From 14672e0318e176af295cd213fe5cd846edfce631 Mon Sep 17 00:00:00 2001
From: Syed Hussain Ather <shussainather@gmail.com>
Date: Fri, 14 Jun 2024 15:52:35 -0400
Subject: [PATCH] Add SWC to NeuroML converter and update documentation

---
 converters/swc_to_nml.py | 46 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 converters/swc_to_nml.py

diff --git a/converters/swc_to_nml.py b/converters/swc_to_nml.py
new file mode 100644
index 00000000..e5e97595
--- /dev/null
+++ b/converters/swc_to_nml.py
@@ -0,0 +1,46 @@
+import neuroml
+from neuroml import Segment, SegmentGroup, Morphology, Cell
+import neuroml.writers as writers
+
+def parse_swc(file_path):
+    with open(file_path, 'r') as file:
+        lines = file.readlines()
+
+    segments = []
+    for line in lines:
+        if not line.startswith('#'):
+            parts = line.strip().split()
+            if len(parts) == 7:
+                id, type, x, y, z, radius, parent = map(float, parts)
+                segment = Segment(
+                    id=int(id),
+                    parent=int(parent) if int(parent) != -1 else None,
+                    proximal=None,
+                    distal=None,
+                    name=f"type_{int(type)}",
+                    group=f"custom_{int(type)}" if int(type) > 3 else None
+                )
+                segments.append(segment)
+
+    return segments
+
+def create_neuroml(segments, output_path):
+    cell = Cell(id="swc_cell")
+    morphology = Morphology(id="morph")
+    cell.morphology = morphology
+
+    for segment in segments:
+        morphology.segments.append(segment)
+
+    doc = neuroml.NeuroMLDocument(id="swc_to_nml")
+    doc.cells.append(cell)
+
+    writers.NeuroMLWriter.write(doc, output_path)
+    print(f"NeuroML file written to {output_path}")
+
+if __name__ == "__main__":
+    swc_file = "path/to/your/input.swc"
+    nml_file = "path/to/your/output.nml"
+    segments = parse_swc(swc_file)
+    create_neuroml(segments, nml_file)
+