Merge pull request #1879 from AllenInstitute/feature/1879-various-upd…

…ates

Extracted parts from #1860

Packages/MIES/MIES_SweepFormula_Helpers.ipf

@@ -38,11 +38,17 @@ End
 /// Here `numBottles` is argument number 0 and mandatory as `defValue` is not present.
 ///
 /// The second argument `size` is optional with 0.5 as default and also defines a list of valid values.
-Function SFH_GetArgumentAsNumeric(variable jsonId, string jsonPath, string graph, string opShort, variable argNum, [variable defValue, WAVE/Z allowedValues, FUNCREF SFH_NumericChecker_Prototype checkFunc])
+Function SFH_GetArgumentAsNumeric(variable jsonId, string jsonPath, string graph, string opShort, variable argNum, [variable defValue, WAVE/Z allowedValues, FUNCREF SFH_NumericChecker_Prototype checkFunc, variable checkDefault])
 
 	string msg, sep, allowedValuesAsStr
 	variable checkExist, numArgs, result, idx, ret
 
+	if(ParamIsDefault(checkDefault))
+		checkDefault = 1
+	else
+		checkDefault = !!checkDefault
+	endif
+
 	if(ParamIsDefault(defValue))
 		checkExist = 1
 	else
@@ -68,6 +74,10 @@ Function SFH_GetArgumentAsNumeric(variable jsonId, string jsonPath, string graph
 		SFH_ASSERT(!checkExist, msg)
 
 		result = defValue
+
+		if(!checkDefault)
+			return result
+		endif
 	endif
 
 	if(!ParamIsDefault(allowedValues))
@@ -112,11 +122,17 @@ End
 /// The second argument `type` is optional with `steam train` as default and a list of allowed values.
 ///
 /// The text argument can be abbreviated as long as it is unique, the unabbreviated result is returned in all cases.
-Function/S SFH_GetArgumentAsText(variable jsonId, string jsonPath, string graph, string opShort, variable argNum, [string defValue, WAVE/T/Z allowedValues, FUNCREF SFH_StringChecker_Prototype checkFunc])
+Function/S SFH_GetArgumentAsText(variable jsonId, string jsonPath, string graph, string opShort, variable argNum, [string defValue, WAVE/T/Z allowedValues, FUNCREF SFH_StringChecker_Prototype checkFunc, variable checkDefault])
 
 	string msg, result, sep, allowedValuesAsStr
 	variable checkExist, numArgs, idx, ret
 
+	if(ParamIsDefault(checkDefault))
+		checkDefault = 1
+	else
+		checkDefault = !!checkDefault
+	endif
+
 	if(ParamIsDefault(defValue))
 		checkExist = 1
 	else
@@ -150,6 +166,10 @@ Function/S SFH_GetArgumentAsText(variable jsonId, string jsonPath, string graph,
 		SFH_ASSERT(!checkExist, msg)
 
 		result = defValue
+
+		if(!checkDefault)
+			return result
+		endif
 	endif
 
 	if(!ParamIsDefault(allowedValues))

Packages/MIES/MIES_SweepFormula_PSX.ipf

@@ -406,11 +406,11 @@ end
 /// - deconvolution
 /// - histogram of deconvolution
 /// - gaussian fit of histogram
-static Function [WAVE sweepDataFiltOff, WAVE sweepDataFiltOffDeconv] PSX_Analysis(WAVE sweepData, WAVE psxKernelFFT, variable filterLow, variable filterHigh)
+static Function [WAVE sweepDataFiltOff, WAVE sweepDataFiltOffDeconv] PSX_Analysis(WAVE sweepData, WAVE psxKernelFFT, variable sweepFilterLow, variable sweepFilterHigh)
 
 	variable offset
 
-	WAVE sweepDataFilt = PSX_FilterSweepData(sweepData, filterLow, filterHigh)
+	WAVE sweepDataFilt = PSX_FilterSweepData(sweepData, sweepFilterLow, sweepFilterHigh)
 
