junifer 0.0.6.dev317__py3-none-any.whl → 0.0.6.dev330__py3-none-any.whl

junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev317'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev317')
+__version__ = version = '0.0.6.dev330'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev330')

junifer/api/queue_context/gnu_parallel_local_adapter.py

@@ -37,6 +37,9 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
         virtual environment of any kind (default None).
     verbose : str, optional
         The level of verbosity (default "info").
+    verbose_datalad : str or None, optional
+        The level of verbosity for datalad. If None, will be the same
+        as ``verbose`` (default None).
     submit : bool, optional
         Whether to submit the jobs (default False).
 
@@ -65,6 +68,7 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
         pre_collect: Optional[str] = None,
         env: Optional[dict[str, str]] = None,
         verbose: str = "info",
+        verbose_datalad: Optional[str] = None,
         submit: bool = False,
     ) -> None:
         """Initialize the class."""
@@ -76,6 +80,7 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
         self._pre_collect = pre_collect
         self._check_env(env)
         self._verbose = verbose
+        self._verbose_datalad = verbose_datalad
         self._submit = submit
 
         self._log_dir = self._job_dir / "logs"
@@ -155,6 +160,11 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
 
     def run(self) -> str:
         """Return run commands."""
+        verbose_args = f"--verbose {self._verbose}"
+        if self._verbose_datalad:
+            verbose_args = (
+                f"{verbose_args} --verbose-datalad {self._verbose_datalad}"
+            )
         return (
             f"#!/usr/bin/env {self._shell}\n\n"
             "# This script is auto-generated by junifer.\n\n"
@@ -169,7 +179,7 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
             f"{self._job_dir.resolve()!s}/{self._executable} "
             f"{self._arguments} run "
             f"{self._yaml_config_path.resolve()!s} "
-            f"--verbose {self._verbose} "
+            f"{verbose_args} "
             f"--element"
         )
 
@@ -184,6 +194,11 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
 
     def collect(self) -> str:
         """Return collect commands."""
+        verbose_args = f"--verbose {self._verbose}"
+        if self._verbose_datalad:
+            verbose_args = (
+                f"{verbose_args} --verbose-datalad {self._verbose_datalad}"
+            )
         return (
             f"#!/usr/bin/env {self._shell}\n\n"
             "# This script is auto-generated by junifer.\n\n"
@@ -193,7 +208,7 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
             f"{self._job_dir.resolve()!s}/{self._executable} "
             f"{self._arguments} collect "
             f"{self._yaml_config_path.resolve()!s} "
-            f"--verbose {self._verbose}"
+            f"{verbose_args}"
         )
 
     def prepare(self) -> None:

junifer/api/queue_context/htcondor_adapter.py

@@ -37,6 +37,9 @@ class HTCondorAdapter(QueueContextAdapter):
         virtual environment of any kind (default None).
     verbose : str, optional
         The level of verbosity (default "info").
+    verbose_datalad : str or None, optional
+        The level of verbosity for datalad. If None, will be the same
+        as ``verbose`` (default None).
     cpus : int, optional
         The number of CPU cores to use (default 1).
     mem : str, optional
@@ -83,6 +86,7 @@ class HTCondorAdapter(QueueContextAdapter):
         pre_collect: Optional[str] = None,
         env: Optional[dict[str, str]] = None,
         verbose: str = "info",
+        verbose_datalad: Optional[str] = None,
         cpus: int = 1,
         mem: str = "8G",
         disk: str = "1G",
@@ -99,6 +103,7 @@ class HTCondorAdapter(QueueContextAdapter):
         self._pre_collect = pre_collect
         self._check_env(env)
         self._verbose = verbose
+        self._verbose_datalad = verbose_datalad
         self._cpus = cpus
         self._mem = mem
         self._disk = disk
@@ -201,10 +206,15 @@ class HTCondorAdapter(QueueContextAdapter):
 
     def run(self) -> str:
         """Return run commands."""
+        verbose_args = f"--verbose {self._verbose} "
+        if self._verbose_datalad is not None:
+            verbose_args = (
+                f"{verbose_args} --verbose-datalad {self._verbose_datalad} "
+            )
         junifer_run_args = (
             "run "
             f"{self._yaml_config_path.resolve()!s} "
-            f"--verbose {self._verbose} "
+            f"{verbose_args}"
             "--element $(element)"
         )
         log_dir_prefix = (
@@ -246,10 +256,16 @@ class HTCondorAdapter(QueueContextAdapter):
 
     def collect(self) -> str:
         """Return collect commands."""
+        verbose_args = f"--verbose {self._verbose} "
+        if self._verbose_datalad is not None:
+            verbose_args = (
+                f"{verbose_args} --verbose-datalad {self._verbose_datalad} "
+            )
+
         junifer_collect_args = (
             "collect "
             f"{self._yaml_config_path.resolve()!s} "
-            f"--verbose {self._verbose}"
+            f"{verbose_args}"
         )
         log_dir_prefix = f"{self._log_dir.resolve()!s}/junifer_collect"
         fixed = (

junifer/cli/cli.py

@@ -45,6 +45,32 @@ __all__ = [
 ]
 
