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Add routines for extracting the stimset epoch #1880

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Add routines for extracting the stimset epoch #1880

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6f97401
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t-b Sep 6, 2023
4640218
SFH_ParseToSelectDataWaveAndRange: Handle non-sweep data gracefully
t-b Sep 8, 2023
947a547
changes
t-b Sep 8, 2023
703eeda
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t-b Sep 8, 2023
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1 change: 1 addition & 0 deletions Packages/MIES/MIES_MiesUtilities.ipf
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Original file line number Diff line number Diff line change
Expand Up @@ -6310,6 +6310,7 @@ Function GetTotalOnsetDelay(numericalValues, sweepNo)
WAVE numericalValues
variable sweepNo

// present since 778969b0 (DC_PlaceDataInITCDataWave: Document all other settings from the DAQ groupbox, 2015-11-26)
return GetLastSettingIndep(numericalValues, sweepNo, "Delay onset auto", DATA_ACQUISITION_MODE) + \
GetLastSettingIndep(numericalValues, sweepNo, "Delay onset user", DATA_ACQUISITION_MODE)
End
Expand Down
17 changes: 13 additions & 4 deletions Packages/MIES/MIES_SweepFormula.ipf
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Expand Up @@ -4625,7 +4625,7 @@ static Function/WAVE SF_OperationApFrequency(variable jsonId, string jsonPath, s
normValue = NaN
Make/FREE/D/N=0 normMean
WAVE/WAVE output = SFH_CreateSFRefWave(graph, opShort, DimSize(input, ROWS))
output = SF_OperationApFrequencyImpl(input[p], level, method, timeFreq, normalize, xAxisType, normValue, normMean)
output = SF_OperationApFrequencyImpl(graph, input[p], level, method, timeFreq, normalize, xAxisType, normValue, normMean)
if(!CmpStr(normalize, SF_OP_APFREQUENCY_NORMOVERSWEEPSAVG) && DimSize(normMean, ROWS))
normValue = mean(normMean)
SF_OperationApFrequencyNormalizeOverSweeps(output, normValue)
Expand Down Expand Up @@ -4659,9 +4659,9 @@ static Function SF_OperationApFrequencyNormalizeOverSweepsImpl(WAVE/Z data, vari
MultiThread data /= normValue
End

static Function/WAVE SF_OperationApFrequencyImpl(WAVE/Z data, variable level, variable method, string yStr, string normStr, string xAxisTypeStr, variable &normOSValue, WAVE normMean)
static Function/WAVE SF_OperationApFrequencyImpl(string graph, WAVE/Z data, variable level, variable method, string yStr, string normStr, string xAxisTypeStr, variable &normOSValue, WAVE normMean)

variable numPeaks, yModeTime, xAxisCount, normalize, normISValue
variable numPeaks, yModeTime, xAxisCount, normalize, normISValue, dataLengthInS
string yUnit

if(!WaveExists(data))
Expand All @@ -4680,7 +4680,16 @@ static Function/WAVE SF_OperationApFrequencyImpl(WAVE/Z data, variable level, va
switch(method)
case SF_APFREQUENCY_FULL:
// number_of_peaks / sweep_length
Make/FREE/D outD = { numPeaks / (DimDelta(data, ROWS) * DimSize(data, ROWS) * MILLI_TO_ONE) }
[WAVE selectData, WAVE selRange] = SFH_ParseToSelectDataWaveAndRange(data)

if(WaveExists(selRange) && SFH_IsFullRange(selRange))
WAVE stimsetRange = SFH_GetStimsetRange(graph, data, selectData)
dataLengthInS = (stimsetRange[1] - stimsetRange[0]) * MILLI_TO_ONE
else
dataLengthInS = DimDelta(data, ROWS) * DimSize(data, ROWS) * MILLI_TO_ONE
endif

Make/FREE/D outD = { numPeaks / dataLengthInS }
yUnit = SelectString(normalize, "Hz [Full]", "normalized frequency [Full]")
SetScale/P y, DimOffset(outD, ROWS), DimDelta(outD, ROWS), yUnit, outD
break
Expand Down
83 changes: 76 additions & 7 deletions Packages/MIES/MIES_SweepFormula_Helpers.ipf
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Expand Up @@ -290,6 +290,14 @@ Function/WAVE SFH_GetFullRange()
return range
End

Function SFH_IsFullRange(WAVE range)

ASSERT(IsNumericWave(range), "Invalid Range wave")
WAVE rangeRef = SFH_GetFullRange()

return EqualWaves(rangeRef, range, EQWAVES_DATA)
End

/// @brief Evaluate range parameter
///
/// Range can be `[100-200]` or implicit as `cursors(A, B)` or a named epoch `E0` or a wildcard expression with epochs `E*`
Expand Down Expand Up @@ -321,12 +329,14 @@ End

