}_{session}_from-MNI152NLin2009cAsym_to-T1w_"
+                        "xfm.h5"
+                    ),
+                    "src": "MNI152NLin2009cAsym",
+                    "dst": "native",
+                    "warper": "ants",
+                },
+                {
+                    "pattern": (
+                        "{subject}/{session}/anat/"
+                        "{subject}_{session}_from-T1w_to-MNI152NLin2009cAsym_"
+                        "xfm.h5"
+                    ),
+                    "src": "native",
+                    "dst": "MNI152NLin2009cAsym",
+                    "warper": "ants",
+                },
+            ],
         },
         replacements=replacements,
     )

{junifer-0.0.6.dev252 → junifer-0.0.6.dev266}/junifer/datagrabber/tests/test_pattern_datalad.py

@@ -15,7 +15,7 @@ from junifer.datagrabber import PatternDataladDataGrabber
 _testing_dataset = {
     "example_bids": {
         "uri": "https://gin.g-node.org/juaml/datalad-example-bids",
-        "commit": "b87897cbe51bf0ee5514becaa5c7dd76491db5ad",
+        "commit": "3f288c8725207ae0c9b3616e093e78cda192b570",
         "id": "8fddff30-6993-420a-9d1e-b5b028c59468",
     },
     "example_bids_ses": {

{junifer-0.0.6.dev252 → junifer-0.0.6.dev266}/junifer/typing/__init__.pyi

@@ -8,6 +8,7 @@ __all__ = [
     "ConditionalDependencies",
     "ExternalDependencies",
     "MarkerInOutMappings",
+    "DataGrabberPatterns",
 ]
 
 from ._typing import (
@@ -20,4 +21,5 @@ from ._typing import (
     ConditionalDependencies,
     ExternalDependencies,
     MarkerInOutMappings,
+    DataGrabberPatterns,
 )

{junifer-0.0.6.dev252 → junifer-0.0.6.dev266}/junifer/typing/_typing.py

@@ -28,6 +28,7 @@ __all__ = [
     "ConditionalDependencies",
     "ExternalDependencies",
     "MarkerInOutMappings",
+    "DataGrabberPatterns",
 ]
 
 
@@ -56,3 +57,6 @@ ConditionalDependencies = Sequence[
 ]
 ExternalDependencies = Sequence[MutableMapping[str, Union[str, Sequence[str]]]]
 MarkerInOutMappings = MutableMapping[str, MutableMapping[str, str]]
+DataGrabberPatterns = dict[
+    str, Union[dict[str, str], Sequence[dict[str, str]]]
+]

{junifer-0.0.6.dev252 → junifer-0.0.6.dev266}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev252
+Version: 0.0.6.dev266
 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-0.0.6.dev252 → junifer-0.0.6.dev266}/junifer.egg-info/SOURCES.txt

@@ -87,12 +87,14 @@ docs/changes/newsfragments/384.misc
 docs/changes/newsfragments/386.bugfix
 docs/changes/newsfragments/387.change
 docs/changes/newsfragments/387.feature
+docs/changes/newsfragments/388.bugfix
 docs/changes/newsfragments/389.enh
 docs/changes/newsfragments/390.change
 docs/changes/newsfragments/390.enh
 docs/changes/newsfragments/391.misc
 docs/changes/newsfragments/392.feature
 docs/changes/newsfragments/393.misc
+docs/changes/newsfragments/398.bugfix
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/dependencies.rst

{junifer-0.0.6.dev252 → junifer-0.0.6.dev266}/tools/create_bids_example_dataset.py

@@ -26,6 +26,8 @@ with TemporaryDirectory() as tmpdir_name:
         fnames = [
             f"anat/{t_sub}_T1w.nii.gz",
             f"anat/{t_sub}_brain_mask.nii.gz",
+            f"anat/{t_sub}_from-MNI152NLin2009cAsym_to-T1w_xfm.h5",
+            f"anat/{t_sub}_from-T1w_to-MNI152NLin2009cAsym_xfm.h5",
             f"func/{t_sub}_task-rest_bold.nii.gz",
             f"func/{t_sub}_task-rest_bold.json",
             f"func/{t_sub}_task-rest_brain_mask.nii.gz",

{junifer-0.0.6.dev252 → junifer-0.0.6.dev266}/tools/create_bids_example_dataset_sessions.py

@@ -31,6 +31,8 @@ with TemporaryDirectory() as tmpdir_name:
             fnames = [
                 f"anat/{t_sub}_{t_ses}_T1w.nii.gz",
                 f"anat/{t_sub}_{t_ses}_brain_mask.nii.gz",
+                f"anat/{t_sub}_{t_ses}_from-MNI152NLin2009cAsym_to-T1w_xfm.h5",
+                f"anat/{t_sub}_{t_ses}_from-T1w_to-MNI152NLin2009cAsym_xfm.h5",
             ]
             if i_ses != 3:  # Session 3 does not have functional data
                 fnames.extend(