parse prerelease tag for AtlasConcepts and Features

Author: AhmetNSimsek

siibra/configuration/factory.py

@@ -180,6 +180,7 @@ def build_atlas(cls, spec):
             spec["@id"],
             spec["name"],
             species=Species.decode(spec.get('species')),
+            prerelease=spec.get("prerelease", False),
         )
         for space_id in spec["spaces"]:
             a._register_space(space_id)
@@ -200,6 +201,7 @@ def build_space(cls, spec):
             modality=spec.get("modality"),
             publications=spec.get("publications", []),
             datasets=cls.extract_datasets(spec),
+            prerelease=spec.get("prerelease", False),
         )
 
     @classmethod
@@ -213,6 +215,7 @@ def build_region(cls, spec):
             datasets=cls.extract_datasets(spec),
             rgb=spec.get("rgb", None),
             spec=spec,
+            prerelease=spec.get("prerelease", False),
         )
 
     @classmethod
@@ -235,6 +238,7 @@ def build_parcellation(cls, spec):
             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
@@ -303,7 +307,8 @@ def build_map(cls, spec):
             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
@@ -421,7 +426,8 @@ def build_volume_of_interest(cls, spec):
             "space_spec": vol._space_spec,
             "providers": vol._providers.values(),
             "datasets": cls.extract_datasets(spec),
-            "id": spec.get("@id", None)
+            "id": spec.get("@id", None),
+            "prerelease": spec.get("prerelease", False),
         }
         modality = spec.get('modality', "")
         if modality == "cell body staining":
@@ -479,7 +485,8 @@ def build_connectivity_matrix(cls, spec):
             "decode_func": decoder_func,
             "anchor": cls.extract_anchor(spec),
             "description": spec.get("description", ""),
-            "datasets": cls.extract_datasets(spec)
+            "datasets": cls.extract_datasets(spec),
+            "prerelease": spec.get("prerelease", False),
         }
         paradigm = spec.get("paradigm")
         if paradigm:
@@ -517,7 +524,8 @@ def build_activity_timeseries(cls, spec):
             "anchor": cls.extract_anchor(spec),
             "description": spec.get("description", ""),
             "datasets": cls.extract_datasets(spec),
-            "timestep": spec.get("timestep")
+            "timestep": spec.get("timestep"),
+            "prerelease": spec.get("prerelease", False),
         }
         paradigm = spec.get("paradigm")
         if paradigm:

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, **kwargs):
         """Construct an empty atlas object with a name and identifier."""
 
         concept.AtlasConcept.__init__(
             self,
             identifier=identifier,
             name=name,
-            species=species
+            species=species,
+            **kwargs
         )
         self._parcellation_ids: List[str] = []
         self._space_ids: List[str] = []

siibra/core/concept.py

@@ -67,7 +67,8 @@ def __init__(
         modality: str = "",
         publications: List[TypePublication] = [],
         datasets: List['TypeDataset'] = [],
-        spec=None
+        spec=None,
+        prerelease: bool = False,
     ):
         """
         Construct a new atlas concept base object.
@@ -94,7 +95,7 @@ def __init__(
             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
@@ -104,6 +105,7 @@ def __init__(
         self.datasets = datasets
         self._spec = spec
         self._CACHED_MATCHES = {}  # we cache match() function results
+        self._prerelease = prerelease
 
     @property
     def description(self):

siibra/core/parcellation.py

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

siibra/core/region.py

@@ -85,6 +85,7 @@ def __init__(
         datasets: list = [],
         rgb: str = None,
         spec=None,
+        prerelease: bool = False,
     ):
         """
         Constructs a new Region object.
@@ -122,7 +123,8 @@ def __init__(
             modality=modality,
             publications=publications,
             datasets=datasets,
-            spec=spec
+            spec=spec,
+            prerelease=prerelease,
         )
 
         # anytree node will take care to use this appropriately

siibra/core/space.py

@@ -38,6 +38,7 @@ def __init__(
         modality: str = "",
         publications: list = [],
         datasets: list = [],
+        prerelease: bool = False,
     ):
         """
         Constructs a new parcellation object.
@@ -75,6 +76,7 @@ def __init__(
             modality=modality,
             publications=publications,
             datasets=datasets,
+            prerelease=prerelease,
         )
         self.volumes = volumes
         for v in self.volumes:

siibra/features/connectivity/regional_connectivity.py

@@ -58,7 +58,8 @@ def __init__(
         datasets: list = [],
         subject: str = "average",
         feature: str = None,
-        id: str = None
+        id: str = None,
+        prerelease: bool = False,
     ):
         """
         Construct a parcellation-averaged connectivity matrix.
@@ -92,7 +93,8 @@ def __init__(
             description=description,
             anchor=anchor,
             datasets=datasets,
-            id=id
+            id=id,
+            prerelease=prerelease
         )
         self.cohort = cohort.upper()
         if isinstance(connector, str) and connector:

siibra/features/feature.py

@@ -99,7 +99,8 @@ def __init__(
         description: str,
         anchor: _anchor.AnatomicalAnchor,
         datasets: List['TypeDataset'] = [],
-        id: str = None
+        id: str = None,
+        prerelease: bool = False,
     ):
         """
         Parameters
@@ -117,6 +118,7 @@ def __init__(
         self._anchor_cached = anchor
         self.datasets = datasets
         self._id = id
+        self._prerelease = prerelease
 
