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Merge pull request #2083 from AllenInstitute/feature/2083-recreate_us…
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…er_epochs

Recreate user epochs for PSQ_Chirp
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@t-b
t-b authored Apr 25, 2024
2 parents e45c216 + 07e3642 commit cb86624
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Showing 11 changed files with 493 additions and 91 deletions.
110 changes: 87 additions & 23 deletions Packages/MIES/MIES_AnalysisFunctions_PatchSeq.ipf
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Original file line number Diff line number Diff line change
Expand Up @@ -446,7 +446,7 @@ static Function PSQ_EvaluateBaselineProperties(string device, STRUCT AnalysisFun
variable leakCurPassedAll, maxLeakCurrent, targetVThreshold
variable rmsShortThreshold, rmsLongThreshold
variable chunkPassedRMSShortOverride, chunkPassedRMSLongOverride, chunkPassedTargetVOverride, chunkPassedLeakCurOverride
string msg, adUnit, ctrl, key, epName, epShortName
string msg, adUnit, ctrl, key

STRUCT PSQ_PulseSettings ps
PSQ_GetPulseSettingsForType(type, ps)
Expand Down Expand Up @@ -596,6 +596,7 @@ static Function PSQ_EvaluateBaselineProperties(string device, STRUCT AnalysisFun
endif
// END TEST

WAVE/T epochWave = GetEpochsWave(device)
for(i = 0; i < NUM_HEADSTAGES; i += 1)

if(!statusHS[i])
Expand All @@ -604,9 +605,7 @@ static Function PSQ_EvaluateBaselineProperties(string device, STRUCT AnalysisFun

DAC = AFH_GetDACFromHeadstage(device, i)
ASSERT(IsFinite(DAC), "Could not determine DAC channel number for HS " + num2istr(i) + " for device " + device)
epName = "Name=Baseline Chunk;Index=" + num2istr(chunk)
epShortName = PSQ_BASELINE_CHUNK_SHORT_NAME_PREFIX + num2istr(chunk)
EP_AddUserEpoch(device, XOP_CHANNEL_TYPE_DAC, DAC, chunkStartTimeMax * MILLI_TO_ONE, (chunkStartTimeMax + chunkLengthTime) * MILLI_TO_ONE, epName, shortname = epShortName)
PSQ_AddBaselineEpoch(epochWave, DAC, chunk, chunkStartTimeMax, chunkLengthTime)

if(chunk == 0)
// store baseline RMS short/long tartget V analysis parameters in labnotebook on first use
Expand Down Expand Up @@ -847,6 +846,22 @@ static Function PSQ_EvaluateBaselineProperties(string device, STRUCT AnalysisFun
endif
End

/// @brief Add base line epoch to user epochs
///
/// @param epochWave 4D epochs wave
/// @param DAC DAC channel number
/// @param chunk number of evaluated chunk
/// @param chunkStartTimeMax start time of chunk in ms
/// @param chunkLengthTime time length of chunk in ms
Function PSQ_AddBaselineEpoch(WAVE epochWave, variable DAC, variable chunk, variable chunkStartTimeMax, variable chunkLengthTime)

string epName, epShortName

epName = "Name=Baseline Chunk;Index=" + num2istr(chunk)
epShortName = PSQ_BASELINE_CHUNK_SHORT_NAME_PREFIX + num2istr(chunk)
EP_AddUserEpoch(epochWave, XOP_CHANNEL_TYPE_DAC, DAC, chunkStartTimeMax * MILLI_TO_ONE, (chunkStartTimeMax + chunkLengthTime) * MILLI_TO_ONE, epName, shortname = epShortName)
End

/// @brief Return the number of chunks
///
/// A chunk is #PSQ_BL_EVAL_RANGE [ms] of baseline.
Expand Down Expand Up @@ -3598,7 +3613,8 @@ static Function PSQ_Ramp_AddEpoch(string device, variable headstage, WAVE wv, st
epBegin = IndexToScale(wv, first, ROWS) * MILLI_TO_ONE
epEnd = IndexToScale(wv, last, ROWS) * MILLI_TO_ONE

