Merge pull request #2339 from AllenInstitute/bugfix/2339-add-power-sp…

…ectrum-setting-to-labnotebook

DA_Ephys: Add power spectrum to labnotebook

Packages/MIES/MIES_Constants.ipf

@@ -39,7 +39,7 @@ Constant SWEEP_EPOCH_VERSION = 9
 /// - New/Changed layers of entries
 ///
 ///@{
-Constant LABNOTEBOOK_VERSION = 78
+Constant LABNOTEBOOK_VERSION = 79
 Constant RESULTS_VERSION     = 3
 ///@}
 

Packages/MIES/MIES_DataConfigurator.ipf

@@ -1212,6 +1212,7 @@ static Function DC_PrepareLBNEntries(string device, STRUCT DataConfigurationResu
 	DC_DocumentChannelProperty(device, "Repeat sweep on async alarm", INDEP_HEADSTAGE, NaN, NaN, var = DAG_GetNumericalValue(device, "Check_Settings_AlarmAutoRepeat"))
 	DC_DocumentChannelProperty(device, AUTOBIAS_PERC_KEY, INDEP_HEADSTAGE, NaN, NaN, var = DAG_GetNumericalValue(device, "setvar_Settings_AutoBiasPerc"))
 	DC_DocumentChannelProperty(device, "Autobias interval", INDEP_HEADSTAGE, NaN, NaN, var = DAG_GetNumericalValue(device, "setvar_Settings_AutoBiasInt"))
+	DC_DocumentChannelProperty(device, "TP power spectrum", INDEP_HEADSTAGE, NaN, NaN, var = DAG_GetNumericalValue(device, "check_settings_show_power"))
 
 	DC_DocumentHardwareProperties(device, s.hardwareType)
 

Packages/MIES/MIES_ExperimentDocumentation.ipf

@@ -801,8 +801,8 @@ Function ED_TPDocumentation(string device)
 	WAVE TPResults  = GetTPResults(device)
 	WAVE statusHS   = DAG_GetChannelState(device, CHANNEL_TYPE_HEADSTAGE)
 
-	Make/FREE/T/N=(3, 12) TPKeyWave
-	Make/FREE/N=(1, 12, LABNOTEBOOK_LAYER_COUNT) TPSettingsWave = NaN
+	Make/FREE/T/N=(3, 13) TPKeyWave
+	Make/FREE/N=(1, 13, LABNOTEBOOK_LAYER_COUNT) TPSettingsWave = NaN
 
 	// add data to TPKeyWave
 	TPKeyWave[0][0] = "TP Baseline Vm" // current clamp
@@ -818,6 +818,7 @@ Function ED_TPDocumentation(string device)
 	TPKeyWave[0][9]  = "DAC"
 	TPKeyWave[0][10] = "ADC"
 	TPKeyWave[0][11] = CLAMPMODE_ENTRY_KEY
+	TPKeyWave[0][12] = "TP power spectrum"
 
 	TPKeyWave[1][0]  = "mV"
 	TPKeyWave[1][1]  = "pA"
@@ -831,6 +832,7 @@ Function ED_TPDocumentation(string device)
 	TPKeyWave[1][9]  = ""
 	TPKeyWave[1][10] = ""
 	TPKeyWave[1][11] = ""
+	TPKeyWave[1][12] = LABNOTEBOOK_BINARY_UNIT
 
 	RTolerance       = TPSettings[%resistanceTol][INDEP_HEADSTAGE]
 	TPKeyWave[2][0]  = "1"                 // Assume a tolerance of 1 mV for V rest
@@ -845,6 +847,7 @@ Function ED_TPDocumentation(string device)
 	TPKeyWave[2][9]  = "0.1"
 	TPKeyWave[2][10] = "0.1"
 	TPKeyWave[2][11] = LABNOTEBOOK_NO_TOLERANCE
+	TPKeyWave[2][12] = LABNOTEBOOK_NO_TOLERANCE
 
 	TPSettingsWave[0][2][0, NUM_HEADSTAGES - 1] = TPResults[%ResistanceInst][r]
 	TPSettingsWave[0][3][0, NUM_HEADSTAGES - 1] = TPResults[%ResistanceSteadyState][r]
@@ -877,6 +880,7 @@ Function ED_TPDocumentation(string device)
 	TPSettingsWave[0][9][0, NUM_HEADSTAGES - 1]  = hsProp[r][%DAC]
 	TPSettingsWave[0][10][0, NUM_HEADSTAGES - 1] = hsProp[r][%ADC]
 	TPSettingsWave[0][11][0, NUM_HEADSTAGES - 1] = hsProp[r][%ClampMode]
+	TPSettingsWave[0][12][INDEP_HEADSTAGE]       = DAG_GetNumericalValue(device, "check_settings_show_power")
 
 	sweepNo = AFH_GetLastSweepAcquired(device)
 	ED_AddEntriesToLabnotebook(TPSettingsWave, TPKeyWave, sweepNo, device, TEST_PULSE_MODE)

