Merge pull request #1032 from AllenInstitute/feature/1032-make-compatible-with-latest-IP9

Make dimension labels valid liberal object names

Author: t-b

Packages/MIES/MIES_Constants.ipf

@@ -623,7 +623,7 @@ Constant HARDWARE_DAC_EXTERNAL_TRIGGER = 0x1
 /// Used to upgrade the GuiStateWave as well as the DA Ephys panel
 Constant DA_EPHYS_PANEL_VERSION           = 53
 Constant DATA_SWEEP_BROWSER_PANEL_VERSION = 30
-Constant WAVEBUILDER_PANEL_VERSION        = 10
+Constant WAVEBUILDER_PANEL_VERSION        = 11
 Constant ANALYSISBROWSER_PANEL_VERSION    =  1
 
 /// Version of the labnotebooks (numerical and textual)
@@ -633,7 +633,7 @@ Constant ANALYSISBROWSER_PANEL_VERSION    =  1
 /// - Changed names of entries
 /// - Changed units or meaning of entries
 /// - New/Changed layers of entries
-Constant LABNOTEBOOK_VERSION = 48
+Constant LABNOTEBOOK_VERSION = 49
 
 /// Version of the stimset wave note
 Constant STIMSET_NOTE_VERSION = 7

Packages/MIES/MIES_DataConfigurator.ipf

@@ -1014,9 +1014,9 @@ static Function DC_PrepareLBNEntries(string panelTitle, STRUCT DataConfiguration
 	DC_DocumentChannelProperty(panelTitle, "Igor Pro version", INDEP_HEADSTAGE, NaN, NaN, str=GetIgorProVersion())
 	DC_DocumentChannelProperty(panelTitle, "Igor Pro build", INDEP_HEADSTAGE, NaN, NaN, str=GetIgorProBuildVersion())
 	DC_DocumentChannelProperty(panelTitle, "Igor Pro bitness", INDEP_HEADSTAGE, NaN, NaN, var=GetArchitectureBits())
-	DC_DocumentChannelProperty(panelTitle, "JSON config file: path", INDEP_HEADSTAGE, NaN, NaN, str=GetUserData(panelTitle, "", EXPCONFIG_UDATA_SOURCEFILE_PATH))
-	DC_DocumentChannelProperty(panelTitle, "JSON config file: SHA-256 hash", INDEP_HEADSTAGE, NaN, NaN, str=GetUserData(panelTitle, "", EXPCONFIG_UDATA_SOURCEFILE_HASH))
-	DC_DocumentChannelProperty(panelTitle, "JSON config file: stimset nwb file path", INDEP_HEADSTAGE, NaN, NaN, str=GetUserData(panelTitle, "", EXPCONFIG_UDATA_STIMSET_NWB_PATH))
+	DC_DocumentChannelProperty(panelTitle, "JSON config file [path]", INDEP_HEADSTAGE, NaN, NaN, str=GetUserData(panelTitle, "", EXPCONFIG_UDATA_SOURCEFILE_PATH))
+	DC_DocumentChannelProperty(panelTitle, "JSON config file [SHA-256 hash]", INDEP_HEADSTAGE, NaN, NaN, str=GetUserData(panelTitle, "", EXPCONFIG_UDATA_SOURCEFILE_HASH))
+	DC_DocumentChannelProperty(panelTitle, "JSON config file [stimset nwb file path]", INDEP_HEADSTAGE, NaN, NaN, str=GetUserData(panelTitle, "", EXPCONFIG_UDATA_STIMSET_NWB_PATH))
 	DC_DocumentChannelProperty(panelTitle, "TP after DAQ", INDEP_HEADSTAGE, NaN, NaN, var=DAG_GetNumericalValue(panelTitle, "check_Settings_TPAfterDAQ"))
 
 	for(i = 0; i < NUM_HEADSTAGES; i += 1)

Packages/MIES/MIES_Debugging.ipf

@@ -551,6 +551,96 @@ Function GetSizeOfAllWavesInExperiment()
 	Edit/K=1 root:list
 End
 