 
+def _validate_optional_verbose(
+    ctx: click.Context, param: str, value: Optional[str]
+):
+    """Validate optional verbose option.
+
+    Parameters
+    ----------
+    ctx : click.Context
+        The context of the command.
+    param : str
+        The parameter to validate.
+    value : str
+        The value to validate.
+
+    Returns
+    -------
+    str or int or None
+        The validated value.
+
+    """
+    if value is None:
+        return value
+    else:
+        return _validate_verbose(ctx, param, value)
+
+
 def _validate_verbose(
     ctx: click.Context, param: str, value: str
 ) -> Union[str, int]:
@@ -105,8 +131,17 @@ def cli() -> None:  # pragma: no cover
     callback=_validate_verbose,
     default="info",
 )
+@click.option(
+    "--verbose-datalad",
+    type=click.UNPROCESSED,
+    callback=_validate_optional_verbose,
+    default=None,
+)
 def run(
-    filepath: click.Path, element: tuple[str], verbose: Union[str, int]
+    filepath: click.Path,
+    element: tuple[str],
+    verbose: Union[str, int],
+    verbose_datalad: Optional[Union[str, int]],
 ) -> None:
     """Run feature extraction.
 
@@ -120,10 +155,12 @@ def run(
         The element(s) to operate on.
     verbose : click.Choice
         The verbosity level: warning, info or debug (default "info").
+    verbose_datalad : click.Choice or None
+        The verbosity level for datalad: warning, info or debug (default None).
 
     """
     # Setup logging
-    configure_logging(level=verbose)
+    configure_logging(level=verbose, level_datalad=verbose_datalad)
     # TODO(synchon): add validation
     # Parse YAML
     config = parse_yaml(filepath)
@@ -167,7 +204,17 @@ def run(
     callback=_validate_verbose,
     default="info",
 )
-def collect(filepath: click.Path, verbose: Union[str, int]) -> None:
+@click.option(
+    "--verbose-datalad",
+    type=click.UNPROCESSED,
+    callback=_validate_optional_verbose,
+    default=None,
+)
+def collect(
+    filepath: click.Path,
+    verbose: Union[str, int],
+    verbose_datalad: Union[str, int, None],
+) -> None:
     """Collect extracted features.
 
     \f
@@ -178,10 +225,12 @@ def collect(filepath: click.Path, verbose: Union[str, int]) -> None:
         The filepath to the configuration file.
     verbose : click.Choice
         The verbosity level: warning, info or debug (default "info").
+    verbose_datalad : click.Choice or None
+        The verbosity level for datalad: warning, info or debug (default None).
 
     """
     # Setup logging
-    configure_logging(level=verbose)
+    configure_logging(level=verbose, level_datalad=verbose_datalad)
     # TODO: add validation
     # Parse YAML
     config = parse_yaml(filepath)
@@ -208,12 +257,19 @@ def collect(filepath: click.Path, verbose: Union[str, int]) -> None:
     callback=_validate_verbose,
     default="info",
 )
+@click.option(
+    "--verbose-datalad",
+    type=click.UNPROCESSED,
+    callback=_validate_optional_verbose,
+    default=None,
+)
 def queue(
     filepath: click.Path,
     element: tuple[str],
     overwrite: bool,
     submit: bool,
     verbose: Union[str, int],
+    verbose_datalad: Union[str, int, None],
 ) -> None:
     """Queue feature extraction.
 
@@ -231,6 +287,8 @@ def queue(
         Whether to submit the job.
     verbose : click.Choice
         The verbosity level: warning, info or debug (default "info").
+    verbose_datalad : click.Choice or None
+        The verbosity level for datalad: warning, info or debug (default None).
 
     Raises
     ------
@@ -239,7 +297,7 @@ def queue(
 
     """
     # Setup logging
-    configure_logging(level=verbose)
+    configure_logging(level=verbose, level_datalad=verbose_datalad)
     # TODO: add validation
     # Parse YAML
     config = parse_yaml(filepath)  # type: ignore
@@ -365,9 +423,16 @@ def selftest(subpkg: str) -> None:
     callback=_validate_verbose,
     default="info",
 )
+@click.option(
+    "--verbose-datalad",
+    type=click.UNPROCESSED,
+    callback=_validate_optional_verbose,
+    default=None,
+)
 def reset(
     filepath: click.Path,
     verbose: Union[str, int],
+    verbose_datalad: Union[str, int, None],
 ) -> None:
     """Reset generated assets.
 
@@ -379,10 +444,12 @@ def reset(
         The filepath to the configuration file.
     verbose : click.Choice
         The verbosity level: warning, info or debug (default "info").
+    verbose_datalad : click.Choice or None
+        The verbosity level for datalad: warning, info or debug (default None).
 
     """
     # Setup logging
-    configure_logging(level=verbose)
+    configure_logging(level=verbose, level_datalad=verbose_datalad)
     # Parse YAML
     config = parse_yaml(filepath)
     # Perform operation
@@ -409,11 +476,18 @@ def reset(
     callback=_validate_verbose,
     default="info",
 )
+@click.option(
+    "--verbose-datalad",
+    type=click.UNPROCESSED,
+    callback=_validate_optional_verbose,
+    default=None,
+)
 def list_elements(
     filepath: click.Path,
     element: tuple[str],
     output_file: Optional[click.Path],
     verbose: Union[str, int],
+    verbose_datalad: Union[str, int, None],
 ) -> None:
     """List elements of a dataset.
 
