siibra 0.4a80__tar.gz → 0.4a82__tar.gz

{siibra-0.4a80/siibra.egg-info → siibra-0.4a82}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: siibra
-Version: 0.4a80
+Version: 0.4a82
 Summary: siibra - Software interfaces for interacting with brain atlases
 Home-page: https://github.com/FZJ-INM1-BDA/siibra-python
 Author: Big Data Analytics Group, Forschungszentrum Juelich, Institute of Neuroscience and Medicine (INM-1)

siibra-0.4a82/siibra/VERSION

@@ -0,0 +1 @@
+0.4a82

{siibra-0.4a80 → siibra-0.4a82}/siibra/configuration/factory.py

@@ -187,6 +187,7 @@ class Factory:
             modality=spec.get("modality"),
             publications=spec.get("publications", []),
             datasets=cls.extract_datasets(spec),
+            prerelease=spec.get("prerelease", False),
         )
 
     @classmethod
@@ -200,6 +201,7 @@ class Factory:
             datasets=cls.extract_datasets(spec),
             rgb=spec.get("rgb", None),
             spec=spec,
+            prerelease=spec.get("prerelease", False),
         )
 
     @classmethod
@@ -222,6 +224,7 @@ class Factory:
             modality=spec.get('modality', ""),
             publications=spec.get("publications", []),
             datasets=cls.extract_datasets(spec),
+            prerelease=spec.get("prerelease", False),
         )
 
         # add version object, if any is specified
@@ -299,7 +302,8 @@ class Factory:
             description=spec.get("description"),
             modality=spec.get("modality"),
             publications=spec.get("publications", []),
-            datasets=cls.extract_datasets(spec)
+            datasets=cls.extract_datasets(spec),
+            prerelease=spec.get("prerelease", False),
         )
 
     @classmethod
@@ -352,6 +356,7 @@ class Factory:
             tsvfile=spec['file'],
             anchor=cls.extract_anchor(spec),
             datasets=cls.extract_datasets(spec),
+            prerelease=spec.get("prerelease", False),
         )
 
     @classmethod
@@ -362,6 +367,7 @@ class Factory:
             layerfiles=spec['layerfiles'],
             anchor=cls.extract_anchor(spec),
             datasets=cls.extract_datasets(spec),
+            prerelease=spec.get("prerelease", False),
         )
 
     @classmethod
@@ -372,6 +378,7 @@ class Factory:
             tsvfile=spec['file'],
             anchor=cls.extract_anchor(spec),
             datasets=cls.extract_datasets(spec),
+            prerelease=spec.get("prerelease", False),
         )
 
     @classmethod
@@ -383,6 +390,7 @@ class Factory:
             url=spec['file'],
             anchor=cls.extract_anchor(spec),
             datasets=cls.extract_datasets(spec),
+            prerelease=spec.get("prerelease", False),
         )
 
     @classmethod
@@ -395,6 +403,7 @@ class Factory:
             "space_spec": vol._space_spec,
             "providers": vol._providers.values(),
             "datasets": cls.extract_datasets(spec),
+            "prerelease": spec.get("prerelease", False),
         }
         modality = spec.get('modality', "")
         if modality == "cell body staining":
@@ -412,6 +421,7 @@ class Factory:
             "space_spec": vol._space_spec,
             "providers": vol._providers.values(),
             "datasets": cls.extract_datasets(spec),
+            "prerelease": spec.get("prerelease", False),
         }
         modality = spec.get('modality', "")
         if modality == "cell body staining":
@@ -461,6 +471,7 @@ class Factory:
             "anchor": cls.extract_anchor(spec),
             "description": spec.get("description", ""),
             "datasets": cls.extract_datasets(spec),
+            "prerelease": spec.get("prerelease", False),
         }
         if modality == "StreamlineCounts":
             return connectivity.StreamlineCounts(**kwargs)
@@ -491,7 +502,8 @@ class Factory:
             "anchor": cls.extract_anchor(spec),
             "description": spec.get("description", ""),
             "datasets": cls.extract_datasets(spec),
-            "timestep": spec.get("timestep", ("1 no_unit"))
+            "timestep": spec.get("timestep", ("1 no_unit")),
+            "prerelease": spec.get("prerelease", False),
         }
         if modality == "Regional BOLD signal":
             kwargs["paradigm"] = spec.get("paradigm", "")

