Latest

.github/workflows/ci-make.yml

@@ -62,7 +62,8 @@ jobs:
         pip install pyNeuroML
         pip install numpy matplotlib
         pip install ruff 
-
+        pip install scipy
+
     - name: Test directly running main program
       run: |
         ./main -p 6  # Note: small population of 6 for quick runtime

.test.2018.mep

@@ -3,4 +3,5 @@ system: Testing activity of some neurons
 experiments:
     Test:
         expected:
-            spike times: [0.17, 8.57, 18.73, 29.09, 39.49, 49.85]
+            spike times: [0.09, 7.21, 17.45, 28.25, 39.05, 49.85]
+

.test.2018gen.mep

@@ -0,0 +1,12 @@
+system: Testing activity of some neurons
+
+experiments:
+    Test:
+        expected:
+            spike times: [0.25, 4.93, 18.25]
+    Test2:
+        expected:
+            spike times: [0.25, 4.93, 18.25]
+    Test3:
+        expected:
+            spike times: [0.25, 4.93, 18.25]

.test.W2D18gen.omt

@@ -0,0 +1,18 @@
+# Framework for running automated tests on Open Source Brain
+# See https://github.com/OpenSourceBrain/osb-model-validation for more details
+
+target: testW2D18gen.py
+engine: Brian2  # This installs Brian2, but all we really need is a Python environment to run the script in
+mep: .test.2018gen.mep
+experiments:
+  Test:
+    observables:
+      spike times:
+        file: 
+          path: testruns/exW2D18gen/act.dat
+          columns: [0, 1]
+          scaling: [1, 1]
+        spike detection: 
+          method: threshold
+          threshold: 1
+        tolerance: 0

.test.W2DCE.mep

@@ -3,4 +3,10 @@ system: Testing activity of some neurons
 experiments:
     Test:
         expected:
-            spike times: [0.405, 8.555]
+            spike times: [0.405, 8.555]
+    Test2:
+        expected:
+            spike times: [0.405, 8.005, 12.155, 17.355]
+    Test3:
+        expected:
+            spike times: [0.455, 8.055, 12.205, 17.355]

.test.W2DSR.omt

@@ -9,7 +9,29 @@ experiments:
     observables:
       spike times:
         file: 
-          path: experiments/exW2DSR/act.dat
+          path: testruns/exW2DSR/act.dat
+          columns: [0,3]
+          scaling: [1, 1]
+        spike detection: 
+          method: threshold
+          threshold: 2
+        tolerance: 0
+  Test2:
+    observables:
+      spike times:
+        file: 
+          path: testruns/exW2DSR_nml/act.dat
+          columns: [0,3]
+          scaling: [1, 1]
+        spike detection: 
+          method: threshold
+          threshold: 2
+        tolerance: 0
+  Test3:
+    observables:
+      spike times:
+        file: 
+          path: testruns/exW2DSR_nml_musc/act.dat
           columns: [0,3]
           scaling: [1, 1]
         spike detection: 

.test.W2DSR18.omt

@@ -0,0 +1,19 @@
+# Framework for running automated tests on Open Source Brain
+# See https://github.com/OpenSourceBrain/osb-model-validation for more details
+
+target: testW2DSR18.py
+engine: Brian2  # This installs Brian2, but all we really need is a Python environment to run the script in
+mep: .test.2018gen.mep
+experiments:
+  Test:
+    observables:
+      spike times:
+        file: 
+          path: testruns/exW2DSR18/act.dat
+          columns: [0, 1]
+          scaling: [1, 1]
+        spike detection: 
+          method: threshold
+          threshold: 1
+        tolerance: 0
+

.test.W2DSR21.mep

@@ -0,0 +1,12 @@
+system: Testing activity of some neurons
+
+experiments:
+    Test:
+        expected:
+            spike times: [50.155, 52.455, 54.705, 57.005, 59.255, 61.555, 63.805, 66.105, 68.355, 70.605, 72.905, 75.155, 77.455, 79.705, 82.005, 84.255, 86.555, 88.805, 91.105, 93.355, 95.605, 97.905, 100.155, 102.455, 104.705, 107.005]
+    Test2:
+        expected:
+            spike times: [50.155, 52.455, 54.705, 57.005, 59.255, 61.555, 63.805, 66.105, 68.355, 70.605, 72.905, 75.155, 77.455, 79.705, 82.005, 84.255, 86.555, 88.805, 91.105, 93.355, 95.605, 97.905, 100.155, 102.455, 104.705, 107.005]
+    Test3:
+        expected:
+            spike times: [50.155, 52.455, 54.705, 57.005, 59.255, 61.555, 63.805, 66.105, 68.355, 70.605, 72.905, 75.155, 77.455, 79.705, 82.005, 84.255, 86.555, 88.805, 91.105, 93.355, 95.605, 97.905, 100.155, 102.455, 104.705, 107.005]