@@ -430,10 +504,12 @@ def list_elements(
         stdout is not performed.
     verbose : click.Choice
         The verbosity level: warning, info or debug (default "info").
+    verbose_datalad : click.Choice or None
+        The verbosity level for datalad: warning, info or debug (default None
 
     """
     # Setup logging
-    configure_logging(level=verbose)
+    configure_logging(level=verbose, level_datalad=verbose_datalad)
     # Parse YAML
     config = parse_yaml(filepath)
     # Fetch datagrabber

junifer/markers/falff/_afni_falff.py

@@ -50,7 +50,7 @@ class AFNIALFF(metaclass=Singleton):
     @lru_cache(maxsize=None, typed=True)
     def compute(
         self,
-        data: "Nifti1Image",
+        input_path: Path,
         highpass: float,
         lowpass: float,
         tr: Optional[float],
@@ -59,8 +59,8 @@ class AFNIALFF(metaclass=Singleton):
 
         Parameters
         ----------
-        data : 4D Niimg-like object
-            Images to process.
+        input_path : pathlib.Path
+            Path to the input data.
         highpass : positive float
             Highpass cutoff frequency.
         lowpass : positive float
@@ -82,19 +82,17 @@ class AFNIALFF(metaclass=Singleton):
         """
         logger.debug("Creating cache for ALFF computation via AFNI")
 
-        # Create component-scoped tempdir
-        tempdir = WorkDirManager().get_tempdir(prefix="afni_alff+falff")
-
-        # Save target data to a component-scoped tempfile
-        nifti_in_file_path = tempdir / "input.nii"  # needs to be .nii
-        nib.save(data, nifti_in_file_path)
+        # Create element-scoped tempdir
+        element_tempdir = WorkDirManager().get_element_tempdir(
+            prefix="afni_lff"
+        )
 
         # Set 3dRSFC command
-        alff_falff_out_path_prefix = tempdir / "alff_falff"
+        lff_out_path_prefix = element_tempdir / "output"
         bp_cmd = [
             "3dRSFC",
-            f"-prefix {alff_falff_out_path_prefix.resolve()}",
-            f"-input {nifti_in_file_path.resolve()}",
+            f"-prefix {lff_out_path_prefix.resolve()}",
+            f"-input {input_path.resolve()}",
             f"-band {highpass} {lowpass}",
             "-no_rsfa -nosat -nodetrend",
         ]
@@ -104,49 +102,48 @@ class AFNIALFF(metaclass=Singleton):
         # Call 3dRSFC
         run_ext_cmd(name="3dRSFC", cmd=bp_cmd)
 
-        # Create element-scoped tempdir so that the ALFF and fALFF maps are
-        # available later as nibabel stores file path reference for
-        # loading on computation
-        element_tempdir = WorkDirManager().get_element_tempdir(
-            prefix="afni_alff_falff"
-        )
-
+        # Read header to get output suffix
+        niimg = nib.load(input_path)
+        header = niimg.header
+        sform_code = header.get_sform(coded=True)[1]
+        if sform_code == 4:
+            output_suffix = "tlrc"
+        else:
+            output_suffix = "orig"
+        # Set params suffix
         params_suffix = f"_{highpass}_{lowpass}_{tr}"
 
         # Convert alff afni to nifti
-        alff_afni_to_nifti_out_path = (
-            element_tempdir / f"alff{params_suffix}_output.nii"
+        alff_nifti_out_path = (
+            element_tempdir / f"output_alff{params_suffix}.nii"
         )  # needs to be .nii
         convert_alff_cmd = [
             "3dAFNItoNIFTI",
-            f"-prefix {alff_afni_to_nifti_out_path.resolve()}",
-            f"{alff_falff_out_path_prefix}_ALFF+orig.BRIK",
+            f"-prefix {alff_nifti_out_path.resolve()}",
+            f"{lff_out_path_prefix}_ALFF+{output_suffix}.BRIK",
         ]
         # Call 3dAFNItoNIFTI
         run_ext_cmd(name="3dAFNItoNIFTI", cmd=convert_alff_cmd)
 
         # Convert falff afni to nifti
-        falff_afni_to_nifti_out_path = (
-            element_tempdir / f"falff{params_suffix}_output.nii"
+        falff_nifti_out_path = (
+            element_tempdir / f"output_falff{params_suffix}.nii"
         )  # needs to be .nii
         convert_falff_cmd = [
             "3dAFNItoNIFTI",
-            f"-prefix {falff_afni_to_nifti_out_path.resolve()}",
-            f"{alff_falff_out_path_prefix}_fALFF+orig.BRIK",
+            f"-prefix {falff_nifti_out_path.resolve()}",
+            f"{lff_out_path_prefix}_fALFF+{output_suffix}.BRIK",
         ]
         # Call 3dAFNItoNIFTI
         run_ext_cmd(name="3dAFNItoNIFTI", cmd=convert_falff_cmd)
 
