From ee974e94d64510224d3fd06f2f84d6330d28cb10 Mon Sep 17 00:00:00 2001
From: bhalla <bhalla@ncbs.res.in>
Date: Thu, 11 Apr 2024 22:21:27 +0530
Subject: [PATCH] Added code and test case for window baseline normalization.

---
 TestJson/epsc_window_baseline_norm.json | 82 +++++++++++++++++++++++++
 findSim.py                              |  9 ++-
 models/loadGABAR.json                   |  7 +++
 models/loadGABAR.py                     | 16 +++++
 4 files changed, 111 insertions(+), 3 deletions(-)
 create mode 100644 TestJson/epsc_window_baseline_norm.json
 create mode 100644 models/loadGABAR.json
 create mode 100644 models/loadGABAR.py

diff --git a/TestJson/epsc_window_baseline_norm.json b/TestJson/epsc_window_baseline_norm.json
new file mode 100644
index 0000000..51e1cb9
--- /dev/null
+++ b/TestJson/epsc_window_baseline_norm.json
@@ -0,0 +1,82 @@
+{
+    "Metadata": {
+        "transcriber": "Upi",
+        "organization": "NCBS",
+        "email": "bhalla@ncbs.res.in",
+        "source": {
+            "sourceType": "other",
+            "doi": "0",
+            "authors": "None",
+            "journal": "None. This is a purely fictional _experiment_ for the purposes of testing findSim",
+            "year": 0,
+            "figure": ""
+        },
+        "testModel": "models/loadGABAR.py",
+        "testMap": "models/loadGABAR.json"
+    },
+    "Experiment": {
+        "design": "TimeSeries",
+        "species": "rat",
+        "cellType": "hippocampal CA1 pyramidal neuron",
+        "notes": "Test removal of baseline in voltage clamp peak estimate"
+    },
+    "Stimuli": [
+        {
+            "timeUnits": "sec",
+            "quantityUnits": "Hz",
+            "entity" : {
+                "name": "synInput",
+                "alias": "synInput"
+            },
+            "field": "rate",
+            "data": [
+                [0,5]
+            ]
+        },
+        {
+            "timeUnits": "sec",
+            "quantityUnits": "mV",
+            "entity" : {
+                "name": "soma",
+                "alias": "soma"
+            },
+            "field": "Vclamp",
+            "data": [
+                [0,-65.0],
+                [0.001,0.0],
+                [0.3,-65.0]
+            ]
+        }
+    ],
+    "Readouts": {
+        "timeUnits": "sec",
+        "quantityUnits": "ratio",
+        "entity" : {
+            "name": "vclamp",
+            "alias": "vclamp"
+            },
+        "field": "current",
+	    "window": {"startt": -0.010, "endt": 0.005, "dt": 0.0005,
+        	"operation": "max", "baseline": "min"
+        },
+        "normalization": {
+            "entity" : {
+                "name": "vclamp",
+                "alias": "vclamp"
+            },
+            "sampling": "start"
+        },
+        "data": [
+            [0.21, 1, 0],
+            [0.23, 1.2, 0],
+            [0.25, 1.2, 0],
+            [0.27, 1.2, 0],
+            [0.29, 1.2, 0]
+        ]
+    },
+    "Modifications": {
+        "subset": [
+            {"name":"all"}
+        ]
+    }
+}
diff --git a/findSim.py b/findSim.py
index 105f482..12ed2e9 100644
--- a/findSim.py
+++ b/findSim.py
@@ -998,7 +998,7 @@ def putStimsInQ( q, stims, pauseHsolve ):
                 val = float(j[1]) * i.quantityScale
             t = float(j[0])*i.timeScale
             heapq.heappush( q, Qentry( t, i, val ) )
-            if isElec:
+            if isElec and pauseHsolve.optimizeElec:
                 # Below we tell the Hsolver to turn off or on for elec calcn.
                 if val == 0.0:
                     heapq.heappush( q, Qentry(t+pauseHsolve.stimSettle, pauseHsolve, 0) )
@@ -1135,6 +1135,9 @@ def parseAndRun( model, stims, readouts, getPlots = False ):
         qe = heapq.heappop( q )
         currt = sw.getCurrentTime()
         if ( qe.t > currt ):
+            print( "currt={:.4f}, qt={:.4f}".format( currt, qe.t) )
+            if qe.t > 1.5:
+                print( qe.entry )
             sw.advanceSimulation( qe.t - currt, doPlot = getPlots )
         if isinstance( qe.entry, Stimulus ):
             sw.deliverStim( qe )
@@ -1176,12 +1179,12 @@ def parseAndRun( model, stims, readouts, getPlots = False ):
     if readouts.useNormalization and readouts.normMode == "each":
         if len( [ y for y in readouts.ratioData if abs(y) < eps ] ) > 0:
             #raise SimError( "runDoser: Normalization1 failed due to zero denominator: " + str( min( readouts.ratioData ) ) )
-            print( "parseAndRun: Normalization1 denom={:.3g} for {}.{}".format(min( readouts.ratioData ), readouts.entities[0], readouts.field ) )
+            print( "parseAndRun: Normalization1 denom={:.3g} for {}.{}".format(min( readouts.ratioData ), readouts.entities, readouts.field ) )
         readouts.simData = [ x/y if abs(y)>= eps else 0.0 for x, y in zip(readouts.simData, readouts.ratioData) ]
     else:
         if abs(norm) < eps:
             #raise SimError( "runDoser: Normalization2 failed due to zero denominator: " + str( norm ) )
-            print( "parseAndRun: Normalization2 denom={:.3g} for {}.{}".format( norm, readouts.entities[0], readouts.field ) )
+            print( "parseAndRun: Normalization2 denom={:.3g} for {}.{}".format( norm, readouts.entities, readouts.field ) )
             readouts.simData = [0.0] *len( readouts.simData )
         else:
             readouts.simData = [ x/norm for x in readouts.simData ]
diff --git a/models/loadGABAR.json b/models/loadGABAR.json
new file mode 100644
index 0000000..6292307
--- /dev/null
+++ b/models/loadGABAR.json
@@ -0,0 +1,7 @@
+{
+    "all":["all"],
+    "soma":["elec/soma"],
+    "synInput":["elec/soma/gabaR/sh/synapse/synInput_rs"],
+    "synapse":["elec/soma/gabaR/sh/synapse"]
+}
+
diff --git a/models/loadGABAR.py b/models/loadGABAR.py
new file mode 100644
index 0000000..903233c
--- /dev/null
+++ b/models/loadGABAR.py
@@ -0,0 +1,16 @@
+import moose
+import rdesigneur as rd
+def load( scaleParam, chemFile ):
+    rdes = rd.rdesigneur(
+        turnOffElec = True,
+        elecDt = 5e-5,
+        chanProto = [['make_GABA()', 'gabaR']],
+        chanDistrib = [
+            ['gabaR', 'soma', 'Gbar', '1' ]],
+        stimList = [['soma', '1','gabaR', 'periodicsyn', '50 * (t > 0.1)']],
+    )
+    return rdes
+
+def build( rdes ):
+    rdes.buildModel()
+    #moose.le( '/model/elec/soma/gabaR/sh/synapse/synInput_rs' )