Fix _get_morphology_loaders to preload only once required morphologie…

…s and metadata.

Add function to update morphology metadata.

bsb_hdf5/morphology_repository.py

@@ -80,6 +80,12 @@ def get_all_meta(self, handle=HANDLED):
             return {}
         return json.loads(handle["morphology_meta"][()], object_hook=meta_object_hook)
 
+    @handles_handles("a")
+    def update_all_meta(self, meta, handle=HANDLED):
+        all_meta = self.get_all_meta(handle=handle)
+        all_meta.update(meta)
+        self.set_all_meta(all_meta, handle=handle)
+
     @handles_handles("a")
     def set_all_meta(self, all_meta, handle=HANDLED):
         if "morphology_meta" in handle:

bsb_hdf5/placement_set.py

@@ -155,8 +155,14 @@ def load_rotations(self, handle=HANDLED):
     @handles_handles("r")
     def load_morphologies(self, handle=HANDLED, allow_empty=False):
         """
-        Load the cell morphologies.
-
+        Preload the cell morphologies.
+
+        :param handle: hdf5 file handler
+        :type handle: hdf5.File
+        :param allow_empty: If False (default), will raise an error in absence of morphologies,
+        :type allow_empty: bool
+        :returns: MorphologySet object containing the loader of all morphologies
+        :rtype: bsb.morphologies.MorphologySet
         :raises: DatasetNotFoundError when the morphology data is not found.
         """
         reader = self._morphology_chunks.get_chunk_reader(handle, True)
@@ -197,18 +203,17 @@ def load_additional(self, key=None, handle=HANDLED):
     @handles_handles("r")
     def _get_morphology_loaders(self, handle=HANDLED):
         stor_mor = {}
+        meta = self._engine.morphologies.get_all_meta()
         for chunk in self.get_loaded_chunks():
             path = self.get_chunk_path(chunk)
             try:
                 _map = handle[path].attrs["morphology_loaders"]
             except KeyError:
                 continue
-            stor_mor.update(
-                (m.name, m)
-                for m in self._engine.morphologies.select(
-                    _MapSelector(ps=self, names=_map)
-                )
-            )
+            for label in _map:
+                if label not in stor_mor and label in meta:
+                    stor_mor[label] = self._engine.morphologies.preload(name=label,
+                                                                        meta=meta[label])
         return stor_mor
 
     @handles_handles("a")
@@ -244,15 +249,20 @@ def append_data(
         Append data to the placement set.
 
         :param chunk: The chunk to store data in.
+        :type chunk: ~bsb.storage.Chunk
         :param positions: Cell positions
         :type positions: :class:`numpy.ndarray`
         :param rotations: Cell rotations
         :type rotations: ~bsb.morphologies.RotationSet
         :param morphologies: Cell morphologies
         :type morphologies: ~bsb.morphologies.MorphologySet
+        :param additional: Additional data to attach to chunck
+        :type additional: dict
         :param count: Amount of entities to place. Excludes the use of any positional,
           rotational or morphological data.
         :type count: int
+        :param handle: h5py file handler
+        :type handle: :class:`h5py.Group`
         """
         if not isinstance(chunk, Chunk):
             chunk = Chunk(chunk, None)
@@ -278,7 +288,7 @@ def append_data(
         if additional is not None:
             for key, ds in additional.items():
                 self.append_additional(key, chunk, ds)
-        self._track_add(handle, chunk, len(positions))
+        self._track_add(handle, chunk, len(positions) if positions is not None else count)
 
     def _append_morphologies(self, chunk, new_set):
         with self.chunk_context([chunk]):
@@ -288,6 +298,17 @@ def _append_morphologies(self, chunk, new_set):
             self._morphology_chunks.append(chunk, morphology_set.get_indices())
 
     def append_entities(self, chunk, count, additional=None):
+        """
+        Append entities to the placement set.
+
+        :param chunk: The chunk to store data in.
+        :type chunk: ~bsb.storage.Chunk
+        :param count: Amount of entities to place. Excludes the use of any positional,
+          rotational or morphological data.
+        :type count: int
+        :param additional: Additional data to attach to chunck
+        :type additional: dict
+        """
         self.append_data(chunk, count=count, additional=additional)
 
     def append_additional(self, name, chunk, data):
@@ -402,12 +423,12 @@ def _track_add(self, handle, chunk, count):
         stats = global_stats.setdefault(
             str(chunk.id), {"placed": 0, "connections": {"inc": 0, "out": 0}}
         )
-        stats["placed"] += count
+        stats["placed"] += int(count)
         handle.attrs["chunks"] = json.dumps(global_stats)
         # Track addition in placement set
         handle[self._path].attrs["len"] = handle[self._path].attrs.get("len", 0) + count
         chunk_stats = json.loads(handle[self._path].attrs.get("chunks", "{}"))
-        chunk_stats[str(chunk.id)] = chunk_stats.get(str(chunk.id), 0) + count
+        chunk_stats[str(chunk.id)] = chunk_stats.get(str(chunk.id), 0) + int(count)
         handle[self._path].attrs["chunks"] = json.dumps(chunk_stats)
 
     @handles_handles("r")