{siibra-0.4a80 → siibra-0.4a82}/siibra/core/atlas.py

@@ -30,14 +30,15 @@ class Atlas(concept.AtlasConcept, configuration_folder="atlases"):
     spaces, as well as common functionalities of those.
     """
 
-    def __init__(self, identifier: str, name: str, species: Species):
+    def __init__(self, identifier: str, name: str, species: Species, prerelease: bool = False):
         """Construct an empty atlas object with a name and identifier."""
 
         concept.AtlasConcept.__init__(
             self,
             identifier=identifier,
             name=name,
-            species=species
+            species=species,
+            prerelease=prerelease
         )
         self._parcellation_ids: List[str] = []
         self._space_ids: List[str] = []

{siibra-0.4a80 → siibra-0.4a82}/siibra/core/concept.py

@@ -51,7 +51,8 @@ class AtlasConcept:
         modality: str = "",
         publications: List[TypePublication] = [],
         datasets: List['TypeDataset'] = [],
-        spec=None
+        spec=None,
+        prerelease: bool = False,
     ):
         """
         Construct a new atlas concept base object.
@@ -78,7 +79,7 @@ class AtlasConcept:
             The preconfigured specification.
         """
         self._id = identifier
-        self.name = name
+        self.name = name if not prerelease else f"[PRERELEASE] {name}"
         self._species_cached = None if species is None \
             else Species.decode(species)  # overwritable property implementation below
         self.shortname = shortname
@@ -87,6 +88,7 @@ class AtlasConcept:
         self._publications = publications
         self.datasets = datasets
         self._spec = spec
+        self._prerelease = prerelease
 
     @property
     def description(self):
@@ -99,7 +101,15 @@ class AtlasConcept:
 
     @property
     def LICENSE(self) -> str:
-        return '\n'.join([ds.LICENSE for ds in self.datasets])
+        licenses = []
+        for ds in self.datasets:
+            if ds.LICENSE is None or ds.LICENSE == "No license information is found.":
+                continue
+            if isinstance(ds.LICENSE, str):
+                licenses.append(ds.LICENSE)
+            if isinstance(ds.LICENSE, list):
+                licenses.extend(ds.LICENSE)
+        return '\n'.join(licenses)
 
     @property
     def doi_or_url(self) -> str:

{siibra-0.4a80 → siibra-0.4a82}/siibra/core/parcellation.py

@@ -82,6 +82,7 @@ class Parcellation(region.Region, configuration_folder="parcellations"):
         modality: str = None,
         publications: list = [],
         datasets: list = [],
+        prerelease: bool = False,
     ):
         """
         Constructs a new parcellation object.
@@ -118,7 +119,8 @@ class Parcellation(region.Region, configuration_folder="parcellations"):
             description=description,
             publications=publications,
             datasets=datasets,
-            modality=modality
+            modality=modality,
+            prerelease=prerelease,
         )
         self._species_cached = Species.decode(species)
         self._id = identifier

{siibra-0.4a80 → siibra-0.4a82}/siibra/core/region.py

@@ -82,6 +82,7 @@ class Region(anytree.NodeMixin, concept.AtlasConcept):
         datasets: list = [],
         rgb: str = None,
         spec=None,
+        prerelease: bool = False,
     ):
         """
         Constructs a new Region object.
@@ -119,7 +120,8 @@ class Region(anytree.NodeMixin, concept.AtlasConcept):
             modality=modality,
             publications=publications,
             datasets=datasets,
-            spec=spec
+            spec=spec,
+            prerelease=prerelease,
         )
 
