Merge pull request #504 in ENG/mies-igor from ~THOMASB/mies-igor:bugf…

…ix/nwb_writing_unassoc_channels to master

* commit 'f83170ca54153cd81a12dd236f9aa6ea5ae92c9e':
  NWB writing: Support unassociated AD channels
  NWB_GetTimeSeriesProperties: Add assertion
  IPNWB#WriteSingleChannel: Use plain TimeSeries for unknown clamp modes
  CreateLBNUnassocKey: Factor out into function

Original-CommitID: 7abbe317b780e5347a36c973cda217f691587b2c

Packages/IPNWB/IPNWB_Writer.ipf

@@ -322,7 +322,8 @@ Function InitTimeSeriesProperties(tsp, channelType, clampMode)
 			// CurrentClampSeries
 			 tsp.missing_fields = "gain;bias_current;bridge_balance;capacitance_compensation"
 		else
-			 ASSERT(0, "Unknown clamp mode")
+			// unassociated channel
+			tsp.missing_fields = ""
 		endif
 	elseif(channelType == CHANNEL_TYPE_DAC)
 		tsp.missing_fields = "gain"
@@ -438,7 +439,7 @@ Function WriteSingleChannel(locationID, path, p, tsp, [chunkedLayout])
 	variable chunkedLayout
 
 	variable groupID, numPlaces, numEntries, i
-	string ancestry, str, source, channelTypeStr, group
+	string ancestry, str, source, channelTypeStr, group, electrodeNumberStr
 
 	chunkedLayout = ParamIsDefault(chunkedLayout) ? 0 : !!chunkedLayout
 
@@ -479,7 +480,13 @@ Function WriteSingleChannel(locationID, path, p, tsp, [chunkedLayout])
 		sprintf str, "%s", channelTypeStr
 	endif
 
-	sprintf source, "Device=%s;Sweep=%d;%s;ElectrodeNumber=%d;ElectrodeName=%s", p.device, p.sweep, str, p.electrodeNumber, p.electrodeName
+	if(IsFinite(p.electrodeNumber))
+		sprintf electrodeNumberStr, "%d", p.electrodeNumber
+	else
+		electrodeNumberStr = "NaN"
+	endif
+
+	sprintf source, "Device=%s;Sweep=%d;%s;ElectrodeNumber=%s;ElectrodeName=%s", p.device, p.sweep, str, electrodeNumberStr, p.electrodeName
 
 	if(strlen(p.channelSuffixDesc) > 0 && strlen(p.channelSuffix) > 0)
 		ASSERT(strsearch(p.channelSuffix, "=", 0) == -1, "channelSuffix must not contain an equals (=) symbol")
@@ -492,29 +499,29 @@ Function WriteSingleChannel(locationID, path, p, tsp, [chunkedLayout])
 		H5_WriteTextAttribute(groupID, "comment", group, str=note(p.data), overwrite=1) // human readable version of description
 	endif
 
-	if(p.channelType == CHANNEL_TYPE_ADC)
+	// only write electrode_name for associated channels
+	if(IsFinite(p.electrodeNumber) && (p.channelType == CHANNEL_TYPE_DAC || p.channelType == CHANNEL_TYPE_ADC))
 		sprintf str, "electrode_%s", p.electrodeName
 		H5_WriteTextDataset(groupID, "electrode_name", str=str, overwrite=1)
+	endif
 
+	if(p.channelType == CHANNEL_TYPE_ADC)
 		if(p.clampMode == V_CLAMP_MODE)
 			ancestry = "TimeSeries;PatchClampSeries;VoltageClampSeries"
 		elseif(p.clampMode == I_CLAMP_MODE)
 			ancestry = "TimeSeries;PatchClampSeries;CurrentClampSeries"
 		elseif(p.clampMode == I_EQUAL_ZERO_MODE)
 			ancestry = "TimeSeries;PatchClampSeries;CurrentClampSeries;IZeroClampSeries"
 		else
-			ancestry = "TimeSeries;PatchClampSeries"
+			ancestry = "TimeSeries"
 		endif
 	elseif(p.channelType == CHANNEL_TYPE_DAC)
-		sprintf str, "electrode_%s", p.electrodeName
-		H5_WriteTextDataset(groupID, "electrode_name", str=str, overwrite=1)
-
 		if(p.clampMode == V_CLAMP_MODE)
 			ancestry = "TimeSeries;PatchClampSeries;VoltageClampStimulusSeries"
 		elseif(p.clampMode == I_CLAMP_MODE)
 			ancestry = "TimeSeries;PatchClampSeries;CurrentClampStimulusSeries"
 		else
-			ancestry = "TimeSeries;PatchClampSeries"
+			ancestry = "TimeSeries"
 		endif
 	else
 		ancestry = "TimeSeries"
@@ -556,7 +563,7 @@ Function WriteSingleChannel(locationID, path, p, tsp, [chunkedLayout])
 		H5_WriteTextAttribute(groupID, "unit", group + "/starting_time", str="Seconds", overwrite=1)
 	endif
 
