properly accumulate 'LFPPops' data from nodes

suny-downstate-medical-center · Apr 15, 2022 · 12ce252 · 12ce252
1 parent b71e8a6
commit 12ce252
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Showing 2 changed files with 16 additions and 1 deletion.
diff --git a/netpyne/sim/gather.py b/netpyne/sim/gather.py
@@ -107,6 +107,8 @@ def gatherData(gatherLFP=True, gatherDipole=True):
                 for k in list(gather[0]['simData'].keys()):  # initialize all keys of allSimData dict
                     if gatherLFP and k == 'LFP':
                         sim.allSimData[k] = np.zeros((gather[0]['simData']['LFP'].shape))
+                    elif gatherLFP and k == 'LFPPops':
+                        sim.allSimData[k] = {p: np.zeros(gather[0]['simData']['LFP'].shape) for p in gather[0]['simData']['LFPPops'].keys()}
                     elif gatherDipole and k == 'dipoleSum':
                         sim.allSimData[k] = np.zeros((gather[0]['simData']['dipoleSum'].shape))
                     elif sim.cfg.recordDipolesHNN and k == 'dipole':
@@ -136,6 +138,9 @@ def gatherData(gatherLFP=True, gatherDipole=True):
                                 sim.allSimData[key] = list(sim.allSimData[key])+list(val) # udpate simData dicts which are Vectors
                         elif gatherLFP and key == 'LFP':
                             sim.allSimData[key] += np.array(val)
+                        elif gatherLFP and key == 'LFPPops':
+                            for p in val:
+                                sim.allSimData[key][p] += np.array(val[p])
                         elif gatherDipole and key == 'dipoleSum':
                             sim.allSimData[key] += np.array(val)
                         elif key not in singleNodeVecs:
@@ -175,6 +180,8 @@ def gatherData(gatherLFP=True, gatherDipole=True):
                 for k in list(gather[0]['simData'].keys()):  # initialize all keys of allSimData dict
                     if gatherLFP and k == 'LFP':
                         sim.allSimData[k] = np.zeros((gather[0]['simData']['LFP'].shape))
+                    elif gatherLFP and k == 'LFPPops':
+                        sim.allSimData[k] = {p: np.zeros(gather[0]['simData']['LFP'].shape) for p in gather[0]['simData']['LFPPops'].keys()}
                     elif gatherDipole and k == 'dipoleSum':
                         sim.allSimData[k] = np.zeros((gather[0]['simData']['dipoleSum'].shape))
                     elif sim.cfg.recordDipolesHNN and k == 'dipole':
@@ -208,6 +215,9 @@ def gatherData(gatherLFP=True, gatherDipole=True):
                                 sim.allSimData[key] = list(sim.allSimData[key])+list(val) # udpate simData dicts which are Vectors
                         elif gatherLFP and key == 'LFP':
                             sim.allSimData[key] += np.array(val)
+                        elif gatherLFP and key == 'LFPPops':
+                            for p in val:
+                                sim.allSimData[key][p] += np.array(val[p])
                         elif gatherDipole and key == 'dipoleSum':
                             sim.allSimData[key] += np.array(val)
                         elif key not in singleNodeVecs:

diff --git a/netpyne/sim/save.py b/netpyne/sim/save.py
@@ -406,6 +406,8 @@ def intervalSave(simTime, gatherLFP=True):
         for k in list(gather[0]['simData'].keys()):  # initialize all keys of allSimData dict
             if gatherLFP and k == 'LFP':
                 sim.allSimData[k] = np.zeros((gather[0]['simData']['LFP'].shape))
+            elif gatherLFP and k == 'LFPPops':
+                sim.allSimData[k] = {p: np.zeros(gather[0]['simData']['LFP'].shape) for p in gather[0]['simData']['LFPPops'].keys()}
             elif sim.cfg.recordDipolesHNN and k == 'dipole':
                 for dk in sim.cfg.recordDipolesHNN:
                     sim.allSimData[k][dk] = np.zeros(len(gather[0]['simData']['dipole'][dk]))
@@ -439,7 +441,10 @@ def intervalSave(simTime, gatherLFP=True):
                         sim.allSimData[key] = list(sim.allSimData[key])+list(val) # udpate simData dicts which are Vectors
                 elif gatherLFP and key == 'LFP':
                     sim.allSimData[key] += np.array(val)
-                elif sim.cfg.recordDipole and key == 'dipoleSum':
+                elif gatherLFP and key == 'LFPPops':
+                    for p in val:
+                        sim.allSimData[key][p] += np.array(val[p])
+                elif key == 'dipoleSum':
                     sim.allSimData[key] += val
                 elif key not in singleNodeVecs:
                     sim.allSimData[key].update(val)           # update simData dicts which are not Vectors