junifer 0.0.4.dev464__py3-none-any.whl → 0.0.4.dev477__py3-none-any.whl

junifer/_version.py

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

junifer/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/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/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/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/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/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.dist-info → junifer-0.0.4.dev477.dist-info}/METADATA

@@ -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: bctpy ==0.6.0 ; extra == 'onthefly'
 [![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.dist-info → junifer-0.0.4.dev477.dist-info}/RECORD

@@ -1,5 +1,5 @@
 junifer/__init__.py,sha256=x1UR2jUcrUdm2HNl-3Qvyi4UUrU6ms5qm2qcmNY7zZk,391
-junifer/_version.py,sha256=rndPcK1qS4_jGEuWxgjS5XohhBKgCIMXhzk3kK5yIA0,428
+junifer/_version.py,sha256=M4X3STs52HWvFyMwLZ_m-ldav_VVRF4lDp3N_LiwSn8,428
 junifer/stats.py,sha256=KUX4jJcLWnlE34coet8EkdFypFd-td4Vtpx5LvlomVs,5879
 junifer/api/__init__.py,sha256=YILu9M7SC0Ri4CVd90fELH2OnK_gvCYAXCoqBNCFE8E,257
 junifer/api/cli.py,sha256=xScav2mF-Jr8JjVFt8kaHuLpX5l_jVTaQGPgQL3VNvA,12881
@@ -133,8 +133,8 @@ junifer/markers/complexity/tests/test_range_entropy_auc.py,sha256=SOpUjFRbNopfMU
 junifer/markers/complexity/tests/test_sample_entropy.py,sha256=3IeDnDgSeFNmUoPxQAJTSZvwN6S04-5r7NDvb0lzHmI,2025
 junifer/markers/complexity/tests/test_weighted_perm_entropy.py,sha256=M7Qt_SFZSmptMi0cBGh5Merd1_3hPieIddl_pz7MWbs,2088
 junifer/markers/falff/__init__.py,sha256=QAUIVtaOFWDL7B8xFrDgsmRum7Q0DCENyDYD1cPMJmM,197
-junifer/markers/falff/falff_base.py,sha256=c1ZVh3S-jgF5FAukYEn18eQnA1fd30EmOpI9E3xlUjg,6094
-junifer/markers/falff/falff_estimator.py,sha256=m1IKT_I3oTRZ2bO0cNnPPRynMECuoEDO9xpLBMkgCgU,12246
+junifer/markers/falff/falff_base.py,sha256=isHD643TvDFg7YJxpopHSrpJlgUwx2fW0tzJeSio6c8,6323
+junifer/markers/falff/falff_estimator.py,sha256=ayXdQWHUyYyeR7NulOPZpYXkjQ2V8HlbHhy-jDKtZI0,12869
 junifer/markers/falff/falff_parcels.py,sha256=UTADrIl96eO_xZ90LtOIt7tuN2eLDPnfIJghr9HAO88,4550
 junifer/markers/falff/falff_spheres.py,sha256=XR2pcBRxjyTZ-J7j_HOjL20_2IHgYO0dI9x4LlQFoVE,5086
 junifer/markers/falff/tests/test_falff_estimator.py,sha256=aVnkFvPqA5mTb9dXegwAJPku8Tf-1jWtDkfXhdcjDj8,8259
@@ -154,10 +154,10 @@ junifer/markers/functional_connectivity/tests/test_functional_connectivity_base.
 junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py,sha256=CN6buyF0hxqzQUefz0KBkQSndwSXoZ5ius-H-WGhslY,3210
 junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py,sha256=KOaMkLf7CEd1H8A92WpZAy6X6VNf6TADzYqsqXqvV4Q,4278
 junifer/markers/reho/__init__.py,sha256=9IfeAxKEVgMWbhud-8T54Le07I4pR6A29sMKeFtvEPg,189
-junifer/markers/reho/reho_base.py,sha256=fy5UwV0SFZC0a930xASxjraJ6cF5qnPDcezzMkz6trA,3861
-junifer/markers/reho/reho_estimator.py,sha256=-ESLzezCM3mNu0lZSpywJtbtiUi65TRho0_3a9vCuUE,19272
-junifer/markers/reho/reho_parcels.py,sha256=AyrtGlb_5r9Pb5f68VcOA1vEtk-jTWAgPVpG4wY6xXo,5833
-junifer/markers/reho/reho_spheres.py,sha256=Si1iGk9RD8Ja_morjmtwZLPwF_YP4i7b0-8_IP5nvIU,6350
+junifer/markers/reho/reho_base.py,sha256=d6oxynZ41EGd7f3zorRww6vMtFYF0PjD6RdAVlLq9BA,3932
+junifer/markers/reho/reho_estimator.py,sha256=88Ki-Ysq7MfmODynA_wk-7tvYdggmB_Z5HDa3gaZeoM,19692
+junifer/markers/reho/reho_parcels.py,sha256=Q-gkB9aO0ncxgEQ68XEQKekpLLu_kXiYC6Xqkv8cdvY,6048
+junifer/markers/reho/reho_spheres.py,sha256=ng5JzYorEnYmFVlxRMOMwkLNFsq2FlMN4o95B_BBVo0,6565
 junifer/markers/reho/tests/test_reho_estimator.py,sha256=V_584X3I5a-XXAIs8YtR4TMuSqhMvGd5E1vcoDj8gQA,10168
 junifer/markers/reho/tests/test_reho_parcels.py,sha256=XJk5VKw6kj31cNrOK5aA2EIlChq1MvPfmf474OQUYqU,5392
 junifer/markers/reho/tests/test_reho_spheres.py,sha256=HSz6Kh92EmtCRovDnSQyeOhtMdNgXFniznS9BzfkuSw,5400
@@ -226,10 +226,10 @@ junifer/utils/fs.py,sha256=Jd9AoV2fIF7pT7KhXsn8T1O1fJ1_SFZgaFuOBAM7DG8,460
 junifer/utils/logging.py,sha256=4kH8j9X_J2bMdnBJMldVF95C5sURa5UAsLmSgRaD9Ig,9117
 junifer/utils/tests/test_fs.py,sha256=WQS7cKlKEZ742CIuiOYYpueeAhY9PqlastfDVpVVtvE,923
 junifer/utils/tests/test_logging.py,sha256=l8oo-AiBV7H6_IzlsNcj__cLeZBUvgIGoaMszD9VaJg,7754
-junifer-0.0.4.dev464.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.4.dev464.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.4.dev464.dist-info/METADATA,sha256=ODotYc3Nl6E6wLjb1V1R49ZoNBUCVvYMVbC78B2n_Oc,7569
-junifer-0.0.4.dev464.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-junifer-0.0.4.dev464.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
-junifer-0.0.4.dev464.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.4.dev464.dist-info/RECORD,,
+junifer-0.0.4.dev477.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.4.dev477.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.4.dev477.dist-info/METADATA,sha256=rRpLolV-SBGOl-4ktutkDrIhIpWnB9fjsFS55rS66QM,7707
+junifer-0.0.4.dev477.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+junifer-0.0.4.dev477.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
+junifer-0.0.4.dev477.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.4.dev477.dist-info/RECORD,,