         # Load nifti
-        alff_data = nib.load(alff_afni_to_nifti_out_path)
-        falff_data = nib.load(falff_afni_to_nifti_out_path)
-
-        # Delete tempdir
-        WorkDirManager().delete_tempdir(tempdir)
+        alff_data = nib.load(alff_nifti_out_path)
+        falff_data = nib.load(falff_nifti_out_path)
 
         return (
             alff_data,
             falff_data,
-            alff_afni_to_nifti_out_path,
-            falff_afni_to_nifti_out_path,
-        )  # type: ignore
+            alff_nifti_out_path,
+            falff_nifti_out_path,
+        )

junifer/markers/falff/_junifer_falff.py

@@ -47,7 +47,7 @@ class JuniferALFF(metaclass=Singleton):
     @lru_cache(maxsize=None, typed=True)
     def compute(
         self,
-        data: "Nifti1Image",
+        input_path: Path,
         highpass: float,
         lowpass: float,
         tr: Optional[float],
@@ -56,8 +56,8 @@ class JuniferALFF(metaclass=Singleton):
 
         Parameters
         ----------
-        data : 4D Niimg-like object
-            Images to process.
+        input_path : pathlib.Path
+            Path to the input data.
         highpass : positive float
             Highpass cutoff frequency.
         lowpass : positive float
@@ -80,9 +80,10 @@ class JuniferALFF(metaclass=Singleton):
         logger.debug("Creating cache for ALFF computation via junifer")
 
         # Get scan data
-        niimg_data = data.get_fdata().copy()
+        niimg = nib.load(input_path)
+        niimg_data = niimg.get_fdata().copy()
         if tr is None:
-            tr = float(data.header["pixdim"][4])  # type: ignore
+            tr = float(niimg.header["pixdim"][4])  # type: ignore
             logger.info(f"`tr` not provided, using `tr` from header: {tr}")
 
         # Bandpass the data within the lowpass and highpass cutoff freqs
@@ -120,19 +121,17 @@ class JuniferALFF(metaclass=Singleton):
         # Calculate ALFF
         alff = numerator / np.sqrt(niimg_data.shape[-1])
         alff_data = nimg.new_img_like(
-            ref_niimg=data,
+            ref_niimg=niimg,
             data=alff,
         )
         falff_data = nimg.new_img_like(
-            ref_niimg=data,
+            ref_niimg=niimg,
             data=falff,
         )
 
-        # Create element-scoped tempdir so that the ALFF and fALFF maps are
-        # available later as nibabel stores file path reference for
-        # loading on computation
+        # Create element-scoped tempdir
         element_tempdir = WorkDirManager().get_element_tempdir(
-            prefix="junifer_alff+falff"
+            prefix="junifer_lff"
         )
         output_alff_path = element_tempdir / "output_alff.nii.gz"
         output_falff_path = element_tempdir / "output_falff.nii.gz"

junifer/markers/falff/falff_base.py

@@ -146,7 +146,7 @@ class ALFFBase(BaseMarker):
             estimator = JuniferALFF()
         # Compute ALFF + fALFF
         alff, falff, alff_path, falff_path = estimator.compute(  # type: ignore
-            data=input_data["data"],
+            input_path=input_data["path"],
             highpass=self.highpass,
             lowpass=self.lowpass,
             tr=self.tr,

junifer/markers/falff/tests/test_falff_spheres.py

@@ -69,7 +69,9 @@ def test_ALFFSpheres(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
             # Fit transform marker on data
             output = marker.fit_transform(element_data)
 
-            assert "Creating cache" in caplog.text
+            # Tests for ALFFParcels run before this with the same data and that
+            # should create the cache
+            assert "Calculating ALFF and fALFF" in caplog.text
 
             # Get BOLD output
             assert "BOLD" in output

junifer/markers/reho/_afni_reho.py

@@ -50,7 +50,7 @@ class AFNIReHo(metaclass=Singleton):
     @lru_cache(maxsize=None, typed=True)
     def compute(
         self,
-        data: "Nifti1Image",
+        input_path: Path,
         nneigh: int = 27,
         neigh_rad: Optional[float] = None,
         neigh_x: Optional[float] = None,
@@ -65,8 +65,8 @@ class AFNIReHo(metaclass=Singleton):
 
         Parameters
         ----------
-        data : 4D Niimg-like object
-            Images to process.
+        input_path : pathlib.Path
+            Path to the input data.
         nneigh : {7, 19, 27}, optional
             Number of voxels in the neighbourhood, inclusive. Can be:
 
@@ -128,19 +128,17 @@ class AFNIReHo(metaclass=Singleton):
         """
         logger.debug("Creating cache for ReHo computation via AFNI")
 
-        # Create component-scoped tempdir
-        tempdir = WorkDirManager().get_tempdir(prefix="afni_reho")
-
-        # Save target data to a component-scoped tempfile
-        nifti_in_file_path = tempdir / "input.nii"  # needs to be .nii
-        nib.save(data, nifti_in_file_path)
+        # Create element-scoped tempdir
+        element_tempdir = WorkDirManager().get_element_tempdir(
+            prefix="afni_reho"
+        )
 
         # Set 3dReHo command
-        reho_out_path_prefix = tempdir / "reho"
+        reho_out_path_prefix = element_tempdir / "output"
         reho_cmd = [
             "3dReHo",
             f"-prefix {reho_out_path_prefix.resolve()}",
-            f"-inset {nifti_in_file_path.resolve()}",
+            f"-inset {input_path.resolve()}",
         ]
         # Check ellipsoidal / cuboidal volume arguments
         if neigh_rad:
@@ -164,28 +162,28 @@ class AFNIReHo(metaclass=Singleton):
         # Call 3dReHo
         run_ext_cmd(name="3dReHo", cmd=reho_cmd)
 
