parse prerelease tag for AtlasConcepts and Features

siibra/configuration/factory.py

@@ -187,6 +187,7 @@ def build_space(cls, spec):
             modality=spec.get("modality"),
             publications=spec.get("publications", []),
             datasets=cls.extract_datasets(spec),
+            prerelease=spec.get("prerelease", False),
         )
 
     @classmethod
@@ -200,6 +201,7 @@ def build_region(cls, spec):
             datasets=cls.extract_datasets(spec),
             rgb=spec.get("rgb", None),
             spec=spec,
+            prerelease=spec.get("prerelease", False),
         )
 
     @classmethod
@@ -222,6 +224,7 @@ 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
@@ -299,7 +302,8 @@ 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
@@ -352,6 +356,7 @@ def build_receptor_density_fingerprint(cls, spec):
             tsvfile=spec['file'],
             anchor=cls.extract_anchor(spec),
             datasets=cls.extract_datasets(spec),
+            prerelease=spec.get("prerelease", False),
         )
 
     @classmethod
@@ -362,6 +367,7 @@ def build_cell_density_fingerprint(cls, spec):
             layerfiles=spec['layerfiles'],
             anchor=cls.extract_anchor(spec),
             datasets=cls.extract_datasets(spec),
+            prerelease=spec.get("prerelease", False),
         )
 
     @classmethod
@@ -372,6 +378,7 @@ def build_receptor_density_profile(cls, spec):
             tsvfile=spec['file'],
             anchor=cls.extract_anchor(spec),
             datasets=cls.extract_datasets(spec),
+            prerelease=spec.get("prerelease", False),
         )
 
     @classmethod
@@ -383,6 +390,7 @@ def build_cell_density_profile(cls, spec):
             url=spec['file'],
             anchor=cls.extract_anchor(spec),
             datasets=cls.extract_datasets(spec),
+            prerelease=spec.get("prerelease", False),
         )
 
     @classmethod
@@ -395,6 +403,7 @@ def build_section(cls, spec):
             "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 @@ def build_volume_of_interest(cls, spec):
             "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 @@ def build_connectivity_matrix(cls, spec):
             "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 @@ def build_activity_timeseries(cls, spec):
             "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/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/core/concept.py

@@ -51,7 +51,8 @@ def __init__(
         modality: str = "",
         publications: List[TypePublication] = [],
         datasets: List['TypeDataset'] = [],
-        spec=None
+        spec=None,
+        prerelease: bool = False,
     ):
         """
         Construct a new atlas concept base object.
@@ -78,7 +79,7 @@ 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
@@ -87,6 +88,7 @@ def __init__(
         self._publications = publications
         self.datasets = datasets
         self._spec = spec
+        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

@@ -82,6 +82,7 @@ def __init__(
         datasets: list = [],
         rgb: str = None,
         spec=None,
+        prerelease: bool = False,
     ):
         """
         Constructs a new Region object.
@@ -119,7 +120,8 @@ 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

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

siibra/features/connectivity/regional_connectivity.py

@@ -51,6 +51,7 @@ def __init__(
         anchor: _anchor.AnatomicalAnchor,
         description: str = "",
         datasets: list = [],
+        prerelease: bool = False,
     ):
         """
         Construct a parcellation-averaged connectivity matrix.
@@ -84,6 +85,7 @@ def __init__(
             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/features/feature.py

@@ -92,7 +92,8 @@ def __init__(
         modality: str,
         description: str,
         anchor: _anchor.AnatomicalAnchor,
-        datasets: List['TypeDataset'] = []
+        datasets: List['TypeDataset'] = [],
+        prerelease: bool = False,
     ):
         """
         Parameters
@@ -109,6 +110,7 @@ def __init__(
         self._description = description
         self._anchor_cached = anchor
         self.datasets = datasets
+        self._prerelease = prerelease
 
     @property
     def modality(self):
@@ -183,7 +185,8 @@ def authors(self):
     @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/features/image/image.py

@@ -62,13 +62,15 @@ def __init__(
         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/features/tabular/cell_density_profile.py

@@ -67,7 +67,8 @@ def __init__(
         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 @@ def __init__(
             unit="detected cells / 0.1mm3",
             anchor=anchor,
             datasets=datasets,
+            prerelease=prerelease,
         )
         self._step = 0.01
         self._url = url

siibra/features/tabular/cortical_profile.py

@@ -52,7 +52,8 @@ def __init__(
         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 @@ def __init__(
             description=description,
             anchor=anchor,
             data=None,  # lazy loader below
-            datasets=datasets
+            datasets=datasets,
+            prerelease=prerelease,
         )
 
     def _check_sanity(self):

siibra/features/tabular/layerwise_cell_density.py

@@ -56,14 +56,16 @@ def __init__(
         layerfiles: list,
         anchor: _anchor.AnatomicalAnchor,
         datasets: list = [],
+        prerelease: bool = False,
     ):
         tabular.Tabular.__init__(
             self,
             description=self.DESCRIPTION,
             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/features/tabular/receptor_density_fingerprint.py

@@ -42,7 +42,8 @@ def __init__(
         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 @@ def __init__(
             anchor=anchor,
             data=None,  # lazy loading below
             datasets=datasets,
+            prerelease=prerelease,
         )
         self._loader = requests.HttpRequest(tsvfile)
 

siibra/features/tabular/receptor_density_profile.py

@@ -39,7 +39,8 @@ def __init__(
         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 @@ def __init__(
             modality=f"{receptor} receptor density",
             anchor=anchor,
             datasets=datasets,
+            prerelease=prerelease,
         )
         self.type = receptor
         self._data_cached = None

siibra/features/tabular/regional_timeseries_activity.py

@@ -47,7 +47,8 @@ def __init__(
         timestep: str,
         description: str = "",
         datasets: list = [],
-        paradigm: str = ""
+        paradigm: str = "",
+        prerelease: bool = False,
     ):
         """
         """
@@ -57,7 +58,8 @@ def __init__(
             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/features/tabular/tabular.py

@@ -44,14 +44,16 @@ def __init__(
         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