siibra 0.4a81__py3-none-any.whl → 0.4a83__py3-none-any.whl

siibra/VERSION

@@ -1 +1 @@
-0.4a81
+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/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/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/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/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/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/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/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/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/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/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/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/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.dist-info → siibra-0.4a83.dist-info}/METADATA

@@ -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.dist-info → siibra-0.4a83.dist-info}/RECORD

@@ -1,12 +1,12 @@
-siibra/VERSION,sha256=g9_JjItOuWjJl9d8unj9O6xgS_VZXN39CB-ynWiIXYc,7
+siibra/VERSION,sha256=8xHFBd8hW3Lc4HP4uzf7eTsjIPJ4yAQgkM8B6QBMfSU,7
 siibra/__init__.py,sha256=qBxxMRyl9RojNt0twQr2LDk1Nyk5eNsPHFxxoIwnpx4,4540
 siibra/commons.py,sha256=PImsqrZBp2Mn_9ZEJOxEOd4i-w_HPMv4sUcHCtN9cPw,25868
 siibra/configuration/__init__.py,sha256=-_Kuf0TfMEdFXiSCTAdcHUL_krA8-cxhJypSNNay53Q,752
 siibra/configuration/configuration.py,sha256=x06QsaqGQbce1d9TuFCCYEgMWJBlLbkt8B3zTfYz5RE,6887
-siibra/configuration/factory.py,sha256=CxJWspLpXPJWB2zeNqgd-2OcyA_tkwTS9IfRmiM5Gao,20585
+siibra/configuration/factory.py,sha256=fpeyl3BbeDsjBdtqd9gNdQ_gEFuZQ1qUmDXYA5rB8Wg,20901
 siibra/core/__init__.py,sha256=z22elfoi5_TscUb17-pBoGyfT_q9PQpvgOgSLEJe2WE,916
 siibra/core/atlas.py,sha256=YwhVWAIT0XGfzKjSuQUNpljdIE4VP4crNQ3VNfTrgKg,7868
-siibra/core/concept.py,sha256=qkxWbfbPStUVN6OL88o5LaQyi4m34xHWtaA1FiHUZsY,9279
+siibra/core/concept.py,sha256=rKR7FO1HaFdy076Dy0y9Bjcdu_tcYUHbxLYNZxH7XTY,9595
 siibra/core/parcellation.py,sha256=f5UEeXWQ3-dsU1YKswXL9nvCPyWSwp0rMqEUlMt8hxw,13951
 siibra/core/region.py,sha256=jp44pOnuazzgpSlbGMjJ0-7xXOJHUYXg4YakXrbbVoM,32887
 siibra/core/relation_qualification.py,sha256=EUU9EPkV0mdCjGUU2hki1rQ5R5U4X2YoFmvwOirO2_E,3641
@@ -16,30 +16,30 @@ siibra/explorer/url.py,sha256=mUAFN7OHfLELfdqqJmSdAkmXJjKCv6Qh5RHtyxNQjfo,5868
 siibra/explorer/util.py,sha256=Z2ruicDL3S_qcxhHHW0GF1q5-r963tJpzgtQmAn8YSM,1424
 siibra/features/__init__.py,sha256=Y5q2M7HoToTcfAdO50jmnPGZybJOi5GyEcbxQRscJjo,1518
 siibra/features/anchor.py,sha256=1w9VuSEWC3oapph8GtbsW26kvMcE7_9ik7281oRMjlE,14245
-siibra/features/feature.py,sha256=4P9g01TALfZhbl2j9Ze11XrtaMnnYFr7vWa7cFPGp3k,20019
+siibra/features/feature.py,sha256=YdIBmyJYFlJby6oIXxK1zFV6FJVr3_eygDynCLCe7vk,20478
 siibra/features/connectivity/__init__.py,sha256=ybKN9OfmabSeTx1I6WSrULu5dT6raefty8QB2XaiUrE,1077
