NWB: Insert recreated epoch data into LNB on NWB_ExportAllData

Epoch data is recreated for each sweep and inserted with the additional
LNB column "PostProcessed" set to 1.

Author: MichaelHuth

Packages/MIES/MIES_Epochs.ipf

@@ -1778,7 +1778,7 @@ End
 /// @param sweepDFR        single sweep folder, e.g. for measurement with a device this wold be DFREF sweepDFR = GetSingleSweepFolder(deviceDFR, sweepNo)
 /// @param sweepNo         sweep number
 /// @returns recreated 4D epoch wave
-static Function/WAVE EP_RecreateEpochsFromLoadedData(WAVE numericalValues, WAVE/T textualValues, DFREF sweepDFR, variable sweepNo)
+Function/WAVE EP_RecreateEpochsFromLoadedData(WAVE numericalValues, WAVE/T textualValues, DFREF sweepDFR, variable sweepNo)
 
 	STRUCT DataConfigurationResult s
 	variable channelNr, plannedTime, acquiredTime, adSize, firstUnacquiredIndex

Packages/MIES/MIES_ExperimentDocumentation.ipf

@@ -125,6 +125,7 @@ static Function ED_InsertRowAfterSweepBlock(WAVE values, variable sweepNo, varia
 		values[rowIndex][][] = NaN
 	endif
 	SetNumberInWaveNote(values, NOTE_INDEX, GetNumberFromWaveNote(values, NOTE_INDEX) + 1)
+	InvalidateLBIndexAndRowCache(values)
 
 	return rowIndex
 End

Packages/MIES/MIES_MiesUtilities_Logbook.ipf

@@ -1951,3 +1951,56 @@ Function/S StringifyLogbookMode(variable mode)
 			break
 	endswitch
 End
+
+Function InsertRecreatedEpochsIntoLBN(WAVE numericalValues, WAVE/T textualValues, string device, variable sweepNo)
+
+	string epochList
+	variable channelNumber, channelType, headstage, gotAssocValues
+
+	DFREF  deviceDFR = GetDeviceDataPath(device)
+	DFREF  sweepDFR  = GetSingleSweepFolder(deviceDFR, sweepNo)
+	WAVE/Z recEpochs = EP_RecreateEpochsFromLoadedData(numericalValues, textualValues, sweepDFR, sweepNo)
+	if(!WaveExists(recEpochs))
+		print "Could not recreate Epochs."
+		return NaN
+	endif
+
+	Make/FREE/T/N=(1, 1) keys
+	Make/FREE/T/N=(1, 1, LABNOTEBOOK_LAYER_COUNT) values, unAssocValues
+
+	for(channelType = 0; channelType < XOP_CHANNEL_TYPE_COUNT; channelType += 1)
+		for(channelNumber = 0; channelNumber < NUM_DA_TTL_CHANNELS; channelNumber += 1)
+			// Currently only implemented for DAC channel type
+			if(channelType != XOP_CHANNEL_TYPE_DAC)
+				continue
+			endif
+
+			epochList = EP_EpochWaveToStr(recEpochs, channelNumber, channelType)
+			if(IsEmpty(epochList))
+				continue
+			endif
+
+			headstage = AFH_GetHeadstageFromChannelNumberAndType(device, channelType, channelNumber)
+			if(IsValidHeadstage(headstage))
+				values[0][0][headstage] = epochList
+				gotAssocValues          = 1
+				continue
+			endif
+			// unassoc channel
+			unAssocValues[0][0][INDEP_HEADSTAGE] = epochList
+			keys[0][0]                           = CreateLBNUnassocKey(EPOCHS_ENTRY_KEY, channelNumber, channelType)
+			ED_AddEntriesToLabnotebook(unAssocValues, keys, sweepNo, device, DATA_ACQUISITION_MODE, insertAsPostProc = 1)
+
+		endfor
+	endfor
+	if(gotAssocValues)
+		keys[0][0] = EPOCHS_ENTRY_KEY
+		ED_AddEntriesToLabnotebook(values, keys, sweepNo, device, DATA_ACQUISITION_MODE, insertAsPostProc = 1)
+	endif
+End
+
+Function InvalidateLBIndexAndRowCache(WAVE values)
+
+	CA_DeleteCacheEntry(CA_CreateLBIndexCacheKey(values))
+	CA_DeleteCacheEntry(CA_CreateLBRowCacheKey(values))
+End

