junifer 0.0.8.dev349__py3-none-any.whl → 0.0.9.dev6__py3-none-any.whl

junifer/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.0.8.dev349'
-__version_tuple__ = version_tuple = (0, 0, 8, 'dev349')
+__version__ = version = '0.0.9.dev6'
+__version_tuple__ = version_tuple = (0, 0, 9, 'dev6')
 
-__commit_id__ = commit_id = 'g2b4aae01d'
+__commit_id__ = commit_id = 'g945cebd37'

junifer/api/functions.py

@@ -21,6 +21,7 @@ from ..markers import BaseMarker
 from ..pipeline import (
     MarkerCollection,
     PipelineComponentRegistry,
+    PipelineStepMixin,
     WorkDirManager,
 )
 from ..preprocess import BasePreprocessor
@@ -70,6 +71,28 @@ def _get_datagrabber(datagrabber_config: dict) -> DataGrabberLike:
     )
 
 
+def _get_datareader(datareader_config: dict) -> PipelineStepMixin:
+    """Get DataReader.
+
+    Parameters
+    ----------
+    datareader_config : dict
+        The config to get the DataReader using.
+
+    Returns
+    -------
+    object
+        The DataReader.
+
+    """
+    return PipelineComponentRegistry().build_component_instance(
+        step="datareader",
+        name=datareader_config.pop("kind"),
+        baseclass=PipelineStepMixin,
+        init_params=datareader_config,
+    )
+
+
 def _get_preprocessor(preprocessing_config: dict) -> PreprocessorLike:
     """Get Preprocessor.
 
@@ -182,6 +205,7 @@ def run(
     storage: dict,
     preprocessors: list[dict] | None = None,
     elements: Elements | None = None,
+    datareader: dict | None = None,
 ) -> None:
     """Run the pipeline on the selected element.
 
@@ -210,6 +234,11 @@ def run(
     elements : list or None, optional
         Element(s) to process. Will be used to index the DataGrabber
         (default None).
+    datareader : dict or None, optional
+        DataReader to use. Must have a key ``kind`` with the kind of
+        DataReader to use. All other keys are passed to the DataReader
+        constructor. If None, will use :class:`.DefaultDataReader`
+        (default None).
 
     Raises
     ------
@@ -249,9 +278,16 @@ def run(
     else:
         built_preprocessors = None
 
+    # Get datareader to use (if provided)
+    if datareader is not None:
+        datareader_object = _get_datareader(datareader.copy())
+    else:
+        datareader_object = None
+
     # Create new marker collection
     mc = MarkerCollection(
         markers=built_markers,
+        datareader=datareader_object,
         preprocessors=built_preprocessors,
         storage=storage_object,
     )

junifer/api/tests/test_functions.py

@@ -21,9 +21,10 @@ from ruamel.yaml import YAML
 
 import junifer.testing.registry  # noqa: F401
 from junifer.api import collect, list_elements, parse_yaml, queue, reset, run
-from junifer.api.decorators import register_marker
+from junifer.api.decorators import register_datareader, register_marker
 from junifer.datagrabber import DataType, PatternDataGrabber
 from junifer.datagrabber.base import BaseDataGrabber
+from junifer.datareader import DefaultDataReader
 from junifer.markers import BaseMarker
 from junifer.pipeline import (
     MarkerCollection,
@@ -224,6 +225,52 @@ def test_run_single_element_with_preprocessing(
     assert len(files) == 1
 
