junifer 0.0.5.dev131__py3-none-any.whl → 0.0.5.dev152__py3-none-any.whl

junifer/__init__.py

@@ -20,3 +20,20 @@ from . import (
     onthefly,
 )
 from ._version import __version__
+
+
+__all__ = [
+    "api",
+    "configs",
+    "data",
+    "datagrabber",
+    "datareader",
+    "markers",
+    "pipeline",
+    "preprocess",
+    "stats",
+    "storage",
+    "utils",
+    "external",
+    "onthefly",
+]

junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.5.dev131'
-__version_tuple__ = version_tuple = (0, 0, 5, 'dev131')
+__version__ = version = '0.0.5.dev152'
+__version_tuple__ = version_tuple = (0, 0, 5, 'dev152')

junifer/api/__init__.py

@@ -7,3 +7,6 @@
 from . import decorators
 from .cli import cli
 from .functions import collect, queue, run
+
+
+__all__ = ["decorators", "cli", "collect", "queue", "run"]

junifer/api/decorators.py

@@ -10,6 +10,15 @@ from typing import Type
 from ..pipeline.registry import register
 
 
+__all__ = [
+    "register_datagrabber",
+    "register_datareader",
+    "register_preprocessor",
+    "register_marker",
+    "register_storage",
+]
+
+
 def register_datagrabber(klass: Type) -> Type:
     """Register DataGrabber.
 

junifer/api/functions.py

@@ -23,6 +23,9 @@ from .queue_context import GnuParallelLocalAdapter, HTCondorAdapter
 from .utils import yaml
 
 
+__all__ = ["run", "collect", "queue", "reset", "list_elements"]
+
+
 def _get_datagrabber(datagrabber_config: Dict) -> BaseDataGrabber:
     """Get DataGrabber.
 
@@ -92,7 +95,7 @@ def run(
     datagrabber : dict
         DataGrabber to use. Must have a key ``kind`` with the kind of
         DataGrabber to use. All other keys are passed to the DataGrabber
-        init function.
+        constructor.
     markers : list of dict
         List of markers to extract. Each marker is a dict with at least two
         keys: ``name`` and ``kind``. The ``name`` key is used to name the
@@ -102,11 +105,11 @@ def run(
     storage : dict
         Storage to use. Must have a key ``kind`` with the kind of
         storage to use. All other keys are passed to the storage
-        init function.
+        constructor.
     preprocessors : list of dict, optional
         List of preprocessors to use. Each preprocessor is a dict with at
         least a key ``kind`` specifying the preprocessor to use. All other keys
-        are passed to the preprocessor init function (default None).
+        are passed to the preprocessor constructor (default None).
     elements : str or tuple or list of str or tuple, optional
         Element(s) to process. Will be used to index the DataGrabber
         (default None).
@@ -188,7 +191,7 @@ def collect(storage: Dict) -> None:
     storage : dict
         Storage to use. Must have a key ``kind`` with the kind of
         storage to use. All other keys are passed to the storage
-        init function.
+        constructor.
 
     """
     storage_params = storage.copy()

junifer/api/parser.py

@@ -14,6 +14,9 @@ from ..utils.logging import logger, raise_error
 from .utils import yaml
 
 
+__all__ = ["parse_yaml"]
+
+
 def parse_yaml(filepath: Union[str, Path]) -> Dict:
     """Parse YAML.
 

junifer/api/queue_context/__init__.py

@@ -6,3 +6,6 @@
 from .queue_context_adapter import QueueContextAdapter
 from .htcondor_adapter import HTCondorAdapter
 from .gnu_parallel_local_adapter import GnuParallelLocalAdapter
+
+
+__all__ = ["QueueContextAdapter", "HTCondorAdapter", "GnuParallelLocalAdapter"]

junifer/api/res/afni/run_afni_docker.sh

@@ -31,7 +31,7 @@ if [ -d "${var}" ]; then
 done
 
 echo "Docker args: ${docker_args[*]}" >&2
-echo "Corrected args for afni: ${corrected_args[*]}" >&2
+echo "Corrected args for AFNI: ${corrected_args[*]}" >&2
 
 cwd=$(pwd)
 cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} afni/afni_make_build ${corrected_args[*]}"

junifer/api/res/ants/run_ants_docker.sh

@@ -31,7 +31,7 @@ if [ -d "${var}" ]; then
 done
 
 echo "Docker args: ${docker_args[*]}" >&2
-echo "Corrected args for fsl: ${corrected_args[*]}" >&2
+echo "Corrected args for ANTs: ${corrected_args[*]}" >&2
 