Packages/MIES/MIES_MiesUtilities_Logbook.ipf

@@ -1347,11 +1347,12 @@ threadsafe static Function FindRange(WAVE wv, variable col, variable val, variab
 
 	if(WaveExists(indizesSourceType)) // entrySourceType could be found
 		WAVE/Z indizes = GetSetIntersection(indizesSetting, indizesSourceType)
-		if(!WaveExists(indizes))
-			return NaN
-		endif
 	else
-		WAVE indizes = indizesSetting
+		WAVE/Z indizes = indizesSetting
+	endif
+
+	if(!WaveExists(indizes))
+		return NaN
 	endif
 
 	numRows = DimSize(indizes, ROWS)
@@ -1372,7 +1373,7 @@ threadsafe static Function FindRange(WAVE wv, variable col, variable val, variab
 	for(i = numRows - 2; i >= 0; i -= 1)
 		index = indizes[i]
 		// a backward search stops when the beginning of the last sequence was found
-		if(index < first - 1)
+		if(index < first - 1 && sourceTypeCol >= 0)
 			if(IsNumeric)
 				for(j = index + 1; j < first; j += 1)
 					if(!IsNaN(wv[j][sourceTypeCol][0]))

Packages/MIES/MIES_WaveDataFolderGetters.ipf

@@ -2367,7 +2367,7 @@ threadsafe Function/WAVE GetLBNidCache(WAVE numericalValues)
 	return wv
 End
 
-static Constant SWEEP_SETTINGS_WAVE_VERSION = 39
+static Constant SWEEP_SETTINGS_WAVE_VERSION = 40
 
 /// @brief Uses the parameter names from the `sourceKey` columns and
 ///        write them as dimension into the columns of dest.
@@ -2513,6 +2513,7 @@ End
 /// - 59: Save amplifier settings
 /// - 60: Require amplifier
 /// - 61: Skip Ahead
+/// - 62: TP power spectrum
 Function/WAVE GetSweepSettingsKeyWave(string device)
 
 	variable versionOfNewWave = SWEEP_SETTINGS_WAVE_VERSION
@@ -2530,9 +2531,9 @@ Function/WAVE GetSweepSettingsKeyWave(string device)
 	if(ExistsWithCorrectLayoutVersion(wv, versionOfNewWave))
 		return wv
 	elseif(WaveExists(wv))
-		Redimension/N=(-1, 62) wv
+		Redimension/N=(-1, 63) wv
 	else
-		Make/T/N=(3, 62) newDFR:$newName/WAVE=wv
+		Make/T/N=(3, 63) newDFR:$newName/WAVE=wv
 	endif
 
 	wv = ""
@@ -2789,6 +2790,10 @@ Function/WAVE GetSweepSettingsKeyWave(string device)
 	wv[%Units][61]     = ""
 	wv[%Tolerance][61] = "1"
 
+	wv[%Parameter][62] = "TP power spectrum"
+	wv[%Units][62]     = LABNOTEBOOK_BINARY_UNIT
+	wv[%Tolerance][62] = LABNOTEBOOK_NO_TOLERANCE
+
 	SetSweepSettingsDimLabels(wv, wv)
 	SetWaveVersion(wv, versionOfNewWave)
 

Packages/MIES/labnotebook_numerical_description.itx

@@ -1,5 +1,5 @@
 IGOR
-WAVES/T/N=(195,6)	labnotebook_numerical_description
+WAVES/T/N=(196,6)	labnotebook_numerical_description
 BEGIN
 	"Name"	"Unit"	"Tolerance"	"Description"	"Headstage Contingency"	"ClampMode"
 	"SweepNum"	""	"-"	"Sweep number: Non-repeating non-negative numeric identifier for sweep time series. Increments in the order of acquisition. Starts at zero."	"ALL"	""
@@ -123,6 +123,7 @@ BEGIN
 	"Autobias"	"On/Off"	"-"	"During the inter trial interval (\"ITI\") autobias adjusts the holding current to maintain the user defined \"Autobias Vcom\" within \"Autobias Vcom variance\". The autobias evaluates a user defined part (\"Autobias (%)\") of the Testpulse baseline at the \"Autobias Interval\" (DaEphys->Settings->Amplifier)."	"DEPEND"	"IC"
 	"Sweep Rollback"	""	"0.1"	"Sweep rollback allows to remove existing sweeps by decreasing the device sweep counter. This entry documents that sweep rollback has happened and the new target sweep number. (removed)"	"INDEP"	""
 	"Skip Sweeps"	""	"0.1"	"Whenever the user issues a \"Skip Sweeps\" command this entry documents the new and to be jumped to sweep number."	"INDEP"	""
+	"TP power spectrum"	"On/Off"	"-"	"Instead of the Testpulse the power spectrum is displayed/saved during TP and TP during ITI"	"INDEP"	""
 	"Async 0 On/Off"	"On/Off"	"-"	"Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.\r\rAlarm is triggered when enabled and minimum or maximum is exceeded.\r\rThe value is stored in a new labnotebook column called \"Async AD$X: $Name\" where X is the asynchronous channel and $Name the title of the entry."	"INDEP"	"IC;VC;I=0"
 	"Async 1 On/Off"	"On/Off"	"-"	"Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.\r\rAlarm is triggered when enabled and minimum or maximum is exceeded.\r\rThe value is stored in a new labnotebook column called \"Async AD$X: $Name\" where X is the asynchronous channel and $Name the title of the entry."	"INDEP"	"IC;VC;I=0"
 	"Async 2 On/Off"	"On/Off"	"-"	"Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.\r\rAlarm is triggered when enabled and minimum or maximum is exceeded.\r\rThe value is stored in a new labnotebook column called \"Async AD$X: $Name\" where X is the asynchronous channel and $Name the title of the entry."	"INDEP"	"IC;VC;I=0"