         # anytree node will take care to use this appropriately

{siibra-0.4a80 → siibra-0.4a82}/siibra/core/space.py

@@ -39,6 +39,7 @@ class Space(AtlasConcept, configuration_folder="spaces"):
         modality: str = "",
         publications: list = [],
         datasets: list = [],
+        prerelease: bool = False,
     ):
         """
         Constructs a new parcellation object.
@@ -76,6 +77,7 @@ class Space(AtlasConcept, configuration_folder="spaces"):
             modality=modality,
             publications=publications,
             datasets=datasets,
+            prerelease=prerelease,
         )
         self.volumes = volumes
         for v in self.volumes:

{siibra-0.4a80 → siibra-0.4a82}/siibra/features/connectivity/regional_connectivity.py

@@ -51,6 +51,7 @@ class RegionalConnectivity(Feature):
         anchor: _anchor.AnatomicalAnchor,
         description: str = "",
         datasets: list = [],
+        prerelease: bool = False,
     ):
         """
         Construct a parcellation-averaged connectivity matrix.
@@ -84,6 +85,7 @@ class RegionalConnectivity(Feature):
             description=description or '\n'.join({ds.description for ds in datasets}),
             anchor=anchor,
             datasets=datasets,
+            prerelease=prerelease,
         )
         self.cohort = cohort.upper()
         self._connector = connector

{siibra-0.4a80 → siibra-0.4a82}/siibra/features/feature.py

@@ -26,8 +26,8 @@ from collections import defaultdict
 from zipfile import ZipFile
 
 if TYPE_CHECKING:
-    from ..retrieval.datasets import EbrainsDataset
-    TypeDataset = EbrainsDataset
+    from ..retrieval.datasets import EbrainsBaseDataset
+    TypeDataset = EbrainsBaseDataset
 
 
 class ParseLiveQueryIdException(Exception):
@@ -92,7 +92,8 @@ class Feature:
         modality: str,
         description: str,
         anchor: _anchor.AnatomicalAnchor,
-        datasets: List['TypeDataset'] = []
+        datasets: List['TypeDataset'] = [],
+        prerelease: bool = False,
     ):
         """
         Parameters
@@ -109,6 +110,7 @@ class Feature:
         self._description = description
         self._anchor_cached = anchor
         self.datasets = datasets
+        self._prerelease = prerelease
 
     @property
     def modality(self):
@@ -162,7 +164,15 @@ class Feature:
 
     @property
     def LICENSE(self) -> str:
-        return '\n'.join([ds.LICENSE for ds in self.datasets])
+        licenses = []
+        for ds in self.datasets:
+            if ds.LICENSE is None or ds.LICENSE == "No license information is found.":
+                continue
+            if isinstance(ds.LICENSE, str):
+                licenses.append(ds.LICENSE)
+            if isinstance(ds.LICENSE, list):
+                licenses.extend(ds.LICENSE)
+        return '\n'.join(licenses)
 
     @property
     def doi_or_url(self) -> str:
@@ -183,7 +193,8 @@ class Feature:
     @property
     def name(self):
         """Returns a short human-readable name of this feature."""
-        return f"{self.__class__.__name__} ({self.modality}) anchored at {self.anchor}"
+        name_ = f"{self.__class__.__name__} ({self.modality}) anchored at {self.anchor}"
+        return name_ if not self._prerelease else f"[PRERELEASE] {name_}"
 
     @classmethod
     def get_instances(cls, **kwargs) -> List['Feature']:

