bsb-core 7.2.2__tar.gz → 7.3.0__tar.gz

{bsb_core-7.2.2 → bsb_core-7.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bsb-core
-Version: 7.2.2
+Version: 7.3.0
 Summary: `bsb-core` is the backbone package contain the essential code of the BSB: A component
 Author-email: Robin De Schepper <robin@alexandria.sc>, Dimitri Rodarie <dimitri.rodarie@unipv.it>
 Requires-Python: >=3.10,<4

{bsb_core-7.2.2 → bsb_core-7.3.0}/bsb/__init__.py

@@ -257,6 +257,7 @@ JobPoolContextError: type["bsb.exceptions.JobPoolContextError"]
 JobPoolError: type["bsb.exceptions.JobPoolError"]
 JobSchedulingError: type["bsb.exceptions.JobSchedulingError"]
 LabelTargetting: type["bsb.simulation.targetting.LabelTargetting"]
+LabellingError: type["bsb.exceptions.LabellingError"]
 Layer: type["bsb.topology.partition.Layer"]
 LayoutError: type["bsb.exceptions.LayoutError"]
 LocationTargetting: type["bsb.simulation.targetting.LocationTargetting"]

{bsb_core-7.2.2 → bsb_core-7.3.0}/bsb/_encoding.py

@@ -58,8 +58,42 @@ class EncodedLabels(np.ndarray):
         cp.labels = {k: v.copy() for k, v in cp.labels.items()}
         return cp
 
+    def remove_labels(self, labels, points):
+        # points can be either a boolean mask or a list of indices
+        if (
+            np.asarray(points).dtype != bool
+            and not len(points)
+            or np.asarray(points).dtype == bool
+            and not np.any(points)
+        ):
+            return
+
+        # A counter that skips existing values.
+        counter = (c for c in itertools.count() if c not in self.labels)
+
+        for i in points:
+            point = self[i]
+            point_labels = self.labels[point].copy()
+            is_in = np.isin(labels, list(point_labels))
+            if np.any(is_in):
+                point_labels -= set(np.array(labels)[is_in])
+                for k, v in self.labels.items():
+                    if point_labels == v:
+                        new_id = k
+                        break
+                else:
+                    new_id = next(counter)
+                    self.labels[new_id] = point_labels
+                self[i] = new_id
+
     def label(self, labels, points):
-        if not len(points):
+        # points can be either a boolean mask or a list of indices
+        if (
+            np.asarray(points).dtype != bool
+            and not len(points)
+            or np.asarray(points).dtype == bool
+            and not np.any(points)
+        ):
             return
         _transitions = {}
         # A counter that skips existing values.
@@ -110,7 +144,9 @@ class EncodedLabels(np.ndarray):
         :param list[str] labels: List of labels
         :rtype: numpy.ndarray[int]
         """
-        labels = set(labels or [])
+        if labels is None:
+            return np.full(self.size, True, dtype=bool)
+        labels = set(labels)
         has_any = [
             k
             for k, v in self.labels.items()

{bsb_core-7.2.2 → bsb_core-7.3.0}/bsb/config/_attrs.py

@@ -399,7 +399,7 @@ def _getref(remote, key):
 
 
 def _getrefname(remote):
-    """Canonical way to retrieve a the name of a remote node."""
+    """Canonical way to retrieve the name of a remote node."""
     try:
         return remote.get_node_name()
     except TypeError:

{bsb_core-7.2.2 → bsb_core-7.3.0}/bsb/exceptions.py

@@ -65,6 +65,7 @@ _t(
             ),
             UnknownGIDError=_e(),
         ),
+        LabellingError=_e(),
         MorphologyError=_e(
             MorphologyRepositoryError=_e(),
             MissingMorphologyError=_e(),
@@ -200,6 +201,7 @@ __all__ = [
     "JobPoolContextError",
     "JobPoolError",
     "JobSchedulingError",
+    "LabellingError",
     "LayoutError",
     "MissingActiveConfigError",
     "MissingMorphologyError",

