junifer 0.0.8.dev290__tar.gz → 0.0.8.dev298__tar.gz

{junifer-0.0.8.dev290/junifer.egg-info → junifer-0.0.8.dev298}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.8.dev290
+Version: 0.0.8.dev298
 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.dev298/docs/changes/newsfragments/522.bugfix

@@ -0,0 +1 @@
+Fix :class:`.TemporalSNRParcels`, :class:`.TemporalSNRSpheres` and :class:`.TemporalSNRMaps` replacing the BOLD data with the tSNR map, so the markers computed after them in a pipeline used the tSNR map instead of the BOLD data by `Fede Raimondo`_

junifer-0.0.8.dev298/docs/changes/newsfragments/522.enh

@@ -0,0 +1 @@
+Raise an error if a marker changes its input data (which is shared with the other markers of a pipeline), checking the values and their contents (arrays, data frames and images) by `Fede Raimondo`_

junifer-0.0.8.dev298/docs/changes/newsfragments/523.misc

@@ -0,0 +1 @@
+Use :class:`.HDF5FeatureStorage` instead of :class:`.SQLiteFeatureStorage` in the tests and documentation, as the latter is only kept for compatibility, and fix the component registry test leaving components de-registered by `Fede Raimondo`_

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/docs/understanding/storage.rst

@@ -21,7 +21,7 @@ The :ref:`Markers <marker>` are responsible for mapping the input
 :ref:`data type <data_types>` to its output :ref:`storage type <storage_types>`
 as shown :ref:`here <extending_markers_input_output>`.
 The storage object in turn declares and provides implementation for
-specific *storage type*. For example, :class:`.SQLiteFeatureStorage` supports
+specific *storage type*. For example, :class:`.HDF5FeatureStorage` supports
 saving ``matrix``, ``vector`` and ``timeseries`` via ``store_matrix``,
 ``store_vector`` and ``store_timeseries`` methods respectively.
 
@@ -88,3 +88,10 @@ Storage Interfaces
      - ``.hdf5``
      - HDF5
      - ``matrix``, ``vector``, ``timeseries``, ``timeseries_2d``, ``scalar_table``
+
+.. note::
+
+   :class:`.HDF5FeatureStorage` is the recommended storage.
+   :class:`.SQLiteFeatureStorage` is only kept for compatibility with features
+   stored in previous versions of ``junifer`` and should not be used for new
+   analyses.

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/docs/using/running.rst

@@ -130,8 +130,8 @@ First we load the storage like so:
 
     from junifer.storage import HDF5FeatureStorage
 
-    # You need to import and use SQLiteFeatureStorage if you chose that
-    # for storage while extracting features
+    # If the features were stored with the legacy SQLiteFeatureStorage,
+    # import and use that class instead
     storage = HDF5FeatureStorage("<path/to/your/collected/file>")
 
 The best way to start analysing would be to list all the extracted features

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/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.dev290'
-__version_tuple__ = version_tuple = (0, 0, 8, 'dev290')
+__version__ = version = '0.0.8.dev298'
+__version_tuple__ = version_tuple = (0, 0, 8, 'dev298')
 
-__commit_id__ = commit_id = 'g64fd8e96c'
+__commit_id__ = commit_id = 'g30ddf7410'

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/api/tests/test_functions.py

@@ -92,7 +92,7 @@ def markers() -> list[dict[str, list[str] | str]]:
 def storage() -> dict[str, str]:
     """Return a storage as a dictionary."""
     return {
-        "kind": "SQLiteFeatureStorage",
+        "kind": "HDF5FeatureStorage",
     }
 
 
@@ -158,7 +158,7 @@ def test_run_single_element(
 
     """
     # Set storage
-    storage["uri"] = str((tmp_path / "out.sqlite").resolve())
+    storage["uri"] = str((tmp_path / "out.hdf5").resolve())
     # Run operations
     with expect:
         run(
@@ -169,7 +169,7 @@ def test_run_single_element(
             elements=element,
         )
         # Check files
-        files = list(tmp_path.glob("*.sqlite"))
+        files = list(tmp_path.glob("*.hdf5"))
         assert len(files) == 1
 
