WIP: NWBv2

Packages/MIES/MIES_AnalysisBrowser.ipf

@@ -579,7 +579,7 @@ End
 static Function AB_LoadSweepsFromNWB(discLocation, dataFolder, device)
 	string discLocation, dataFolder, device
 
-	variable h5_fileID, h5_groupID
+	variable h5_fileID, h5_groupID, nwbVersion
 	string channelList
 
 	Wave/I sweeps = GetAnalysisChannelSweepWave(dataFolder, device)
@@ -588,33 +588,33 @@ static Function AB_LoadSweepsFromNWB(discLocation, dataFolder, device)
 	h5_fileID = IPNWB#H5_OpenFile(discLocation)
 
 	// load from /acquisition/timeseries
-	channelList = IPNWB#ReadAcquisition(h5_fileID)
-	h5_groupID  = IPNWB#OpenAcquisition(h5_fileID)
+	nwbVersion = IPNWB#ReadNWBVersion(h5_fileID)
+	channelList = IPNWB#ReadAcquisition(h5_fileID, nwbVersion)
+	h5_groupID  = IPNWB#OpenAcquisition(h5_fileID, nwbVersion)
 	Wave/T acquisition = GetAnalysisChannelAcqWave(dataFolder, device)
-	AB_StoreChannelsBySweep(h5_groupID, channelList, sweeps, acquisition)
+	AB_StoreChannelsBySweep(h5_groupID, nwbVersion, channelList, sweeps, acquisition)
 	HDF5CloseGroup/Z h5_groupID
 
 	// load from /stimulus/presentation
 	channelList = IPNWB#ReadStimulus(h5_fileID)
 	h5_groupID  = IPNWB#OpenStimulus(h5_fileID)
 	Wave/T stimulus = GetAnalysisChannelStimWave(dataFolder, device)
-	AB_StoreChannelsBySweep(h5_groupID, channelList, sweeps, stimulus)
+	AB_StoreChannelsBySweep(h5_groupID, nwbVersion, channelList, sweeps, stimulus)
 	HDF5CloseGroup/Z h5_groupID
 
 	// close hdf5 file
 	IPNWB#H5_CloseFile(h5_fileID)
 End
 
 /// @brief Store channelList in storage wave according to index in sweeps wave
-static Function AB_StoreChannelsBySweep(groupID, channelList, sweeps, storage)
-	variable groupID
+static Function AB_StoreChannelsBySweep(groupID, nwbVersion, channelList, sweeps, storage)
+	variable groupID, nwbVersion
 	string channelList
 	Wave/I sweeps
 	Wave/T storage
 
-	variable numChannels, numSweeps, i
+	variable numChannels, numSweeps, i, sweepNo
 	string channelString
-	STRUCT IPNWB#ReadChannelParams channel
 
 	numChannels = ItemsInList(channelList)
 	numSweeps = GetNumberFromWaveNote(sweeps, NOTE_INDEX)
@@ -624,13 +624,13 @@ static Function AB_StoreChannelsBySweep(groupID, channelList, sweeps, storage)
 
 	for(i = 0; i < numChannels; i += 1)
 		channelString = StringFromList(i, channelList)
-		IPNWB#LoadSourceAttribute(groupID, channelString, channel)
-		FindValue/I=(channel.sweep)/S=0 sweeps
+		sweepNo = IPNWB#LoadSweepNumber(groupID, channelString, nwbVersion)
+		FindValue/I=(sweepNo)/S=0 sweeps
 		if(V_Value == -1)
 			numSweeps += 1
 			EnsureLargeEnoughWave(sweeps, minimumSize = numSweeps, dimension = ROWS, initialValue = -1)
 			EnsureLargeEnoughWave(storage, minimumSize = numSweeps, dimension = ROWS)
-			sweeps[numSweeps - 1] = channel.sweep
+			sweeps[numSweeps - 1] = sweepNo
 			storage[numSweeps - 1] = AddListItem(channelString, "")
 		else
 			storage[V_Value] = AddListItem(channelString, storage[V_Value])
@@ -1547,7 +1547,7 @@ static Function AB_LoadSweepFromNWB(discLocation, sweepDFR, device, sweep)
 	variable sweep
 
 	string channelList
-	variable h5_fileID, h5_groupID, numSweeps
+	variable h5_fileID, h5_groupID, numSweeps, version
 
 	Wave/T nwb = AB_GetMap(discLocation)
 
@@ -1573,20 +1573,21 @@ static Function AB_LoadSweepFromNWB(discLocation, sweepDFR, device, sweep)
 
 	// open NWB file
 	h5_fileID = IPNWB#H5_OpenFile(discLocation)
+	version = IPNWB#ReadNWBVersion(h5_fileID)
 