Packages/MIES/MIES_NeuroDataWithoutBorders.ipf

@@ -479,7 +479,6 @@ static Function NWB_AddDeviceSpecificData(STRUCT NWBAsyncParameters &s, variable
 
 	AddModificationTimeEntry(s.locationID, s.nwbVersion)
 	NWB_AddDevice(s)
-	NWB_WriteLabnotebooksAndComments(s)
 	NWB_WriteTestpulseData(s, writeStoredTestPulses)
 End
 
@@ -588,12 +587,13 @@ End
 /// @param overwrite             [optional, defaults to false] overwrite any existing NWB file with the same name, only
 ///                              used when overrideFilePath is passed
 /// @param verbose               [optional, defaults to true] get diagnostic output to the command line
+/// @param recreateEpochs        [optional, defaults to false] when set to true, epoch information is recreated if the version of the data in the experiment is older than the latest version
 ///
 /// @return 0 on success, non-zero on failure
-Function NWB_ExportAllData(variable nwbVersion, [string device, string overrideFullFilePath, string overrideFileTemplate, variable writeStoredTestPulses, variable writeIgorHistory, variable compressionMode, variable keepFileOpen, variable overwrite, variable verbose])
+Function NWB_ExportAllData(variable nwbVersion, [string device, string overrideFullFilePath, string overrideFileTemplate, variable writeStoredTestPulses, variable writeIgorHistory, variable compressionMode, variable keepFileOpen, variable overwrite, variable verbose, variable recreateEpochs])
 
 	string list, name, fileName
-	variable locationID, sweep, createdNewNWBFile, argCheck
+	variable locationID, sweep, createdNewNWBFile, argCheck, epochVersion
 	string stimsetList = ""
 
 	if(ParamIsDefault(keepFileOpen))
@@ -630,6 +630,8 @@ Function NWB_ExportAllData(variable nwbVersion, [string device, string overrideF
 		verbose = !!verbose
 	endif
 
+	recreateEpochs = ParamIsDefault(recreateEpochs) ? 0 : !!recreateEpochs
+
 	argCheck = ParamIsDefault(overrideFullFilePath) + ParamIsDefault(overrideFileTemplate)
 	ASSERT(argCheck >= 1 && argCheck <= 2, "Either arg overrideFullFilePath or arg overrideFileTemplate must be given or none (auto-gen)")
 
@@ -736,6 +738,13 @@ Function NWB_ExportAllData(variable nwbVersion, [string device, string overrideF
 			WAVE s.DAQDataWave   = TextSweepToWaveRef(sweepWave)
 			WAVE s.DAQConfigWave = configWave
 
+			if(recreateEpochs)
+				epochVersion = GetLastSettingIndep(s.numericalValues, s.sweep, "Epochs Version", DATA_ACQUISITION_MODE, defValue = NaN)
+				if(IsNaN(epochVersion) || epochVersion < SWEEP_EPOCH_VERSION)
+					InsertRecreatedEpochsIntoLBN(s.numericalValues, s.textualValues, s.device, s.sweep)
+				endif
+			endif
+
 			NWB_AppendSweepLowLevel(s)
 			stimsetList += AB_GetStimsetFromPanel(device, sweep)
 
@@ -744,6 +753,8 @@ Function NWB_ExportAllData(variable nwbVersion, [string device, string overrideF
 		endfor
 		LOG_AddEntry(PACKAGE_MIES, "export", keys = {"size [MiB]"}, values = {num2str(NWB_GetExportedFileSize(device))})
 
+		NWB_WriteLabnotebooksAndComments(s)
+
 		NWB_AppendStimset(nwbVersion, s.locationID, stimsetList, compressionMode)
 
 		if(writeIgorHistory)