 
@@ -191,7 +191,7 @@ def test_run_single_element_with_preprocessing(
 
     """
     # Set storage
-    storage["uri"] = str((tmp_path / "out.sqlite").resolve())
+    storage["uri"] = str((tmp_path / "out.hdf5").resolve())
     # Run operations
     run(
         workdir={"path": tmp_path, "cleanup": False},
@@ -209,7 +209,7 @@ def test_run_single_element_with_preprocessing(
         elements=["sub-01"],
     )
     # Check files
-    files = list(tmp_path.glob("*.sqlite"))
+    files = list(tmp_path.glob("*.hdf5"))
     assert len(files) == 1
 
 
@@ -250,7 +250,7 @@ def test_run_multi_element_multi_output(
 
     """
     # Set storage
-    storage["uri"] = str((tmp_path / "out.sqlite").resolve())
+    storage["uri"] = str((tmp_path / "out.hdf5").resolve())
     storage["single_output"] = False  # type: ignore
     # Run operations
     with expect:
@@ -262,7 +262,7 @@ def test_run_multi_element_multi_output(
             elements=element,
         )
         # Check files
-        files = list(tmp_path.glob("*.sqlite"))
+        files = list(tmp_path.glob("*.hdf5"))
         assert len(files) == 2
 
 
@@ -287,7 +287,7 @@ def test_run_multi_element_single_output(
 
     """
     # Set storage
-    storage["uri"] = str((tmp_path / "out.sqlite").resolve())
+    storage["uri"] = str((tmp_path / "out.hdf5").resolve())
     storage["single_output"] = True  # type: ignore
     # Run operations
     run(
@@ -298,9 +298,9 @@ def test_run_multi_element_single_output(
         elements=["sub-01", "sub-03"],
     )
     # Check files
-    files = list(tmp_path.glob("*.sqlite"))
+    files = list(tmp_path.glob("*.hdf5"))
     assert len(files) == 1
-    assert files[0].name == "out.sqlite"
+    assert files[0].name == "out.hdf5"
 
 
 def test_run_and_collect(
@@ -324,7 +324,7 @@ def test_run_and_collect(
 
     """
     # Set storage
-    uri = tmp_path / "out.sqlite"
+    uri = tmp_path / "out.hdf5"
     storage["uri"] = str(uri.resolve())
     storage["single_output"] = False  # type: ignore
     # Run operations
@@ -343,9 +343,9 @@ def test_run_and_collect(
     )
     elements = dg.get_elements()  # type: ignore
     # This should create one file per element
-    files = list(tmp_path.glob("*.sqlite"))
+    files = list(tmp_path.glob("*.hdf5"))
     assert len(files) == len(elements)
-    # But the test.sqlite file should not exist
+    # But the test.hdf5 file should not exist
     assert not uri.exists()
     # Collect in storage
     collect(storage)
@@ -660,7 +660,7 @@ def test_reset_run(
 
     """
     # Create storage
-    storage["uri"] = tmp_path / "test_reset_run.sqlite"  # type: ignore
+    storage["uri"] = tmp_path / "test_reset_run.hdf5"  # type: ignore
     # Run operation to generate files
     run(
         workdir=tmp_path,
@@ -711,7 +711,7 @@ def test_reset_queue(
     with monkeypatch.context() as m:
         m.chdir(tmp_path)
         # Create storage
-        storage["uri"] = "test_reset_queue.sqlite"
+        storage["uri"] = "test_reset_queue.hdf5"
         # Set job name
         if job_name is None:
             job_name = "junifer_job"

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/cli/tests/data/gmd_mean.yaml

@@ -10,5 +10,5 @@ markers:
     parcellation: TianxS2x3TxMNInonlinear2009cAsym
     method: mean
 storage:
-  kind: SQLiteFeatureStorage
-  uri: /Users/fraimondo/dev/tbox/junifer/scratch/db/test.sqlite
+  kind: HDF5FeatureStorage
+  uri: /Users/fraimondo/dev/tbox/junifer/scratch/db/test.hdf5

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/cli/tests/data/gmd_mean_htcondor.yaml

@@ -9,8 +9,8 @@ markers:
     parcellation: TianxS2x3TxMNInonlinear2009cAsym
     method: mean
 storage:
-  kind: SQLiteFeatureStorage
-  uri: /Users/fraimondo/dev/tbox/junifer/scratch/db/test.sqlite
+  kind: HDF5FeatureStorage
+  uri: /Users/fraimondo/dev/tbox/junifer/scratch/db/test.hdf5
 queue:
   jobname: TestHTCondorQueue
   kind: HTCondor