-        # Create element-scoped tempdir so that the ReHo map is
-        # available later as nibabel stores file path reference for
-        # loading on computation
-        element_tempdir = WorkDirManager().get_element_tempdir(
-            prefix="afni_reho"
-        )
+        # Read header to get output suffix
+        niimg = nib.load(input_path)
+        header = niimg.header
+        sform_code = header.get_sform(coded=True)[1]
+        if sform_code == 4:
+            output_suffix = "tlrc"
+        else:
+            output_suffix = "orig"
+
         # Convert afni to nifti
-        reho_afni_to_nifti_out_path = (
+        reho_nifti_out_path = (
             element_tempdir / "output.nii"  # needs to be .nii
         )
         convert_cmd = [
             "3dAFNItoNIFTI",
-            f"-prefix {reho_afni_to_nifti_out_path.resolve()}",
-            f"{reho_out_path_prefix}+orig.BRIK",
+            f"-prefix {reho_nifti_out_path.resolve()}",
+            f"{reho_out_path_prefix}+{output_suffix}.BRIK",
         ]
         # Call 3dAFNItoNIFTI
         run_ext_cmd(name="3dAFNItoNIFTI", cmd=convert_cmd)
 
         # Load nifti
-        output_data = nib.load(reho_afni_to_nifti_out_path)
-
-        # Delete tempdir
-        WorkDirManager().delete_tempdir(tempdir)
+        output_data = nib.load(reho_nifti_out_path)
 
-        return output_data, reho_afni_to_nifti_out_path  # type: ignore
+        return output_data, reho_nifti_out_path

junifer/markers/reho/_junifer_reho.py

@@ -48,15 +48,15 @@ class JuniferReHo(metaclass=Singleton):
     @lru_cache(maxsize=None, typed=True)
     def compute(
         self,
-        data: "Nifti1Image",
+        input_path: Path,
         nneigh: int = 27,
     ) -> tuple["Nifti1Image", Path]:
         """Compute ReHo map.
 
         Parameters
         ----------
-        data : 4D Niimg-like object
-            Images to process.
+        input_path : pathlib.Path
+            Path to the input data.
         nneigh : {7, 19, 27, 125}, optional
             Number of voxels in the neighbourhood, inclusive. Can be:
 
@@ -89,7 +89,8 @@ class JuniferReHo(metaclass=Singleton):
         logger.debug("Creating cache for ReHo computation via junifer")
 
         # Get scan data
-        niimg_data = data.get_fdata()
+        niimg = nib.load(input_path)
+        niimg_data = niimg.get_fdata().copy()
         # Get scan dimensions
         n_x, n_y, n_z, _ = niimg_data.shape
 
@@ -119,7 +120,7 @@ class JuniferReHo(metaclass=Singleton):
         # after #299 is merged
         # Calculate whole brain mask
         mni152_whole_brain_mask = nmask.compute_brain_mask(
-            target_img=data,
+            target_img=niimg,
             threshold=0.5,
             mask_type="whole-brain",
         )
@@ -227,7 +228,7 @@ class JuniferReHo(metaclass=Singleton):
 
         # Create new image like target image
         output_data = nimg.new_img_like(
-            ref_niimg=data,
+            ref_niimg=niimg,
             data=reho_map,
             copy_header=False,
         )

junifer/markers/reho/reho_base.py

@@ -125,7 +125,7 @@ class ReHoBase(BaseMarker):
             estimator = JuniferReHo()
         # Compute reho
         reho_map, reho_map_path = estimator.compute(  # type: ignore
-            data=input_data["data"],
+            input_path=input_data["path"],
             **reho_params,
         )
 

junifer/utils/logging.py

@@ -4,6 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import os
 import sys
 
 
@@ -16,7 +17,7 @@ import logging
 import warnings
 from pathlib import Path
 from subprocess import PIPE, Popen, TimeoutExpired
-from typing import NoReturn, Optional, Union
+from typing import ClassVar, NoReturn, Optional, Union
 from warnings import warn
 
 import datalad
@@ -80,6 +81,59 @@ class WrapStdOut(logging.StreamHandler):
             raise AttributeError(f"'file' object has not attribute '{name}'")
 