 cwd=$(pwd)
 cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} antsx/ants ${corrected_args[*]}"

junifer/api/res/fsl/run_fsl_docker.sh

@@ -31,7 +31,7 @@ if [ -d "${var}" ]; then
 done
 
 echo "Docker args: ${docker_args[*]}" >&2
-echo "Corrected args for fsl: ${corrected_args[*]}" >&2
+echo "Corrected args for FSL: ${corrected_args[*]}" >&2
 
 cwd=$(pwd)
 cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} brainlife/fsl ${corrected_args[*]}"

junifer/configs/juseless/__init__.py

@@ -4,3 +4,6 @@
 # License: AGPL
 
 from . import datagrabbers
+
+
+__all__ = ["datagrabbers"]

junifer/configs/juseless/datagrabbers/__init__.py

@@ -10,3 +10,12 @@ from .camcan_vbm import JuselessDataladCamCANVBM
 from .ixi_vbm import JuselessDataladIXIVBM
 from .ucla import JuselessUCLA
 from .ukb_vbm import JuselessDataladUKBVBM
+
+
+__all__ = [
+    "JuselessDataladAOMICID1000VBM",
+    "JuselessDataladCamCANVBM",
+    "JuselessDataladIXIVBM",
+    "JuselessUCLA",
+    "JuselessDataladUKBVBM",
+]

junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py

@@ -11,6 +11,9 @@ from ....api.decorators import register_datagrabber
 from ....datagrabber import PatternDataladDataGrabber
 
 
+__all__ = ["JuselessDataladAOMICID1000VBM"]
+
+
 @register_datagrabber
 class JuselessDataladAOMICID1000VBM(PatternDataladDataGrabber):
     """Concrete implementation for Juseless AOMIC ID1000 VBM data fetching.

junifer/configs/juseless/datagrabbers/camcan_vbm.py

@@ -12,6 +12,9 @@ from ....api.decorators import register_datagrabber
 from ....datagrabber import PatternDataladDataGrabber
 
 
+__all__ = ["JuselessDataladCamCANVBM"]
+
+
 @register_datagrabber
 class JuselessDataladCamCANVBM(PatternDataladDataGrabber):
     """Concrete implementation for Juseless CamCAN VBM data fetching.

junifer/configs/juseless/datagrabbers/ixi_vbm.py

@@ -13,6 +13,9 @@ from ....datagrabber import PatternDataladDataGrabber
 from ....utils import raise_error
 
 
+__all__ = ["JuselessDataladIXIVBM"]
+
+
 @register_datagrabber
 class JuselessDataladIXIVBM(PatternDataladDataGrabber):
     """Concrete implementation for Juseless IXI VBM data fetching.

junifer/configs/juseless/datagrabbers/ucla.py

@@ -12,6 +12,9 @@ from ....datagrabber import PatternDataGrabber
 from ....utils import raise_error
 
 
+__all__ = ["JuselessUCLA"]
+
+
 @register_datagrabber
 class JuselessUCLA(PatternDataGrabber):
     """Concrete implementation for Juseless UCLA data fetching.

junifer/configs/juseless/datagrabbers/ukb_vbm.py

@@ -12,6 +12,9 @@ from ....api.decorators import register_datagrabber
 from ....datagrabber import PatternDataladDataGrabber
 
 
+__all__ = ["JuselessDataladUKBVBM"]
+
+
 @register_datagrabber
 class JuselessDataladUKBVBM(PatternDataladDataGrabber):
     """Concrete implementation for Juseless UKB VBM data fetching.

junifer/data/__init__.py

@@ -28,3 +28,23 @@ from .masks import (
 from .template_spaces import get_template, get_xfm
 
 from . import utils
+
+
+__all__ = [
+    "list_coordinates",
+    "load_coordinates",
+    "register_coordinates",
+    "get_coordinates",
+    "list_parcellations",
+    "load_parcellation",
+    "register_parcellation",
+    "merge_parcellations",
+    "get_parcellation",
+    "list_masks",
+    "load_mask",
+    "register_mask",
+    "get_mask",
+    "get_template",
+    "get_xfm",
+    "utils",
+]

junifer/data/coordinates.py

@@ -16,6 +16,14 @@ from ..pipeline import WorkDirManager
 from ..utils import logger, raise_error, run_ext_cmd
 