 	WAVE/ZZ sweepDataFiltOff
 	[sweepDataFiltOff, offset] = PSX_OffsetSweepData(sweepDataFilt)
@@ -696,7 +696,7 @@ static Function/WAVE PSX_CreateOverrideResults(variable numEvents, WAVE/T combos
 	return wv
 End
 
-static Function PSX_OperationSweepGathering(string graph, WAVE/WAVE psxKernelDataset, variable parameterJsonID, variable filterLow, variable filterHigh, variable index, WAVE/WAVE output)
+static Function PSX_OperationSweepGathering(string graph, WAVE/WAVE psxKernelDataset, variable parameterJsonID, variable sweepFilterLow, variable sweepFilterHigh, variable index, WAVE/WAVE output)
 
 	string key, comboKey, psxParametersAnalyzePeaks, cacheKey
 
@@ -717,7 +717,7 @@ static Function PSX_OperationSweepGathering(string graph, WAVE/WAVE psxKernelDat
 		WAVE sweepDataFiltOff       = psxAnalyzePeaksFromCache[%sweepDataFiltOff]
 		WAVE sweepDataFiltOffDeconv = psxAnalyzePeaksFromCache[%sweepDataFiltOffDeconv]
 	else
-		[WAVE sweepDataFiltOff, WAVE sweepDataFiltOffDeconv] = PSX_Analysis(sweepData, psxKernelFFT, filterLow, filterHigh)
+		[WAVE sweepDataFiltOff, WAVE sweepDataFiltOffDeconv] = PSX_Analysis(sweepData, psxKernelFFT, sweepFilterLow, sweepFilterHigh)
 
 		Make/FREE/WAVE/N=(2) psxAnalyzePeaks
 		SetDimensionLabels(psxAnalyzePeaks, "sweepDataFiltOff;sweepDataFiltOffDeconv", ROWS)
@@ -4090,7 +4090,7 @@ End
 // ...
 Function/WAVE PSX_Operation(variable jsonId, string jsonPath, string graph)
 
-	variable numberOfSDs, filterLow, filterHigh, parameterJsonID, numCombos, i, addedData, kernelAmp
+	variable numberOfSDs, sweepFilterLow, sweepFilterHigh, parameterJsonID, numCombos, i, addedData, kernelAmp
 	variable maxTauFactor, peakThresh
 	string parameterPath, id, psxParameters, dataUnit
 
@@ -4100,8 +4100,8 @@ Function/WAVE PSX_Operation(variable jsonId, string jsonPath, string graph)
 
 	try
 		numberOfSDs   = SFH_GetArgumentAsNumeric(jsonID, jsonPath, graph, SF_OP_PSX, 2, defValue = PSX_NUMBER_OF_SDS_DEFAULT, checkFunc = IsStrictlyPositiveAndFinite)
-		filterLow     = SFH_GetArgumentAsNumeric(jsonID, jsonPath, graph, SF_OP_PSX, 3, defValue = PSX_DEFAULT_FILTER_LOW)
-		filterHigh    = SFH_GetArgumentAsNumeric(jsonID, jsonPath, graph, SF_OP_PSX, 4, defValue = PSX_DEFAULT_FILTER_HIGH)
+		sweepFilterLow     = SFH_GetArgumentAsNumeric(jsonID, jsonPath, graph, SF_OP_PSX, 3, defValue = PSX_DEFAULT_FILTER_LOW)
+		sweepFilterHigh    = SFH_GetArgumentAsNumeric(jsonID, jsonPath, graph, SF_OP_PSX, 4, defValue = PSX_DEFAULT_FILTER_HIGH)
 		maxTauFactor  = SFH_GetArgumentAsNumeric(jsonID, jsonPath, graph, SF_OP_PSX, 5, defValue = PSX_DEFAULT_MAX_TAU_FACTOR, checkFunc = IsStrictlyPositiveAndFinite)
 		WAVE riseTime = SFH_GetArgumentAsWave(jsonID, jsonPath, graph, SF_OP_PSX, 6, defOp = "psxRiseTime()", singleResult = 1)
 		ASSERT(IsNumericWave(riseTime), "Invalid return from psxRiseTime")
@@ -4111,8 +4111,8 @@ Function/WAVE PSX_Operation(variable jsonId, string jsonPath, string graph)
 		JSON_AddTreeObject(parameterJsonID, parameterPath)
 		JSON_AddString(parameterJsonID, parameterPath + "/id", id)
 		JSON_AddVariable(parameterJsonID, parameterPath + "/numberOfSDs", numberOfSDs)
-		JSON_AddVariable(parameterJsonID, parameterPath + "/filterLow", filterLow)
-		JSON_AddVariable(parameterJsonID, parameterPath + "/filterHigh", filterHigh)
+		JSON_AddVariable(parameterJsonID, parameterPath + "/sweepFilterLow", sweepFilterLow)
+		JSON_AddVariable(parameterJsonID, parameterPath + "/sweepFilterHigh", sweepFilterHigh)
 		JSON_AddVariable(parameterJsonID, parameterPath + "/maxTauFactor", maxTauFactor)
 		parameterPath = SF_META_USER_GROUP + PSX_JWN_PARAMETERS + "/" + SF_OP_PSX_RISETIME
 		JSON_AddTreeObject(parameterJsonID, parameterPath)
@@ -4138,7 +4138,7 @@ Function/WAVE PSX_Operation(variable jsonId, string jsonPath, string graph)
 		endfor
 