EP_AddUserEpoch(device, XOP_CHANNEL_TYPE_DAC, DAC, epBegin, epEnd, tags, shortName = shortName)
WAVE/T epochWave = GetEpochsWave(device)
EP_AddUserEpoch(epochWave, XOP_CHANNEL_TYPE_DAC, DAC, epBegin, epEnd, tags, shortName = shortName)
End

/// @brief Determine if we have three passing sweeps with the same DAScale value
Expand Down Expand Up @@ -4670,8 +4686,7 @@ End
///
/// Zero is the DA/AD wave zero.
static Function [variable epBegin, variable epEnd] PSQ_CR_GetSpikeEvaluationRange(string device, variable sweepNo, variable headstage)
variable DAC, totalOnsetDelay, chirpStart, chirpEnd
string tags, shortname
variable DAC, totalOnsetDelay

WAVE numericalValues = GetLBNumericalValues(device)
WAVE textualValues = GetLBTextualValues(device)
Expand All @@ -4694,7 +4709,28 @@ static Function [variable epBegin, variable epEnd] PSQ_CR_GetSpikeEvaluationRang

WAVE durations = PSQ_GetPulseDurations(device, PSQ_CHIRP, sweepNo, totalOnsetDelay)

chirpStart = totalOnsetDelay + PSQ_BL_EVAL_RANGE
WAVE/T epochWave = GetEpochsWave(device)
[epBegin, epEnd] = PSQ_CR_AddSpikeEvaluationEpoch(epochsWave, DAC, headstage, durations, totalOnsetDelay)

return [epBegin * ONE_TO_MILLI, epEnd * ONE_TO_MILLI]
End

/// @brief Adds PSQ_Chirp spike evaluation epoch
///
/// @param epochsWave 4d epochs wave
/// @param DAC DAC number
/// @param headstage headstage number
/// @param durations pulse duration wave
/// @param totalOnsetDelayMS totalOnsetDelay in ms
///
/// @retval epBegin epoch begin in s
/// @retval epEnd epoch end in s
Function [variable epBegin, variable epEnd] PSQ_CR_AddSpikeEvaluationEpoch(WAVE/T epochsWave, variable DAC, variable headstage, WAVE durations, variable totalOnsetDelayMS)

variable chirpStart, chirpEnd
string tags, shortName

chirpStart = totalOnsetDelayMS + PSQ_BL_EVAL_RANGE
chirpEnd = chirpStart + durations[headstage]

epBegin = chirpStart * MILLI_TO_ONE
Expand All @@ -4703,9 +4739,9 @@ static Function [variable epBegin, variable epEnd] PSQ_CR_GetSpikeEvaluationRang
sprintf tags, "Type=Chirp spike evaluation"
sprintf shortName, "CR_SE"

EP_AddUserEpoch(device, XOP_CHANNEL_TYPE_DAC, DAC, epBegin, epEnd, tags, shortName = shortName)
EP_AddUserEpoch(epochsWave, XOP_CHANNEL_TYPE_DAC, DAC, epBegin, epEnd, tags, shortName = shortName)

return [epBegin * ONE_TO_MILLI, epEnd * ONE_TO_MILLI]
return [epBegin, epEnd]
End

/// @brief Return the begin/start [ms] of the chirp bounds evaluation range
Expand All @@ -4714,7 +4750,7 @@ End
static Function [variable epBegin, variable epEnd] PSQ_CR_GetChirpEvaluationRange(string device, variable sweepNo, variable headstage, variable requestedCycles)

variable DAC, stimsetQC
string name, tags, regexp, shortname, key
string name, tags, shortname, key

WAVE numericalValues = GetLBNumericalValues(device)
WAVE textualValues = GetLBTextualValues(device)
Expand All @@ -4733,10 +4769,7 @@ static Function [variable epBegin, variable epEnd] PSQ_CR_GetChirpEvaluationRang
return [epBegin, epEnd]
endif

sprintf regexp, "^(E1_TG_C%d|E1_TG_C%d)$", 0, requestedCycles - 1
WAVE/T/Z fullCycleEpochs = EP_GetEpochs(numericalValues, textualValues, NaN, XOP_CHANNEL_TYPE_DAC, DAC, \
regexp, treelevel = 2, epochsWave = epochsWave)