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/cli/tests/test_cli.py

@@ -222,7 +222,7 @@ def test_queue(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
         # Working directory
         contents["workdir"] = str(tmp_path.resolve())
         # Storage
-        contents["storage"]["uri"] = str((tmp_path / "out.sqlite").resolve())
+        contents["storage"]["uri"] = str((tmp_path / "out.hdf5").resolve())
         # Write new test config
         outfile = tmp_path / "in.yaml"
         yaml.dump(contents, stream=outfile)
@@ -274,7 +274,7 @@ def test_reset(
         # Working directory
         contents["workdir"] = str(tmp_path.resolve())
         # Storage
-        contents["storage"]["uri"] = str((tmp_path / "out.sqlite").resolve())
+        contents["storage"]["uri"] = str((tmp_path / "out.hdf5").resolve())
         # Write new test config
         outfile = tmp_path / "in.yaml"
         yaml.dump(contents, stream=outfile)

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/base.py

@@ -16,10 +16,12 @@ from ..pipeline import PipelineStepMixin, UpdateMetaMixin
 from ..storage import StorageType
 from ..typing import MarkerInOutMappings, StorageLike
 from ..utils import ensure_list_or_none, raise_error
+from .utils import _changed_paths, _fingerprint
 
 
 __all__ = ["BaseMarker"]
 
+
 _log = structlog.get_logger("junifer")
 logger = _log.bind(pkg="markers", step="marker")
 
@@ -212,7 +214,7 @@ class BaseMarker(BaseModel, ABC, PipelineStepMixin, UpdateMetaMixin):
         output : dict
             The computed result as a dictionary to store.
         storage : storage-like
-            The storage class, for example, SQLiteFeatureStorage.
+            The storage class, for example, HDF5FeatureStorage.
 
         """
         s_type = self.storage_type(data_type, feature)
@@ -231,7 +233,7 @@ class BaseMarker(BaseModel, ABC, PipelineStepMixin, UpdateMetaMixin):
         input : dict
             The Junifer Data object.
         storage : storage-like, optional
-            The storage class, for example, SQLiteFeatureStorage.
+            The storage class, for example, HDF5FeatureStorage.
 
         Returns
         -------
@@ -257,8 +259,17 @@ class BaseMarker(BaseModel, ABC, PipelineStepMixin, UpdateMetaMixin):
                 # Copy metadata
                 t_meta = t_input["meta"].copy()
                 t_meta["type"] = t.value
-                # Compute marker
+                # Compute marker, checking it does not change the data, as
+                # it is shared with the markers computed afterwards
+                fingerprint = _fingerprint(input)
                 t_out = self.compute(input=t_input, extra_input=extra_input)
+                changed = _changed_paths(fingerprint, _fingerprint(input))
+                if changed:
+                    raise_error(
+                        f"Marker {self.name} changed its input data, which is "
+                        f"shared with the other markers: {', '.join(changed)}",
+                        klass=RuntimeError,
+                    )
                 # Initialize empty dictionary if no storage object is provided
                 if storage is None:
                     out[t] = {}

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/complexity/tests/test_hurst_exponent.py

@@ -15,7 +15,7 @@ pytest.importorskip("neurokit2")
 from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.complexity import HurstExponent
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import (
     PartlyCloudyTestingDataGrabber,
 )
@@ -83,6 +83,6 @@ def test_store(element_data: dict, tmp_path: Path) -> None:
     # Initialize the marker
     marker = HurstExponent(parcellation=PARCELLATION)
     # Create storage
-    storage = SQLiteFeatureStorage(uri=tmp_path / "test_hurst_exponent.sqlite")
+    storage = HDF5FeatureStorage(uri=tmp_path / "test_hurst_exponent.hdf5")
     # Compute the marker and store
     marker.fit_transform(input=element_data, storage=storage)

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/complexity/tests/test_multiscale_entropy_auc.py

@@ -15,7 +15,7 @@ pytest.importorskip("neurokit2")
 from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.complexity import MultiscaleEntropyAUC
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import (
     PartlyCloudyTestingDataGrabber,
 )
@@ -83,8 +83,8 @@ def test_store(element_data: dict, tmp_path: Path) -> None:
     # Initialize the marker
     marker = MultiscaleEntropyAUC(parcellation=PARCELLATION)
     # Create storage
-    storage = SQLiteFeatureStorage(
-        uri=tmp_path / "test_multiscale_entropy_auc.sqlite"
+    storage = HDF5FeatureStorage(
+        uri=tmp_path / "test_multiscale_entropy_auc.hdf5"
     )
     # Compute the marker and store
     marker.fit_transform(input=element_data, storage=storage)

