Take feature.id from config if available

Author: AhmetNSimsek

siibra/configuration/factory.py

@@ -365,6 +365,7 @@ def build_receptor_density_fingerprint(cls, spec):
             tsvfile=spec['file'],
             anchor=cls.extract_anchor(spec),
             datasets=cls.extract_datasets(spec),
+            id=spec.get("id", None)
         )
 
     @classmethod
@@ -375,6 +376,7 @@ def build_cell_density_fingerprint(cls, spec):
             layerfiles=spec['layerfiles'],
             anchor=cls.extract_anchor(spec),
             datasets=cls.extract_datasets(spec),
+            id=spec.get("id", None)
         )
 
     @classmethod
@@ -385,6 +387,7 @@ def build_receptor_density_profile(cls, spec):
             tsvfile=spec['file'],
             anchor=cls.extract_anchor(spec),
             datasets=cls.extract_datasets(spec),
+            id=spec.get("id", None)
         )
 
     @classmethod
@@ -396,6 +399,7 @@ def build_cell_density_profile(cls, spec):
             url=spec['file'],
             anchor=cls.extract_anchor(spec),
             datasets=cls.extract_datasets(spec),
+            id=spec.get("id", None)
         )
 
     @classmethod
@@ -408,6 +412,7 @@ def build_section(cls, spec):
             "space_spec": vol._space_spec,
             "providers": vol._providers.values(),
             "datasets": cls.extract_datasets(spec),
+            "id": spec.get("id", None)
         }
         modality = spec.get('modality', "")
         if modality == "cell body staining":
@@ -425,6 +430,7 @@ 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)
         }
         modality = spec.get('modality', "")
         if modality == "cell body staining":
@@ -495,7 +501,8 @@ def build_connectivity_matrix(cls, spec):
                 "filename": filename,
                 "subject": fkey if files_indexed_by == "subject" else "average",
                 "feature": fkey if files_indexed_by == "feature" else None,
-                "connector": repo_connector or base_url + filename
+                "connector": repo_connector or base_url + filename,
+                "id": spec.get("id", None)
             })
             conn_by_file.append(conn_cls(**kwargs))
         return conn_by_file
@@ -528,7 +535,8 @@ def build_activity_timeseries(cls, spec):
         for fkey, filename in files.items():
             kwargs.update({
                 "filename": filename,
-                "subject": fkey
+                "subject": fkey,
+                "id": spec.get("id", None)
             })
             timeseries_by_file.append(timeseries_cls(**kwargs))
         return timeseries_by_file

siibra/features/connectivity/regional_connectivity.py

@@ -57,7 +57,8 @@ def __init__(
         description: str = "",
         datasets: list = [],
         subject: str = "average",
-        feature: str = None
+        feature: str = None,
+        id: str = None
     ):
         """
         Construct a parcellation-averaged connectivity matrix.
@@ -91,6 +92,7 @@ def __init__(
             description=description,
             anchor=anchor,
             datasets=datasets,
+            id=id
         )
         self.cohort = cohort.upper()
         if isinstance(connector, str) and connector:

siibra/features/feature.py

@@ -98,7 +98,8 @@ def __init__(
         modality: str,
         description: str,
         anchor: _anchor.AnatomicalAnchor,
-        datasets: List['TypeDataset'] = []
+        datasets: List['TypeDataset'] = [],
+        id: str = None
     ):
         """
         Parameters
@@ -115,6 +116,7 @@ def __init__(
         self._description = description
         self._anchor_cached = anchor
         self.datasets = datasets
+        self._id = id
 
     @property
     def modality(self):
@@ -262,6 +264,9 @@ def last_match_description(self):
 
     @property
     def id(self):
+        if self._id:
+            return self._id
+
         prefix = ''
         for ds in self.datasets:
             if hasattr(ds, "id"):

siibra/features/image/image.py

@@ -63,13 +63,15 @@ def __init__(
         providers: List[provider.VolumeProvider],
         region: str = None,
         datasets: List = [],
+        id: str = None
     ):
         feature.Feature.__init__(
             self,
             modality=modality,
             description=None,  # lazy implementation below!
             anchor=None,  # lazy implementation below!
-            datasets=datasets
+            datasets=datasets,
+            id=id
         )
 
         _volume.Volume.__init__(

siibra/features/tabular/cell_density_profile.py

@@ -69,7 +69,8 @@ def __init__(
         patch: int,
         url: str,
         anchor: _anchor.AnatomicalAnchor,
-        datasets: list = []
+        datasets: list = [],
+        id: str = None
     ):
         """
         Generate a cell density profile from a URL to a cloud folder
@@ -82,6 +83,7 @@ def __init__(
             unit="cells / 0.1mm3",
             anchor=anchor,
             datasets=datasets,
+            id=id
         )
         self._step = 0.01
         self._url = url

siibra/features/tabular/cortical_profile.py

@@ -56,7 +56,8 @@ def __init__(
         values: Union[list, np.ndarray] = None,
         unit: str = None,
         boundary_positions: Dict[Tuple[int, int], float] = None,
-        datasets: list = []
+        datasets: list = [],
+        id: str = None
     ):
         """Initialize profile.
 
@@ -96,7 +97,8 @@ def __init__(
             description=description,
             anchor=anchor,
             data=None,  # lazy loader below
-            datasets=datasets
+            datasets=datasets,
+            id=id
         )
 
     def _check_sanity(self):

siibra/features/tabular/layerwise_cell_density.py

@@ -56,14 +56,16 @@ def __init__(
         layerfiles: list,
         anchor: _anchor.AnatomicalAnchor,
         datasets: list = [],
+        id: str = None
     ):
         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
+            id=id
         )
         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 = [],
+        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.
@@ -54,6 +55,7 @@ def __init__(
             anchor=anchor,
             data=None,  # lazy loading below
             datasets=datasets,
+            id=id
         )
         self._loader = requests.HttpRequest(tsvfile)
 

siibra/features/tabular/receptor_density_profile.py

@@ -41,7 +41,8 @@ def __init__(
         receptor: str,
         tsvfile: str,
         anchor: _anchor.AnatomicalAnchor,
-        datasets: list = []
+        datasets: list = [],
+        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 @@ def __init__(
             modality="Receptor density",
             anchor=anchor,
             datasets=datasets,
+            id=id
         )
         self.receptor = receptor
         self._data_cached = None

siibra/features/tabular/regional_timeseries_activity.py

@@ -48,7 +48,8 @@ def __init__(
         timestep: str,
         description: str = "",
         datasets: list = [],
-        subject: str = "average"
+        subject: str = "average",
+        id: str = None
     ):
         """
         """
@@ -58,7 +59,8 @@ def __init__(
             description=description,
             anchor=anchor,
             datasets=datasets,
-            data=None  # lazy loading below
+            data=None,  # lazy loading below
+            id=id
         )
         self.cohort = cohort.upper()
         if isinstance(connector, str) and 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 = [],
+        id: str = None
     ):
         feature.Feature.__init__(
             self,
             modality=modality,
             description=description,
             anchor=anchor,
-            datasets=datasets
+            datasets=datasets,
+            id=id
         )
         self._data_cached = data