 		for(i = 0; i < numCombos; i += 1)
-			PSX_OperationSweepGathering(graph, psxKernelDataset, parameterJsonID, filterLow, filterHigh, i, output)
+			PSX_OperationSweepGathering(graph, psxKernelDataset, parameterJsonID, sweepFilterLow, sweepFilterHigh, i, output)
 		endfor
 
 		[WAVE hist, WAVE fit, peakThresh, dataUnit] = PSX_CalculatePeakThreshold(output, numCombos, numberOfSDs)

Packages/MIES/MIES_Utilities.ipf

@@ -3424,35 +3424,6 @@ Function/WAVE ExtractFromSubrange(listOfRanges, dim)
 	return ranges
 End
 
-/// @brief Check if a name for an object adheres to the strict naming rules
-///
-/// @see `DisplayHelpTopic "Standard Object Names"`
-///
-/// UTF_NOINSTRUMENTATION
-threadsafe Function IsValidObjectName(string name)
-	return NameChecker(name, 0)
-End
-
-/// UTF_NOINSTRUMENTATION
-threadsafe Function IsStrictlyPositiveAndFinite(variable var)
-
-	return var > 0 && var < inf
-End
-
-/// @brief Check if a name for an object adheres to the liberal naming rules
-///
-/// @see `DisplayHelpTopic "Liberal Object Names"`
-///
-/// UTF_NOINSTRUMENTATION
-threadsafe Function IsValidLiberalObjectName(string name)
-	return NameChecker(name, 1)
-End
-
-/// UTF_NOINSTRUMENTATION
-threadsafe static Function NameChecker(string name, variable liberal)
-	return !cmpstr(name, CleanupName(name, !!liberal, MAX_OBJECT_NAME_LENGTH_IN_BYTES))
-End
-
 /// @brief Find an integer `x` which is larger than `a` but the
 /// smallest possible power of `p`.
 ///
@@ -6770,26 +6741,6 @@ Function GetDayOfWeek(variable seconds)
 	return str2num(dayOfWeek)
 End
 
-/// @brief Return the truth if `val` is in the range `]0, 1[`
-threadsafe Function BetweenZeroAndOneExc(variable val)
-	return val > 0.0 && val < 1.0
-End
-
-/// @brief Return the truth if `val` is in the range `[0, 1]`
-threadsafe Function BetweenZeroAndOne(variable val)
-	return val >= 0.0 && val <= 1.0
-End
-
-/// @brief Return the truth if `val` is in the range `]0, 100[`
-threadsafe Function BetweenZeroAndOneHoundredExc(variable val)
-	return val > 0.0 && val < 100.0
-End
-
-/// @brief Return the truth if `val` is in the range `[0, 100]`
-threadsafe Function BetweenZeroAndOneHoundred(variable val)
-	return val >= 0.0 && val <= 100.0
-End
-
 /// @brief Upper case the first character in an ASCII string
 threadsafe Function/S UpperCaseFirstChar(string str)
 

