EP: Add stimset epoch times based in index length

- stimset epoch times are now setup in epochs based
  on length data saved on stimset creation for the epochs

Packages/MIES/MIES_Epochs.ipf

@@ -310,7 +310,7 @@ static Function EP_AddEpochsFromStimSetNote(string device, STRUCT DataConfigurat
 	variable epochCount, totalDuration, poissonDistribution, cycleNr
 	variable epochNr, pulseNr, numPulses, epochType, flipping, pulseToPulseLength, stimEpochAmplitude, amplitude, i, j
 	variable logicalPulseOffset
-	variable stimsetSize
+	variable stimsetSize, stimepochOffset, logicalStimepochOffset
 	variable pulseDuration, halfCycleNr, hasFullCycle, hasIncompleteCycleAtStart, hasIncompleteCycleAtEnd
 	variable subsubEpochBegin, subsubEpochEnd, numInflectionPoints, incompleteCycleNr
 	string type
@@ -320,36 +320,68 @@ static Function EP_AddEpochsFromStimSetNote(string device, STRUCT DataConfigurat
 	string shortNameEpTypePTBaseline
 	string stimNote = note(stimset)
 
+	WAVE/WAVE dataWave = GetDAQDataWave(device, DATA_ACQUISITION_MODE)
+	WAVE data = dataWave[0]
+
 	ASSERT(!IsEmpty(stimNote), "Stimset note is empty.")
 
 	stopCollectionPoint = ROVar(GetStopCollectionPoint(device))
 
 	scale = channelType == XOP_CHANNEL_TYPE_TTL ? 1 : scale
 	stimsetSize = DimSize(stimset, ROWS)
 
-	stimsetEnd = min(stimsetBegin + setLength, (stopCollectionPoint - 1) * s.samplingInterval)
-	epSweepTags = ReplaceStringByKey(EPOCH_TYPE_KEY, "", "Stimset", STIMSETKEYNAME_SEP, EPOCHNAME_SEP)
-	EP_AddEpoch(device, channel, channelType, stimsetBegin, stimsetEnd, epSweepTags, EPOCH_SN_STIMSET, 0)
-
 	epochCount = WB_GetWaveNoteEntryAsNumber(stimNote, STIMSET_ENTRY, key="Epoch Count")
 	ASSERT(IsFinite(epochCount), "Could not find Epoch Count in stimset wave note.")
+	flipping = WB_GetWaveNoteEntryAsNumber(stimNote, STIMSET_ENTRY, key = "Flip")
 
-	Make/FREE/D/N=(epochCount) duration, sweepOffset
+	Make/FREE/D/N=(epochCount) stimepochDuration, stimepochOffsetTime, stimEpochLength
+	stimepochLength[] = WB_GetWaveNoteEntryAsNumber(stimNote, EPOCH_ENTRY, sweep = sweep, epoch = p, key = EPOCH_LENGTH_INDEX_KEY)
+	for(epochNr = 0; epochNr < epochCount; epochNr += 1)
+		logicalStimepochOffset = flipping ? stimsetSize - stimepochOffset - stimepochLength[epochNr] : stimepochOffset
+		stimepochOffsetTime[epochNr] = limit(IndexAfterDecimation(logicalStimepochOffset, s.decimationFactor) + 1, 0, Inf) * s.samplingInterval
+		stimepochOffset += stimepochLength[epochNr]
+	endfor
 
-	duration[] = WB_GetWaveNoteEntryAsNumber(stimNote, EPOCH_ENTRY, key="Duration", sweep=sweep, epoch=p)
-	duration *= MILLI_TO_MICRO
-	totalDuration = sum(duration)
+	for(epochNr = 0; epochNr < epochCount; epochNr += 1)
+		if(flipping)
+			if(epochNr > 0)
+				stimepochDuration[epochNr] = stimepochOffsetTime[epochNr - 1] - stimepochOffsetTime[epochNr]
+			else
+				stimepochDuration[epochNr] = (IndexAfterDecimation(stimepochLength[epochNr] + 0.5, s.decimationFactor) + 0) * s.samplingInterval
+			endif
+		else
+			if(epochNr < epochCount - 1)
+				stimepochDuration[epochNr] = stimepochOffsetTime[epochNr + 1] - stimepochOffsetTime[epochNr]
+			else
+				stimepochDuration[epochNr] = (IndexAfterDecimation(stimepochOffset, s.decimationFactor) + 1) * s.samplingInterval - stimepochOffsetTime[epochNr]
+			endif
+		endif
+		ASSERT(stimepochDuration[epochNr] > 0, "Epoch duration must be greater than zero")
+	endfor
+	totalDuration = sum(stimepochDuration)
 
