junifer 0.0.4.dev464__tar.gz → 0.0.4.dev477__tar.gz

{junifer-0.0.4.dev464 → junifer-0.0.4.dev477}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev464
+Version: 0.0.4.dev477
 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>
@@ -73,6 +73,7 @@ Requires-Dist: sphinxcontrib-mermaid<0.10,>=0.8.1; extra == "docs"
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/charliermarsh/ruff)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8176570.svg)](https://doi.org/10.5281/zenodo.8176570)
+[![FAIR checklist badge](https://fairsoftwarechecklist.net/badge.svg)](https://fairsoftwarechecklist.net/v0.2?f=31&a=32113&i=32322&r=133)
 
 ## About
 

{junifer-0.0.4.dev464 → junifer-0.0.4.dev477}/README.md

@@ -12,6 +12,7 @@
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/charliermarsh/ruff)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8176570.svg)](https://doi.org/10.5281/zenodo.8176570)
+[![FAIR checklist badge](https://fairsoftwarechecklist.net/badge.svg)](https://fairsoftwarechecklist.net/v0.2?f=31&a=32113&i=32322&r=133)
 
 ## About
 

junifer-0.0.4.dev477/docs/changes/newsfragments/286.bugfix

@@ -0,0 +1 @@
+Pass down input path if input space is "native" for ``ReHoEstimator`` and ``ALFFEstimator``, else use respective compute maps by `Fede Raimondo`_ and `Synchon Mandal`_

junifer-0.0.4.dev477/docs/changes/newsfragments/294.misc

@@ -0,0 +1 @@
+Update ``pyproject.toml`` and add FAIR shield in ``README.md`` by `Synchon Mandal`_

{junifer-0.0.4.dev464 → junifer-0.0.4.dev477}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.4.dev464'
-__version_tuple__ = version_tuple = (0, 0, 4, 'dev464')
+__version__ = version = '0.0.4.dev477'
+__version_tuple__ = version_tuple = (0, 0, 4, 'dev477')

{junifer-0.0.4.dev464 → junifer-0.0.4.dev477}/junifer/markers/falff/falff_base.py

@@ -148,6 +148,9 @@ class ALFFBase(BaseMarker):
 
         estimator = ALFFEstimator()
 
+        # If the input data space is "native", then alff_path and falff_path
+        # both point to the input data path as it might be required to use
+        # in get_corrdinates() for transforming coordinates to native space.
         alff, falff, alff_path, falff_path = estimator.fit_transform(
             use_afni=self.use_afni,
             input_data=input,

{junifer-0.0.4.dev464 → junifer-0.0.4.dev477}/junifer/markers/falff/falff_estimator.py

@@ -308,17 +308,16 @@ class ALFFEstimator:
         if use_afni:
             # Create new temporary directory before using AFNI
             self.temp_dir_path = WorkDirManager().get_tempdir(prefix="falff")
-            output = self._compute_alff_afni(
+            return self._compute_alff_afni(
                 data=data,
                 highpass=highpass,
                 lowpass=lowpass,
                 tr=tr,
             )
-        else:
-            output = self._compute_alff_python(
-                data, highpass=highpass, lowpass=lowpass, tr=tr
-            )
-        return output
+
+        return self._compute_alff_python(
+            data, highpass=highpass, lowpass=lowpass, tr=tr
+        )
 
     def fit_transform(
         self,
@@ -350,16 +349,18 @@ class ALFFEstimator:
         Niimg-like object
             fALFF map.
         pathlib.Path
-            The path to the ALFF map as NIfTI.
+            The path to the ALFF map as NIfTI or the input data path if the
+            input data space is "native".
         pathlib.Path
-            The path to the fALFF map as NIfTI.
+            The path to the fALFF map as NIfTI or the input data path if the
+            input data space is "native".
 
         """
         bold_path = input_data["path"]
         bold_data = input_data["data"]
         # Clear cache if file path is different from when caching was done
         if self._file_path != bold_path:
-            logger.info(f"Removing fALFF map cache at {self._file_path}.")
+            logger.info(f"Removing fALFF map cache for {self._file_path}.")
             # Clear the cache
             self._compute.cache_clear()
             # Clear temporary directory files
@@ -368,12 +369,20 @@ class ALFFEstimator:
             # Set the new file path
             self._file_path = bold_path
         else:
-            logger.info(f"Using fALFF map cache at {self._file_path}.")
+            logger.info(f"Using fALFF map cache for {self._file_path}.")
         # Compute
-        return self._compute(
+        alff_map, falff_map, alff_map_path, falff_map_path = self._compute(
             use_afni=use_afni,
             data=bold_data,
             highpass=highpass,
             lowpass=lowpass,
             tr=tr,
         )
+        # If the input data space is native already, the original path should
+        # be propagated down as it might be required for transforming
+        # coordinates to native space via get_coordinates(), else the alff
+        # / falff map path should be passed for use later if required.
+        if input_data["space"] == "native":
+            return alff_map, falff_map, input_data["path"], input_data["path"]
+
+        return alff_map, falff_map, alff_map_path, falff_map_path

{junifer-0.0.4.dev464 → junifer-0.0.4.dev477}/junifer/markers/reho/reho_base.py

@@ -110,7 +110,8 @@ class ReHoBase(BaseMarker):
         Niimg-like object
             The ReHo map as NIfTI.
         pathlib.Path
-            The path to the ReHo map as NIfTI.
+            The path to the ReHo map as NIfTI or the input data path if the
+            input data space is "native".
 