{bsb_core-7.2.2 → bsb_core-7.3.0}/bsb/storage/interfaces.py

@@ -386,6 +386,7 @@ class PlacementSet(Interface):
         self._type = cell_type
         self._tag = cell_type.name
         self._morphology_labels = None
+        self._labels = None
 
     @abc.abstractmethod
     def __len__(self):  # pragma: nocover
@@ -605,7 +606,6 @@ class PlacementSet(Interface):
         """
         pass
 
-    @abc.abstractmethod
     def set_label_filter(self, labels):  # pragma: nocover
         """
         Should limit the scope of the placement set to the given labels.
@@ -613,7 +613,16 @@ class PlacementSet(Interface):
         :param labels: List of labels
         :type labels: list[str]
         """
-        pass
+        self._labels = labels
+
+    def get_label_filter(self):  # pragma: nocover
+        """
+        Get the labels used to limit the scope of the placement set.
+
+        :param labels: List of labels
+        :type labels: list[str]
+        """
+        return self._labels
 
     @abc.abstractmethod
     def set_morphology_label_filter(self, morphology_labels):  # pragma: nocover
@@ -629,6 +638,17 @@ class PlacementSet(Interface):
         """
         pass
 
+    @abc.abstractmethod
+    def label_by_mask(self, labels, mask):  # pragma: nocover
+        """
+        Should label the masked with the given labels.
+
+        :param list[str] labels: List of labels
+        :param list[bool] mask: Array of boolean for each cell to label
+        :raises: LabellingError if the array provided has invalid shape.
+        """
+        pass
+
     @abc.abstractmethod
     def label(self, labels, cells):  # pragma: nocover
         """
@@ -638,6 +658,31 @@ class PlacementSet(Interface):
         :type labels: list[str]
         :param cells: Array of cells in this set to label.
         :type cells: list[int]
+        :raises: LabellingError if the ids provided are invalid.
+        """
+        pass
+
+    @abc.abstractmethod
+    def remove_labels_by_mask(self, labels, mask):  # pragma: nocover
+        """
+        Should remove the provided labels assigned to the masked cells.
+
+        :param list[str] labels: List of labels
+        :param list[bool] mask: Array of boolean for each cell to label
+        :raises: LabellingError if the array provided has invalid shape.
+        """
+        pass
+
+    @abc.abstractmethod
+    def remove_labels(self, labels, cells):
+        """
+        Should remove the provided labels assigned to the cells.
+
+        :param labels: List of labels
+        :type labels: list[str]
+        :param cells: Array of cells in this set to remove labels.
+        :type cells: list[int]
+        :raises: LabellingError if the ids provided are invalid.
         """
         pass
 
@@ -654,8 +699,8 @@ class PlacementSet(Interface):
     @abc.abstractmethod
     def get_labelled(self, labels=None):  # pragma: nocover
         """
-        Should return the ids of the cells labelled with given labels. If labels are not
-        provided, will filter non labelled cells.
+        Should return the ids of the cells labelled with given labels.
+        To filter non labelled cells, set labels to empty list.
 
         :param labels: List of labels
         :type labels: list[str]
@@ -667,10 +712,11 @@ class PlacementSet(Interface):
     def get_label_mask(self, labels=None):  # pragma: nocover
         """
         Should return a mask that fits the placement set for the cells with given labels.
-        If labels are not provided, will filter non labelled cells.
+        To filter non labelled cells, set labels to empty list.
 
         :param labels: List of labels
         :type labels: list[str]
+        :rtype: numpy.ndarray[bool]
         """
         pass
 

{bsb_core-7.2.2 → bsb_core-7.3.0}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "flit_core.buildapi"
 
 [project]
 name = "bsb-core"
-version = "7.2.2"
+version = "7.3.0"
 readme = "README.md"
 requires-python = ">=3.10,<4"
 dynamic = [ "description" ]