     @property
     def modality(self):
@@ -199,7 +201,8 @@ def authors(self):
     def name(self):
         """Returns a short human-readable name of this feature."""
         readable_class_name = sub("([a-z])([A-Z])", r"\g<1> \g<2>", self.__class__.__name__)
-        return sub("([b,B]ig [b,B]rain)", "BigBrain", readable_class_name)
+        name_ = sub("([b,B]ig [b,B]rain)", "BigBrain", readable_class_name)
+        return name_ if not self._prerelease else f"[PRERELEASE] {name_}"
 
     @classmethod
     def _get_instances(cls, **kwargs) -> List['Feature']:
@@ -724,7 +727,7 @@ class CompoundFeature(Feature):
     def __init__(
         self,
         elements: List['Feature'],
-        queryconcept: Union[region.Region, parcellation.Parcellation, space.Space]
+        queryconcept: Union[region.Region, parcellation.Parcellation, space.Space],
     ):
         """
         A compound of several features of the same type with an anchor created
@@ -757,7 +760,8 @@ def __init__(
             modality=modality,
             description="\n".join({f.description for f in elements}),
             anchor=self._feature_type._merge_anchors([f.anchor for f in elements]),
-            datasets=list(dict.fromkeys([ds for f in elements for ds in f.datasets]))
+            datasets=list(dict.fromkeys([ds for f in elements for ds in f.datasets])),
+            prerelease=all(f._prerelease for f in elements),
         )
         self._queryconcept = queryconcept
         self._merged_feature_cached = None
@@ -833,7 +837,8 @@ def name(self) -> str:
             for k, v in self._compounding_attributes.items()
             if k != 'modality'
         ])
-        return f"{len(self)} {readable_feature_type} features{f' {groupby}' if groupby else ''}"
+        cf_name = f"{len(self)} {readable_feature_type} features{f' {groupby}' if groupby else ''}"
+        return cf_name if not self._prerelease else f"[PRERELEASE] {cf_name}"
 
     @property
     def id(self) -> str:

siibra/features/image/image.py

@@ -63,15 +63,17 @@ def __init__(
         providers: List[provider.VolumeProvider],
         region: str = None,
         datasets: List = [],
-        id: str = None
+        id: str = None,
+        prerelease: bool = False,
     ):
         feature.Feature.__init__(
             self,
             modality=modality,
             description=None,  # lazy implementation below!
             anchor=None,  # lazy implementation below!
             datasets=datasets,
-            id=id
+            id=id,
+            prerelease=prerelease
         )
 
         _volume.Volume.__init__(

siibra/features/tabular/cell_density_profile.py

@@ -70,7 +70,8 @@ def __init__(
         url: str,
         anchor: _anchor.AnatomicalAnchor,
         datasets: list = [],
-        id: str = None
+        id: str = None,
+        prerelease: bool = False,
     ):
         """
         Generate a cell density profile from a URL to a cloud folder
@@ -83,7 +84,8 @@ def __init__(
             unit="cells / 0.1mm3",
             anchor=anchor,
             datasets=datasets,
-            id=id
+            id=id,
+            prerelease=prerelease,
         )
         self._step = 0.01
         self._url = url

siibra/features/tabular/cortical_profile.py

@@ -57,7 +57,8 @@ def __init__(
         unit: str = None,
         boundary_positions: Dict[Tuple[int, int], float] = None,
         datasets: list = [],
-        id: str = None
+        id: str = None,
+        prerelease: bool = False,
     ):
         """Initialize profile.
 
@@ -98,7 +99,8 @@ def __init__(
             anchor=anchor,
             data=None,  # lazy loader below
             datasets=datasets,
-            id=id
+            id=id,
+            prerelease=prerelease,
         )
 
     def _check_sanity(self):

siibra/features/tabular/receptor_density_fingerprint.py

@@ -43,7 +43,8 @@ def __init__(
         tsvfile: str,
         anchor: _anchor.AnatomicalAnchor,
         datasets: list = [],
-        id: str = None
+        id: str = None,
+        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.
@@ -55,7 +56,8 @@ def __init__(
             anchor=anchor,
             data=None,  # lazy loading below
             datasets=datasets,
-            id=id
+            id=id,
+            prerelease=prerelease,
         )
         self._loader = requests.HttpRequest(tsvfile)
 

siibra/features/tabular/receptor_density_profile.py

@@ -42,7 +42,8 @@ def __init__(
         tsvfile: str,
         anchor: _anchor.AnatomicalAnchor,
         datasets: list = [],
-        id: str = None
+        id: str = None,
+        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.
@@ -53,7 +54,8 @@ def __init__(
             modality="Receptor density",
             anchor=anchor,
             datasets=datasets,
-            id=id
+            id=id,
+            prerelease=prerelease
         )
         self.receptor = receptor
         self._data_cached = None

siibra/features/tabular/regional_timeseries_activity.py

@@ -49,7 +49,8 @@ def __init__(
         description: str = "",
         datasets: list = [],
         subject: str = "average",
-        id: str = None
+        id: str = None,
+        prerelease: bool = False,
     ):
         """
         """
@@ -60,7 +61,8 @@ def __init__(
             anchor=anchor,
             datasets=datasets,
             data=None,  # lazy loading below
-            id=id
+            id=id,
+            prerelease=prerelease,
         )
         self.cohort = cohort.upper()
         if isinstance(connector, str) and connector:

siibra/features/tabular/tabular.py

@@ -45,15 +45,17 @@ def __init__(
         anchor: _anchor.AnatomicalAnchor,
         data: pd.DataFrame,  # sample x feature dimension
         datasets: list = [],
-        id: str = None
+        id: str = None,
+        prerelease: bool = False,
     ):
         feature.Feature.__init__(
             self,
             modality=modality,
             description=description,
             anchor=anchor,
             datasets=datasets,
-            id=id
+            id=id,
+            prerelease=prerelease
         )
         self._data_cached = data