remove placement-algo dep

requirements/base.pip

@@ -1,4 +1,3 @@
-atlas_analysis>=0.0.5
 bluepymm>=0.8.5
 bluepyparallel>=0.0.8
 brainbuilder>=0.20
@@ -19,7 +18,6 @@ neurom>=3.2.2,<4
 neurots>=3.6,<4
 numpy>=1.26.4
 pandas>=1.5.3
-placement_algorithm>=2.3.1
 PyYAML>=6
 region_grower>=1.3,<2
 scipy>=1.10

src/synthesis_workflow/synthesis.py

@@ -19,8 +19,13 @@
 from neurom.check.morphology_checks import has_apical_dendrite
 from neurom.core.dataformat import COLS
 from neurots import extract_input
-from placement_algorithm.app import utils
-from placement_algorithm.app.choose_morphologies import Master as ChooseMorphologyMaster
+
+try:
+    from placement_algorithm.app.choose_morphologies import Master as ChooseMorphologyMaster
+
+    with_placement_algo = True
+except ImportError:
+    with_placement_algo = False
 from tmd.io.io import load_population
 from tqdm import tqdm
 from voxcell import CellCollection
@@ -279,7 +284,7 @@ def create_axon_morphologies_tsv(
             f"Either 'morphs_df_path' or all the following parameter should be None: {_params}"
         )
 
-    if all(check_placement_params.values()):
+    if all(check_placement_params.values()) and with_placement_algo:
         L.info("Use placement algorithm for axons")
 
         kwargs = {
@@ -320,7 +325,7 @@ def create_axon_morphologies_tsv(
                 random_state=42,
             )["name"].to_list()
 
-        utils.dump_morphology_list(axon_morphs, axon_morphs_path)
+        axon_morphs.to_csv(axon_morphs_path, sep="\t", na_rep="N/A")
 
 
 def get_target_length(soma_layer, target_layer, cortical_thicknesses):

src/synthesis_workflow/tasks/synthesis.py

@@ -21,7 +21,6 @@
 from neurots.generate.orientations import fit_3d_angles
 from neurots.validator import validate_neuron_distribs
 from neurots.validator import validate_neuron_params
-from placement_algorithm.app.compact_annotations import _collect_annotations
 from region_grower.synthesize_morphologies import SynthesizeMorphologies
 from region_grower.utils import NumpyEncoder
 from tqdm import tqdm
@@ -33,6 +32,7 @@
 from synthesis_workflow.synthesis import get_axon_base_dir
 from synthesis_workflow.synthesis import get_neurite_types
 from synthesis_workflow.synthesis import rescale_morphologies
+from synthesis_workflow.utils import collect_annotations
 from synthesis_workflow.tasks.circuit import SliceCircuit
 from synthesis_workflow.tasks.config import CircuitConfig
 from synthesis_workflow.tasks.config import DiametrizerConfig
@@ -280,7 +280,7 @@ class CreateAnnotationsFile(WorkflowTask):
     def run(self):
         """Actual process of the task."""
         # pylint: disable=protected-access
-        annotations = _collect_annotations(self.annotation_dir, self.morph_db)
+        annotations = collect_annotations(self.annotation_dir, self.morph_db)
 
         with open(self.destination, "w", encoding="utf-8") as f:
             json.dump(annotations, f, indent=4, sort_keys=True)

src/synthesis_workflow/utils.py

@@ -3,6 +3,8 @@
 import json
 import logging
 from pathlib import Path
+from tqdm import tqdm
+import lxml.etree
 
 import dictdiffer
 import numpy as np
@@ -192,3 +194,40 @@ def create_circuit_config(nodes_file, morphology_path):
             "edges": [],
         }
     }
+
+
+def parse_annotations(filepath):
+    """Parse XML with morphology annotations."""
+    etree = lxml.etree.parse(filepath)
+    result = {}
+    for elem in etree.findall("placement"):
+        attr = dict(elem.attrib)
+        rule_id = attr.pop("rule")
+        if rule_id in result:
+            raise KeyError(f"Duplicate annotation for rule '{rule_id}'")
+        result[rule_id] = attr
+    return result
+
+
+def parse_morphdb(filepath):
+    """Parse (ext)neuronDB.dat file."""
+    columns = ["morphology", "layer", "mtype"]
+    first_row = pd.read_csv(filepath, sep=r"\s+", header=None, nrows=1)
+    if first_row.shape[1] > 3:
+        columns.append("etype")
+    return pd.read_csv(
+        filepath, sep=r"\s+", names=columns, usecols=columns, na_filter=False, dtype={"layer": str}
+    )
+
+
+def collect_annotations(annotation_dir, morphdb_path):
+    result = {}
+    if morphdb_path is None:
+        for filepath in tqdm(Path(annotation_dir).glob("*.xml")):
+            result[Path(filepath).stem] = parse_annotations(filepath)
+    else:
+        morphdb = parse_morphdb(morphdb_path)
+        for morph in tqdm(morphdb["morphology"].unique()):
+            filepath = Path(annotation_dir) / (morph + ".xml")
+            result[morph] = parse_annotations(filepath)
+    return result