.test.W2DSR21.omt

@@ -0,0 +1,40 @@
+# Framework for running automated tests on Open Source Brain
+# See https://github.com/OpenSourceBrain/osb-model-validation for more details
+
+target: testW2DSR21.py
+engine: Brian2  # This installs Brian2, but all we really need is a Python environment to run the script in
+mep: .test.W2DSR21.mep
+experiments:
+  Test:
+    observables:
+      spike times:
+        file: 
+          path: testruns/exW2DSR21_nml/act.dat
+          columns: [0, 3]
+          scaling: [1, 1]
+        spike detection: 
+          method: threshold
+          threshold: 0.5
+        tolerance: 0.031
+  Test2:
+    observables:
+      spike times:
+        file: 
+          path: testruns/exW2DSR21/act.dat
+          columns: [0, 3]
+          scaling: [1, 1]
+        spike detection: 
+          method: threshold
+          threshold: 0.5
+        tolerance: 0
+  Test3:
+    observables:
+      spike times:
+        file: 
+          path: testruns/exW2DSR21_nml_musc/act.dat
+          columns: [0, 3]
+          scaling: [1, 1]
+        spike detection: 
+          method: threshold
+          threshold: 0.5
+        tolerance: 0.031

.test.osc_sim.mep

@@ -0,0 +1,12 @@
+system: Testing activity of some neurons
+
+experiments:
+    Test2:
+        expected:
+            spike times: [11.005, 13.655, 16.305, 18.955]
+    Test3:
+        expected:
+            spike times: [11.005, 13.655, 16.305, 18.955]
+    Test4:
+        expected:
+            spike times: [11.005, 13.655, 16.305, 18.955]

.test.osc_sim.omt

@@ -0,0 +1,41 @@
+# Framework for running automated tests on Open Source Brain
+# See https://github.com/OpenSourceBrain/osb-model-validation for more details
+
+target: run_osc_sim.py
+engine: Brian2  # This installs Brian2, but all we really need is a Python environment to run the script in
+mep: .test.osc_sim.mep
+experiments:
+    Test2:
+        observables:
+            spike times:
+                file: 
+                    path: experiments/osc_sim_nml/act.dat
+                    columns: [0, 3]
+                    scaling: [1, 1]
+                spike detection: 
+                    method: threshold
+                    threshold: 0.5
+                tolerance: 0.0
+
+    Test3:
+        observables:
+            spike times:
+                file: 
+                    path: experiments/osc_sim_nml_musc/act.dat
+                    columns: [0, 3]
+                    scaling: [1, 1]
+                spike detection: 
+                    method: threshold
+                    threshold: 0.5
+                tolerance: 0.0
+    Test4:
+        observables:
+            spike times:
+                file: 
+                    path: experiments/osc_sim/act.dat
+                    columns: [0, 3]
+                    scaling: [1, 1]
+                spike detection: 
+                    method: threshold
+                    threshold: 0.5
+                tolerance: 0.0

.test.osc_sim_21.mep

@@ -0,0 +1,12 @@
+system: Testing activity of some neurons
+
+experiments:
+    Test2:
+        expected:
+            spike times: [10.655, 12.705, 14.755, 16.805, 18.855]
+    Test3:
+        expected:
+            spike times: [10.655, 12.705, 14.755, 16.805, 18.855]
+    Test4:
+        expected:
+            spike times: [10.655, 12.705, 14.755, 16.805, 18.855]

.test.osc_sim_21.omt

@@ -0,0 +1,41 @@
+# Framework for running automated tests on Open Source Brain
+# See https://github.com/OpenSourceBrain/osb-model-validation for more details
+
+target: run_osc_sim_21.py
+engine: Brian2  # This installs Brian2, but all we really need is a Python environment to run the script in
+mep: .test.osc_sim_21.mep
+experiments:
+    Test2:
+        observables:
+            spike times:
+                file: 
+                    path: experiments/osc_sim_21_nml/act.dat
+                    columns: [0, 3]
+                    scaling: [1, 1]
+                spike detection: 
+                    method: threshold
+                    threshold: 0.5
+                tolerance: 0.0
+
+    Test3:
+        observables:
+            spike times:
+                file: 
+                    path: experiments/osc_sim_21_nml_musc/act.dat
+                    columns: [0, 3]
+                    scaling: [1, 1]
+                spike detection: 
+                    method: threshold
+                    threshold: 0.5
+                tolerance: 0.0
+    Test4:
+        observables:
+            spike times:
+                file: 
+                    path: experiments/osc_sim_21/act.dat
+                    columns: [0, 3]
+                    scaling: [1, 1]
+                spike detection: 
+                    method: threshold
+                    threshold: 0.5
+                tolerance: 0.0