 
+def test_run_single_element_with_datareader(
+    tmp_path: Path,
+    markers: list[dict[str, str]],
+    storage: dict[str, str],
+) -> None:
+    """Test run function with single element and a DataReader.
+
+    Parameters
+    ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
+    markers : list of dict
+        Testing markers as list of dictionary.
+    storage : dict
+        Testing storage as dictionary.
+
+    """
+
+    @register_datareader
+    class CountingDataReader(DefaultDataReader):
+        """DataReader counting the elements it reads."""
+
+        n_read: ClassVar[int] = 0
+
+        def _fit_transform(self, input, params=None):
+            CountingDataReader.n_read += 1
+            return super()._fit_transform(input, params)
+
+    # Set storage
+    storage["uri"] = str((tmp_path / "out.hdf5").resolve())
+    # Run operations
+    run(
+        workdir=tmp_path,
+        datagrabber=_datagrabber.copy(),
+        markers=markers,
+        storage=storage,
+        elements=["sub-01"],
+        datareader={"kind": "CountingDataReader"},
+    )
+    # Check the DataReader was used
+    assert CountingDataReader.n_read == 1
+    # Check files
+    files = list(tmp_path.glob("*.hdf5"))
+    assert len(files) == 1
+
+
 @pytest.mark.parametrize(
     "element, expect",
     [

junifer/cli/cli.py

@@ -193,6 +193,8 @@ def run(
     markers = config["markers"]
     # Fetch storage
     storage = config["storage"]
+    # Fetch datareader
+    datareader = config.get("datareader")
     # Fetch preprocessors
     preprocessors = config.get("preprocess")
     # Convert to list if single preprocessor
@@ -208,6 +210,7 @@ def run(
         storage=storage,
         preprocessors=preprocessors,
         elements=elements,
+        datareader=datareader,
     )
 
 

{junifer-0.0.8.dev349.dist-info → junifer-0.0.9.dev6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.8.dev349
+Version: 0.0.9.dev6
 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-0.0.8.dev349.dist-info → junifer-0.0.9.dev6.dist-info}/RECORD