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/complexity/tests/test_perm_entropy.py

@@ -15,7 +15,7 @@ pytest.importorskip("neurokit2")
 from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.complexity import PermEntropy
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import (
     PartlyCloudyTestingDataGrabber,
 )
@@ -83,6 +83,6 @@ def test_store(element_data: dict, tmp_path: Path) -> None:
     # Initialize the marker
     marker = PermEntropy(parcellation=PARCELLATION)
     # Create storage
-    storage = SQLiteFeatureStorage(uri=tmp_path / "test_perm_entropy.sqlite")
+    storage = HDF5FeatureStorage(uri=tmp_path / "test_perm_entropy.hdf5")
     # Compute the marker and store
     marker.fit_transform(input=element_data, storage=storage)

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/complexity/tests/test_range_entropy.py

@@ -15,7 +15,7 @@ pytest.importorskip("neurokit2")
 from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.complexity import RangeEntropy
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import (
     PartlyCloudyTestingDataGrabber,
 )
@@ -83,6 +83,6 @@ def test_store(element_data: dict, tmp_path: Path) -> None:
     # Initialize the marker
     marker = RangeEntropy(parcellation=PARCELLATION)
     # Create storage
-    storage = SQLiteFeatureStorage(uri=tmp_path / "test_range_entropy.sqlite")
+    storage = HDF5FeatureStorage(uri=tmp_path / "test_range_entropy.hdf5")
     # Compute the marker and store
     marker.fit_transform(input=element_data, storage=storage)

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/complexity/tests/test_range_entropy_auc.py

@@ -15,7 +15,7 @@ pytest.importorskip("neurokit2")
 from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.complexity import RangeEntropyAUC
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import (
     PartlyCloudyTestingDataGrabber,
 )
@@ -83,8 +83,6 @@ def test_store(element_data: dict, tmp_path: Path) -> None:
     # Initialize the marker
     marker = RangeEntropyAUC(parcellation=PARCELLATION)
     # Create storage
-    storage = SQLiteFeatureStorage(
-        uri=tmp_path / "test_range_entropy_auc.sqlite"
-    )
+    storage = HDF5FeatureStorage(uri=tmp_path / "test_range_entropy_auc.hdf5")
     # Compute the marker and store
     marker.fit_transform(input=element_data, storage=storage)

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/complexity/tests/test_sample_entropy.py

@@ -15,7 +15,7 @@ pytest.importorskip("neurokit2")
 from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.complexity import SampleEntropy
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import (
     PartlyCloudyTestingDataGrabber,
 )
@@ -83,6 +83,6 @@ def test_store(element_data: dict, tmp_path: Path) -> None:
     # Initialize the marker
     marker = SampleEntropy(parcellation=PARCELLATION)
     # Create storage
-    storage = SQLiteFeatureStorage(uri=tmp_path / "test_sample_entropy.sqlite")
+    storage = HDF5FeatureStorage(uri=tmp_path / "test_sample_entropy.hdf5")
     # Compute the marker and store
     marker.fit_transform(input=element_data, storage=storage)

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/complexity/tests/test_weighted_perm_entropy.py

@@ -15,7 +15,7 @@ pytest.importorskip("neurokit2")
 from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.complexity import WeightedPermEntropy
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import (
     PartlyCloudyTestingDataGrabber,
 )
@@ -83,8 +83,8 @@ def test_store(element_data: dict, tmp_path: Path) -> None:
     # Initialize the marker
     marker = WeightedPermEntropy(parcellation=PARCELLATION)
     # Create storage
-    storage = SQLiteFeatureStorage(
-        uri=tmp_path / "test_weighted_perm_entropy.sqlite"
+    storage = HDF5FeatureStorage(
+        uri=tmp_path / "test_weighted_perm_entropy.hdf5"
     )
     # Compute the marker and store
     marker.fit_transform(input=element_data, storage=storage)

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/falff/tests/test_falff_parcels.py

