Merge pull request #71 from GazzolaLab/feature/optimization

Optimization modules

.pre-commit-config.yaml

@@ -1,13 +1,13 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: check-json
       - id: end-of-file-fixer
       - id: requirements-txt-fixer
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 24.3.0
     hooks:
       - id: black
         additional_dependencies: ["click==8.0.4"]

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "miv-simulator"
-version = "0.0.3"
+version = "0.0.4"
 description = "Mind-in-Vitro simulator"
 readme = "README.md"
 authors = []
@@ -28,6 +28,7 @@ matplotlib = "^3.6.0"
 quantities = "^0.15.0"
 pydantic = "^2.3.0"
 neuron = "^8.2.3"
+distgfs = {version = "^1.1.0", optional = true}
 
 
 [tool.poetry.dev-dependencies]
@@ -88,6 +89,7 @@ check-config = "scripts.tools.check_config:main"
 cut-slice = "scripts.tools.cut_slice:main"
 sample-cells = "scripts.tools.sample_cells:main"
 reposition-trees = "scripts.tools.reposition_trees:main"
+optimize-network = "scripts.optimization.optimize_network:main_cli"
 
 
 [build-system]

src/miv_simulator/cells.py

@@ -315,7 +315,6 @@ def __init__(
         self.random.seed(self.gid)
         self.spike_detector = None
         self.spike_onset_delay = 0.0
-        self.is_reduced = True
         if not isinstance(cell_config, BRKconfig):
             raise RuntimeError(
                 "BRKneuron: argument cell_attrs must be of type BRKconfig"
@@ -422,6 +421,10 @@ def ais(self):
     def hillock(self):
         return self.nodes["hillock"]
 
+    @property
+    def is_reduced(self):
+        return True
+
 
 class PRneuron:
     """
@@ -458,7 +461,6 @@ def __init__(
         self.random.seed(self.gid)
         self.spike_detector = None
         self.spike_onset_delay = 0.0
-        self.is_reduced = True
         if not isinstance(cell_config, PRconfig):
             raise RuntimeError(
                 "PRneuron: argument cell_attrs must be of type PRconfig"
@@ -558,6 +560,10 @@ def ais(self):
     def hillock(self):
         return self.nodes["hillock"]
 
+    @property
+    def is_reduced(self):
+        return True
+
 
 class SCneuron:
     """
@@ -611,7 +617,6 @@ def __init__(
         self.random.seed(self.gid)
         self.spike_detector = None
         self.spike_onset_delay = 0.0
-        self.is_reduced = True
 
         SC_nrn = h.SC_nrn()
 
@@ -678,6 +683,10 @@ def ais(self) -> List[Any]:
     def hillock(self):
         return self.nodes["hillock"]
 
+    @property
+    def is_reduced(self):
+        return True
+
 
 class BiophysCell:
     """
@@ -951,20 +960,18 @@ def import_morphology_from_hoc(
     sec_info_dict = {}
     root_sec = None
     for sec_type, sec_index_list in default_hoc_sec_lists.items():
-        hoc_sec_attr_name = sec_type
+        hoc_sec_attr_name = f"{sec_type}_list"
         if not hasattr(hoc_cell, hoc_sec_attr_name):
-            hoc_sec_attr_name = f"{sec_type}_list"
+            hoc_sec_attr_name = sec_type
         if hasattr(hoc_cell, hoc_sec_attr_name) and (
             getattr(hoc_cell, hoc_sec_attr_name) is not None
         ):
             sec_list = list(getattr(hoc_cell, hoc_sec_attr_name))
+            hoc_obj = getattr(hoc_cell, hoc_sec_attr_name)
             if hasattr(hoc_cell, sec_index_list):
                 sec_indexes = list(getattr(hoc_cell, sec_index_list))
             else:
-                raise AttributeError(
-                    "import_morphology_from_hoc: %s is not an attribute of the hoc cell"
-                    % sec_index_list
-                )
+                sec_indexes = list(range(len(sec_list)))
             if sec_type == "soma":
                 root_sec = sec_list[0]
             for sec, index in zip(sec_list, sec_indexes):
@@ -1355,6 +1362,34 @@ def filter_nodes(
     return result
 