-	if(p.channelType == CHANNEL_TYPE_ADC || p.channelType == CHANNEL_TYPE_TTL)
+	if(strlen(p.stimSet) > 0 && (p.channelType == CHANNEL_TYPE_ADC || p.channelType == CHANNEL_TYPE_TTL))
 		// custom data not specified by NWB spec
 		H5_WriteTextDataset(groupID, "stimulus_description", str=p.stimSet, overwrite=1)
 		MarkAsCustomEntry(groupID, "stimulus_description")

Packages/MIES/MIES_DataConfiguratorITC.ipf

@@ -997,7 +997,7 @@ static Function DC_DocumentChannelProperty(panelTitle, entry, headstage, channel
 	endif
 
 	// headstage is not finite, so the channel is unassociated
-	sprintf ua_entry, "%s UNASSOC_%d", entry, channelNumber
+	ua_entry = CreateLBNUnassocKey(entry, channelNumber)
 
 	if(!ParamIsDefault(var))
 		colData = FindDimLabel(sweepDataLNB, COLS, ua_entry)

Packages/MIES/MIES_MiesUtilities.ipf

@@ -2993,3 +2993,15 @@ Function/S GetDefaultElectrodeName(headstage)
 
 	return num2str(headstage)
 End
+
+/// @brief Create a labnotebook key for unassociated channels
+Function/S CreateLBNUnassocKey(setting, channelNumber)
+	string setting
+	variable channelNumber
+
+	string key
+
+	sprintf key, "%s UNASSOC_%d", setting, channelNumber
+
+	return key
+End

Packages/MIES/MIES_NeuroDataWithoutBorders.ipf

@@ -427,6 +427,8 @@ static Function NWB_AppendSweepLowLevel(locationID, panelTitle, ITCDataWave, ITC
 	WAVE/T textualValues = GetLBTextualValues(panelTitle)
 	WAVE/T textualKeys   = GetLBTextualKeys(panelTitle)
 
+	Make/FREE/N=(DimSize(ITCDataWave, COLS)) writtenDataColumns = 0
+
 	// comment denotes the introducing comment of the labnotebook entry
 	// 9b35fdad (Add the clamp mode to the labnotebook for acquired data, 2015-04-26)
 	WAVE/Z clampMode = GetLastSetting(numericalValues, sweep, "Clamp Mode")
@@ -501,11 +503,12 @@ static Function NWB_AppendSweepLowLevel(locationID, panelTitle, ITCDataWave, ITC
 		params.stimset         = stimSets[i]
 
 		if(IsFinite(adc))
-			path                 = "/acquisition/timeseries"
-			params.channelNumber = ADCs[i]
-			params.channelType   = ITC_XOP_CHANNEL_TYPE_ADC
-			col                  = AFH_GetITCDataColumn(ITCChanConfigWave, params.channelNumber, params.channelType)
-			WAVE params.data     = ExtractOneDimDataFromSweep(ITCChanConfigWave, ITCDataWave, col)
+			path                    = "/acquisition/timeseries"
+			params.channelNumber    = ADCs[i]
+			params.channelType      = ITC_XOP_CHANNEL_TYPE_ADC
+			col                     = AFH_GetITCDataColumn(ITCChanConfigWave, params.channelNumber, params.channelType)
+			writtenDataColumns[col] = 1
+			WAVE params.data        = ExtractOneDimDataFromSweep(ITCChanConfigWave, ITCDataWave, col)
 			NWB_GetTimeSeriesProperties(params, tsp)
 			params.groupIndex    = IsFinite(params.groupIndex) ? params.groupIndex : IPNWB#GetNextFreeGroupIndex(locationID, path)
 			IPNWB#WriteSingleChannel(locationID, path, params, tsp, chunkedLayout=chunkedLayout)
@@ -514,11 +517,12 @@ static Function NWB_AppendSweepLowLevel(locationID, panelTitle, ITCDataWave, ITC
 		DEBUGPRINT_ELAPSED(refTime)
 