Packages/MIES/MIES_Utilities_Checks.ipf

@@ -0,0 +1,73 @@
+#pragma TextEncoding = "UTF-8"
+#pragma rtGlobals=3 // Use modern global access method and strict wave access.
+#pragma rtFunctionErrors=1
+
+#ifdef AUTOMATED_TESTING
+#pragma ModuleName=MIES_Checks
+#endif
+
+/// @file MIES_Utilities_Checks.ipf
+/// @brief Threadsafe check functions which comply with either SFH_NumericChecker_Prototype or SFH_StringChecker_Prototype
+
+/// @brief Check if a name for an object adheres to the strict naming rules
+///
+/// @see `DisplayHelpTopic "Standard Object Names"`
+///
+/// UTF_NOINSTRUMENTATION
+threadsafe Function IsValidObjectName(string name)
+	return NameChecker(name, 0)
+End
+
+/// @brief Check if a name for an object adheres to the liberal naming rules
+///
+/// @see `DisplayHelpTopic "Liberal Object Names"`
+///
+/// UTF_NOINSTRUMENTATION
+threadsafe Function IsValidLiberalObjectName(string name)
+	return NameChecker(name, 1)
+End
+
+/// UTF_NOINSTRUMENTATION
+threadsafe static Function NameChecker(string name, variable liberal)
+	return !cmpstr(name, CleanupName(name, !!liberal, MAX_OBJECT_NAME_LENGTH_IN_BYTES))
+End
+
+/// UTF_NOINSTRUMENTATION
+threadsafe Function IsStrictlyPositiveAndFinite(variable var)
+
+	return var > 0 && var < inf
+End
+
+/// UTF_NOINSTRUMENTATION
+threadsafe Function IsNullOrPositiveAndFinite(variable var)
+
+	return var >= 0 && var < inf
+End
+
+/// @brief Return the truth if `val` is in the range `]0, 1[`
+///
+/// UTF_NOINSTRUMENTATION
+threadsafe Function BetweenZeroAndOneExc(variable val)
+	return val > 0.0 && val < 1.0
+End
+
+/// @brief Return the truth if `val` is in the range `[0, 1]`
+///
+/// UTF_NOINSTRUMENTATION
+threadsafe Function BetweenZeroAndOne(variable val)
+	return val >= 0.0 && val <= 1.0
+End
+
+/// @brief Return the truth if `val` is in the range `]0, 100[`
+///
+/// UTF_NOINSTRUMENTATION
+threadsafe Function BetweenZeroAndOneHoundredExc(variable val)
+	return val > 0.0 && val < 100.0
+End
+
+/// @brief Return the truth if `val` is in the range `[0, 100]`
+///
+/// UTF_NOINSTRUMENTATION
+threadsafe Function BetweenZeroAndOneHoundred(variable val)
+	return val >= 0.0 && val <= 100.0
+End

Packages/MIES_Include.ipf

@@ -234,6 +234,7 @@ End
 #include "MIES_TestPulse_Multi"
 #include "MIES_TraceUserData"
 #include "MIES_Utilities"
+#include "MIES_Utilities_Checks"
 #include "MIES_WaveBuilder"
 #include "MIES_WaveBuilderPanel"
 #include "MIES_WaveBuilder_Macro"

Packages/tests/Basic/UTF_Basic.ipf

@@ -26,6 +26,7 @@
 #include "UTF_UpgradeDataFolderLocation"
 #include "UTF_UpgradeWaveLocationAndGetIt"
 #include "UTF_Utils"
+#include "UTF_UtilsChecks"
 #include "UTF_WaveAveraging"
 #include "UTF_WaveBuilder"
 #include "UTF_WaveBuilderRegression"
@@ -115,6 +116,7 @@ Function RunWithOpts([string testcase, string testsuite, variable allowdebug, va
 	list = AddListItem("UTF_UpgradeDataFolderLocation.ipf", list, ";", inf)
 	list = AddListItem("UTF_UpgradeWaveLocationAndGetIt.ipf", list, ";", inf)
 	list = AddListItem("UTF_Utils.ipf", list, ";", inf)
+	list = AddListItem("UTF_UtilsChecks.ipf", list, ";", inf)
 	list = AddListItem("UTF_WaveAveraging.ipf", list, ";", inf)
 	list = AddListItem("UTF_WaveBuilder.ipf", list, ";", inf)
 	list = AddListItem("UTF_WaveBuilderRegression.ipf", list, ";", inf)