         References
         ----------

{junifer-0.0.4.dev464 → junifer-0.0.4.dev477}/junifer/markers/reho/reho_estimator.py

@@ -462,12 +462,9 @@ class ReHoEstimator:
         if use_afni:
             # Create new temporary directory before using AFNI
             self.temp_dir_path = WorkDirManager().get_tempdir(prefix="reho")
-            output, output_path = self._compute_reho_afni(data, **reho_params)
-        else:
-            output, output_path = self._compute_reho_python(
-                data, **reho_params
-            )
-        return output, output_path
+            return self._compute_reho_afni(data, **reho_params)
+
+        return self._compute_reho_python(data, **reho_params)
 
     def fit_transform(
         self,
@@ -491,14 +488,15 @@ class ReHoEstimator:
         Niimg-like object
             The ReHo map as NIfTI.
         pathlib.Path
-            The path to the ReHo map as NIfTI.
+            The path to the ReHo map as NIfTI or the input data path if the
+            input data space is "native".
 
         """
         bold_path = input_data["path"]
         bold_data = input_data["data"]
         # Clear cache if file path is different from when caching was done
         if self._file_path != bold_path:
-            logger.info(f"Removing ReHo map cache at {self._file_path}.")
+            logger.info(f"Removing ReHo map cache for {self._file_path}.")
             # Clear the cache
             self._compute.cache_clear()
             # Clear temporary directory files
@@ -507,9 +505,19 @@ class ReHoEstimator:
             # Set the new file path
             self._file_path = bold_path
         else:
-            logger.info(f"Using ReHo map cache at {self._file_path}.")
+            logger.info(f"Using ReHo map cache for {self._file_path}.")
         # Compute
-        return self._compute(use_afni, bold_data, **reho_params)
+        reho_map, reho_map_path = self._compute(
+            use_afni, bold_data, **reho_params
+        )
+        # If the input data space is native already, the original path should
+        # be propagated down as it might be required for transforming
+        # coordinates to native space via get_coordinates(), else the reho map
+        # path should be passed for use later if required.
+        if input_data["space"] == "native":
+            return reho_map, input_data["path"]
+
+        return reho_map, reho_map_path
 
 
 def _kendall_w_reho(

{junifer-0.0.4.dev464 → junifer-0.0.4.dev477}/junifer/markers/reho/reho_parcels.py

@@ -127,6 +127,9 @@ class ReHoParcels(ReHoBase):
         """
         logger.info("Calculating ReHo for parcels.")
         # Calculate reho map
+        # If the input data space is "native", then reho_file_path points to
+        # the input data path as it might be required to use in
+        # get_coordinates() for transforming coordinates to native space.
         if self.reho_params is not None:
             reho_map, reho_file_path = self.compute_reho_map(
                 input=input, **self.reho_params

{junifer-0.0.4.dev464 → junifer-0.0.4.dev477}/junifer/markers/reho/reho_spheres.py

@@ -139,6 +139,9 @@ class ReHoSpheres(ReHoBase):
         """
         logger.info("Calculating ReHo for spheres.")
         # Calculate reho map
+        # If the input data space is "native", then reho_file_path points to
+        # the input data path as it might be required to use in
+        # get_coordinates() for transforming coordinates to native space.
         if self.reho_params is not None:
             reho_map, reho_file_path = self.compute_reho_map(
                 input=input, **self.reho_params

{junifer-0.0.4.dev464 → junifer-0.0.4.dev477}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev464
+Version: 0.0.4.dev477
 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>
@@ -73,6 +73,7 @@ Requires-Dist: sphinxcontrib-mermaid<0.10,>=0.8.1; extra == "docs"
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/charliermarsh/ruff)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8176570.svg)](https://doi.org/10.5281/zenodo.8176570)
+[![FAIR checklist badge](https://fairsoftwarechecklist.net/badge.svg)](https://fairsoftwarechecklist.net/v0.2?f=31&a=32113&i=32322&r=133)
 
 ## About
 

{junifer-0.0.4.dev464 → junifer-0.0.4.dev477}/junifer.egg-info/SOURCES.txt

@@ -94,8 +94,10 @@ docs/changes/newsfragments/281.bugfix
 docs/changes/newsfragments/281.misc
 docs/changes/newsfragments/282.bugfix
 docs/changes/newsfragments/283.bugfix
+docs/changes/newsfragments/286.bugfix
 docs/changes/newsfragments/288.misc
 docs/changes/newsfragments/291.doc
+docs/changes/newsfragments/294.misc
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/extension.rst

{junifer-0.0.4.dev464 → junifer-0.0.4.dev477}/pyproject.toml

@@ -1,9 +1,5 @@
 [build-system]
-requires = [
-  "setuptools >= 61.0.0",
-  "wheel",
-  "setuptools_scm[toml] >= 6.2"
-]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -45,9 +41,9 @@ dependencies = [
     "pandas>=1.4.0,<2.2",
     "nibabel>=3.2.0,<5.11",
     "nilearn>=0.9.0,<=0.11.0",
-    "sqlalchemy>=1.4.27,<= 2.1.0",
+    "sqlalchemy>=1.4.27,<=2.1.0",
     "ruamel.yaml>=0.17,<0.18",
-    "importlib_metadata; python_version < '3.10'",
+    "importlib_metadata; python_version<'3.10'",
     "h5py>=3.8.0,<3.10",
 ]
 dynamic = ["version"]
@@ -153,7 +149,7 @@ extend-exclude = [
     "examples",
     "tools",
 ]
-extend-ignore = [
+ignore = [
     # Use of `functools.lru_cache` or `functools.cache` on methods can lead to
     # memory leaks. The cache may retain instance references, preventing garbage
     # collection.
@@ -187,6 +183,8 @@ known-third-party =[
     "nilearn",
     "sqlalchemy",
     "yaml",
+    "bct",
+    "neurokit2",
     "pytest",
 ]