 		if(IsFinite(dac))
-			path                 = "/stimulus/presentation"
-			params.channelNumber = DACs[i]
-			params.channelType   = ITC_XOP_CHANNEL_TYPE_DAC
-			col                  = AFH_GetITCDataColumn(ITCChanConfigWave, params.channelNumber, params.channelType)
-			WAVE params.data     = ExtractOneDimDataFromSweep(ITCChanConfigWave, ITCDataWave, col)
+			path                    = "/stimulus/presentation"
+			params.channelNumber    = DACs[i]
+			params.channelType      = ITC_XOP_CHANNEL_TYPE_DAC
+			col                     = AFH_GetITCDataColumn(ITCChanConfigWave, params.channelNumber, params.channelType)
+			writtenDataColumns[col] = 1
+			WAVE params.data        = ExtractOneDimDataFromSweep(ITCChanConfigWave, ITCDataWave, col)
 			NWB_GetTimeSeriesProperties(params, tsp)
 			params.groupIndex    = IsFinite(params.groupIndex) ? params.groupIndex : IPNWB#GetNextFreeGroupIndex(locationID, path)
 			IPNWB#WriteSingleChannel(locationID, path, params, tsp, chunkedLayout=chunkedLayout)
@@ -543,10 +547,11 @@ static Function NWB_AppendSweepLowLevel(locationID, panelTitle, ITCDataWave, ITC
 
 		listOfStimsets = GetTTLstimSets(numericalValues, textualValues, sweep, i)
 
-		params.clampMode     = NaN
-		params.channelNumber = i
-		params.channelType   = ITC_XOP_CHANNEL_TYPE_TTL
-		col                  = AFH_GetITCDataColumn(ITCChanConfigWave, params.channelNumber, params.channelType)
+		params.clampMode        = NaN
+		params.channelNumber    = i
+		params.channelType      = ITC_XOP_CHANNEL_TYPE_TTL
+		col                     = AFH_GetITCDataColumn(ITCChanConfigWave, params.channelNumber, params.channelType)
+		writtenDataColumns[col] = 1
 
 		WAVE data = ExtractOneDimDataFromSweep(ITCChanConfigWave, ITCDataWave, col)
 		DFREF dfr = NewFreeDataFolder()
@@ -580,6 +585,31 @@ static Function NWB_AppendSweepLowLevel(locationID, panelTitle, ITCDataWave, ITC
 	endfor
 
 	DEBUGPRINT_ELAPSED(refTime)
+
+	numEntries = DimSize(writtenDataColumns, ROWS)
+	for(i = 0; i < numEntries; i += 1)
+
+		if(writtenDataColumns[i])
+			continue
+		endif
+
+		// unassociated channel data
+		// can currently be ADC only
+		path                   = "/acquisition/timeseries"
+		ASSERT(ITCChanConfigWave[i][0] == ITC_XOP_CHANNEL_TYPE_ADC, "Unexpected channel type")
+		params.clampMode       = NaN
+		params.electrodeNumber = NaN
+		params.electrodeName   = ""
+		params.channelType     = ITCChanConfigWave[i][0]
+		params.channelNumber   = ITCChanConfigWave[i][1]
+		params.stimSet         = ""
+		NWB_GetTimeSeriesProperties(params, tsp)
+		WAVE params.data       = ExtractOneDimDataFromSweep(ITCChanConfigWave, ITCDataWave, i)
+		params.groupIndex      = IsFinite(params.groupIndex) ? params.groupIndex : IPNWB#GetNextFreeGroupIndex(locationID, path)
+		IPNWB#WriteSingleChannel(locationID, path, params, tsp, chunkedLayout=chunkedLayout)
+	endfor
+
+	DEBUGPRINT_ELAPSED(refTime)
 End
 
 static Function NWB_WriteStimsetTemplateWaves(locationID, stimSet, chunkedLayout)
@@ -632,6 +662,15 @@ static Function NWB_GetTimeSeriesProperties(p, tsp)
 
 	IPNWB#InitTimeSeriesProperties(tsp, p.channelType, p.clampMode)
 
+	// unassociated channel
+	if(!IsFinite(p.clampMode))
+		return NaN
+	endif
+
+	if(strlen(tsp.missing_fields) > 0)
+		ASSERT(IsFinite(p.electrodeNumber), "Expected finite electrode number with non empty \"missing_fields\"")
+	endif
+
 	if(p.channelType == ITC_XOP_CHANNEL_TYPE_ADC)
 		if(p.clampMode == V_CLAMP_MODE)
 			// VoltageClampSeries: datasets