Add task to build a circuit MV3 file

Change-Id: I239c3d97a364a7437fffa9ed3921eb1b1a45a4fe

synthesis_workflow/synthesis.py

@@ -12,6 +12,7 @@
 from joblib import Parallel
 from tqdm import tqdm
 
+from brainbuilder.app.cells import _place as place
 from morphio.mut import Morphology
 from neuroc.scale import scale_section
 from neuroc.scale import ScaleParameters
@@ -542,3 +543,34 @@ def _process_scaling_rule(
             slope,
             intercept,
         )
+
+
+def build_circuit(
+    cell_composition_path,
+    mtype_taxonomy_path,
+    atlas_path,
+    density_factor=0.01,
+    seed=None,
+):
+    """Based on YAML cell composition recipe, build a circuit as MVD3 file with:
+    - cell positions
+    - required cell properties: 'layer', 'mtype', 'etype'
+    - additional cell properties prescribed by the recipe and / or atlas
+    """
+    if seed is not None:
+        np.random.seed(seed)
+    return place(
+        composition_path=cell_composition_path,
+        mtype_taxonomy_path=mtype_taxonomy_path,
+        atlas_url=atlas_path,
+        mini_frequencies_path=None,
+        atlas_cache=None,
+        region=None,
+        mask_dset=None,
+        density_factor=density_factor,
+        soma_placement="basic",
+        atlas_properties=None,
+        sort_by=None,
+        append_hemisphere=False,
+        input_path=None,
+    )

synthesis_workflow/tasks/luigi_tools.py

@@ -124,7 +124,11 @@ def __getattribute__(self, name):
         return tmp
 
     def __setattr__(self, name, value):
-        if value is None and name in self.get_param_names():
+        try:
+            global_params = self._global_params
+        except AttributeError:
+            global_params = {}
+        if value is None and name in global_params:
             L.warning(
                 "The Parameter '%s' of the task '%s' is set to None, thus the global "
                 "value will be taken frow now on",

synthesis_workflow/tasks/synthesis.py

@@ -14,6 +14,7 @@
 
 from ..synthesis import add_scaling_rules_to_parameters
 from ..synthesis import apply_substitutions
+from ..synthesis import build_circuit
 from ..synthesis import build_distributions
 from ..synthesis import create_axon_morphologies_tsv
 from ..synthesis import get_axon_base_dir
@@ -398,3 +399,42 @@ def run(self):
     def output(self):
         """"""
         return luigi.LocalTarget(self.rescaled_morphs_df_path)
+
+
+class BuildCircuit(WorkflowTask):
+    """Generate cell positions and me-types from atlas, compositions and taxonomy.
+
+    Args:
+        cell_composition_path (str): path to the cell composition file (YAML)
+        mtype_taxonomy_path (str): path to the taxonomy file (tsv)
+        density_factor (float): density factor
+        seed (int): pseudo-random generator seed
+    """
+
+    cell_composition_path = luigi.Parameter(
+        description="path to the cell composition file (YAML)"
+    )
+    mtype_taxonomy_path = luigi.Parameter(description="path to the taxonomy file (tsv)")
+    density_factor = luigi.NumericalParameter(
+        default=0.01,
+        var_type=float,
+        min_value=0,
+        max_value=1,
+        description="The density of positions generated from the atlas",
+    )
+    seed = luigi.IntParameter(default=None, description="pseudo-random generator seed")
+
+    def run(self):
+        """"""
+        cells = build_circuit(
+            self.cell_composition_path,
+            self.mtype_taxonomy_path,
+            CircuitConfig().atlas_path,
+            self.density_factor,
+            self.seed,
+        )
+        cells.save(self.output().path)
+
+    def output(self):
+        """"""
+        return luigi.LocalTarget(CircuitConfig().circuit_somata_path)