 
+class ColorFormatter(logging.Formatter):
+    """Color formatter for logging messages.
+
+    Parameters
+    ----------
+    fmt : str
+        The format string for the logging message.
+    datefmt : str, optional
+        The format string for the date.
+
+    """
+
+    BLACK, RED, GREEN, YELLOW, BLUE, MAGENTA, CYAN, WHITE = range(8)
+
+    COLORS: ClassVar[dict[str, int]] = {
+        "WARNING": YELLOW,
+        "INFO": GREEN,
+        "DEBUG": BLUE,
+        "CRITICAL": MAGENTA,
+        "ERROR": RED,
+    }
+
+    RESET_SEQ: str = "\033[0m"
+    COLOR_SEQ: str = "\033[1;%dm"
+    BOLD_SEQ: str = "\033[1m"
+
+    def __init__(self, fmt: str, datefmt: Optional[str] = None) -> None:
+        """Initialize the ColorFormatter."""
+        logging.Formatter.__init__(self, fmt, datefmt)
+
+    def format(self, record: logging.LogRecord) -> str:
+        """Format the log record.
+
+        Parameters
+        ----------
+        record : logging.LogRecord
+            The log record to format.
+
+        Returns
+        -------
+        str
+            The formatted log record.
+
+        """
+        levelname = record.levelname
+        if levelname in self.COLORS:
+            levelname_color = (
+                self.COLOR_SEQ % (30 + self.COLORS[levelname]) + levelname
+            )
+            record.levelname = levelname_color + self.RESET_SEQ
+        return logging.Formatter.format(self, record)
+
+
 def _get_git_head(path: Path) -> str:
     """Aux function to read HEAD from git.
 
@@ -237,11 +291,51 @@ def log_versions(tbox_path: Optional[Path] = None) -> None:
         pass
 
 
+def _can_use_color(handler: logging.Handler) -> bool:
+    """Check if color can be used in the logging output.
+
+    Parameters
+    ----------
+    handler : logging.Handler
+        The logging handler to check for color support.
+
+    Returns
+    -------
+    bool
+        Whether color can be used in the logging output.
+
+    """
+    if isinstance(handler, logging.FileHandler):
+        # Do not use colors in file handlers
+        return False
+    else:
+        stream = handler.stream
+        if hasattr(stream, "isatty") and stream.isatty():
+            valid_terms = [
+                "xterm-256color",
+                "xterm-kitty",
+                "xterm-color",
+            ]
+            this_term = os.getenv("TERM", None)
+            if this_term is not None:
+                if this_term in valid_terms:
+                    return True
+                if this_term.endswith("256color") or this_term.endswith("256"):
+                    return True
+                if this_term == "dumb" and os.getenv("CI", False):
+                    return True
+            if os.getenv("COLORTERM", False):
+                return True
+        # No TTY, no color
+        return False
+
+
 def configure_logging(
     level: Union[int, str] = "WARNING",
     fname: Optional[Union[str, Path]] = None,
     overwrite: Optional[bool] = None,
     output_format=None,
+    level_datalad: Union[int, str, None] = None,
 ) -> None:
     """Configure the logging functionality.
 
@@ -264,6 +358,10 @@ def configure_logging(
         e.g., ``"%(asctime)s - %(levelname)s - %(message)s"``.
         If None, default string format is used
         (default ``"%(asctime)s - %(name)s - %(levelname)s - %(message)s"``).
+    level_datalad : int or {"DEBUG", "INFO", "WARNING", "ERROR"}, optional
+        The level of the messages to print for datalad. If string, it will be
+        interpreted as elements of logging. If None, it will be set as the
+        ``level`` parameter (default None).
 
     """
     _close_handlers(logger)  # close relevant logger handlers
@@ -297,11 +395,22 @@ def configure_logging(
         #     "%(asctime)s [%(levelname)s] %(message)s "
         #     "(%(filename)s:%(lineno)s)"
         # )
-    formatter = logging.Formatter(fmt=output_format)
+    if _can_use_color(lh):
+        formatter = ColorFormatter(fmt=output_format)
+    else:
+        formatter = logging.Formatter(fmt=output_format)
 
     lh.setFormatter(formatter)  # set formatter
     logger.setLevel(level)  # set level
-    datalad.log.lgr.setLevel(level)  # set level for datalad
+
+    # Set datalad logging level accordingly
+    if level_datalad is not None:
+        if isinstance(level_datalad, str):
+            level_datalad = _logging_types[level_datalad]
+    else:
+        level_datalad = level
+    datalad.log.lgr.setLevel(level_datalad)  # set level for datalad
+
     logger.addHandler(lh)  # set handler
     log_versions()  # log versions of installed packages
 

{junifer-0.0.6.dev317.dist-info → junifer-0.0.6.dev330.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev317
+Version: 0.0.6.dev330
 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.dev317.dist-info → junifer-0.0.6.dev330.dist-info}/RECORD