 
+__all__ = [
+    "register_coordinates",
+    "list_coordinates",
+    "get_coordinates",
+    "load_coordinates",
+]
+
+
 # Path to the VOIs
 _vois_path = Path(__file__).parent / "VOIs"
 

junifer/data/masks.py

@@ -35,6 +35,16 @@ from .utils import closest_resolution
 if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
+
+__all__ = [
+    "compute_brain_mask",
+    "register_mask",
+    "list_masks",
+    "get_mask",
+    "load_mask",
+]
+
+
 # Path to the masks
 _masks_path = Path(__file__).parent / "masks"
 

junifer/data/parcellations.py

@@ -30,6 +30,15 @@ if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
 
+__all__ = [
+    "register_parcellation",
+    "list_parcellations",
+    "get_parcellation",
+    "load_parcellation",
+    "merge_parcellations",
+]
+
+
 # A dictionary containing all supported parcellations and their respective
 # valid parameters.
 

junifer/data/template_spaces.py

@@ -15,6 +15,9 @@ from ..utils import logger, raise_error
 from .utils import closest_resolution
 
 
+__all__ = ["get_xfm", "get_template"]
+
+
 def get_xfm(
     src: str, dst: str, xfms_dir: Union[str, Path, None] = None
 ) -> Path:  # pragma: no cover

junifer/data/utils.py

@@ -7,6 +7,9 @@ import numpy as np
 from ..utils.logging import logger
 
 
+__all__ = ["closest_resolution"]
+
+
 def closest_resolution(
     resolution: Optional[Union[float, int]],
     valid_resolution: Union[List[float], List[int], np.ndarray],

junifer/datagrabber/__init__.py

@@ -16,3 +16,18 @@ from .aomic import DataladAOMICID1000, DataladAOMICPIOP1, DataladAOMICPIOP2
 from .hcp1200 import HCP1200, DataladHCP1200
 from .multiple import MultipleDataGrabber
 from .dmcc13_benchmark import DMCC13Benchmark
+
+
+__all__ = [
+    "BaseDataGrabber",
+    "DataladDataGrabber",
+    "PatternDataGrabber",
+    "PatternDataladDataGrabber",
+    "DataladAOMICID1000",
+    "DataladAOMICPIOP1",
+    "DataladAOMICPIOP2",
+    "HCP1200",
+    "DataladHCP1200",
+    "MultipleDataGrabber",
+    "DMCC13Benchmark",
+]

junifer/datagrabber/aomic/__init__.py

@@ -7,3 +7,6 @@
 from .id1000 import DataladAOMICID1000
 from .piop1 import DataladAOMICPIOP1
 from .piop2 import DataladAOMICPIOP2
+
+
+__all__ = ["DataladAOMICID1000", "DataladAOMICPIOP1", "DataladAOMICPIOP2"]

junifer/datagrabber/aomic/id1000.py

@@ -14,6 +14,9 @@ from ...api.decorators import register_datagrabber
 from ..pattern_datalad import PatternDataladDataGrabber
 
 
+__all__ = ["DataladAOMICID1000"]
+
+
 @register_datagrabber
 class DataladAOMICID1000(PatternDataladDataGrabber):
     """Concrete implementation for datalad-based data fetching of AOMIC ID1000.

junifer/datagrabber/aomic/piop1.py

@@ -16,6 +16,9 @@ from ...utils import raise_error
 from ..pattern_datalad import PatternDataladDataGrabber
 
 
+__all__ = ["DataladAOMICPIOP1"]
+
+
 @register_datagrabber
 class DataladAOMICPIOP1(PatternDataladDataGrabber):
     """Concrete implementation for pattern-based data fetching of AOMIC PIOP1.

junifer/datagrabber/aomic/piop2.py

@@ -16,6 +16,9 @@ from ...utils import raise_error
 from ..pattern_datalad import PatternDataladDataGrabber
 
 
+__all__ = ["DataladAOMICPIOP2"]
+
+
 @register_datagrabber
 class DataladAOMICPIOP2(PatternDataladDataGrabber):
     """Concrete implementation for pattern-based data fetching of AOMIC PIOP2.

junifer/datagrabber/base.py

@@ -14,6 +14,9 @@ from ..utils import logger, raise_error
 from .utils import validate_types
 
 
+__all__ = ["BaseDataGrabber"]
+
+
 class BaseDataGrabber(ABC, UpdateMetaMixin):
     """Abstract base class for DataGrabber.
 