@@ -1,13 +1,13 @@
 junifer/__init__.py,sha256=2McgH1yNue6Z1V26-uN_mfMjbTcx4CLhym-DMBl5xA4,266
 junifer/__init__.pyi,sha256=SsTvgq2Dod6UqJN96GH1lCphH6hJQQurEJHGNhHjGUI,508
-junifer/_version.py,sha256=913VI4mfcgL8gv1u73-Z9x0UsteJJKKCSifYKT9Cxlw,545
+junifer/_version.py,sha256=mxTtW49B4vO_Y8j5kOe5ACVr91pjDNIjy8g8J52bupM,541
 junifer/conftest.py,sha256=zNA1SDU5MtF1Wp_6nbo1PRYtN4gsYjH1PTBFa_PfWLw,2856
 junifer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/stats.py,sha256=dOENKWWVjXq--OebL4pci_4UYEDKjxR_lWYvcus7OOc,6247
 junifer/api/__init__.py,sha256=aAXW_KAEGQ8aAP5Eni2G1R4MWBF7UgjKOgM6akLuJco,252
 junifer/api/__init__.pyi,sha256=weBgoe0MwCaSAmoDl-4sAaYxsshNFbSDAUYHi-CoE7o,255
 junifer/api/decorators.py,sha256=7yFhb63zRuyd9uyV_8e7gr4oD0yvZAC4So6CYlwm4tY,4723
-junifer/api/functions.py,sha256=Oxu4KNUZIOQWMtWUqAyjTtsnOjsVzH_39Gj1jTODu9M,21118
+junifer/api/functions.py,sha256=6sLdXKWFYgOfQsGqNtK2lEmwuqoRY24MU2cXaQ7qCYg,22153
 junifer/api/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/api/queue_context/__init__.py,sha256=glr8x4aMm4EvVrHywDIlugdNlwD1RzqV2FTDNPqYQZ4,204
 junifer/api/queue_context/__init__.pyi,sha256=L1snkn0qGyzxIM8_d5LNMrpYYu9ecC0favO334QqId4,391
@@ -41,10 +41,10 @@ junifer/api/res/fsl/img2imgcoord,sha256=Zmaw3oJYrEltcXiPyEubXry9ppAq3SND52tdDWGg
 junifer/api/res/fsl/run_fsl_docker.sh,sha256=cFkGz0Kx6pp9R3c0N-lgP703IbmN7LuCtrbuqAdgtd0,1293
 junifer/api/res/fsl/std2imgcoord,sha256=-X5wRH6XMl0yqnTACJX6MFhO8DFOEWg42MHRxGvimXg,49
 junifer/api/tests/test_decorators.py,sha256=2-ajsMWqXvGdHDnNU4ueSd5GcJ8ROIYOX8tFrJINbaI,2062
-junifer/api/tests/test_functions.py,sha256=2fxBQChqMYztiGCsoE4Jo04ol1LBs9qJthftYY3cOL8,45732
+junifer/api/tests/test_functions.py,sha256=_8ymqJILPQ2YNrHhC5RpCUWpa3WC2aSC7UT5OepMFDQ,47046
 junifer/cli/__init__.py,sha256=L0gTMTtz8s09_adrqgJtufbwqTSfSYhh5MMPifrneQY,378
 junifer/cli/__init__.pyi,sha256=PiV4znUnzSeuSSJGz-RT8N21PiMqoSMwYcypi7nt2Js,40
-junifer/cli/cli.py,sha256=p_yC3jVqM-hmWL-Ik17f24gP8ofYhN9Bb7WOZ5gWbkA,16121
+junifer/cli/cli.py,sha256=DNSK7eRpDMxGpBgDRX3rzqy3Ny26HF2sHcLuQiMrn64,16217
 junifer/cli/parser.py,sha256=kUGFxZzGJzGEv5Ws9og5eV6T08-Teza6nktGS6jKu4I,3704
 junifer/cli/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/cli/utils.py,sha256=Db_Q4XPR9bcfTeCkG59-eOKCqXv2lY2DF1NsDqtLcFs,3325
@@ -393,10 +393,10 @@ junifer/utils/tests/test_config.py,sha256=7ltIXuwb_W4Mv_1dxQWyiyM10XgUAfsWKV6D_i
 junifer/utils/tests/test_fs.py,sha256=WQS7cKlKEZ742CIuiOYYpueeAhY9PqlastfDVpVVtvE,923
 junifer/utils/tests/test_helpers.py,sha256=fJ3NfwR6QXB4RuZvFFo9v02_RXJjIQCFig8pLnT3sLQ,1803
 junifer/utils/tests/test_logging.py,sha256=kptAMU-N7r-Buu_H0JGKjGTsVKyjN3FwFelrRrbL4g0,2947
-junifer-0.0.8.dev349.dist-info/licenses/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.8.dev349.dist-info/licenses/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.8.dev349.dist-info/METADATA,sha256=_GCXc9O4PcED0iB6iATIlUx-qY8RDAsTd51tXaCwKas,9116
-junifer-0.0.8.dev349.dist-info/WHEEL,sha256=16fc_9Rp854SLcdhaDEjr0u65p0e3FhZxihNgcnCE98,91
-junifer-0.0.8.dev349.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
-junifer-0.0.8.dev349.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.8.dev349.dist-info/RECORD,,
+junifer-0.0.9.dev6.dist-info/licenses/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.9.dev6.dist-info/licenses/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.9.dev6.dist-info/METADATA,sha256=SO9mWZukleFFL2dzsXti1tk2mif9HQYww0USfFcpoK0,9114
+junifer-0.0.9.dev6.dist-info/WHEEL,sha256=mOdXR9C3wMVov7cSY8PY-XCzo3SmmWCHvGQr5csJoao,91
+junifer-0.0.9.dev6.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
+junifer-0.0.9.dev6.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.9.dev6.dist-info/RECORD,,

{junifer-0.0.8.dev349.dist-info → junifer-0.0.9.dev6.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (84.1.0)
+Generator: setuptools (84.2.1)
 Root-Is-Purelib: true
 Tag: py3-none-any