/// @brief Returns a range from a epochName
///
/// @param graph name of databrowser graph
/// @param graph name of databrowser graph
/// @param epochName name epoch
/// @param sweep number of sweep
/// @param channel number of DA channel
/// @param sweep number of sweep
/// @param chanType type of channel
/// @param channel number of DA channel
///
/// @returns a 1D wave with two elements, [startTime, endTime] in ms, if no epoch could be resolved [NaN, NaN] is returned
Function/WAVE SFH_GetRangeFromEpoch(string graph, string epochName, variable sweep, variable channel)
Function/WAVE SFH_GetRangeFromEpoch(string graph, string epochName, variable sweep, variable chanType, variable channel)

string regex
variable numEpochs
Expand All @@ -347,7 +357,7 @@ Function/WAVE SFH_GetRangeFromEpoch(string graph, string epochName, variable swe
endif

regex = "^" + epochName + "$"
WAVE/T/Z epochs = EP_GetEpochs(numericalValues, textualValues, sweep, XOP_CHANNEL_TYPE_DAC, channel, regex)
WAVE/T/Z epochs = EP_GetEpochs(numericalValues, textualValues, sweep, chanType, channel, regex)
if(!WaveExists(epochs))
return range
endif
Expand Down Expand Up @@ -951,10 +961,12 @@ Function [WAVE selectData, WAVE range] SFH_ParseToSelectDataWaveAndRange(WAVE sw
WAVE/Z range = JWN_GetTextWaveFromWaveNote(sweepData, SF_META_RANGE)

if(!WaveExists(range))
WAVE range = JWN_GetNumericWaveFromWaveNote(sweepData, SF_META_RANGE)
WAVE/Z range = JWN_GetNumericWaveFromWaveNote(sweepData, SF_META_RANGE)
endif

ASSERT(HasOneValidEntry(range), "Empty range")
if(!WaveExists(range) || !HasOneValidEntry(range))
return [$"", $""]
endif

WAVE selectData = SFH_NewSelectDataWave(1, 1)

Expand Down Expand Up @@ -1238,3 +1250,60 @@ Function SFH_CheckArgumentCount(variable jsonId, string jsonPath, string opShort

return numArgs
End

/// @brief Return a SF range in ms with the stimset range
///
/// Returns the full range if it is not sweep data.
Function/WAVE SFH_GetStimsetRange(string graph, WAVE data, WAVE selectData)

variable sweepNo, channel, chanType, dDAQ, oodDAQ, onsetDelay, terminationDelay, lengthInMS

sweepNo = selectData[0][%SWEEP]
channel = selectData[0][%CHANNELNUMBER]
chanType = selectData[0][%CHANNELTYPE]

// stimset epoch "ST" does not include any onset or termination delay and only the stimset epochs
// and it also works with dDAQ/oodDAQ
WAVE range = SFH_GetRangeFromEpoch(graph, "ST", sweepNo, chanType, channel)

if(!SFH_IsEmptyRange(range))
return range
endif

// data prior to 13b3499d (Add short names for Epochs stored in epoch name, 2021-09-06)
// try the long name instead
WAVE range = SFH_GetRangeFromEpoch(graph, "Stimset;", sweepNo, chanType, channel)

if(!SFH_IsEmptyRange(range))
return range
endif

// data prior to a2172f03 (Added generations of epoch information wave, 2019-05-22)
// remove total onset delay and termination delay iff we have neither dDAQ nor oodDAQ enabled
WAVE/Z numericalValues = BSP_GetLogbookWave(graph, LBT_LABNOTEBOOK, LBN_NUMERICAL_VALUES, sweepNumber = sweepNo)
ASSERT(WaveExists(numericalValues), "Missing numerical labnotebook")

// 778969b0 (DC_PlaceDataInITCDataWave: Document all other settings from the DAQ groupbox, 2015-11-26)
dDAQ = GetLastSettingIndep(numericalValues, sweepNo, "Distributed DAQ", DATA_ACQUISITION_MODE)
SFH_ASSERT(dDAQ != 1, "Can not gather stimset range with dDAQ data")

// d102c07d (Add new data acquisition mode: Optimized overlap distributed acquisition, 2016-08-10)
oodDAQ = GetLastSettingIndep(numericalValues, sweepNo, "Optimized Overlap dDAQ", DATA_ACQUISITION_MODE)
SFH_ASSERT(oodDAQ != 1, "Can not gather stimset range with oodDAQ data")

onsetDelay = GetTotalOnsetDelay(numericalValues, sweepNo)

// 778969b0 (DC_PlaceDataInITCDataWave: Document all other settings from the DAQ groupbox, 2015-11-26)
terminationDelay = GetLastSettingIndep(numericalValues, sweepNo, "Delay termination", DATA_ACQUISITION_MODE)

lengthInMS = DimDelta(data, ROWS) * DimSize(data, ROWS)

WAVE range = SFH_GetEmptyRange()

range[0] = onsetDelay
range[1] = lengthInMS - onsetDelay - terminationDelay

ASSERT(range[0] < range[1], "Invalid range")

return range
End
2 changes: 2 additions & 0 deletions Packages/MIES/MIES_SweepFormula_PSX.ipf
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Expand Up @@ -707,6 +707,7 @@ static Function PSX_OperationSweepGathering(string graph, WAVE/WAVE psxKernelDat
WAVE sweepData = psxKernelDataset[%$key]

[WAVE selectData, WAVE range] = SFH_ParseToSelectDataWaveAndRange(sweepData)
ASSERT(WaveExists(selectData) && WaveExists(range), "Could not recreate select/range wave")
comboKey = PSX_GenerateComboKey(graph, selectData, range)

psxParametersAnalyzePeaks = PSX_GetPSXParameters(parameterJSONID, PSX_CACHE_KEY_ANALYZE_PEAKS)
Expand Down Expand Up @@ -756,6 +757,7 @@ static Function PSX_OperationImpl(string graph, variable parameterJSONID, string
endif

[WAVE selectData, WAVE range] = SFH_ParseToSelectDataWaveAndRange(sweepData)
ASSERT(WaveExists(selectData) && WaveExists(range), "Could not recreate select/range wave")
comboKey = PSX_GenerateComboKey(graph, selectData, range)

psxParametersEvents = PSX_GetPSXParameters(parameterJSONID, PSX_CACHE_KEY_EVENTS)
Expand Down