WAVE/Z/T fullCycleEpochs = PSQ_CR_GetFullCycleEpochs(numericalValues, textualValues, DAC, epochsWave, requestedCycles)
if(!WaveExists(fullCycleEpochs))
printf "Could not find chirp cycles in epoch 1.\r"
ControlWindowToFront()
Expand All @@ -4758,15 +4791,43 @@ static Function [variable epBegin, variable epEnd] PSQ_CR_GetChirpEvaluationRang
return [NaN, NaN]
endif

[epBegin, epEnd] = PSQ_CR_AddCycleEvaluationEpoch(epochsWave, fullCycleEpochs, DAC)

return [epBegin * ONE_TO_MILLI, epEnd * ONE_TO_MILLI]
End

/// @brief Add PSQ_Chirp cycle evaluation epoch
///
/// @param epochsWave 4d epoch wave
/// @param fullCycleEpochs 2d epoch wave with epochs of full cycles (sorted)
/// @param DAC DAC number
///
/// @retval epBegin epoch begin in s
/// @retval epEnd epoch end in s
Function [variable epBegin, variable epEnd] PSQ_CR_AddCycleEvaluationEpoch(WAVE/T epochsWave, WAVE/T fullCycleEpochs, variable DAC)

string tags, shortName

epBegin = str2num(fullCycleEpochs[0][EPOCH_COL_STARTTIME])
epEnd = str2num(fullCycleEpochs[DimSize(fullCycleEpochs, ROWS) - 1][EPOCH_COL_ENDTIME])

sprintf tags, "Type=Chirp cycles evaluation"
sprintf shortName, "CR_CE"

EP_AddUserEpoch(device, XOP_CHANNEL_TYPE_DAC, DAC, epBegin, epEnd, tags, shortName = shortName)
EP_AddUserEpoch(epochsWave, XOP_CHANNEL_TYPE_DAC, DAC, epBegin, epEnd, tags, shortName = shortName)

return [epBegin * ONE_TO_MILLI, epEnd * ONE_TO_MILLI]
return [epBegin, epEnd]
End

Function/WAVE PSQ_CR_GetFullCycleEpochs(WAVE numericalValues, WAVE/T textualValues, variable DAC, WAVE/T epochsWave, variable requestedCycles)

string regexp

sprintf regexp, "^(E1_TG_C%d|E1_TG_C%d)$", 0, requestedCycles - 1
WAVE/T/Z fullCycleEpochs = EP_GetEpochs(numericalValues, textualValues, NaN, XOP_CHANNEL_TYPE_DAC, DAC, \
regexp, treelevel = 2, epochsWave = epochsWave)

return fullCycleEpochs
End

/// @brief Manually force the pre/post set events
Expand Down Expand Up @@ -5245,15 +5306,16 @@ static Function PSQ_CreateTestpulseLikeEpoch(string device, variable DAC, string
sprintf tags, "Type=Testpulse Like;Index=%d", tpIndex
sprintf shortName, "TP%d", tpIndex

EP_AddUserEpoch(device, XOP_CHANNEL_TYPE_DAC, DAC, epBegin, epEnd, tags, shortName = shortName)
WAVE/T epochWave = GetEpochsWave(device)
EP_AddUserEpoch(epochWave, XOP_CHANNEL_TYPE_DAC, DAC, epBegin, epEnd, tags, shortName = shortName)

// pre TP baseline
// same epBegin as full TP
epEnd = epBegin + prePulseTP
sprintf tags, "Type=Testpulse Like;SubType=Baseline;Index=%d;", tpIndex
sprintf shortName, "TP%d_B0", tpIndex

EP_AddUserEpoch(device, XOP_CHANNEL_TYPE_DAC, DAC, epBegin, epEnd, tags, shortName = shortName)
EP_AddUserEpoch(epochWave, XOP_CHANNEL_TYPE_DAC, DAC, epBegin, epEnd, tags, shortName = shortName)

// pulse TP
epBegin = epEnd
Expand All @@ -5262,15 +5324,15 @@ static Function PSQ_CreateTestpulseLikeEpoch(string device, variable DAC, string
sprintf tags, "Type=Testpulse Like;SubType=Pulse;Amplitude=%g;Index=%d;", amplitude, tpIndex
sprintf shortName, "TP%d_P", tpIndex

