started work on a parameter scanning method

vivarium_models/library/scan.py

@@ -0,0 +1,37 @@
+from vivarium.core.engine import Engine, pf
+
+class Scan():
+    def __init__(
+            self,
+            parameter_sets,
+            simulator_class,
+            total_time,
+            metrics=()):
+
+        self.parameter_sets = parameter_sets
+        self.simulator_class = simulator_class
+        self.total_time = total_time
+        self.metrics = metrics
+
+    def run_simulation(self, parameters):
+        simulator = self.simulator_class(parameters['parameters']).generate()
+        engine = Engine(
+            processes=simulator['processes'],
+            topology=simulator['topology'],
+            initial_state=parameters['states'])
+        engine.update(self.total_time)
+        return engine.emitter.get_data()
+
+    def run_scan(self):
+        results = {}
+        for id, parameter_set in self.parameter_sets.items():
+            data = self.run_simulation(parameter_set)
+            metrics = [
+                metric(data)
+                for metric in self.metrics]
+            results[id] = {
+                'data': data,
+                'metrics': metrics}
+        return results
+
+

vivarium_models/processes/readdy_actin_process.py

@@ -3,12 +3,13 @@
 from vivarium.core.process import Process
 from vivarium.core.engine import Engine, pf
 from vivarium.core.composition import simulate_process
+from vivarium.core.control import run_library_cli
 
 from tqdm import tqdm
 from simularium_models_util.actin import ActinSimulation, ActinUtil, ActinTestData
 from simularium_models_util import ReaddyUtil
 from vivarium_models.util import create_monomer_update
-
+from vivarium_models.library.scan import Scan
 
 NAME = "ReaDDy_actin"
 
@@ -238,23 +239,26 @@ def run_readdy_actin_process():
         return output
 
 
-def test_readdy_actin_process():
+def get_monomer_data():
     monomer_data = ActinTestData.linear_actin_monomers()
     monomer_data["box_center"] = np.array([3000.0, 1000.0, 1000.0])
     monomer_data["box_size"] = 500.0
+    return {'monomers': monomer_data}
+
+
+def test_readdy_actin_process():
+    monomer_data = get_monomer_data()
     readdy_actin_process = ReaddyActinProcess()
 
     engine = Engine(
-        {
+        **{
             "processes": {"readdy_actin_process": readdy_actin_process},
             "topology": {
                 "readdy_actin_process": {
                     "monomers": ("monomers",),
                 },
             },
-            "initial_state": {
-                "monomers": monomer_data,
-            },
+            "initial_state": monomer_data,
         }
     )
 
@@ -264,5 +268,43 @@ def test_readdy_actin_process():
     print(pf(output))
 
 
+def test_scan_readdy():
+    monomer_data = get_monomer_data()
+
+    parameters = {
+        '1': {
+            'parameters': {
+                'actin_concentration': 100.0,
+                'arp23_concentration': 5.0},
+            'states': monomer_data},
+        '2': {
+            'parameters': {
+                'actin_concentration': 200.0,
+                'arp23_concentration': 10.0},
+            'states': monomer_data},
+        '3': {
+            'parameters': {
+                'actin_concentration': 300.0,
+                'arp23_concentration': 20.0},
+            'states': monomer_data}}
+
+    metrics = []
+
+    scan = Scan(
+        parameters,
+        ReaddyActinProcess,
+        0.0000001,
+        metrics=metrics)
+
+    results = scan.run_scan()
+
+    import ipdb; ipdb.set_trace()
+
+
+library = {
+    '0': test_readdy_actin_process,
+    '1': test_scan_readdy}
+
+
 if __name__ == "__main__":
-    test_readdy_actin_process()
+    run_library_cli(library)