Merge pull request #677 from suny-downstate-medical-center/dipole-sum…

…-save-load-improvements added saving and gathering 'LFPPops' and 'dipoleSum' where it was missing
suny-downstate-medical-center · Apr 15, 2022 · 522f377 · 522f377
2 parents eeb677f + 12ce252
commit 522f377
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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:
@@ -469,6 +479,12 @@ def sort(popKeyAndValue):
                             for p in value:
                                 allSimData['LFPPops'][p] += np.array(value[p])
 
+                        elif key == 'dipoleSum':
+                            if key not in allSimData.keys():
+                                allSimData[key] = value
+                            else:
+                                allSimData[key] += value
+
                         elif key not in singleNodeVecs:
                             allSimData[key].update(value)
 

diff --git a/netpyne/sim/save.py b/netpyne/sim/save.py
@@ -406,9 +406,13 @@ 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]))
+            elif sim.cfg.recordDipole and k == 'dipoleSum':
+                sim.allSimData[k] = np.zeros(gather[0]['simData']['dipoleSum'].shape)
             else:
                 sim.allSimData[k] = {}
 
@@ -437,6 +441,11 @@ 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 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
                 if 'xElectrodeTransferResistances' in node: