Added prepDilution field to scale responses to active fraction of prep volume

Author: upibhalla

FindSim-Schema.json

@@ -188,6 +188,11 @@
                     "minimum": 0.0, 
                     "maximum": 5000 
                 },
+                "prepDilution": {"type": "number", 
+               		"description": "Active portion of prep may be much smaller than the total volume taken, for example, synaptic spine signals in background of whole slice prep. Typical dilution in that case would be 10, so any ratiometric readout should be scaled by 10x. Best used for normalized readouts.",
+                    "minimum": 1e-6, 
+					"default": 1.0
+                },
                 "normalization": {"type": "object",
                     "properties": {
                         "sampling": {"type": "string",

findSim.py

@@ -289,6 +289,7 @@ def __init__( self, findsim, exptFile = "", isPlotOnly = False ):
         self.findsim = findsim
         self.exptFile = exptFile
         ro = findsim["Readouts"]
+        self.prepDilution = ro.get( "prepDilution", 1.0 )
         self.directParamData = ro.get( "paramdata" )
         self.isPlotOnly = isPlotOnly
         self.simData = []
@@ -307,11 +308,25 @@ def __init__( self, findsim, exptFile = "", isPlotOnly = False ):
             self.data = ro.get("data") # For most kinds of data
             if self.data:
                 for i in self.data: # force it to have [t, v, sem] in each row
+                    # Scale it by the estimated dilution of active sample
+                    # over total sample, eg spine vol over entire tissue.
+                    if "normalization" in ro:
+                        i[1] = 1+ (i[1]-1) * self.prepDilution
+                    else:
+                        i[1] *= self.prepDilution
                     if len( i ) == 2:
                         i.append( 0 )
                     assert( len( i ) == 3 )
 
             self.bardata = ro.get( "bardata" )  # only for barcharts
+            if self.bardata:
+                if "normalization" in ro:
+                    for bb in self.bardata:
+                        bb['value'] = 1 + (bb['value']-1)*self.prepDilution
+                else:
+                    for bb in self.bardata:
+                        bb['value'] *= self.prepDilution
+
             self.tabulateOutput = False
             self.generate = None
             self.generateFile = None
@@ -465,7 +480,7 @@ def digestSteadyStateRun( self, ref, ret ):
 
 
         # Finally assign the simData.
-        self.simData = [ x/y for x, y in zip( ret, ref ) ]
+        self.simData = [ x/y for x, y in zip(ret, ref) ]
 
     def displayPlots( self, fname, modelLookup, stims, hideSubplots, exptType, bigFont = False, labelPos = None, deferPlot = False ):
         if self.isPlotOnly: