Separate neuroml load

Author: pgleeson

.gitignore

@@ -0,0 +1 @@
+__pycache__

load.py

@@ -2,81 +2,6 @@
 
 import sys
 
-from pyneuroml import pynml
-from pyneuroml.utils import extract_position_info
-from neuroml import Cell
-
-
-pl = pv.Plotter()
-
-filename = sys.argv[1] if len(sys.argv) == 2 else "c302_D_Full.net.nml"
-
-nml_doc = pynml.read_neuroml2_file(filename, include_includes=True)
-
-print("Loaded NeuroML file: %s" % filename)
-
-
-(
-    cell_id_vs_cell,
-    pop_id_vs_cell,
-    positions,
-    pop_id_vs_color,
-    pop_id_vs_radii,
-) = extract_position_info(nml_doc, False)
-
-factor = 0.2
-
-while pop_id_vs_cell:
-    pop_id, cell = pop_id_vs_cell.popitem()
-    pos_pop = positions[pop_id]  # type: typing.Dict[typing.Any, typing.List[float]]
-
-    print("Pop: %s has %i of component %s" % (pop_id, len(pos_pop), cell.id))
-
-    radius = pop_id_vs_radii[pop_id] if pop_id in pop_id_vs_radii else 10
-    color = pop_id_vs_color[pop_id] if pop_id in pop_id_vs_color else "r"
-
-    if type(cell) is Cell:
-        print("Loading a cell with %i segments" % len(cell.morphology.segments))
-
-        cell_meshes = pv.MultiBlock()
-
-        for seg in cell.morphology.segments:
-            p = cell.get_actual_proximal(seg.id)
-            d = seg.distal
-            width = (p.diameter + d.diameter) / 4
-            # print("Creating %s" % (seg))
-
-            if cell.get_segment_length(seg.id) == 0:
-                seg_mesh = pv.Sphere(
-                    center=(p.x * factor, p.z * factor, -1 * p.y * factor),
-                    radius=p.diameter * factor / 2,
-                )
-
-                pl.add_mesh(seg_mesh, color=color)
-            else:
-                seg_mesh = pv.Tube(
-                    pointa=(p.x * factor, p.z * factor, -1 * p.y * factor),
-                    pointb=(d.x * factor, d.z * factor, -1 * d.y * factor),
-                    resolution=1,
-                    radius=width * factor,
-                    n_sides=15,
-                )
-
-            cell_meshes.append(seg_mesh)
-
-        while pos_pop:
-            cell_index, pos = pos_pop.popitem()
-            pp = [pos[0] * factor, pos[2] * factor, -1 * pos[1] * factor]
-            print("Plotting %s(%i) at %s, %s" % (cell.id, cell_index, pos, pp))
-            cell_mesh = cell_meshes.copy()
-            for i in range(len(cell_mesh)):
-                cell_mesh[i].translate(pp, inplace=True)
-            pl.add_mesh(cell_mesh, color=color, smooth_shading=True)
-
-    else:
-        sphere = pv.Sphere(center=(pos[0], pos[1], pos[2]), radius=radius)
-
-        pl.add_mesh(sphere, color=color)
 
 '''
 
@@ -237,8 +162,15 @@ def create_mesh(step):
 
 '''
 
-pl.set_background("white")
-pl.add_axes()
 
+if __name__ == "__main__":
+    pl = pv.Plotter()
+
+    from neuromlmodel import add_neuroml_model
+
+    add_neuroml_model(pl)
+    pl.set_background("white")
+    pl.add_axes()
 
-pl.show()
+    if "-nogui" not in sys.argv:
+        pl.show()

neuromlmodel.py

@@ -0,0 +1,88 @@
+import pyvista as pv
+
+import sys
+
+from pyneuroml import pynml
+from pyneuroml.utils import extract_position_info
+from neuroml import Cell
+
+
+def add_neuroml_model(pl):
+    filename = "c302_D_Full.net.nml"
+
+    nml_doc = pynml.read_neuroml2_file(filename, include_includes=True)
+
+    print("Loaded NeuroML file: %s" % filename)
+
+    (
+        cell_id_vs_cell,
+        pop_id_vs_cell,
+        positions,
+        pop_id_vs_color,
+        pop_id_vs_radii,
+    ) = extract_position_info(nml_doc, False)
+
+    factor = 0.2
+
+    while pop_id_vs_cell:
+        pop_id, cell = pop_id_vs_cell.popitem()
+        pos_pop = positions[pop_id]  # type: typing.Dict[typing.Any, typing.List[float]]
+
+        print("Pop: %s has %i of component %s" % (pop_id, len(pos_pop), cell.id))
+
+        radius = pop_id_vs_radii[pop_id] if pop_id in pop_id_vs_radii else 10
+        color = pop_id_vs_color[pop_id] if pop_id in pop_id_vs_color else "r"
+
+        if type(cell) is Cell:
+            print("Loading a cell with %i segments" % len(cell.morphology.segments))
+
+            cell_meshes = pv.MultiBlock()
+
+            for seg in cell.morphology.segments:
+                p = cell.get_actual_proximal(seg.id)
+                d = seg.distal
+                width = (p.diameter + d.diameter) / 4
+                # print("Creating %s" % (seg))
+
+                if cell.get_segment_length(seg.id) == 0:
+                    seg_mesh = pv.Sphere(
+                        center=(p.x * factor, p.z * factor, -1 * p.y * factor),
+                        radius=p.diameter * factor / 2,
+                    )
+
+                    pl.add_mesh(seg_mesh, color=color)
+                else:
+                    seg_mesh = pv.Tube(
+                        pointa=(p.x * factor, p.z * factor, -1 * p.y * factor),
+                        pointb=(d.x * factor, d.z * factor, -1 * d.y * factor),
+                        resolution=1,
+                        radius=width * factor,
+                        n_sides=15,
+                    )
+
+                cell_meshes.append(seg_mesh)
+
+            while pos_pop:
+                cell_index, pos = pos_pop.popitem()
+                pp = [pos[0] * factor, pos[2] * factor, -1 * pos[1] * factor]
+                print("Plotting %s(%i) at %s, %s" % (cell.id, cell_index, pos, pp))
+                cell_mesh = cell_meshes.copy()
+                for i in range(len(cell_mesh)):
+                    cell_mesh[i].translate(pp, inplace=True)
+                pl.add_mesh(cell_mesh, color=color, smooth_shading=True)
+
+        else:
+            sphere = pv.Sphere(center=(pos[0], pos[1], pos[2]), radius=radius)
+
+            pl.add_mesh(sphere, color=color)
+
+
+if __name__ == "__main__":
+    pl = pv.Plotter()
+
+    add_neuroml_model(pl)
+    pl.set_background("white")
+    pl.add_axes()
+
+    if "-nogui" not in sys.argv:
+        pl.show()

test.sh

@@ -3,4 +3,5 @@ set -ex
 ruff format *.py
 ruff check *.py
 
-python load.py
+python neuromlmodel.py -nogui 
+python load.py -nogui