 	ASSERT(IsFinite(totalDuration), "Expected finite totalDuration")
 	ASSERT(IsFinite(stimsetBegin), "Expected finite stimsetBegin")
+
 	stimsetEndLogical = stimsetBegin + totalDuration
+	stimsetEnd = min(stimsetBegin + setLength, stopCollectionPoint * s.samplingInterval)
+// This assertion should be valid if the acquisition was not aborted early.
+//	ASSERT(stimsetEndLogical == stimsetEnd, "Logical stimset end is inconsistent with actual stimset end")
 
-	if(epochCount > 1)
-		sweepOffset[0] = 0
-		sweepOffset[1,] = sweepOffset[p - 1] + duration[p - 1]
-	endif
+	epSweepTags = ReplaceStringByKey(EPOCH_TYPE_KEY, "", "Stimset", STIMSETKEYNAME_SEP, EPOCHNAME_SEP)
+	EP_AddEpoch(device, channel, channelType, stimsetBegin, stimsetEnd, epSweepTags, EPOCH_SN_STIMSET, 0)
 
-	flipping = WB_GetWaveNoteEntryAsNumber(stimNote, STIMSET_ENTRY, key = "Flip")
+	// If decimationFactor < 1 then stimsetEndLogical < stimsetEnd (if acquisition was not stopped early)
+	// because the round function in the decimation shifts effectively the stimset by 0.5 * WAVEBUILDER_MIN_SAMPINT to the left.
+	// Thus, after decimation the end is shifted to the left as well, potentially leaving remaining sample points in the DA wave.
+	//
+	// Case 2: stimsets with multiple sweeps where each sweep has a different length (due to delta mechanism)
+	// result in 2D stimset waves where all sweeps have the same length
+	// therefore we must add a baseline epoch after all defined epochs
+	if(stimsetEnd > stimsetEndLogical)
+		tags = ReplaceStringByKey(EPOCH_TYPE_KEY, "", EPOCH_BASELINE_REGION_KEY, STIMSETKEYNAME_SEP, EPOCHNAME_SEP)
+		EP_AddEpoch(device, channel, channelType, stimsetEndLogical, stimsetEnd, tags, EPOCH_SN_STIMSET + "_" + EPOCH_SN_STIMSETBLTRAIL, 1)
+	endif
 
 	epSweepTags = ReplaceStringByKey(EPOCH_TYPE_KEY, "", "Epoch", STIMSETKEYNAME_SEP, EPOCHNAME_SEP)
 
@@ -358,14 +390,9 @@ static Function EP_AddEpochsFromStimSetNote(string device, STRUCT DataConfigurat
 		epochType = WB_ToEpochType(type)
 		stimEpochAmplitude = WB_GetWaveNoteEntryAsNumber(stimNote, EPOCH_ENTRY, key="Amplitude", sweep=sweep, epoch=epochNr)
 		amplitude = scale * stimEpochAmplitude
-		if(flipping)
-			// in case of oodDAQ cutOff stimsetEndLogical can be greater than stimsetEnd, thus epochEnd can be greater than stimsetEnd
-			epochEnd = stimsetEndLogical - sweepOffset[epochNr]
-			epochBegin = epochEnd - duration[epochNr]
-		else
-			epochBegin = sweepOffset[epochNr] + stimsetBegin
-			epochEnd = epochBegin + duration[epochNr]
-		endif
+
+		epochBegin = stimepochOffsetTime[epochNr] + stimsetBegin
+		epochEnd = epochBegin + stimepochDuration[epochNr]
 
 		if(epochBegin >= stimsetEnd)
 			// sweep epoch starts beyond stimset end
@@ -595,14 +622,6 @@ static Function EP_AddEpochsFromStimSetNote(string device, STRUCT DataConfigurat
 		endif
 
 	endfor
-
-	// stimsets with multiple sweeps where each sweep has a different length (due to delta mechanism)
-	// result in 2D stimset waves where all sweeps have the same length
-	// therefore we must add a baseline epoch after all defined epochs
-	if(stimsetEnd > stimsetEndLogical)
-		tags = ReplaceStringByKey(EPOCH_TYPE_KEY, "", EPOCH_BASELINE_REGION_KEY, STIMSETKEYNAME_SEP, EPOCHNAME_SEP)
-		EP_AddEpoch(device, channel, channelType, stimsetEndLogical, stimsetEnd, tags, EPOCH_SN_STIMSET + "_" + EPOCH_SN_STIMSETBLTRAIL, 1)
-	endif
 End
 
 /// @brief Sorts all epochs per channel number / channel type in EpochsWave