Morphologies reworked to branch centric structure of arrays (#129)

* initial write up of reworked morphologies & repo loading

* merged initial write up and TrueMorphology into Morphology class

* moved MRs that are addressed by path to test MR folder

* Removed dead code, added `flatten`

* Renamed `branches_iterator` to `branch_iter` and it uses `yield from`

* Fixed undefined `vec`

* Removed preload, turned compartments into cached property

* Added invalid branch labels checking function

* Pass scaffold to morphology from _morphology

* Catch missing branch vector datasets

* Compartments were misconstructed from 1 set of coords, added pairwise

* Bumped errr version for correct exception names during tests

* Added first batch of morphology tests

* crude seperation of Morphology from config. All vars still "morphology"

* Disabled outdated parts. Will work towards enabling arbz.

* bumped errr in requirements

* Rewrote arbz import, saving and loading of morphologies

* regenerated morphology repositories

* skip some broken tests

* Removed old storage code. Fixed some graph code errors

* Use latest dbbs_models version for PC target sets

* Added morphology labelling

* Added arborize multi-labels. closes #126

* enabled placement tests

* removed morphos.hdf5

* removed MR gitignore exception

* Started work on dynamic test MR's, "fixed" empty KDTree error

* updated main MR

* Restored connectivity

* Fixed postprocessing test

* Try dbbs bump for key error

* Added circular morphology error

* Added morpho warning

* Upgraded to patch 2.2.0 for functional SectionRef

* Added conceptual docs on morphologies

* Dynamic test files. (closes #120)

* Fixed morphology & nest tests

* Fixed entity test

* Changed rounding of step

* Fixed fiber_intersection test

* Added fixes for missing MR files

* duplicate .h5 file to top lvl, to be sure

* removed test print

* Expect an extra point at seam of branches (closes #132)

* v3.6.0b0 - Branched SoA morphologies

* Completed basic testing of morphologies.py

* Added placeholder tests

bsb/__init__.py

@@ -1,3 +1,3 @@
-__version__ = "3.5.0b1"
+__version__ = "3.6.0b0"
 
 from .reporting import set_verbosity, report, warn

bsb/config.py

@@ -5,7 +5,7 @@
 import os, sys, site
 from inspect import isclass
 from .models import CellType, Layer
-from .morphologies import Morphology as BaseMorphology
+from .morphologies import Representation
 from .connectivity import ConnectionStrategy, FiberTransform
 from .placement import PlacementStrategy
 from .output import OutputFormatter, HDF5Formatter
@@ -666,7 +666,7 @@ def init_morphology(self, section, cell_type_name):
         name = cell_type_name + "_morphology"
         node_name = "cell_types.{}.morphology".format(cell_type_name)
         morphology_class = assert_attr(section, "class", node_name)
-        morphology = load_configurable_class(name, morphology_class, BaseMorphology)
+        morphology = load_configurable_class(name, morphology_class, Representation)
         fill_configurable_class(morphology, section, excluded=["class"])
         self.add_morphology(morphology)
         return morphology

bsb/connectivity/connectome/glomerulus_granule.py

@@ -26,12 +26,8 @@ def validate(self):
                 )
             mr = self.scaffold.morphology_repository
             morphology = mr.get_morphology(morphologies[0])
-            dendritic_compartments = morphology.get_compartments(["dendrites"])
-            dendrites = {}
-            for c in dendritic_compartments:
-                # Store the last found compartment of each dendrite
-                dendrites[c.section_id] = c
-            self.dendritic_claws = [c.id for c in dendrites.values()]
+            branches = morphology.get_branches(["dendrites"])
+            self.dendritic_claws = [branch.to_compartments()[-1] for branch in branches]
             self.morphology = morphology
 
     def connect(self):
@@ -108,6 +104,7 @@ def connectome_glom_grc(
             # Add morphology & compartment information
             morpho_map = [self.morphology.morphology_name]
             morphologies = np.zeros((len(connectome), 2))
+            # Store a map between the granule cell ids and the available claw compartments
             granule_dendrite_occupation = {
                 g[0]: self.dendritic_claws.copy() for g in granules
             }
@@ -126,7 +123,7 @@ def connectome_glom_grc(
                     raise ConnectivityError(
                         "Attempt to connect a glomerulus to a fully saturated granule cell."
                     )
-                compartments.append([0, unoccupied_claw])
+                compartments.append([0, unoccupied_claw.id])
             self.scaffold.connect_cells(
                 self,
                 connectome,

bsb/connectivity/detailed/fiber_intersection.py

@@ -100,9 +100,7 @@ def connect(self):
         for c, (from_cell, from_morpho) in enumerate(from_morphology_set):
             # (1) Extract the FiberMorpho object for each branch in the from_compartments
             # of the presynaptic morphology
-            compartments = from_morpho.get_compartments(
-                compartment_types=from_compartments
-            )
+            compartments = from_morpho.get_compartments(from_compartments)
             morpho_rotation = from_cell.rotation
             fm = FiberMorphology(compartments, morpho_rotation)
 