EP_AddUserEpoch(device, XOP_CHANNEL_TYPE_DAC, DAC, epBegin, epEnd, tags, shortName = shortName)
EP_AddUserEpoch(epochWave, XOP_CHANNEL_TYPE_DAC, DAC, epBegin, epEnd, tags, shortName = shortName)

// post TP baseline
epBegin = epEnd
epEnd = epBegin + postPulseTP
sprintf tags, "Type=Testpulse Like;SubType=Baseline;Index=%d;", tpIndex
sprintf shortName, "TP%d_B1", tpIndex

EP_AddUserEpoch(device, XOP_CHANNEL_TYPE_DAC, DAC, epBegin, epEnd, tags, shortName = shortName)
EP_AddUserEpoch(epochWave, XOP_CHANNEL_TYPE_DAC, DAC, epBegin, epEnd, tags, shortName = shortName)

return epEnd
End
Expand Down Expand Up @@ -5698,6 +5760,7 @@ static Function PSQ_SE_CreateEpochs(string device, variable headstage, string pa

wbBegin = 0
wbEnd = totalOnsetDelay * MILLI_TO_ONE
WAVE/T epochWave = GetEpochsWave(device)
for(i = 0; i < numEpochs; i += 1)
duration = ST_GetStimsetParameterAsVariable(setName, "Duration", epochIndex = i) * MILLI_TO_ONE

Expand Down Expand Up @@ -5727,7 +5790,7 @@ static Function PSQ_SE_CreateEpochs(string device, variable headstage, string pa
epEnd = epBegin + chunkLength

[tags, shortName] = PSQ_CreateBaselineChunkSelectionStrings(userEpochIndexBLC)
EP_AddUserEpoch(device, XOP_CHANNEL_TYPE_DAC, DAC, epBegin, epEnd, tags, shortName = shortName)
EP_AddUserEpoch(epochWave, XOP_CHANNEL_TYPE_DAC, DAC, epBegin, epEnd, tags, shortName = shortName)
userEpochIndexBLC += 1
elseif(i == 1 || i == 4 || i == 7 || i == 12 || i == 15 || i == 18)
epBegin = wbBegin
Expand Down Expand Up @@ -6115,6 +6178,7 @@ static Function PSQ_CreateBaselineChunkSelectionEpochs(string device, variable h

wbBegin = 0
wbEnd = totalOnsetDelay * MILLI_TO_ONE
WAVE/T epochWave = GetEpochsWave(device)
for(i = 0; i < numEpochs; i += 1)
duration = ST_GetStimsetParameterAsVariable(setName, "Duration", epochIndex = i) * MILLI_TO_ONE

Expand All @@ -6139,7 +6203,7 @@ static Function PSQ_CreateBaselineChunkSelectionEpochs(string device, variable h
epEnd = epBegin + chunkLength

[tags, shortName] = PSQ_CreateBaselineChunkSelectionStrings(index)
EP_AddUserEpoch(device, XOP_CHANNEL_TYPE_DAC, DAC, epBegin, epEnd, tags, shortName = shortName)
EP_AddUserEpoch(epochWave, XOP_CHANNEL_TYPE_DAC, DAC, epBegin, epEnd, tags, shortName = shortName)
index += 1
endfor

Expand Down
3 changes: 2 additions & 1 deletion Packages/MIES/MIES_Constants.ipf
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Original file line number Diff line number Diff line change
Expand Up @@ -1119,7 +1119,8 @@ Constant PSQ_CALC_METHOD_RMS = 0x2 // root-mean-square (rms)

Constant PSQ_BL_FAILED = 1

StrConstant PSQ_BASELINE_CHUNK_SHORT_NAME_PREFIX = "BLC"
StrConstant PSQ_BASELINE_CHUNK_SHORT_NAME_PREFIX = "BLC"
StrConstant PSQ_BASELINE_CHUNK_SHORT_NAME_RE_MATCHER = "^U_BLC[[:digit:]]+$"
/// @}

/// @name PatchSeq labnotebook constants
Expand Down
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