Packages/tests/Basic/UTF_Utils.ipf

@@ -3690,17 +3690,6 @@ Function FLW_RequiresNumericWave()
 	endtry
 End
 
-Function/WAVE InfiniteValues()
-
-	Make/FREE wv = {NaN, Inf, -Inf}
-
-	SetDimLabel ROWS, 0, $"NaN", wv
-	SetDimLabel ROWS, 1, $"Inf", wv
-	SetDimLabel ROWS, 2, $"-Inf", wv
-
-	return wv
-End
-
 // UTF_TD_GENERATOR InfiniteValues
 Function FLW_RequiresFiniteLevel([var])
 	variable var
@@ -7142,58 +7131,6 @@ static Function GetDayOfWeekTest()
 	endtry
 End
 
-static Function BetweenZeroAndOneX()
-
-	FUNCREF SFH_NumericChecker_Prototype f = BetweenZeroAndOne
-	CHECK(FuncRefIsAssigned(FuncRefInfo(f)))
-
-	CHECK_EQUAL_VAR(BetweenZeroAndOne(-2.0), 0)
-	CHECK_EQUAL_VAR(BetweenZeroAndOne(0.0), 1)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneExc(0 + 1e-15), 1)
-	CHECK_EQUAL_VAR(BetweenZeroAndOne(0.1), 1)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneExc(1.0 - 1e-14), 1)
-	CHECK_EQUAL_VAR(BetweenZeroAndOne(1.0), 1)
-	CHECK_EQUAL_VAR(BetweenZeroAndOne(2.0), 0)
-
-	FUNCREF SFH_NumericChecker_Prototype f = BetweenZeroAndOneExc
-	CHECK(FuncRefIsAssigned(FuncRefInfo(f)))
-
-	// excluding the borders
-	CHECK_EQUAL_VAR(BetweenZeroAndOneExc(-2.0), 0)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneExc(0), 0)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneExc(0 + 1e-15), 1)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneExc(0.1), 1)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneExc(1.0 - 1e-14), 1)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneExc(1.0), 0)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneExc(2.0), 0)
-End
-
-static Function BetweenZeroAndOneHoundredX()
-
-	FUNCREF SFH_NumericChecker_Prototype f = BetweenZeroAndOneHoundred
-	CHECK(FuncRefIsAssigned(FuncRefInfo(f)))
-
-	CHECK_EQUAL_VAR(BetweenZeroAndOneHoundred(-2.0), 0)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneHoundred(0.0), 1)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneHoundredExc(0 + 1e-15), 1)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneHoundred(0.1), 1)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneHoundredExc(100.0 - 1e-14), 1)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneHoundred(1.0), 1)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneHoundred(102.0), 0)
-
-	FUNCREF SFH_NumericChecker_Prototype f = BetweenZeroAndOneHoundredExc
-	CHECK(FuncRefIsAssigned(FuncRefInfo(f)))
-
-	// excluding the borders
-	CHECK_EQUAL_VAR(BetweenZeroAndOneHoundredExc(-2.0), 0)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneHoundredExc(0), 0)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneHoundredExc(0 + 1e-15), 1)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneHoundredExc(0.1), 1)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneHoundredExc(100.0 - 1e-14), 1)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneHoundredExc(100.0), 0)
-	CHECK_EQUAL_VAR(BetweenZeroAndOneHoundredExc(102.0), 0)
-End
-
 static Function TestUpperCaseFirstChar()
 
 	string ret = UpperCaseFirstChar("")