HillTau fixes: less memory leak, go faster over settle phase of runs.

Author: upibhalla

findSim.py

@@ -190,6 +190,11 @@ def load( findsim ):
     load = staticmethod( load )
 
     def minInterval( self ):
+        """
+        This function checks if stim steps up from zero at t>0.
+        I think for plotting? Maybe for numerical stability. Either way,
+        it inserts a very small nonzero value just before the step.
+        """
         ret = 1000.0
         lastt = 0.0
         lastval = 0.0
@@ -208,9 +213,9 @@ def minInterval( self ):
                 if (not isElec) and (t - lastt) >= 100.0 and lastval < 1e-7 and val > 0.5e-4: 
                     # Have to insert intermediate step in data.
                     newdata.append( [float(d[0]), 1e-6 / self.quantityScale] )
-                    newt = t + (t - lastt)/( 100.0 * self.timeScale )
+                    newt = t + (t - lastt)/100.0
                     #print( "inserting: ", [d[0], 1e-6], [newt, d[1]] )
-                    newdata.append( [newt, d[1]] )
+                    newdata.append( [newt/self.timeScale, d[1]] )
                     ret = min( ret, (t - lastt)/100.0 )
                 else:
                     newdata.append( [d[0], d[1]] )
@@ -1002,7 +1007,7 @@ def __lt__( self, other ):
 
 def putStimsInQ( q, stims, pauseHsolve ):
     for i in stims:
-        isElec = i.field in ['Im', 'current', 'Vclamp'] or (i.field=='rate' and 'syn' in i.entities[0])
+        isElec = i.field in ['Im', 'current', 'Vclamp'] or (i.field=='rate' and 'syn' in i.entity['name'])
         for j in i.data:
             if len(j) == 0:
                 continue
@@ -1147,7 +1152,8 @@ def parseAndRun( model, stims, readouts, getPlots = False ):
         currt = sw.getCurrentTime()
         if ( qe.t > currt ):
             #print( "currt={:.4f}, qt={:.4f}".format( currt, qe.t) )
-            sw.advanceSimulation( qe.t - currt, doPlot = getPlots )
+            sw.advanceSimulation( qe.t - currt, doPlot = getPlots, 
+                    doSettle = (i==0) )
         if isinstance( qe.entry, Stimulus ):
             sw.deliverStim( qe )
             #print( "DELIVER STIM {} {} {} {}".format( qe.entry.entities, qe.entry.field, qe.entry.data, qe.val ) )
@@ -1502,9 +1508,9 @@ def runit( expt, model, stims, readouts, getPlots = False ):
 def getInitParams( modelFile, mapFile, paramList ):
     # ParamList as strings of objpath.field 
     if modelFile.split('.')[-1] == "json":
-        sw = SimWrapHillTau( mapFile = mapFile, ignoreMissingObj = False, silent = False, exptFile = "" )
+        sw = SimWrapHillTau( mapFile = mapFile, ignoreMissingObj = False, silent = False, exptFile = "getInitParams" )
     else:
-        sw = SimWrapMoose( mapFile = mapFile, ignoreMissingObj = False, silent = False, exptFile = "" )
+        sw = SimWrapMoose( mapFile = mapFile, ignoreMissingObj = False, silent = False, exptFile = "getInitParams" )
 
     sw.deleteSimulation()
     sw.loadModelFile( modelFile, silentDummyModify, [], "", "" )
@@ -1565,6 +1571,9 @@ def innerMain( exptFile, scoreFunc = defaultScoreFunc, modelFile = "", mapFile =
     readouts.tabulateOutput = tabulateOutput
     readouts.generate = generate
 
+    if not silent:
+        print( "FindSim: doing expt ", exptFile )
+
     if mapFile != "":
         mapFile = mapFile
     else:

simWrapHillTau.py

@@ -527,11 +527,59 @@ def makeReadoutPlots( self, readouts ):
                 self.numMainPlots = numPlots
         self.plots = [[]]*numPlots
 
-    def fillPlots( self ): # takes plots from sim and puts the numpy arrays of the plot values from sim into the return. Also returns main plot dt as a float, and the number of main plots.
+    def old_fillPlots( self ): 
+        # takes plots from sim and puts the numpy arrays of the plot values from sim into the return. Also returns main plot dt as a float, and the number of main plots.
         tempArray = np.array(self.model.plotvec).transpose()
         for index, plotNum in self.plotPath.values():
             self.plots[plotNum] = tempArray[index]
         return [ np.array( i ) for i in self.plots], [self.plotDt] * len( self.plots ), self.numMainPlots
+
+    def fillPlots(self):
+        """
+        takes plots from sim and puts the numpy arrays of the plot values from 
+        sim into the return. Also returns main plot dt as a float, and the 
+        number of main plots.
+        Optimized using AI.
+        """
+        tempArray = np.array(self.model.plotvec).transpose()
+    
+        # If there are no plots specified, return early.
+        if not self.plotPath:
+            return [], [], self.numMainPlots
+    
+        # Get the desired row indices and their corresponding plot numbers.
+        # We assume self.plotPath.values() yields (index, plotNum) tuples.
+        path_values = list(self.plotPath.values())
+        indices_to_select = [item[0] for item in path_values]
+        plot_num_keys = [item[1] for item in path_values]
+    
+        # Use advanced indexing to select all required plots in a single operation.
+        # This creates one new, compact array with only the data you need.
+        selected_plots = tempArray[indices_to_select]
+    
+        # Populate self.plots with views into the selected_plots array.
+        # This avoids creating a new copy for each plot.
+        for i, key in enumerate(plot_num_keys):
+            self.plots[key] = selected_plots[i]
+    
+        # The original function returned a list of 1D arrays. 
+        # `list(selected_plots)`
+        # does this efficiently without making a final, unnecessary copy.
+        output_plots = list(selected_plots)
+    
+        return output_plots, [self.plotDt] * len(output_plots), self.numMainPlots
+
+
+
+
+
+
+
+
+
+
+
+
 
     def deliverStim( self, qe ):
         field = qe.entry.field
@@ -668,7 +716,7 @@ def getObjParam( self, entity, field, isSilent = False ):
         if not entity in self.modelLookup:
             if self.ignoreMissingObj or isSilent:
                 return -2.0
-            raise SimError( "SimWrapHillTau::getObjParam: Entity {} not found".format( entity ) )
+            raise SimError( "SimWrapHillTau::getObjParam: {}: Entity {} not found".format( self.exptFile, entity ) )
         elms = self.modelLookup[entity]
         if len( elms ) != 1:
             if isSilent:
@@ -727,7 +775,7 @@ def steadyStateStims(self, stimList, responseList, isSeries = False, settleTime
                         self.setField( elm, "conc", value * scale )
                         self.setField( elm, "concInit", value * scale )
                 self.reinitSimulation()
-                self.advanceSimulation( settleTime, doPlot = False )
+                self.advanceSimulation( settleTime, doPlot = False, doSettle = True )
                 for elm, field, oldval in orig:
                     self.setField( elm, field, oldval )
                     if field == 'conc':