{siibra-0.4a80 → siibra-0.4a82}/siibra/features/image/image.py

@@ -62,13 +62,15 @@ class Image(feature.Feature, _volume.Volume):
         providers: List[_volume.VolumeProvider],
         region: str = None,
         datasets: List = [],
+        prerelease: bool = False,
     ):
         feature.Feature.__init__(
             self,
             modality=modality,
             description=None,  # lazy implementation below!
             anchor=None,  # lazy implementation below!
-            datasets=datasets
+            datasets=datasets,
+            prerelease=prerelease,
         )
 
         _volume.Volume.__init__(

{siibra-0.4a80 → siibra-0.4a82}/siibra/features/tabular/cell_density_profile.py

@@ -67,7 +67,8 @@ class CellDensityProfile(
         patch: int,
         url: str,
         anchor: _anchor.AnatomicalAnchor,
-        datasets: list = []
+        datasets: list = [],
+        prerelease: bool = False,
     ):
         """
         Generate a cell density profile from a URL to a cloud folder
@@ -80,6 +81,7 @@ class CellDensityProfile(
             unit="detected cells / 0.1mm3",
             anchor=anchor,
             datasets=datasets,
+            prerelease=prerelease,
         )
         self._step = 0.01
         self._url = url

{siibra-0.4a80 → siibra-0.4a82}/siibra/features/tabular/cortical_profile.py

@@ -52,7 +52,8 @@ class CorticalProfile(tabular.Tabular):
         values: Union[list, np.ndarray] = None,
         unit: str = None,
         boundary_positions: Dict[Tuple[int, int], float] = None,
-        datasets: list = []
+        datasets: list = [],
+        prerelease: bool = False,
     ):
         """Initialize profile.
 
@@ -92,7 +93,8 @@ class CorticalProfile(tabular.Tabular):
             description=description,
             anchor=anchor,
             data=None,  # lazy loader below
-            datasets=datasets
+            datasets=datasets,
+            prerelease=prerelease,
         )
 
     def _check_sanity(self):

{siibra-0.4a80 → siibra-0.4a82}/siibra/features/tabular/layerwise_cell_density.py

@@ -56,6 +56,7 @@ class LayerwiseCellDensity(
         layerfiles: list,
         anchor: _anchor.AnatomicalAnchor,
         datasets: list = [],
+        prerelease: bool = False,
     ):
         tabular.Tabular.__init__(
             self,
@@ -63,7 +64,8 @@ class LayerwiseCellDensity(
             modality="Cell body density",
             anchor=anchor,
             datasets=datasets,
-            data=None  # lazy loading below
+            data=None,  # lazy loading below
+            prerelease=prerelease,
         )
         self.unit = "# detected cells/0.1mm3"
         self._filepairs = list(zip(segmentfiles, layerfiles))

{siibra-0.4a80 → siibra-0.4a82}/siibra/features/tabular/receptor_density_fingerprint.py

@@ -42,7 +42,8 @@ class ReceptorDensityFingerprint(
         self,
         tsvfile: str,
         anchor: _anchor.AnatomicalAnchor,
-        datasets: list = []
+        datasets: list = [],
+        prerelease: bool = False,
     ):
         """ Generate a receptor fingerprint from a URL to a .tsv file
         formatted according to the structure used by Palomero-Gallagher et al.
@@ -54,6 +55,7 @@ class ReceptorDensityFingerprint(
             anchor=anchor,
             data=None,  # lazy loading below
             datasets=datasets,
+            prerelease=prerelease,
         )
         self._loader = requests.HttpRequest(tsvfile)
 

{siibra-0.4a80 → siibra-0.4a82}/siibra/features/tabular/receptor_density_profile.py

@@ -39,7 +39,8 @@ class ReceptorDensityProfile(
         receptor: str,
         tsvfile: str,
         anchor: _anchor.AnatomicalAnchor,
-        datasets: list = []
+        datasets: list = [],
+        prerelease: bool = False,
     ):
         """Generate a receptor density profile from a URL to a .tsv file
         formatted according to the structure used by Palomero-Gallagher et al.
@@ -50,6 +51,7 @@ class ReceptorDensityProfile(
             modality=f"{receptor} receptor density",
             anchor=anchor,
             datasets=datasets,
+            prerelease=prerelease,
         )
         self.type = receptor
         self._data_cached = None