@@ -1,6 +1,6 @@
 junifer/__init__.py,sha256=2McgH1yNue6Z1V26-uN_mfMjbTcx4CLhym-DMBl5xA4,266
 junifer/__init__.pyi,sha256=SsTvgq2Dod6UqJN96GH1lCphH6hJQQurEJHGNhHjGUI,508
-junifer/_version.py,sha256=ysdlII3ZUlFBiHIzSCvasFtc1CMEpYMsiJEwLoFxjKQ,428
+junifer/_version.py,sha256=ib7p2sRvl9n6dHPTqNlqVwUPPOKf5EKIksHMk7EQqno,428
 junifer/conftest.py,sha256=PWYkkRDU8ly2lYwv7VBKMHje4et6HX7Yey3Md_I2KbA,613
 junifer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/stats.py,sha256=e9aaagMGtgpRfW3Wdpz9ocpnYld1IWylCDcjFUgX9Mk,6225
@@ -11,8 +11,8 @@ junifer/api/functions.py,sha256=Tq1LKoxJuHHylcCFJ6SrPoPriIsnTLdbQ5K6w8gdTE8,1369
 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=LoDQFGZ9wCDmgx5a1_nhKo4zOSvqViXZ8V882DksF7U,246
-junifer/api/queue_context/gnu_parallel_local_adapter.py,sha256=HBsH9ql0AnU87KfiUEpQ7rCakbFEf4dlz8JzYdlqEpg,9542
-junifer/api/queue_context/htcondor_adapter.py,sha256=MihS26FJX92_0ysoJm-INP1YUoRcnU_S_WVCgbkoD08,13214
+junifer/api/queue_context/gnu_parallel_local_adapter.py,sha256=hFeLoqqHiB7JXE5cwkVDRX00tjKyK60xAxvE1uO7OOk,10178
+junifer/api/queue_context/htcondor_adapter.py,sha256=9TXtPhBsDdGFgkIhtsySFCi4QUjerUXMq5kMHpxNg90,13878
 junifer/api/queue_context/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/api/queue_context/queue_context_adapter.py,sha256=a6UE8xavDfuaZbkWYsayVs6l-rwIrbpFSpqSyHsEeYY,1577
 junifer/api/queue_context/tests/test_gnu_parallel_local_adapter.py,sha256=Nv_0axIW4SOE7-TyQXd_nM_0A_kDiFAgrkQcmQafW_s,6585
@@ -43,7 +43,7 @@ junifer/api/res/fsl/std2imgcoord,sha256=-X5wRH6XMl0yqnTACJX6MFhO8DFOEWg42MHRxGvi
 junifer/api/tests/test_functions.py,sha256=PPkjs_FqjZZgsEa3a81ulzPxLskVh5HmnaG8TaNCwR0,18084
 junifer/cli/__init__.py,sha256=DS3kZKHeVDxt6d1MLBerZ2fcAwrEBHee5JOBhOLajUI,197
 junifer/cli/__init__.pyi,sha256=PiV4znUnzSeuSSJGz-RT8N21PiMqoSMwYcypi7nt2Js,40
-junifer/cli/cli.py,sha256=Q0l7dBclLrM0P5MU2G0MA7W8u23VtqIQdwaeoOy-_ws,13519
+junifer/cli/cli.py,sha256=LvtkFMvnxuoviAhs0bki6P4GMda6ZvNsJi4_QF00va8,15691
 junifer/cli/parser.py,sha256=ouVnk4NrOmVMNnQDMsqAjt2BaOT05bNJq0LVRsIakXI,8358
 junifer/cli/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/cli/utils.py,sha256=AbPQC0Kl-tHMNKiPxp_01gLAGD3IGoLbsq3rXyPMM-c,3116
@@ -208,14 +208,14 @@ junifer/markers/complexity/tests/test_sample_entropy.py,sha256=rfbiguVq7CUwYIvYB
 junifer/markers/complexity/tests/test_weighted_perm_entropy.py,sha256=yDWKEaUbxrnrG6J2NlktLfwSBre5OuXd63kEof7t8PM,2373
 junifer/markers/falff/__init__.py,sha256=qxdx_3FsVrn7h3gtbocK0ZmvqZwPQZGKuVkPm31ejNM,217
 junifer/markers/falff/__init__.pyi,sha256=X-q2zBjUX0imQ37yN2Cg5gKfDvq8sh_9y2hRH4g5ufY,120
-junifer/markers/falff/_afni_falff.py,sha256=D_hhT-rfWXeIe-Pwh4pK2O7N9Q07VyMOUHeAz6Ooudo,4518
-junifer/markers/falff/_junifer_falff.py,sha256=TnZ6T8u0f0YitJ7KRk4gMcC1tv6UW8m4VVcvcjGRsL0,4450
-junifer/markers/falff/falff_base.py,sha256=XZcBfXA74tWrW--uCALkRLl1tB7toR3_HfzPJUblz8g,4909
+junifer/markers/falff/_afni_falff.py,sha256=PYkSOFMyaHoGYDvmBjKLW1ALyWBe7yI36JBqZ71ji2c,4223
+junifer/markers/falff/_junifer_falff.py,sha256=1PsavcopVjPtfmPZsnNi5ynl2GTfnCx9qjuKDb7YejE,4347
+junifer/markers/falff/falff_base.py,sha256=WtJTMRn_Vmv9RZaaeLeyZpCsQc8QgB3UqIPWsUI3Lh4,4915
 junifer/markers/falff/falff_parcels.py,sha256=sSb6QLaJKpL0GCTRWW3RnpOZCoy1f9lDLgJ0I_W_LlM,6017
 junifer/markers/falff/falff_spheres.py,sha256=GrakJYPB01y9BNBXM8WzWaae0mC-S06txiycvfBGcj0,6656
 junifer/markers/falff/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/markers/falff/tests/test_falff_parcels.py,sha256=Z3n1i8dkYbdXgouUjfIif9yLv5MubBEdrtAA-a6kRcc,4349
-junifer/markers/falff/tests/test_falff_spheres.py,sha256=-VLEvFaF8CMCN_7FLYCSfP7MMjy-gm1Zgu13je5Pku8,4373