+/// @brief Check that all stored waves (permanent and free) adhere to the liberal naming rules.
+///
+/// These are only enforced since IP9 beta9 or later.
+///
+/// @return Number of waves not matching
+Function CheckAllDimensionLabels()
+	string msg, path
+	variable i, numWaves, failures
+
+	WAVE/T allWaves = ListToTextWave(GetListOfObjects($"root:", ".*", fullPath=1, recursive=1), ";")
+	WAVE/T allWavesUnique = GetUniqueEntries(allWaves)
+	WaveClear allWaves
+
+	numWaves = DimSize(allWavesUnique, ROWS)
+	for(i = 0; i < numWaves; i += 1)
+		path = allWavesUnique[i]
+		WAVE wv = $path
+		msg = CheckDimensionLabels(wv)
+
+		if(!IsEmpty(msg))
+			printf "Wave %s:\r", path
+			print msg
+			failures += 1
+		endif
+	endfor
+
+	return failures
+End
+
+threadsafe static Function/S CheckDimensionLabels(WAVE/Z wv)
+	variable i, numDims, j, size, numMatches, numEntries, idx
+	string entry
+	string msg = ""
+	string text = ""
+
+	if(!WaveExists(wv))
+		return msg
+	endif
+
+	numDims = WaveDims(wv)
+
+	for(i = 0; i < numDims; i += 1)
+		size = DimSize(wv, i)
+
+		Make/FREE/T/N=(size + 1) lbls
+		Multithread lbls[] = GetDimLabel(wv, i, p - 1)
+		Make/FREE/N=(size + 1) valid
+		Multithread valid[] = IsValidLiberalObjectName(lbls[p])
+
+		FindValue/UOFV/V=0 valid
+
+		if(V_Value >= 0)
+			WAVE/Z indizes = FindIndizes(valid, col = 0, var = 0)
+			numMatches = WaveExists(indizes) ? DimSize(indizes, ROWS) : 0
+
+			for(j = 0; j < numMatches; j += 1)
+				sprintf text, "dimension %d, element %d, label %s\r", i, indizes[j], lbls[indizes[j]]
+				msg += text
+			endfor
+		endif
+	endfor
+
+	// call recursively if it is a wave reference wave
+	if(IsWaveRefWave(wv))
+		WAVE/WAVE waveRef = wv
+		// use a linearized index to check all holded waves
+		numEntries = numpnts(waveRef)
+		Make/FREE/T/N=(numEntries) results
+		Multithread results[] = CheckDimensionLabels(waveRef[p])
+
+		if(HasOneValidEntry(results))
+			WAVE/Z indizes = FindIndizes(results, col = 0, prop = PROP_NON_EMPTY)
+			numMatches = WaveExists(indizes) ? DimSize(indizes, ROWS) : 0
+
+			for(i = 0; i < numMatches; i += 1)
+				idx = indizes[i]
+				entry = results[idx]
+
+				if(IsEmpty(entry))
+					continue
+				endif
+
+				sprintf text, "Wave ref wave has wave with the following invalid dimension label (invalid linear index %d): %s", idx, entry
+			endfor
+		endif
+	endif
+
+	return msg
+End
+
 // see tools/functionprofiling.sh
 Function DEBUG_STOREFUNCTION()
 	string funcName = GetRTStackInfo(2)

Packages/MIES/MIES_ExperimentDocumentation.ipf

@@ -437,7 +437,6 @@ static Function/Wave ED_FindIndizesAndRedimension(incomingKey, key, values, rowI
 	numCols = DimSize(incomingKey, COLS)
 	for(i = 0; i < numCols; i += 1)
 		searchStr = incomingKey[0][i]
-		ASSERT(!isEmpty(searchStr), "Incoming key can not be empty")
 
 		FindValue/TXOP=4/TEXT=(searchStr) key
 		col = floor(V_value / numKeyRows)
@@ -449,6 +448,7 @@ static Function/Wave ED_FindIndizesAndRedimension(incomingKey, key, values, rowI
 			sprintf msg, "Found key \"%s\" from incoming column %d in key column %d", incomingKey[0][i], i, idx
 			DEBUGPRINT(msg)
 		else
+			ASSERT(IsValidLiberalObjectName(searchStr), "Incoming key is not a valid liberal object name: " + searchStr)
 			idx = numKeyCols + numAdditions
 			EnsureLargeEnoughWave(key, minimumSize=idx, dimension=COLS)
 			key[0, lastValidIncomingKeyRow][idx] = incomingKey[p][i]

Packages/MIES/MIES_StimsetAPI.ipf

@@ -165,7 +165,7 @@ End
 static Function/S ST_ParameterStringValues(string entry)
 	// translate passed string values which are numeric internally
 	//                                  WBP_GetDeltaModes() WBP_GetNoiseTypes()               WBP_GetNoiseBuildResolution() WBP_GetTriggerTypes()             WBP_GetPulseTypes()
-	Make/FREE/T translateableEntries = {"^.* op$",          "Noise Type: White, Pink, Brown", "Build resolution (index)",   "Trigonometric function Sin/Cos", "Pulse train type (index)"}
+	Make/FREE/T translateableEntries = {"^.* op$",          "Noise Type [White, Pink, Brown]", "Build resolution (index)",   "Trigonometric function Sin/Cos", "Pulse train type (index)"}
 
 	if(GrepString(entry, translateableEntries[0]))
 		return WBP_GetDeltaModes()

Packages/MIES/MIES_Utilities.ipf

@@ -3422,11 +3422,21 @@ End
 
 /// @brief Check if a name for an object adheres to the strict naming rules
 ///
-/// @see `DisplayHelpTopic "ObjectName"`
-threadsafe Function IsValidObjectName(name)
-	string name
+/// @see `DisplayHelpTopic "Standard Object Names"`
+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"`
+threadsafe Function IsValidLiberalObjectName(string name)
+	return NameChecker(name, 1)
+End
 
-	return !cmpstr(name, CleanupName(name, 0, MAX_OBJECT_NAME_LENGTH_IN_BYTES))
+threadsafe static Function NameChecker(string name, variable liberal)
+   // @todo remove the IsEmpty check once this is resolved upstream.
+	return !IsEmpty(name) && !cmpstr(name, CleanupName(name, !!liberal, MAX_OBJECT_NAME_LENGTH_IN_BYTES))
 End
 
 /// @brief Find an integer `x` which is larger than `a` but the