{siibra-0.4a80 → siibra-0.4a82}/siibra/features/tabular/regional_timeseries_activity.py

@@ -47,7 +47,8 @@ class RegionalTimeseriesActivity(tabular.Tabular):
         timestep: str,
         description: str = "",
         datasets: list = [],
-        paradigm: str = ""
+        paradigm: str = "",
+        prerelease: bool = False,
     ):
         """
         """
@@ -57,7 +58,8 @@ class RegionalTimeseriesActivity(tabular.Tabular):
             description=description or '\n'.join({ds.description for ds in datasets}),
             anchor=anchor,
             datasets=datasets,
-            data=None  # lazy loading below
+            data=None,  # lazy loading below
+            prerelease=prerelease
         )
         self.cohort = cohort.upper()
         self._connector = connector

{siibra-0.4a80 → siibra-0.4a82}/siibra/features/tabular/tabular.py

@@ -44,14 +44,16 @@ class Tabular(feature.Feature):
         modality: str,
         anchor: _anchor.AnatomicalAnchor,
         data: pd.DataFrame,  # sample x feature dimension
-        datasets: list = []
+        datasets: list = [],
+        prerelease: bool = False,
     ):
         feature.Feature.__init__(
             self,
             modality=modality,
             description=description,
             anchor=anchor,
-            datasets=datasets
+            datasets=datasets,
+            prerelease=prerelease,
         )
         self._data_cached = data
 

{siibra-0.4a80 → siibra-0.4a82}/siibra/livequeries/bigbrain.py

@@ -21,6 +21,7 @@ from ..commons import logger
 from ..locations import point, pointset
 from ..core import region
 from ..retrieval import requests, cache
+from ..retrieval.datasets import GenericDataset
 
 import numpy as np
 from typing import List
@@ -36,6 +37,37 @@ class WagstylProfileLoader:
     _profiles = None
     _vertices = None
     _boundary_depths = None
+    DATASET = GenericDataset(
+        name="HIBALL workshop on cortical layers",
+        contributors=[
+            'Konrad Wagstyl',
+            'Stéphanie Larocque',
+            'Guillem Cucurull',
+            'Claude Lepage',
+            'Joseph Paul Cohen',
+            'Sebastian Bludau',
+            'Nicola Palomero-Gallagher',
+            'Lindsay B. Lewis',
+            'Thomas Funck',
+            'Hannah Spitzer',
+            'Timo Dickscheid',
+            'Paul C. Fletcher',
+            'Adriana Romero',
+            'Karl Zilles',
+            'Katrin Amunts',
+            'Yoshua Bengio',
+            'Alan C. Evans'
+        ],
+        url="https://github.com/kwagstyl/cortical_layers_tutorial/",
+        description="Cortical profiles of BigBrain staining intensities computed by Konrad Wagstyl, "
+        "as described in the publication 'Wagstyl, K., et al (2020). BigBrain 3D atlas of "
+        "cortical layers: Cortical and laminar thickness gradients diverge in sensory and "
+        "motor cortices. PLoS Biology, 18(4), e3000678. "
+        "http://dx.doi.org/10.1371/journal.pbio.3000678."
+        "The data is taken from the tutorial at "
+        "https://github.com/kwagstyl/cortical_layers_tutorial. Each vertex is "
+        "assigned to the regional map when queried."
+    )
 
     def __init__(self):
         if self._profiles is None:
@@ -174,6 +206,7 @@ class BigBrainProfileQuery(query.LiveQuery, args=[], FeatureType=bigbrain_intens
                     boundaries=boundary_depths[i, :],
                     location=point.Point(coords[i, :], 'bigbrain')  # points are warped into BigBrain
                 )
+                prof.datasets = [WagstylProfileLoader.DATASET]
                 result.append(prof)
 
