siibra 0.4a81__tar.gz → 0.4a83__tar.gz

{siibra-0.4a81/siibra.egg-info → siibra-0.4a83}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: siibra
-Version: 0.4a81
+Version: 0.4a83
 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-0.4a83/siibra/VERSION

@@ -0,0 +1 @@
+0.4a83

{siibra-0.4a81 → siibra-0.4a83}/siibra/configuration/factory.py

@@ -357,6 +357,7 @@ class Factory:
             anchor=cls.extract_anchor(spec),
             datasets=cls.extract_datasets(spec),
             prerelease=spec.get("prerelease", False),
+            id=spec.get("@id", None),
         )
 
     @classmethod
@@ -368,6 +369,7 @@ class Factory:
             anchor=cls.extract_anchor(spec),
             datasets=cls.extract_datasets(spec),
             prerelease=spec.get("prerelease", False),
+            id=spec.get("@id", None),
         )
 
     @classmethod
@@ -379,6 +381,7 @@ class Factory:
             anchor=cls.extract_anchor(spec),
             datasets=cls.extract_datasets(spec),
             prerelease=spec.get("prerelease", False),
+            id=spec.get("@id", None),
         )
 
     @classmethod
@@ -391,6 +394,7 @@ class Factory:
             anchor=cls.extract_anchor(spec),
             datasets=cls.extract_datasets(spec),
             prerelease=spec.get("prerelease", False),
+            id=spec.get("@id", None),
         )
 
     @classmethod
@@ -404,6 +408,7 @@ class Factory:
             "providers": vol._providers.values(),
             "datasets": cls.extract_datasets(spec),
             "prerelease": spec.get("prerelease", False),
+            "id": spec.get("@id", None),
         }
         modality = spec.get('modality', "")
         if modality == "cell body staining":
@@ -422,6 +427,7 @@ class Factory:
             "providers": vol._providers.values(),
             "datasets": cls.extract_datasets(spec),
             "prerelease": spec.get("prerelease", False),
+            "id": spec.get("@id", None),
         }
         modality = spec.get('modality', "")
         if modality == "cell body staining":
@@ -472,6 +478,7 @@ class Factory:
             "description": spec.get("description", ""),
             "datasets": cls.extract_datasets(spec),
             "prerelease": spec.get("prerelease", False),
+            "id": spec.get("@id", None),
         }
         if modality == "StreamlineCounts":
             return connectivity.StreamlineCounts(**kwargs)
@@ -504,6 +511,7 @@ class Factory:
             "datasets": cls.extract_datasets(spec),
             "timestep": spec.get("timestep", ("1 no_unit")),
             "prerelease": spec.get("prerelease", False),
+            "id": spec.get("@id", None),
         }
         if modality == "Regional BOLD signal":
             kwargs["paradigm"] = spec.get("paradigm", "")

{siibra-0.4a81 → siibra-0.4a83}/siibra/core/concept.py

@@ -101,7 +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-0.4a81 → siibra-0.4a83}/siibra/features/connectivity/regional_connectivity.py

@@ -52,6 +52,7 @@ class RegionalConnectivity(Feature):
         description: str = "",
         datasets: list = [],
         prerelease: bool = False,
+        id: str = None,
     ):
         """
         Construct a parcellation-averaged connectivity matrix.
@@ -86,6 +87,7 @@ class RegionalConnectivity(Feature):
             anchor=anchor,
             datasets=datasets,
             prerelease=prerelease,
+            id=id,
         )
         self.cohort = cohort.upper()
         self._connector = connector

{siibra-0.4a81 → siibra-0.4a83}/siibra/features/feature.py

@@ -94,6 +94,8 @@ class Feature:
         anchor: _anchor.AnatomicalAnchor,
         datasets: List['TypeDataset'] = [],
         prerelease: bool = False,
+        id: str = None,
+
     ):
         """
         Parameters
@@ -111,6 +113,7 @@ class Feature:
         self._anchor_cached = anchor
         self.datasets = datasets
         self._prerelease = prerelease
+        self._id = id
 
     @property
     def modality(self):
@@ -164,7 +167,15 @@ 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:
@@ -247,12 +258,16 @@ class Feature:
 
     @property
     def id(self):
+        if self._id:
+            return self._id
+
         prefix = ''
         for ds in self.datasets:
             if hasattr(ds, "id"):
                 prefix = ds.id + '--'
                 break
-        return prefix + md5(self.name.encode("utf-8")).hexdigest()
+        name_ = self.name.lstrip("[PRERELEASE] ")
+        return prefix + md5(name_.encode("utf-8")).hexdigest()
 
     def _export(self, fh: ZipFile):
         """

{siibra-0.4a81 → siibra-0.4a83}/siibra/features/image/image.py

@@ -63,6 +63,7 @@ class Image(feature.Feature, _volume.Volume):
         region: str = None,
         datasets: List = [],
         prerelease: bool = False,
+        id: str = None,
     ):
         feature.Feature.__init__(
             self,
@@ -71,6 +72,7 @@ class Image(feature.Feature, _volume.Volume):
             anchor=None,  # lazy implementation below!
             datasets=datasets,
             prerelease=prerelease,
+            id=id,
         )
 