 
+def get_mech_rules_dict(cell, **rules):
+    """
+    Used by modify_mech_param. Takes in a series of arguments and constructs a validated rules dictionary that will be
+    used to update a cell's mechanism dictionary.
+    :param cell: :class:'BiophysCell'
+    :param rules: dict
+    :return: dict
+    """
+    rules_dict = {
+        name: rules[name]
+        for name in (
+            name
+            for name in ["value", "origin"]
+            if name in rules and rules[name] is not None
+        )
+    }
+    if "origin" in rules_dict:
+        origin_type = rules_dict["origin"]
+        valid_sec_types = [
+            sec_type for sec_type in cell.nodes if len(cell.nodes[sec_type]) > 0
+        ]
+        if origin_type not in valid_sec_types + ["parent", "branch_origin"]:
+            raise ValueError(
+                f"get_mech_rules_dict: cannot inherit from invalid origin type: {origin_type}"
+            )
+    return rules_dict
+
+
 def report_topology(
     env: AbstractEnv, cell: BiophysCell, node: Optional[SectionNode] = None
 ) -> None:
@@ -1782,12 +1817,14 @@ def init_circuit_context(
                             syn_name,
                             zip_longest(
                                 weights_syn_ids,
-                                [
-                                    {"weight": Promise(expr_closure, [x])}
-                                    for x in weights_values
-                                ]
-                                if expr_closure
-                                else [{"weight": x} for x in weights_values],
+                                (
+                                    [
+                                        {"weight": Promise(expr_closure, [x])}
+                                        for x in weights_values
+                                    ]
+                                    if expr_closure
+                                    else [{"weight": x} for x in weights_values]
+                                ),
                             ),
                             multiple=multiple_weights,
                             append=append_weights,
@@ -2058,11 +2095,16 @@ def make_biophys_cell(
         )
         _, tree_dict = next(tree_attr_iter)
 
+    hoc_cell = make_hoc_cell(
+        env, population_name, gid, neurotree_dict=tree_dict
+    )
+
     cell = BiophysCell(
+        env=env,
         gid=gid,
         population_name=population_name,
+        hoc_cell=hoc_cell,
         neurotree_dict=tree_dict,
-        env=env,
         mech_file_path=mech_file_path,
         mech_dict=mech_dict,
     )
@@ -2474,3 +2516,14 @@ def record_cell(
                             recs.append(rec)
 
     return recs
+
+
+default_reduced_cell_constructors = {
+    "pr_nrn": make_PR_cell,
+    "brk_nrn": make_BRK_cell,
+    "sc_nrn": make_SC_cell,
+}
+
+
+def get_reduced_cell_constructor(template_name):
+    return default_reduced_cell_constructors.get(template_name.lower(), None)

src/miv_simulator/clamps/cell.py

@@ -111,23 +111,11 @@ def init_biophys_cell(
     else:
         correct_for_spines_flag = False
 
+    reduced_cons = cells.get_reduced_cell_constructor(template_name)
+
     ## Load cell gid and its synaptic attributes and connection data
-    if template_name.lower() == "pr_nrn":
-        cell = cells.make_PR_cell(
-            env,
-            pop_name,
-            gid,
-            tree_dict=cell_dict.get("morph", None),
-            synapses_dict=cell_dict.get("synapse", None),
-            connection_graph=cell_dict.get("connectivity", None),
-            weight_dict=cell_dict.get("weight", None),
-            mech_dict=mech_dict,
-            load_synapses=True,
-            load_weights=load_weights,
-            load_edges=load_connections,
-        )
-    elif template_name.lower() == "sc_nrn":
-        cell = cells.make_SC_cell(
+    if reduced_cons is not None:
+        cell = reduced_cons(
             env,
             pop_name,
             gid,