junifer/datagrabber/datalad_base.py

@@ -21,6 +21,9 @@ from ..utils import logger, raise_error, warn_with_log
 from .base import BaseDataGrabber
 
 
+__all__ = ["DataladDataGrabber"]
+
+
 class DataladDataGrabber(BaseDataGrabber):
     """Abstract base class for datalad-based data fetching.
 

junifer/datagrabber/hcp1200/__init__.py

@@ -5,3 +5,6 @@
 
 from .hcp1200 import HCP1200
 from .datalad_hcp1200 import DataladHCP1200
+
+
+__all__ = ["HCP1200", "DataladHCP1200"]

junifer/datagrabber/hcp1200/datalad_hcp1200.py

@@ -14,6 +14,9 @@ from ...api.decorators import register_datagrabber
 from .hcp1200 import HCP1200
 
 
+__all__ = ["DataladHCP1200"]
+
+
 @register_datagrabber
 class DataladHCP1200(DataladDataGrabber, HCP1200):
     """Concrete implementation for datalad-based data fetching of HCP1200.

junifer/datagrabber/hcp1200/hcp1200.py

@@ -14,6 +14,9 @@ from ..pattern import PatternDataGrabber
 from ..utils import raise_error
 
 
+__all__ = ["HCP1200"]
+
+
 @register_datagrabber
 class HCP1200(PatternDataGrabber):
     """Concrete implementation for pattern-based data fetching of HCP1200.

junifer/datagrabber/multiple.py

@@ -11,6 +11,9 @@ from ..utils import raise_error
 from .base import BaseDataGrabber
 
 
+__all__ = ["MultipleDataGrabber"]
+
+
 class MultipleDataGrabber(BaseDataGrabber):
     """Concrete implementation for multi sourced data fetching.
 

junifer/datagrabber/pattern.py

@@ -18,6 +18,9 @@ from .base import BaseDataGrabber
 from .utils import validate_patterns, validate_replacements
 
 
+__all__ = ["PatternDataGrabber"]
+
+
 # Accepted formats for confounds specification
 _CONFOUNDS_FORMATS = ("fmriprep", "adhoc")
 

junifer/datagrabber/pattern_datalad.py

@@ -12,6 +12,9 @@ from .datalad_base import DataladDataGrabber
 from .pattern import PatternDataGrabber
 
 
+__all__ = ["PatternDataladDataGrabber"]
+
+
 @register_datagrabber
 class PatternDataladDataGrabber(DataladDataGrabber, PatternDataGrabber):
     """Concrete implementation for pattern and datalad based data fetching.

junifer/datagrabber/utils.py

@@ -9,6 +9,9 @@ from typing import Dict, List
 from ..utils import logger, raise_error
 
 
+__all__ = ["validate_types", "validate_replacements", "validate_patterns"]
+
+
 # Define schema for pattern-based datagrabber's patterns
 PATTERNS_SCHEMA = {
     "T1w": {

junifer/datareader/__init__.py

@@ -6,3 +6,6 @@
 # License: AGPL
 
 from .default import DefaultDataReader
+
+
+__all__ = ["DefaultDataReader"]

junifer/datareader/default.py

@@ -15,6 +15,9 @@ from ..pipeline import PipelineStepMixin, UpdateMetaMixin
 from ..utils.logging import logger, warn_with_log
 
 
+__all__ = ["DefaultDataReader"]
+
+
 # Map each file extension to a type
 _extensions = {
     ".nii": "NIFTI",

junifer/external/nilearn/junifer_nifti_spheres_masker.py

@@ -10,9 +10,9 @@ from nilearn import image, masking
 from nilearn._utils.class_inspect import get_params
 from nilearn._utils.niimg import img_data_dtype
 from nilearn._utils.niimg_conversions import (
-    _safe_get_data,
     check_niimg_3d,
     check_niimg_4d,
+    safe_get_data,
 )
 from nilearn.maskers import NiftiSpheresMasker
 from nilearn.maskers.base_masker import _filter_and_extract
@@ -104,7 +104,7 @@ def _apply_mask_and_get_affinity(
 