@@ -15,7 +15,7 @@ from junifer.datareader import DefaultDataReader
 from junifer.markers import ALFFImpl, ALFFParcels
 from junifer.pipeline import WorkDirManager
 from junifer.pipeline.utils import _check_afni
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
@@ -90,9 +90,7 @@ def test_ALFFParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
             # Reset log capture
             caplog.clear()
             # Initialize storage
-            storage = SQLiteFeatureStorage(
-                uri=tmp_path / "falff_parcels.sqlite"
-            )
+            storage = HDF5FeatureStorage(uri=tmp_path / "falff_parcels.hdf5")
             # Fit transform marker on data with storage
             marker.fit_transform(
                 input=element_data,

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/falff/tests/test_falff_spheres.py

@@ -15,7 +15,7 @@ from junifer.datareader import DefaultDataReader
 from junifer.markers import ALFFImpl, ALFFSpheres
 from junifer.pipeline import WorkDirManager
 from junifer.pipeline.utils import _check_afni
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
@@ -93,9 +93,7 @@ def test_ALFFSpheres(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
             # Reset log capture
             caplog.clear()
             # Initialize storage
-            storage = SQLiteFeatureStorage(
-                uri=tmp_path / "falff_spheres.sqlite"
-            )
+            storage = HDF5FeatureStorage(uri=tmp_path / "falff_spheres.hdf5")
             # Fit transform marker on data with storage
             marker.fit_transform(
                 input=element_data,

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/functional_connectivity/tests/test_crossparcellation_functional_connectivity.py

@@ -13,7 +13,7 @@ from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers import CrossParcellationFC
 from junifer.pipeline import WorkDirManager
-from junifer.storage import SQLiteFeatureStorage, Upsert
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
@@ -85,9 +85,8 @@ def test_store(tmp_path: Path) -> None:
             parcellation_two=parcellation_two,
             corr_method="spearman",
         )
-        storage = SQLiteFeatureStorage(
-            uri=tmp_path / "test_crossparcellation.sqlite",
-            upsert=Upsert.Ignore,
+        storage = HDF5FeatureStorage(
+            uri=tmp_path / "test_crossparcellation.hdf5",
         )
         # Fit transform marker on data with storage
         crossparcellation.fit_transform(input=element_data, storage=storage)

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_parcels.py

@@ -11,7 +11,7 @@ import pytest
 from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.functional_connectivity import EdgeCentricFCParcels
-from junifer.storage import SQLiteFeatureStorage, Upsert
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
@@ -67,8 +67,8 @@ def test_EdgeCentricFCParcels(
         assert len(set(edge_fc_bold["col_names"])) == n_edges
 
         # Store
-        storage = SQLiteFeatureStorage(
-            uri=tmp_path / "test_edge_fc_parcels.sqlite", upsert=Upsert.Ignore
+        storage = HDF5FeatureStorage(
+            uri=tmp_path / "test_edge_fc_parcels.hdf5",
         )
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_spheres.py

@@ -11,7 +11,7 @@ import pytest
 from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.functional_connectivity import EdgeCentricFCSpheres
-from junifer.storage import SQLiteFeatureStorage, Upsert
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
 
 
@@ -69,8 +69,8 @@ def test_EdgeCentricFCSpheres(
         assert len(set(edge_fc_bold["col_names"])) == n_edges
 
         # Store
-        storage = SQLiteFeatureStorage(
-            uri=tmp_path / "test_edge_fc_spheres.sqlite", upsert=Upsert.Ignore
+        storage = HDF5FeatureStorage(
+            uri=tmp_path / "test_edge_fc_spheres.hdf5",
         )
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py

@@ -20,7 +20,7 @@ from junifer.datareader import DefaultDataReader
 from junifer.markers import (
     FunctionalConnectivityParcels,
 )
-from junifer.storage import SQLiteFeatureStorage, Upsert
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
@@ -105,8 +105,8 @@ def test_FunctionalConnectivityParcels(
         )
 
         # Store
-        storage = SQLiteFeatureStorage(
-            uri=tmp_path / "test_fc_parcels.sqlite", upsert=Upsert.Ignore
+        storage = HDF5FeatureStorage(
+            uri=tmp_path / "test_fc_parcels.hdf5",
         )
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py

@@ -21,7 +21,7 @@ from junifer.datareader import DefaultDataReader
 from junifer.markers.functional_connectivity import (
     FunctionalConnectivitySpheres,
 )
-from junifer.storage import SQLiteFeatureStorage, Upsert
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
 