.test.osc_sim_21all.mep

@@ -0,0 +1,12 @@
+system: Testing activity of some neurons
+
+experiments:
+    Test2:
+        expected:
+            spike times: [10.105, 12.355, 14.605, 16.855, 19.105]
+    Test3:
+        expected:
+            spike times: [10.105, 12.355, 14.605, 16.855, 19.105]
+    Test4:
+        expected:
+            spike times: [10.105, 12.355, 14.605, 16.855, 19.105]

.test.osc_sim_21all.omt

@@ -0,0 +1,41 @@
+# Framework for running automated tests on Open Source Brain
+# See https://github.com/OpenSourceBrain/osb-model-validation for more details
+
+target: run_osc_sim_21all.py
+engine: Brian2  # This installs Brian2, but all we really need is a Python environment to run the script in
+mep: .test.osc_sim_21all.mep
+experiments:
+    Test2:
+        observables:
+            spike times:
+                file: 
+                    path: experiments/osc_sim_21all_nml/act.dat
+                    columns: [0, 3]
+                    scaling: [1, 1]
+                spike detection: 
+                    method: threshold
+                    threshold: 0.5
+                tolerance: 0.0
+
+    Test3:
+        observables:
+            spike times:
+                file: 
+                    path: experiments/osc_sim_21all_nml_musc/act.dat
+                    columns: [0, 3]
+                    scaling: [1, 1]
+                spike detection: 
+                    method: threshold
+                    threshold: 0.5
+                tolerance: 0.0
+    Test4:
+        observables:
+            spike times:
+                file: 
+                    path: experiments/osc_sim_21all/act.dat
+                    columns: [0, 3]
+                    scaling: [1, 1]
+                spike detection: 
+                    method: threshold
+                    threshold: 0.5
+                tolerance: 0.0

F2_fig_behavior.py

@@ -8,7 +8,9 @@
 import neuromlLocal.utils as utils
 
 
-def make_fig(plot_format):
+def make_fig(model_name):
+    plot_format = utils.plot_formats[model_name]
+
     file_prefix = "sim_"
     if not os.path.isfile(hf.rename_file(file_prefix + "ns.dat")):
         file_prefix = ""
@@ -60,7 +62,9 @@ def make_fig(plot_format):
     if "plot_cell_unit" in plot_format:
         plot_cell_unit = plot_format["plot_cell_unit"]
     plot_col_divs = plot_format["plot_col_divs"]
-    cell_names = utils.getCellNames(network_json_data)
+    # cell_names = utils.getCellNames(network_json_data)
+    cell_names = utils.default_cells[model_name]["names"]
+
     step_size = network_json_data["Evolutionary Optimization Parameters"]["StepSize"][
         "value"
     ]
@@ -198,6 +202,9 @@ def plot_worm(ax, k):
     ):
         ind1 = utils.getIndOfNthVal(cell, cell_names, plot_cell_unit)
         if ind1 is None:
+            print(cell_names)
+            print(cell)
+            print(plot_cell_unit)
             print("Index error")
             exit()
         print("cell ind is ", ind1)

RoyalSociety2018/Worm.cpp

@@ -174,14 +174,14 @@ Worm::Worm(TVector<double> &v,double output)
 void Worm::InitializeState(RandomState &rs)
 {
     t = 0.0;
-    n.RandomizeCircuitState(-0.5, 0.5, rs);
-    h.RandomizeCircuitState(-0.5, 0.5, rs);
+    //n.RandomizeCircuitState(-0.5, 0.5, rs);
+    //h.RandomizeCircuitState(-0.5, 0.5, rs);
     //n.RandomizeCircuitState(0.4, 0.4, rs); //fix initial conditions
     //h.RandomizeCircuitState(0.4, 0.4, rs); //fix initial conditions
-    /* for (int i = 1; i <= n.size; i++)
+    for (int i = 1; i <= n.size; i++)
         n.SetNeuronState(i, (i-0.5)/n.size);
     for (int i = 1; i <= h.size; i++)
-        h.SetNeuronState(i, (i-0.5)/h.size); */
+        h.SetNeuronState(i, (i-0.5)/h.size); 
     b.InitializeBodyState();
     m.InitializeMuscleState();
 }