         _volume.Volume.__init__(

{siibra-0.4a81 → siibra-0.4a83}/siibra/features/tabular/cell_density_profile.py

@@ -69,6 +69,7 @@ class CellDensityProfile(
         anchor: _anchor.AnatomicalAnchor,
         datasets: list = [],
         prerelease: bool = False,
+        id: str = None,
     ):
         """
         Generate a cell density profile from a URL to a cloud folder
@@ -82,6 +83,7 @@ class CellDensityProfile(
             anchor=anchor,
             datasets=datasets,
             prerelease=prerelease,
+            id=id,
         )
         self._step = 0.01
         self._url = url

{siibra-0.4a81 → siibra-0.4a83}/siibra/features/tabular/cortical_profile.py

@@ -54,6 +54,7 @@ class CorticalProfile(tabular.Tabular):
         boundary_positions: Dict[Tuple[int, int], float] = None,
         datasets: list = [],
         prerelease: bool = False,
+        id: str = None,
     ):
         """Initialize profile.
 
@@ -95,6 +96,7 @@ class CorticalProfile(tabular.Tabular):
             data=None,  # lazy loader below
             datasets=datasets,
             prerelease=prerelease,
+            id=id,
         )
 
     def _check_sanity(self):

{siibra-0.4a81 → siibra-0.4a83}/siibra/features/tabular/layerwise_cell_density.py

@@ -57,6 +57,7 @@ class LayerwiseCellDensity(
         anchor: _anchor.AnatomicalAnchor,
         datasets: list = [],
         prerelease: bool = False,
+        id: str = None,
     ):
         tabular.Tabular.__init__(
             self,
@@ -66,6 +67,7 @@ class LayerwiseCellDensity(
             datasets=datasets,
             data=None,  # lazy loading below
             prerelease=prerelease,
+            id=id,
         )
         self.unit = "# detected cells/0.1mm3"
         self._filepairs = list(zip(segmentfiles, layerfiles))

{siibra-0.4a81 → siibra-0.4a83}/siibra/features/tabular/receptor_density_fingerprint.py

@@ -44,6 +44,7 @@ class ReceptorDensityFingerprint(
         anchor: _anchor.AnatomicalAnchor,
         datasets: list = [],
         prerelease: bool = False,
+        id: str = None,
     ):
         """ Generate a receptor fingerprint from a URL to a .tsv file
         formatted according to the structure used by Palomero-Gallagher et al.
@@ -56,6 +57,7 @@ class ReceptorDensityFingerprint(
             data=None,  # lazy loading below
             datasets=datasets,
             prerelease=prerelease,
+            id=id,
         )
         self._loader = requests.HttpRequest(tsvfile)
 

{siibra-0.4a81 → siibra-0.4a83}/siibra/features/tabular/receptor_density_profile.py

@@ -41,6 +41,7 @@ class ReceptorDensityProfile(
         anchor: _anchor.AnatomicalAnchor,
         datasets: list = [],
         prerelease: bool = False,
+        id: str = None,
     ):
         """Generate a receptor density profile from a URL to a .tsv file
         formatted according to the structure used by Palomero-Gallagher et al.
@@ -52,6 +53,7 @@ class ReceptorDensityProfile(
             anchor=anchor,
             datasets=datasets,
             prerelease=prerelease,
+            id=id
         )
         self.type = receptor
         self._data_cached = None

{siibra-0.4a81 → siibra-0.4a83}/siibra/features/tabular/regional_timeseries_activity.py

@@ -49,6 +49,7 @@ class RegionalTimeseriesActivity(tabular.Tabular):
         datasets: list = [],
         paradigm: str = "",
         prerelease: bool = False,
+        id: str = None,
     ):
         """
         """
@@ -59,7 +60,8 @@ class RegionalTimeseriesActivity(tabular.Tabular):
             anchor=anchor,
             datasets=datasets,
             data=None,  # lazy loading below
-            prerelease=prerelease
+            prerelease=prerelease,
+            id=id,
         )
         self.cohort = cohort.upper()
         self._connector = connector

{siibra-0.4a81 → siibra-0.4a83}/siibra/features/tabular/tabular.py

@@ -46,6 +46,7 @@ class Tabular(feature.Feature):
         data: pd.DataFrame,  # sample x feature dimension
         datasets: list = [],
         prerelease: bool = False,
+        id: str = None,
     ):
         feature.Feature.__init__(
             self,
@@ -54,6 +55,7 @@ class Tabular(feature.Feature):
             anchor=anchor,
             datasets=datasets,
             prerelease=prerelease,
+            id=id,
         )
         self._data_cached = data
 

{siibra-0.4a81 → siibra-0.4a83}/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-0.4a81 → siibra-0.4a83/siibra.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: siibra
-Version: 0.4a81
+Version: 0.4a83
 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-0.4a81/siibra/VERSION

@@ -1 +0,0 @@
-0.4a81