Add neuron.obj blender file

Author: pgleeson

.github/workflows/non_omv.yml

@@ -25,6 +25,5 @@ jobs:
     - name: Run Python scripts
       run: |
         echo "Running non OMV tests..."
-        cd Python
         pip install -r requirements.txt
         ./test.sh

app.py

@@ -1,6 +1,7 @@
 from neuromlmodel import add_neuroml_model  # noqa: F401
 from siberneticmodel import add_sibernetic_model  # noqa: F401
 from virtualworm import add_virtualworm_muscles  # noqa: F401
+from virtualworm import add_virtualworm_neurons  # noqa: F401
 
 import pyvista as pv
 import sys
@@ -37,12 +38,16 @@
 
 plotter = pv.Plotter()
 
-add_neuroml_model(plotter, somas_only=True)
-add_sibernetic_model(plotter)
+
 add_virtualworm_muscles(plotter)
+# add_virtualworm_neurons(plotter)
+add_neuroml_model(plotter, "NeuroML2/c302_D_Full.net.nml", somas_only=True)
+add_sibernetic_model(plotter)
 
 
 plotter.set_viewup([0, 10, 0])
+# plotter.remove_scalar_bar("RegionId")
+# plotter.remove_scalar_bar("types")
 
 
 print("Created the scene...")

load.py

@@ -1,181 +1,25 @@
 import pyvista as pv
-
 import sys
 
-
-'''
-
-points = []
-
-types = []
-
-file = "pressure_buffer.txt"
-file = "position_buffer.txt"
-if len(sys.argv) == 2:
-    file = sys.argv[1]
-
-colours = {1.1: "lightblue", 2.1: "green", 2.2: "turquoise", 3: "#eeeeee"}
-colours = {1.1: "blue", 2.2: "turquoise"}
-
-line_count = 0
-pcount = 0
-
-all_points = []
-all_point_types = []
-
-time_count = 0
-
-logStep = None
-
-include_boundary = False
-
-for line in open(file):
-    ws = line.split()
-    # print(ws)
-    if line_count == 6:
-        numOfElasticP = int(ws[0])
-    if line_count == 7:
-        numOfLiquidP = int(ws[0])
-    if line_count == 8:
-        numOfBoundaryP = int(ws[0])
-    if line_count == 9:
-        timeStep = float(ws[0])
-    if line_count == 10:
-        logStep = int(ws[0])
-
-    if len(ws) == 4:
-        type = float(ws[3])
-
-        if not (type == 3 and not include_boundary):
-            points.append([float(ws[0]), float(ws[1]), float(ws[2])])
-            types.append(type)
-
-    if logStep is not None:
-        pcount += 1
-
-        if pcount == numOfBoundaryP + numOfElasticP + numOfLiquidP:
-            print(
-                "End of one batch of %i added, %i total points at line %i, time: %i"
-                % (len(points), pcount, line_count, time_count)
-            )
-            all_points.append(points)
-            all_point_types.append(types)
-
-            points = []
-            types = []
-            pcount = 0
-            numOfBoundaryP = 0
-
-            time_count += 1
-
-    line_count += 1
-
-# all_points_np = np.array(all_points)
-
-print(
-    "Loaded positions with %i elastic, %i liquid and %i boundary points (%i total), %i lines"
-    % (
-        numOfElasticP,
-        numOfLiquidP,
-        numOfBoundaryP,
-        numOfElasticP + numOfLiquidP + numOfBoundaryP,
-        line_count,
-    )
-)
-
-print("Num of time points found: %i" % len(all_points))
-
-pl.set_background("lightgrey")
-
-last_mesh = None
-
-
-import time
-
-def create_mesh(step):
-    step_count = step
-    value = step_count
-    global last_mesh
-    index = int(value)
-
-    print("Changing to time point: %s (%s) " % (index, value))
-    curr_points = all_points[index]
-    curr_types = all_point_types[index]
-    if last_mesh is None:
-        last_mesh = pv.PolyData(curr_points)
-        last_mesh["types"] = curr_types
-        last_mesh.translate((0, -1000, 0), inplace=True)
-        print(last_mesh)
-
-        # last_actor =
-        pl.add_mesh(
-            last_mesh,
-            render_points_as_spheres=True,
-            cmap=[c for c in colours.values()],
-            point_size=3,
-        )
-    else:
-        last_mesh.points = curr_points
-        last_mesh.translate((0, -00, -100), inplace=True)
-
-    pl.render()
-
-    time.sleep(0.1)
-
-    return
-
-
-create_mesh(0)
-
-max_time = len(all_points) - 1
-pl.add_slider_widget(create_mesh, rng=[0, max_time], value=max_time, title="Time point")
-pl.add_timer_event(max_steps=5, duration=2, callback=create_mesh)
-
-
-mesh = pv.read("bwm.obj")
-mesh.scale(20, inplace=True)
-mesh.translate((-40, 0, 0), inplace=True)
-
-pl.add_mesh(mesh, smooth_shading=True, color="green")
-
-mesh2 = pv.read("neurons.obj")
-mesh2.scale(20, inplace=True)
-mesh2.translate((-80, 0, 0), inplace=True)
-
-pl.add_mesh(mesh2, smooth_shading=True, color="orange")
-"""
-conn = mesh2.connectivity('all')
-print(conn)
-# Format scalar bar text for integer values.
-scalar_bar_args = dict(
-    fmt='%.f',
-)
-
-cpos = [(10.5, 12.2, 18.3), (0.0, 0.0, 0.0), (0.0, 1.0, 0.0)]
-
-conn.plot(
-    categories=True,
-    cmap='jet',
-    scalar_bar_args=scalar_bar_args,
-    cpos=cpos,
-)"""
-
-'''
-
+from virtualworm import add_virtualworm_muscles
+from virtualworm import add_virtualworm_neurons
+from neuromlmodel import add_neuroml_model
+from siberneticmodel import add_sibernetic_model
 
 if __name__ == "__main__":
-    pl = pv.Plotter()
+    plotter = pv.Plotter()
 
-    from virtualworm import add_virtualworm_muscles
-    from neuromlmodel import add_neuroml_model
-    from siberneticmodel import add_sibernetic_model
+    add_virtualworm_muscles(plotter)
+    add_virtualworm_neurons(plotter)
+    add_neuroml_model(plotter, "NeuroML2/c302_D_Full.net.nml", somas_only=False)
+    add_sibernetic_model(plotter)
 
-    add_virtualworm_muscles(pl)
-    add_neuroml_model(pl, somas_only=True)
-    add_sibernetic_model(pl)
+    plotter.set_background("white")
+    plotter.set_viewup([0, 10, 0])
 
-    pl.set_background("white")
-    pl.add_axes()
+    plotter.add_axes()
+    plotter.remove_scalar_bar("RegionId")
+    plotter.remove_scalar_bar("types")
 
     if "-nogui" not in sys.argv:
-        pl.show()
+        plotter.show()