 	// load acquisition
 	Wave/T acquisition = GetAnalysisChannelAcqWave(nwb[%DataFolder], device)
 	channelList = acquisition[V_Value]
-	h5_groupID = IPNWB#OpenAcquisition(h5_fileID)
-	if(AB_LoadSweepFromNWBgeneric(h5_groupID, channelList, sweepDFR, configSweep))
+	h5_groupID = IPNWB#OpenAcquisition(h5_fileID, version)
+	if(AB_LoadSweepFromNWBgeneric(h5_groupID, version, channelList, sweepDFR, configSweep))
 		return 1
 	endif
 
 	// load stimulus
 	Wave/T stimulus = GetAnalysisChannelStimWave(nwb[%DataFolder], device)
 	channelList = stimulus[V_Value]
 	h5_groupID = IPNWB#OpenStimulus(h5_fileID)
-	if(AB_LoadSweepFromNWBgeneric(h5_groupID, channelList, sweepDFR, configSweep))
+	if(AB_LoadSweepFromNWBgeneric(h5_groupID, version, channelList, sweepDFR, configSweep))
 		return 1
 	endif
 
@@ -1596,8 +1597,9 @@ static Function AB_LoadSweepFromNWB(discLocation, sweepDFR, device, sweep)
 	return 0
 End
 
-static Function AB_LoadSweepFromNWBgeneric(h5_groupID, channelList, sweepDFR, configSweep)
-	variable h5_groupID
+/// @todo nwbVersion
+static Function AB_LoadSweepFromNWBgeneric(h5_groupID, version, channelList, sweepDFR, configSweep)
+	variable h5_groupID, version
 	string channelList
 	DFREF sweepDFR
 	Wave/I configSweep
@@ -1611,10 +1613,7 @@ static Function AB_LoadSweepFromNWBgeneric(h5_groupID, channelList, sweepDFR, co
 
 	for(i = 0; i < numChannels; i += 1)
 		channel = StringFromList(i, channelList)
-
-		// use AnalyseChannelName as a fallback if properties from the source attribute are missing
 		IPNWB#AnalyseChannelName(channel, p)
-		IPNWB#LoadSourceAttribute(h5_groupID, channel, p)
 
 		switch(p.channelType)
 			case ITC_XOP_CHANNEL_TYPE_DAC:
@@ -1625,7 +1624,7 @@ static Function AB_LoadSweepFromNWBgeneric(h5_groupID, channelList, sweepDFR, co
 				break
 			case ITC_XOP_CHANNEL_TYPE_ADC:
 				channelName = "AD"
-				wave loaded = IPNWB#LoadTimeseries(h5_groupID, channel)
+				wave loaded = IPNWB#LoadTimeseries(h5_groupID, channel, version)
 				channelName += "_" + num2str(p.channelNumber)
 				fakeConfigWave = 1
 				break
@@ -1661,6 +1660,7 @@ static Function AB_LoadSweepFromNWBgeneric(h5_groupID, channelList, sweepDFR, co
 			default:
 				ASSERT(0, "unknown channel type " + num2str(p.channelType))
 		endswitch
+		ASSERT(WaveExists(loaded), "No Wave loaded")
 
 		if(waveNoteLoaded == 0)
 			SVAR/Z test = sweepDFR:note

Packages/MIES/MIES_Constants.ipf

@@ -792,6 +792,7 @@ StrConstant PRESSURE_STARTSEAL      = "Initial Seal Pressure (psi)"
 StrConstant PRESSURE_MAXSEAL        = "Maximum Seal Pressure (psi)"
 StrConstant TP_AFTER_DAQ            = "Activate TP after DAQ"
 StrConstant EXPORT_NWB              = "Export to NWB"
+StrConstant NWB_VERSION             = "NWB Version"
 StrConstant APPEND_ASYNC            = "Append Asynchronous reading to wave note"
 StrConstant SYNC_MIES_MCC           = "Sync MIES to MCC"
 StrConstant ENABLE_I_EQUAL_ZERO     = "Switch clamp modes via I equal zero"

Packages/MIES/MIES_DAEphys.ipf

@@ -403,6 +403,7 @@ Function DAP_EphysPanelStartUpSettings()
 	CheckBox check_Settings_TPAfterDAQ WIN = $panelTitle, value= 0
 
 	CheckBox Check_Settings_NwbExport WIN = $panelTitle,value= 0
+	PopupMenu Popup_Settings_NwbVersion WIN = $panelTitle, mode=2, popvalue="2"
 