@@ -393,9 +391,10 @@ def transform_branch(self, branch, offset):
 
         if not self.shared:
             # Compute branch direction - to check that PFs have 2 branches, left and right
-            branch_dir = branch._compartments[0].end - branch._compartments[0].start
-            # Normalize branch_dir vector
-            branch_dir = branch_dir / np.linalg.norm(branch_dir)
+            branch_dir = self.get_branch_direction(branch)
+            # If the entire branch consists of compartments without direction, do nothing.
+            if branch_dir is False:
+                return
 
             num_comp = len(branch._compartments)
 
@@ -409,7 +408,6 @@ def transform_branch(self, branch, offset):
                 # the branch direction and the original morphology/parent branch
                 if branch.orientation is None:
                     transversal_vector = np.cross(branch_dir, [0, 1, 0])
-                    # branch.orientation =
                 else:
                     transversal_vector = np.cross(branch_dir, branch.orientation)
 
@@ -454,3 +452,12 @@ def transform_branch(self, branch, offset):
                     )
                     # The new end is the start of the adjacent compartment
                     branch._compartments[comp + 1].start = branch._compartments[comp].end
+
+    def get_branch_direction(self, branch):
+        for comp in branch._compartments:
+            branch_dir = comp.end - comp.start
+            if not np.sum(branch_dir):
+                continue
+            # Normalize branch_dir vector
+            branch_dir = branch_dir / np.linalg.norm(branch_dir)
+            return branch_dir

bsb/connectivity/detailed/touch_detection.py

@@ -197,25 +197,19 @@ def intersect_compartments(self, touch_info, candidate_map):
         )
 
     def get_compartment_intersections(self, touch_info, from_pos, to_pos):
-        from_morphology = touch_info.from_morphology
-        to_morphology = touch_info.to_morphology
+        from_morpho = touch_info.from_morphology
+        to_morpho = touch_info.to_morphology
         query_points = (
-            to_morphology.get_compartment_positions(types=touch_info.to_cell_compartments)
+            to_morpho.get_compartment_positions(touch_info.to_cell_compartments)
             + to_pos
             - from_pos
         )
-        from_tree = from_morphology.get_compartment_tree(
-            compartment_types=touch_info.from_cell_compartments
-        )
+        from_tree = from_morpho.get_compartment_tree(touch_info.from_cell_compartments)
         compartment_hits = from_tree.query_radius(
             query_points, self.compartment_intersection_radius
         )
-        from_map = from_morphology.get_compartment_submask(
-            compartment_types=touch_info.from_cell_compartments
-        )
-        to_map = to_morphology.get_compartment_submask(
-            compartment_types=touch_info.to_cell_compartments
-        )
+        from_map = from_morpho.get_compartment_submask(touch_info.from_cell_compartments)
+        to_map = to_morpho.get_compartment_submask(touch_info.to_cell_compartments)
         intersections = []
         for i in range(len(compartment_hits)):
             hits = compartment_hits[i]

bsb/exceptions.py

@@ -41,6 +41,7 @@
             MissingMorphologyError=_e(),
             IncompleteMorphologyError=_e(),
             MorphologyDataError=_e(),
+            CircularMorphologyError=_e("morphology", "component").set(list_details=True),
             CompartmentError=_e(),
         ),
         TreeError=_e(),
@@ -78,6 +79,10 @@ class PlacementWarning(ScaffoldWarning):
     pass
 
 
+class MorphologyWarning(ScaffoldWarning):
+    pass
+
+
 class ConnectivityWarning(ScaffoldWarning):
     pass
 

bsb/models.py

@@ -632,9 +632,7 @@ def load_morpho(scaffold, morpho_ind, compartment_types=None):
                 self._morphology_map[morpho_ind]
             )
             m._set_index = morpho_ind
-            m.voxelize(
-                N, compartments=m.get_compartments(compartment_types=compartment_types)
-            )
+            m.voxelize(N, compartments=m.get_compartments(compartment_types))
             return m
 
         # Load and voxelize only the unique morphologies present in the morphology map.