Use MorphIO Collections. (#4)

.pylintrc

@@ -1,5 +1,5 @@
 [MESSAGES CONTROL]
-disable=fixme,invalid-name,len-as-condition,no-else-return,cyclic-import,import-outside-toplevel,useless-object-inheritance,self-assigning-variable,line-too-long,logging-fstring-interpolation,too-many-locals,too-many-branches,too-many-statements,no-member,unspecified-encoding,too-many-arguments,dangerous-default-value,similarities,too-many-lines,consider-using-f-string,broad-exception-caught,too-many-return-statements,eval-used
+disable=fixme,invalid-name,len-as-condition,no-else-return,cyclic-import,import-outside-toplevel,useless-object-inheritance,self-assigning-variable,line-too-long,logging-fstring-interpolation,too-many-locals,too-many-branches,too-many-statements,no-member,unspecified-encoding,too-many-arguments,dangerous-default-value,similarities,too-many-lines,consider-using-f-string,broad-exception-caught,too-many-return-statements,eval-used,too-many-positional-arguments
 
 [FORMAT]
 # Maximum number of characters on a single line.

connectome_manipulator/access_functions.py

@@ -5,8 +5,6 @@
 
 """Collection of function for flexible nodes/edges access, to be used by model building and manipulation operations"""
 
-from pathlib import Path
-
 import numpy as np
 import pandas as pd
 
@@ -57,20 +55,6 @@ def get_nodes(nodes, selection=None):
     return result
 
 
-def get_morphology_paths(nodes, selection, morpho_helper, extension="swc"):
-    """Return paths to morphology files corresponding to `selection`.
-
-    Args:
-        nodes: a bluepysnap node set
-        selection (libsonata.Selection): a selection of nodes
-        morpho_helper: a bluepysnap MorphoHelper instance
-        extension (str): expected filetype extension of the morph file.
-    """
-    morpho_dir = morpho_helper.get_morphology_dir(extension)
-    result = get_nodes(nodes, selection)
-    return [Path(morpho_dir, f"{name}.{extension}") for name in result[Node.MORPHOLOGY]]
-
-
 def orientations(nodes, node_sel=None):
     """Node orientation(s) as a list of numpy arrays.
 

connectome_manipulator/connectome_manipulation/manipulation/base.py

@@ -15,7 +15,7 @@
 
 from bluepysnap.morph import MorphHelper
 from bluepysnap.sonata_constants import Node
-from morphio.mut import Morphology
+from morphio import Collection
 import numpy as np
 
 from connectome_manipulator import access_functions
@@ -94,12 +94,13 @@ def __init__(self, nodes, writer=None, split_index=0, split_total=1):
 
     def _get_tgt_morphs(self, morph_ext, tgt_node_sel):
         """Access function (incl. transformation!), using specified format (swc/h5/...)"""
-        morphology_paths = access_functions.get_morphology_paths(
-            self.nodes[1], tgt_node_sel, self.morpho_helper, morph_ext
-        )
+        morpho_dir = self.morpho_helper.get_morphology_dir(morph_ext)
+        collection = Collection(morpho_dir, [f".{morph_ext}"])
+        result = access_functions.get_nodes(self.nodes[1], tgt_node_sel)
+
         morphologies = []
-        for mp in morphology_paths:
-            morphologies.append(Morphology(mp))
+        for morpho_name in result[Node.MORPHOLOGY]:
+            morphologies.append(collection.load(morpho_name, mutable=True))
         return self._transform(morphologies, tgt_node_sel)
 
     def _transform(self, morphs, node_sel):

connectome_manipulator/connectome_manipulation/manipulation/conn_rewiring.py

@@ -337,7 +337,7 @@ def apply(
             tgt_morphs = [None] * num_tgt
 
         log.info(
-            f"Rewiring afferent {syn_class} connections to {num_tgt} ({amount_pct}%) of {len(tgt_sel)} target neurons in current split (total={num_tgt_total}, sel_src={sel_src}, sel_dest={sel_dest}, keep_indegree={keep_indegree}, gen_method={gen_method}, keep_conns={keep_conns}, reuse_conns={reuse_conns}, syn_pos_mode={syn_pos_mode}{', morph_ext=' + morph_ext if syn_pos_mode=='random' else ''}, rewire_mode={rewire_mode})"
+            f"Rewiring afferent {syn_class} connections to {num_tgt} ({amount_pct}%) of {len(tgt_sel)} target neurons in current split (total={num_tgt_total}, sel_src={sel_src}, sel_dest={sel_dest}, keep_indegree={keep_indegree}, gen_method={gen_method}, keep_conns={keep_conns}, reuse_conns={reuse_conns}, syn_pos_mode={syn_pos_mode}{', morph_ext=' + morph_ext if syn_pos_mode == 'random' else ''}, rewire_mode={rewire_mode})"
         )
 
         # Init/reset static variables (function attributes) related to generation methods which need only be initialized once [for better performance]

connectome_manipulator/model_building/conn_props.py

@@ -397,7 +397,7 @@ def merge_uniq(vals, cnts):
             conn_prop_model["p"][sidx, tidx, pidx] = c / np.sum(c)
 
     log.info(
-        f"Interpolated {missing_list.shape[0]} missing values. Interpolation level counts: { {k: level_counts[k] for k in sorted(level_counts.keys())} }"
+        f"Interpolated {missing_list.shape[0]} missing values. Interpolation level counts: {{k: level_counts[k] for k in sorted(level_counts.keys())}}"
     )
 
     # Create model properties dictionary

pyproject.toml

@@ -9,4 +9,3 @@ include = 'connectome_manipulator\/.*\.py$|tests\/.*\.py$|doc\/source\/conf\.py$
 pythonpath = [
   "."
 ]
-