 	SetVariable min_AsyncAD_00 WIN = $panelTitle,value= _NUM:0
 	SetVariable max_AsyncAD_00 WIN = $panelTitle,value= _NUM:0
@@ -2347,7 +2348,7 @@ Function DAP_CheckSettings(panelTitle, mode)
 	endfor
 
 	if(DAG_GetNumericalValue(panelTitle, "Check_Settings_NwbExport"))
-		NWB_PrepareExport()
+		NWB_PrepareExport(DAG_GetNumericalValue(panelTitle, "Popup_Settings_NwbVersion"))
 	endif
 
 	return 0

Packages/MIES/MIES_DAEphys_Macro.ipf

@@ -3217,6 +3217,11 @@ Window DA_Ephys() : Panel
 	CheckBox Check_Settings_NwbExport,userdata(ResizeControlsInfo) += A"zzzzzzzzzzzz!!#u:Du]k<zzzzzzzzzzz"
 	CheckBox Check_Settings_NwbExport,userdata(ResizeControlsInfo) += A"zzz!!#u:Du]k<zzzzzzzzzzzzzz!!!"
 	CheckBox Check_Settings_NwbExport,value= 0
+	PopupMenu Popup_Settings_NwbVersion,pos={139.00,231.00},size={69.00,19.00},proc=DAP_PopMenuProc_UpdateGuiState,title="version"
+	PopupMenu Popup_Settings_NwbVersion,help={"Set the NWB Version of the export when using triggered export from DA_Ephys"}
+	PopupMenu Popup_Settings_NwbVersion,userdata(tabcontrol)=  "ADC"
+	PopupMenu Popup_Settings_NwbVersion,userdata(tabnum)=  "5"
+	PopupMenu Popup_Settings_NwbVersion,mode=2,popvalue="2",value= #"\"1;2\""
 	SetVariable setvar_DataAcq_OnsetDelayUser,pos={289.00,636.00},size={167.00,18.00},bodyWidth=50,disable=1,proc=DAP_SetVar_UpdateGuiState,title="User onset delay (ms)"
 	SetVariable setvar_DataAcq_OnsetDelayUser,help={"A global parameter that delays the onset time of a set after the initiation of data acquistion. Data acquisition start time is NOT delayed. Useful when set(s) have insufficient baseline epoch."}
 	SetVariable setvar_DataAcq_OnsetDelayUser,userdata(tabnum)=  "0"

Packages/MIES/MIES_Debugging.ipf

@@ -560,3 +560,25 @@ Function GetSizeOfAllWavesInExperiment()
 
 	Edit/K=1 root:list
 End
+
+// see tools/functionprofiling.sh
+Function DEBUG_STOREFUNCTION()
+	string funcName = GetRTStackInfo(2)
+	string callchain = GetRTStackInfo(0)
+	string caller = StringFromList(0, callchain)
+
+	WAVE/Z wv = root:functionids
+	if(!WaveExists(wv))
+		WAVE/T functionids = ListToTextWave(FunctionList("*", ";", "KIND:18,WIN:"), ";")
+		Duplicate functionids root:functionids/WAVE=wv
+	endif
+	WAVE/Z count = root:functioncount
+	if(!WaveExists(count))
+		Make/U/L/N=(DimSize(wv, 0)) root:functioncount = 0
+		WAVE count = root:functioncount
+	endif
+	FindValue/TEXT=(funcName) wv
+	if(V_Value != -1)
+		count[V_Value] += 1
+	endif
+End

Packages/MIES/MIES_ExperimentConfig.ipf

@@ -406,6 +406,8 @@ static Function ExpConfig_DAEphysSettings(panelTitle, UserSettings)
 	PGC_SetAndActivateControl(panelTitle,"check_Settings_TP_SaveTP", val = str2numSafe(UserSettings[V_value][%SettingValue]))
 	FindValue /TXOP = 4 /TEXT = EXPORT_NWB UserSettings
 	PGC_SetAndActivateControl(panelTitle,"Check_Settings_NwbExport", val = str2numSafe(UserSettings[V_value][%SettingValue]))
+	FindValue /TXOP = 4 /TEXT = NWB_VERSION UserSettings
+	PGC_SetAndActivateControl(panelTitle,"Popup_Settings_NwbVersion", val = str2numSafe(UserSettings[V_value][%SettingValue]))
 	FindValue /TXOP = 4 /TEXT = APPEND_ASYNC UserSettings
 	PGC_SetAndActivateControl(panelTitle,"Check_Settings_Append", val = str2numSafe(UserSettings[V_value][%SettingValue]))
 	FindValue /TXOP = 4 /TEXT = SYNC_MIES_MCC UserSettings

Packages/MIES/MIES_Menu.ipf

@@ -31,9 +31,11 @@ Menu "Mies Panels"
 	"-"
 	SubMenu "Neurodata Without Borders (NWB)"
 		"Export all data into NWB"             , /Q, NWB_ExportWithDialog(NWB_EXPORT_DATA)
+		"-"
+		"Export all data into NWBv1 (legacy)"  , /Q, NWB_ExportWithDialog(NWB_EXPORT_DATA, nwbVersion = 1)
+		"-"
 		"Export all stimsets into NWB"         , /Q, NWB_ExportWithDialog(NWB_EXPORT_STIMSETS)
 		"Load Stimsets from NWB"               , /Q, NWB_LoadAllStimsets()
-		"-"
 	End
 	"-"
 	"About MIES"                               , /Q, OpenAboutDialog()