+junifer/markers/falff/tests/test_falff_spheres.py,sha256=PGsxFjMxsH8HxIHVtdcQcX8suFa18ma_12Almknzn88,4503
 junifer/markers/functional_connectivity/__init__.py,sha256=dGTn69eS7a3rylMQh_wKlO28UmYGjsoDEGu4q5sgQFA,230
 junifer/markers/functional_connectivity/__init__.pyi,sha256=qfw6WVyE65u-5NZNi0xPa8zZVtkRfFvwyl4jHH2Xl00,539
 junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py,sha256=uLdVGywmL7qrzloh1YBL4g4tPiamA47MgHF2DQH0JTU,5733
@@ -233,10 +233,10 @@ junifer/markers/functional_connectivity/tests/test_functional_connectivity_parce
 junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py,sha256=A9OtFdndiSGOcPHH-QLPh6qoiD03A6KjM_emwxAlPg0,4145
 junifer/markers/reho/__init__.py,sha256=WZf4A0XaRThjl8SlFOhvTLUfhTHp5koLxZgowsgTSAE,211
 junifer/markers/reho/__init__.pyi,sha256=_aFb-Ry_EP2OMU6xRL4GlfuDpSl_egHllL-fz7vXjcE,118
-junifer/markers/reho/_afni_reho.py,sha256=YBqNYipZO8EFM4Jmek_A36zr9n4nTR0RVDPpxjJKLxM,6466
-junifer/markers/reho/_junifer_reho.py,sha256=86oBH8UtWsHJJGz2-uRXAjdGNHvaSV6Xu1v7-9AJqLs,9340
+junifer/markers/reho/_afni_reho.py,sha256=SOWR5y9AYKfw1wj2Z4Wy7ckMUVTmeS378bayvPPVqqo,6225
+junifer/markers/reho/_junifer_reho.py,sha256=14ObaRa2-0JzcoYLJyhnx4bgPCpTdciDXmrn9-gPv20,9387
 junifer/markers/reho/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-junifer/markers/reho/reho_base.py,sha256=Amji7hNtkT9D-teJ2tTzDsVHKRXETDwhICDKa8ZGehY,4071
+junifer/markers/reho/reho_base.py,sha256=Q88TbhIM4rQWdeQPLwwxwZ9DrR8l09orD1rdTkSYDtc,4077
 junifer/markers/reho/reho_parcels.py,sha256=UE1ia3uqbmTcZMc_FI625xVPLxBYvwpfrcvhekopbkI,6392
 junifer/markers/reho/reho_spheres.py,sha256=FCC2qncC85Kd82hg-MOu4T7NAKEkXHUaCcwC9taau9Y,6996
 junifer/markers/reho/tests/test_reho_parcels.py,sha256=bRtDi91qRcRYaRqqQjuSU6NuNz-KwLVCoTYo-e5VmsI,4075
@@ -334,17 +334,17 @@ junifer/utils/_config.py,sha256=cfxyv1bfklID2atQseu6y3J7mZrCXPwnGEfBSImG9CM,3054
 junifer/utils/_yaml.py,sha256=jpTroTI2rajECj0RXGCXaOwLpad858WzI7Jg-eXJ_jU,336
 junifer/utils/fs.py,sha256=M3CKBLh4gPS6s9giyopgb1hHMXzLb6k3cung2wHVBjs,492
 junifer/utils/helpers.py,sha256=QcfdHPhrYKTf6o5eSOIvDxqmIAxlp9SqmCEdR10jbIY,2033
-junifer/utils/logging.py,sha256=DRWcKwez56Mfh5PyLQSaKgL0Cc_Om8qfO8zGHTHB5Vo,9769
+junifer/utils/logging.py,sha256=8rWEtZPohugiB7niF9yvybi79w3Sj5xcaImJhsuXxks,12998
 junifer/utils/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/utils/singleton.py,sha256=iATJMdzsSVE9akTI4DDycubhAl98t0EdO17gwgOjAYA,1189
 junifer/utils/tests/test_config.py,sha256=7ltIXuwb_W4Mv_1dxQWyiyM10XgUAfsWKV6D_iE-XU0,1540
 junifer/utils/tests/test_fs.py,sha256=WQS7cKlKEZ742CIuiOYYpueeAhY9PqlastfDVpVVtvE,923
 junifer/utils/tests/test_helpers.py,sha256=k5qqfxK8dFyuewTJyR1Qn6-nFaYNuVr0ysc18bfPjyU,929
 junifer/utils/tests/test_logging.py,sha256=duO4ou365hxwa_kwihFtKPLaL6LC5XHiyhOijrrngbA,8009
-junifer-0.0.6.dev317.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.6.dev317.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.6.dev317.dist-info/METADATA,sha256=aQiIDdr_Ov-v0da-VOALNQiJe1FIGM-Xz32tTTqlW00,8429
-junifer-0.0.6.dev317.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-junifer-0.0.6.dev317.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
-junifer-0.0.6.dev317.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.6.dev317.dist-info/RECORD,,
+junifer-0.0.6.dev330.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.6.dev330.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.6.dev330.dist-info/METADATA,sha256=LkxGgT6R7p-H0fZTaFoWi71TBNqAnRpuXVa9w6DUhZ4,8429
+junifer-0.0.6.dev330.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+junifer-0.0.6.dev330.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
+junifer-0.0.6.dev330.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.6.dev330.dist-info/RECORD,,