 siibra/features/connectivity/functional_connectivity.py,sha256=AkRYufi4r3CeV50FLaI6kjKraQ4t9G58iPn521HRRGk,1407
-siibra/features/connectivity/regional_connectivity.py,sha256=hK372Dhn-Bn8ALj-Gmwm1sv9HjKXfznOsHfRVNmGcO0,15360
+siibra/features/connectivity/regional_connectivity.py,sha256=PlMO13p9uYB1h72qVPRKqDkyHEtkbWLLD3yxYGz4twU,15403
 siibra/features/connectivity/streamline_counts.py,sha256=ngl7xCiCUOyflyBvjZYa3ShOmtf21E5e0A_BeWfFtSQ,1064
 siibra/features/connectivity/streamline_lengths.py,sha256=0a09Dag-eRvs1KgHSU47I3xQwbgHICsDozhZyuNzQME,1067
 siibra/features/connectivity/tracing_connectivity.py,sha256=pyTMTLvkJL3ftk56s0AbT8dHexV4EyuTJ2yX27kLGfc,1083
 siibra/features/dataset/__init__.py,sha256=5h_wstfa3h35emL1qoKOtcFOiIjKZX9oIy-GwsChEyc,748
 siibra/features/dataset/ebrains.py,sha256=wdb1-4ovHE1duw2a9NSU0PYgqnlt8-f4pLsGwfTa8xw,2542
 siibra/features/image/__init__.py,sha256=UIECVLwKYKeuCPNa4WcjcLDuNr_3JxCyiOQSjBRf36U,1013
-siibra/features/image/image.py,sha256=rr9sF2PZbmTgeGRASdIB-sl-3dBYYr5SJfrUnj1xygM,3305
+siibra/features/image/image.py,sha256=1K4u6X6q2CV8avguE56LQQSe5ziahnLr8QFIdvMmFKE,3348
 siibra/features/image/sections.py,sha256=d4TQSs6nIKQ5vgi89htERfWOMgnvOA9k4LhaXBMWNbE,961
 siibra/features/image/volume_of_interest.py,sha256=DIv9GNOptfungLddA_CfrrCfY8p36rbWCT9xkE6K66w,2654
 siibra/features/tabular/__init__.py,sha256=3DBwa8JtGd-npeOyyw6kJzcveKXadbqSATyJtTnY3-w,1176
 siibra/features/tabular/bigbrain_intensity_profile.py,sha256=-dXzznb6r1BhMjE8jOeugbZ3MjXo0AJkTtOw25SehYs,2238
-siibra/features/tabular/cell_density_profile.py,sha256=RmeROeC76QOqc0D9z2QsFGWCqF3OtT55NJs65D3ii3k,9166
-siibra/features/tabular/cortical_profile.py,sha256=tf5RSILGSvqc4QbWgQPkl9r5bKLGiHvEX0z53_A73D8,9620
+siibra/features/tabular/cell_density_profile.py,sha256=QICybWoFvyzyH0sVA79Q8WUEmXZLyIdge6arfOLkV78,9209
+siibra/features/tabular/cortical_profile.py,sha256=xxJ3vwqBxGg0X2g_Zoslj6v12hNc-iPMlKkGBRjifgs,9663
 siibra/features/tabular/gene_expression.py,sha256=YqUicjGC0rkPXSWZwJtUjgxCIcfekeGk9nkWT0EZceE,4965
 siibra/features/tabular/layerwise_bigbrain_intensities.py,sha256=w6AxLPyUxHBOQlkNPgr4O4xARTzmmXenEHA0nbUDgbo,2161
-siibra/features/tabular/layerwise_cell_density.py,sha256=x0--ySigfrkCjuyU54bmqzC89Hj2ceXGUd6ij0FXBEE,4237
-siibra/features/tabular/receptor_density_fingerprint.py,sha256=yXCtWypgs6M6_ItgK63wRVymstweSRnR_OUU01TMfu0,7234
-siibra/features/tabular/receptor_density_profile.py,sha256=XBxNvUf9RyDpDx7fLBN_aOEZOKtT2KX3livrE0C1Nn8,3647
-siibra/features/tabular/regional_timeseries_activity.py,sha256=jNqGK6sNM5E5Mp_UeuPA-BZ31yX6Osi7_TQPSyynLGE,9018
-siibra/features/tabular/tabular.py,sha256=Yjxg-CRFNdSGUeQ9wzDU0XJL2nXqGUVHZr129c8X4Io,5072
+siibra/features/tabular/layerwise_cell_density.py,sha256=FHIG4YfVkVFq466bZU_6UN-OqSlW1lV97B_hgAqqGwg,4280