     # Compute world coordinates of all in-mask voxels.
     if niimg is None:
-        mask, affine = masking._load_mask_img(mask_img)
+        mask, affine = masking.load_mask_img(mask_img)
         # Get coordinate for all voxels inside of mask
         mask_coords = np.asarray(np.nonzero(mask)).T.tolist()
         X = None
@@ -118,21 +118,21 @@ def _apply_mask_and_get_affinity(
             target_shape=niimg.shape[:3],
             interpolation="nearest",
         )
-        mask, _ = masking._load_mask_img(mask_img)
+        mask, _ = masking.load_mask_img(mask_img)
         mask_coords = list(zip(*np.where(mask != 0)))
 
-        X = masking._apply_mask_fmri(niimg, mask_img)
+        X = masking.apply_mask_fmri(niimg, mask_img)
 
     elif niimg is not None:
         affine = niimg.affine
-        if np.isnan(np.sum(_safe_get_data(niimg))):
+        if np.isnan(np.sum(safe_get_data(niimg))):
             warn_with_log(
                 "The imgs you have fed into fit_transform() contains NaN "
                 "values which will be converted to zeroes."
             )
-            X = _safe_get_data(niimg, True).reshape([-1, niimg.shape[3]]).T
+            X = safe_get_data(niimg, True).reshape([-1, niimg.shape[3]]).T
         else:
-            X = _safe_get_data(niimg).reshape([-1, niimg.shape[3]]).T
+            X = safe_get_data(niimg).reshape([-1, niimg.shape[3]]).T
 
         mask_coords = list(np.ndindex(niimg.shape[:3]))
 

junifer/markers/__init__.py

@@ -24,3 +24,24 @@ from .temporal_snr import (
     TemporalSNRSpheres,
 )
 from .brainprint import BrainPrint
+
+
+__all__ = [
+    "BaseMarker",
+    "MarkerCollection",
+    "RSSETSMarker",
+    "ParcelAggregation",
+    "SphereAggregation",
+    "FunctionalConnectivityParcels",
+    "FunctionalConnectivitySpheres",
+    "CrossParcellationFC",
+    "EdgeCentricFCParcels",
+    "EdgeCentricFCSpheres",
+    "ReHoParcels",
+    "ReHoSpheres",
+    "ALFFParcels",
+    "ALFFSpheres",
+    "TemporalSNRParcels",
+    "TemporalSNRSpheres",
+    "BrainPrint",
+]

junifer/markers/base.py

@@ -15,16 +15,22 @@ if TYPE_CHECKING:
     from junifer.storage import BaseFeatureStorage
 
 
+__all__ = ["BaseMarker"]
+
+
 class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
     """Abstract base class for all markers.
 
+    For every interface that is required, one needs to provide a concrete
+    implementation of this abstract class.
+
     Parameters
     ----------
-    on : str or list of str
-        The kind of data to apply the marker to. By default, will work on all
-        available data.
+    on : str or list of str or None, optional
+        The data type to apply the marker on. If None,
+        will work on all available data types (default None).
     name : str, optional
-        The name of the marker. By default, it will use the class name as the
+        The name of the marker. If None, will use the class name as the
         name of the marker (default None).
 
     Raises
@@ -192,17 +198,25 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
         for type_ in self._on:
             if type_ in input.keys():
                 logger.info(f"Computing {type_}")
+                # Get data dict for data type
                 t_input = input[type_]
+                # Pass the other data types as extra input, removing
+                # the current type
                 extra_input = input.copy()
                 extra_input.pop(type_)
+                logger.debug(
+                    f"Extra data type for feature extraction: "
+                    f"{extra_input.keys()}"
+                )
+                # Copy metadata
                 t_meta = t_input["meta"].copy()
                 t_meta["type"] = type_
-
+                # Compute marker
                 t_out = self.compute(input=t_input, extra_input=extra_input)
                 t_out["meta"] = t_meta
-
+                # Update metadata for step
                 self.update_meta(t_out, "marker")
-
+                # Check storage
                 if storage is not None:
                     logger.info(f"Storing in {storage}")
                     self.store(type_=type_, out=t_out, storage=storage)

junifer/markers/brainprint.py

@@ -43,6 +43,9 @@ if TYPE_CHECKING:
     from junifer.storage import BaseFeatureStorage
 
 
+__all__ = ["BrainPrint"]
+
+
 @register_marker
 class BrainPrint(BaseMarker):
     """Class for BrainPrint.

junifer/markers/collection.py

@@ -19,6 +19,9 @@ if TYPE_CHECKING:
     from junifer.datagrabber import BaseDataGrabber
 
 
+__all__ = ["MarkerCollection"]
+
+
 class MarkerCollection:
     """Class for marker collection.