Packages/tests/Basic/UTF_Labnotebook.ipf

@@ -98,6 +98,15 @@ Function GetLastSettingEntrySourceTypes()
 	CHECK_EQUAL_WAVES(DAQSettings, {0, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN}, mode = WAVE_DATA)
 	CHECK_EQUAL_WAVES(TPSettings, {1, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN}, mode = WAVE_DATA)
 
+	// no entry source otherwise the same labnotebook as above
+	WAVE/SDFR=dfr numericalValues_with_sweep_rb_no_type
+	WAVE   numericalValues = PrepareLBNNumericalValues(numericalValues_with_sweep_rb_no_type)
+	WAVE/Z DAQSettings     = GetLastSetting(numericalValues, 0, "DAC", DATA_ACQUISITION_MODE)
+	WAVE/Z TPSettings      = GetLastSetting(numericalValues, 0, "DAC", TEST_PULSE_MODE)
+
+	CHECK_EQUAL_WAVES(DAQSettings, {0, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN}, mode = WAVE_DATA)
+	CHECK_EQUAL_WAVES(TPSettings, {1, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN}, mode = WAVE_DATA)
+
 	// contains two times sweep 73, created with sweep rollback and a trailing TP
 	// and does not have entry source type information
 	WAVE/SDFR=dfr numericalValues_no_type_with_sweep_rb_with_tp
@@ -222,6 +231,22 @@ Function GetLastSettingFindsNaNSweep()
 	CHECK_EQUAL_WAVES(settings, settingsRef, mode = WAVE_DATA, tol = 1e-13)
 End
 
+Function GetLastSettingOnlyTPData()
+
+	DFREF dfr = root:Labnotebook_misc:
+
+	// check that we can find the first entries of the testpulse which have sweepNo == NaN
+	WAVE/SDFR=dfr numericalValues_only_TP
+	WAVE numericalValues = PrepareLBNNumericalValues(numericalValues_only_TP)
+
+	WAVE/Z settings = GetLastSetting(numericalValues, NaN, "TP power spectrum", TEST_PULSE_MODE)
+	Make/D/FREE settingsRef = {NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, 1}
+	CHECK_EQUAL_WAVES(settings, settingsRef, mode = WAVE_DATA)
+
+	WAVE/Z settings = GetLastSetting(numericalValues, NaN, "TP power spectrum", DATA_ACQUISITION_MODE)
+	CHECK_WAVE(settings, NULL_WAVE)
+End
+
 static Function GetLastSettingFindsWithinNonConsecutiveSweepOrder()
 
 	string   key

Packages/tests/HardwareBasic/UTF_TestPulseAndTPDuringDAQ.ipf

@@ -1164,6 +1164,13 @@ static Function RunPowerSpectrum_REENTRY([string str])
 	CHECK_EQUAL_VAR(0, sweepDataLNB[0][%$STIMSET_SCALE_FACTOR_KEY][0])
 	CHECK_EQUAL_VAR(0, sweepDataLNB[0][%$STIMSET_SCALE_FACTOR_KEY][1])
 
+	WAVE numericalValues = GetLBNumericalValues(str)
+
+	WAVE/Z powerSpectrum = GetLastSetting(numericalValues, sweepNo, "TP power spectrum", DATA_ACQUISITION_MODE)
+	CHECK_WAVE(powerSpectrum, NULL_WAVE)
+
+	WAVE/Z powerSpectrum = GetLastSetting(numericalValues, sweepNo, "TP power spectrum", TEST_PULSE_MODE)
+	CHECK_EQUAL_WAVES(powerSpectrum, {NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, 1}, mode = WAVE_DATA)
 End
 
 // UTF_TD_GENERATOR DeviceNameGeneratorMD1
@@ -1266,6 +1273,9 @@ static Function TPDuringDAQwithPS_REENTRY([string str])
 	daGain = DAG_GetNumericalValue(str, GetSpecialControlLabel(CHANNEL_TYPE_DAC, CHANNEL_CONTROL_SCALE), index = 0)
 
 	CHECK_EQUAL_WAVES(stimScale, {tpAmp, daGain, NaN, NaN, NaN, NaN, NaN, NaN, NaN}, mode = WAVE_DATA)
+
+	WAVE/Z powerSpectrum = GetLastSetting(numericalValues, sweepNo, "TP power spectrum", DATA_ACQUISITION_MODE)
+	CHECK_EQUAL_WAVES(powerSpectrum, {NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, 1}, mode = WAVE_DATA)
 End
 
 // UTF_TD_GENERATOR v0:SingleMultiDeviceDAQ