+siibra/features/tabular/receptor_density_fingerprint.py,sha256=3aH7hepvx1Qx-qpqA5hV2Qv_e6vF32pfpf-JFpLq1s0,7277
+siibra/features/tabular/receptor_density_profile.py,sha256=yNczKA0OnEro01fIbQMtaKY936YlWbHQTsYtaCKDjJo,3689
+siibra/features/tabular/regional_timeseries_activity.py,sha256=9ZXAewiStc28ef3EN4qUoEX7em77aR9TbBpr7kDeqGg,9062
+siibra/features/tabular/tabular.py,sha256=kqlSWJzK95Ft9UbXaPIBkxJZQwO1ss42gHdOMflbwZY,5115
 siibra/livequeries/__init__.py,sha256=rpJKroYqtujIkvAUlavOIHUlP4Yg73U27Se44aZms2Q,1013
 siibra/livequeries/allen.py,sha256=a0-F1Wk8ocJcJBm1pZLv9BvHjdv2iPeM56xmkN-g-r4,12252
 siibra/livequeries/bigbrain.py,sha256=4HPBWCiciAdDgItaiQDY85ZVFBtcrBzp1oOAYCL3ldg,9935
@@ -52,7 +52,7 @@ siibra/locations/point.py,sha256=ZPfjcGgxBvZrXNJ7HA4qLk9xr-0ZlA2Nj_5z8w4IZzw,126
 siibra/locations/pointset.py,sha256=Wp-qlU3hdlLlEc3WU-QodpL_70It7GQf9FctnYLXsQI,7159
 siibra/retrieval/__init__.py,sha256=pAJ2WsNk9tVY1RddmXzya1iFgJXJarO4TVCJTob1Ej0,1062
 siibra/retrieval/cache.py,sha256=9Wssws2YHiI_OW4EZp72OzYV9nw8h5cAEAakSxtRMts,5143
-siibra/retrieval/datasets.py,sha256=hmzTIAJ50fK302crWXlNjA27NrVNBdks8xTx8tb2uvM,11174
+siibra/retrieval/datasets.py,sha256=zDiSgbmL6aqnZpYrJMcfbv2c_Kh-2KMwmHQTJkdF9GM,11267
 siibra/retrieval/repositories.py,sha256=wYE3oYcIBgD3WOqIerS3darsg_TSrfpdDJ72l2uytak,25961
 siibra/retrieval/requests.py,sha256=tRmgocvob7619e_4Vw-dVd8R3JJ95UGkVyESXF2EBE0,22013
 siibra/retrieval/exceptions/__init__.py,sha256=_w996kp5rxuvi-_iLhrByrH2OtApxm_TykthkaQvKpo,874
@@ -67,8 +67,8 @@ siibra/volumes/nifti.py,sha256=nGSCedjpsiy43XIiHQ2SRy9rPRK8Ci9QDq4AHKclCck,9030
 siibra/volumes/parcellationmap.py,sha256=phoMzNLI3Ig9rWvuD_c1yBm3ejLxAJGXtTHMXqw-ivc,44243
 siibra/volumes/sparsemap.py,sha256=j41ozLSgKri68-KDsqo46gEs4lT4aYsf2yMF4l-ruCo,21752
 siibra/volumes/volume.py,sha256=h_KrdDkpeoENnOrE7BlTZNXaZQGTrJXHX0eSyArxF-4,11667
-siibra-0.4a81.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-siibra-0.4a81.dist-info/METADATA,sha256=tVcIwpPs7lmGR0VaD7guc8dlw8PQoI1RiMJ7RUpfvG0,8328
-siibra-0.4a81.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-siibra-0.4a81.dist-info/top_level.txt,sha256=NF0OSGLL0li2qyC7MaU0iBB5Y9S09_euPpvisD0-8Hg,7
-siibra-0.4a81.dist-info/RECORD,,
+siibra-0.4a83.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+siibra-0.4a83.dist-info/METADATA,sha256=GTH5UFZL3sWOPTnHxwXGpUiNCpd9G6t73mtDiMuIZYE,8328
+siibra-0.4a83.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
+siibra-0.4a83.dist-info/top_level.txt,sha256=NF0OSGLL0li2qyC7MaU0iBB5Y9S09_euPpvisD0-8Hg,7
+siibra-0.4a83.dist-info/RECORD,,

{siibra-0.4a81.dist-info → siibra-0.4a83.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.1.0)
+Generator: setuptools (75.2.0)
 Root-Is-Purelib: true
 Tag: py3-none-any