 
@@ -106,8 +106,8 @@ def test_FunctionalConnectivitySpheres(
         )
 
         # Store
-        storage = SQLiteFeatureStorage(
-            uri=tmp_path / "test_fc_spheres.sqlite", upsert=Upsert.Ignore
+        storage = HDF5FeatureStorage(
+            uri=tmp_path / "test_fc_spheres.hdf5",
         )
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/reho/tests/test_reho_parcels.py

@@ -14,7 +14,7 @@ from junifer.datareader import DefaultDataReader
 from junifer.markers import ReHoImpl, ReHoParcels
 from junifer.pipeline import WorkDirManager
 from junifer.pipeline.utils import _check_afni
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import (
     ADHDTestingDataGrabber,
     PartlyCloudyTestingDataGrabber,
@@ -74,9 +74,7 @@ def test_ReHoParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
             # Reset log capture
             caplog.clear()
             # Initialize storage
-            storage = SQLiteFeatureStorage(
-                uri=tmp_path / "reho_parcels.sqlite"
-            )
+            storage = HDF5FeatureStorage(uri=tmp_path / "reho_parcels.hdf5")
             # Fit transform marker on data with storage
             marker.fit_transform(
                 input=element_data,

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/reho/tests/test_reho_spheres.py

@@ -14,7 +14,7 @@ from junifer.datareader import DefaultDataReader
 from junifer.markers import ReHoImpl, ReHoSpheres
 from junifer.pipeline import WorkDirManager
 from junifer.pipeline.utils import _check_afni
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
 
 
@@ -72,9 +72,7 @@ def test_ReHoSpheres(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
             # Reset log capture
             caplog.clear()
             # Initialize storage
-            storage = SQLiteFeatureStorage(
-                uri=tmp_path / "reho_spheres.sqlite"
-            )
+            storage = HDF5FeatureStorage(uri=tmp_path / "reho_spheres.hdf5")
             # Fit transform marker on data with storage
             marker.fit_transform(
                 input=element_data,

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/temporal_snr/temporal_snr_base.py

@@ -104,7 +104,9 @@ class TemporalSNRBase(BaseMarker):
             "img.std(axis=-1).squeeze()", img=input["data"]
         )
         mask_img = nimg.math_img("(stdv_img != 0)", stdv_img=stdv_img)
-        input["data"] = nimg.math_img(
+        # Aggregate the tSNR image, without changing the input
+        aggregation_input = dict(input.items())
+        aggregation_input["data"] = nimg.math_img(
             "np.divide(mean_img, stdv_img, where=mask_img.astype(bool))",
             mean_img=mean_img,
             stdv_img=stdv_img,
@@ -113,8 +115,8 @@ class TemporalSNRBase(BaseMarker):
         # Perform necessary aggregation and return
         return {
             "tsnr": {
-                **self.aggregate(input=input, extra_input=extra_input)[
-                    "aggregation"
-                ]
+                **self.aggregate(
+                    input=aggregation_input, extra_input=extra_input
+                )["aggregation"]
             }
         }

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/temporal_snr/tests/test_temporal_snr_maps.py

@@ -28,7 +28,10 @@ def test_TemporalSNRMaps_computation() -> None:
             input_type=DataType.BOLD, output_feature="tsnr"
         )
         # Fit-transform the data
+        bold_img = element_data["BOLD"]["data"]
         tsnr_parcels = marker.fit_transform(element_data)
+        # The input is not changed
+        assert element_data["BOLD"]["data"] is bold_img
         tsnr_parcels_bold = tsnr_parcels["BOLD"]["tsnr"]
 
         assert "data" in tsnr_parcels_bold

{junifer-0.0.8.dev290 → junifer-0.0.8.dev298}/junifer/markers/temporal_snr/tests/test_temporal_snr_parcels.py

@@ -30,7 +30,10 @@ def test_TemporalSNRParcels_computation() -> None:
             input_type=DataType.BOLD, output_feature="tsnr"
         )
         # Fit-transform the data
+        bold_img = element_data["BOLD"]["data"]
         tsnr_parcels = marker.fit_transform(element_data)
+        # The input is not changed
+        assert element_data["BOLD"]["data"] is bold_img
         tsnr_parcels_bold = tsnr_parcels["BOLD"]["tsnr"]
 
         assert "data" in tsnr_parcels_bold