         return result
@@ -216,6 +249,7 @@ class LayerwiseBigBrainIntensityQuery(query.LiveQuery, args=[], FeatureType=laye
                 stds=[matched_profiles[layer_labels == layer].std() for layer in range(1, 7)],
             )
             assert fp.matches(subregion)  # to create an assignment result
+            fp.datasets = [WagstylProfileLoader.DATASET]
             result.append(fp)
 
         return result

{siibra-0.4a80 → siibra-0.4a82}/siibra/retrieval/datasets.py

@@ -56,6 +56,10 @@ class EbrainsBaseDataset(ABC):
     def name(self) -> str:
         raise NotImplementedError
 
+    @abstractproperty
+    def LICENSE(self) -> List[str]:
+        raise NotImplementedError
+
     @abstractproperty
     def urls(self) -> List[EbrainsDatasetUrl]:
         raise NotImplementedError

{siibra-0.4a80 → siibra-0.4a82}/siibra/volumes/parcellationmap.py

@@ -87,6 +87,7 @@ class Map(concept.AtlasConcept, configuration_folder="maps"):
         modality: str = None,
         publications: list = [],
         datasets: list = [],
+        prerelease: bool = False,
     ):
         """
         Constructs a new parcellation object.
@@ -131,7 +132,8 @@ class Map(concept.AtlasConcept, configuration_folder="maps"):
             description=description,
             publications=publications,
             datasets=datasets,
-            modality=modality
+            modality=modality,
+            prerelease=prerelease,
         )
 
         # Since the volumes might include 4D arrays, where the actual

{siibra-0.4a80 → siibra-0.4a82}/siibra/volumes/sparsemap.py

@@ -225,7 +225,8 @@ class SparseMap(parcellationmap.Map):
         description: str = "",
         modality: str = None,
         publications: list = [],
-        datasets: list = []
+        datasets: list = [],
+        prerelease: bool = False,
     ):
         parcellationmap.Map.__init__(
             self,
@@ -240,6 +241,7 @@ class SparseMap(parcellationmap.Map):
             publications=publications,
             datasets=datasets,
             volumes=volumes,
+            prerelease=prerelease,
         )
         self._sparse_index_cached = None
 

{siibra-0.4a80 → siibra-0.4a82}/siibra/volumes/volume.py

@@ -202,6 +202,19 @@ class Volume:
         else:
             raise ValueError(f"Invalid format requested: {format}")
 
+        # ensure the voi is inside the template
+        voi = kwargs.get("voi", None)
+        if isinstance(voi, _boundingbox.BoundingBox) and voi.space is not None:
+            tmplt_bbox = voi.space.get_template().boundingbox
+            intersection_bbox = voi.intersection(tmplt_bbox)
+            if intersection_bbox is None:
+                raise RuntimeError(f"voi provided ({voi}) lies out side the voxel space of the {voi.space.name} template.")
+            if intersection_bbox.minpoint != voi.minpoint or intersection_bbox.maxpoint != voi.maxpoint:
+                logger.info(
+                    f"Since provided voi lies outside the template ({voi.space}) it is clipped as: {intersection_bbox}"
+                )
+                kwargs["voi"] = intersection_bbox
+
         # try the selected format only
         for try_count in range(6):
             try:

{siibra-0.4a80 → siibra-0.4a82/siibra.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: siibra
-Version: 0.4a80
+Version: 0.4a82
 Summary: siibra - Software interfaces for interacting with brain atlases
 Home-page: https://github.com/FZJ-INM1-BDA/siibra-python
 Author: Big Data Analytics Group, Forschungszentrum Juelich, Institute of Neuroscience and Medicine (INM-1)

siibra-0.4a80/siibra/VERSION

@@ -1 +0,0 @@
-0.4a80