GetAllFilesRecursivelyFromPath: Speed it up with custom extension #2403

t-b · 2025-04-14T18:08:30Z

We used to always perform alias/shortcut handling even when we only look for certain file suffixes.

But we only have to try following these if they can be part of the returned list.

So for the common case of Windows OS and a extension which does not match .lnk we can skip the alias resolving.

When we do have aliases we also first call GetFileFolderInfo and only if we have an alias ResolveAlias again, skipping another GetFileFolderInfo for the case when the pointed to file is not an alias.

This allows to gather 100k files on a 1Gb/s network link in under 60s.

Function Dostuff()

	Newpath/O testPath "Y:"

	beginfunctionProfiling(testTime = 50000)
	string result = getAllfilesRecursivelyFromPath("testPath", extension = ".mp3")
	endfunctionProfiling()
	printf  "Number of files: %d\r", ItemsInList(result, "|")
End

gives

Total time: 54.4173, Time in Function code: 54.3973 (100%)
Top function percentages:
Function MIES_Utilities_File.ipf GetAllFilesRecursivelyFromPath: 99%

Annotated Top Functions:

*******************************************************************************************
Function: MIES_Utilities_File.ipf MIES_Utilities_File.ipf#GetAllFilesRecursivelyFromPath; Percent total 99%
*******************************************************************************************
[00]          	|Function/S GetAllFilesRecursivelyFromPath(string pathName, [string extension])
[00]          	|
[00]          	|	string fileOrPath, folders, subFolderPathName, fileName
[00]          	|	string files, allFilesList
[00]          	|	string allFiles         = ""
[00]*         	|	string foldersFromAlias = ""
[00]          	|	variable err, isWindows
[00]          	|
[00]          	|#ifdef WINDOWS
[00]          	|	isWindows = 1
[00]          	|#endif
[00]          	|
[01]*         	|	PathInfo $pathName
[00]          	|	ASSERT(V_flag, "Given symbolic path does not exist")
[00]          	|
[00]          	|	if(ParamIsDefault(extension))
[00]          	|		extension = "????"
[00]          	|	endif
[00]          	|
[00]          	|	AssertOnAndClearRTError()
[70]*******   	|	allFilesList = IndexedFile($pathName, -1, extension, "????", FILE_LIST_SEP); err = GetRTError(1)
[00]          	|
[00]*         	|	if(isWindows && cmpstr(extension, "????") && cmpstr(extension, ".lnk"))
[00]          	|		allFiles = AddPrefixToEachListItem(S_path, allFilesList, sep = FILE_LIST_SEP)
[00]          	|	else
[00]          	|		// try to resolve aliases/shortcuts when we can have them
[00]          	|		WAVE/T allFilesInDir = ListToTextWave(allFilesList, FILE_LIST_SEP)
[00]          	|		for(fileName : allFilesInDir)
[00]          	|
[00]          	|			GetFileFolderInfo/P=$pathName/Q/Z fileName
[00]          	|
[00]          	|			if(V_Flag != 0)
[00]          	|				// error querying file
[00]          	|				continue
[00]          	|			endif
[00]          	|
[00]          	|			if(V_IsAliasShortcut)
[00]          	|				fileOrPath = ResolveAlias(fileName, pathName = pathName)
[00]          	|
[00]          	|				// redo the check
[00]          	|				GetFileFolderInfo/P=$pathName/Q/Z fileOrPath
[00]          	|
[00]          	|				if(V_Flag != 0)
[00]          	|					// error querying file/folder pointed to by alias
[00]          	|					continue
[00]          	|				endif
[00]          	|			endif
[00]          	|
[00]          	|			if(V_isFile)
[00]          	|				allFiles = AddListItem(S_path, allFiles, FILE_LIST_SEP, Inf)
[00]          	|			elseif(V_isFolder)
[00]          	|				foldersFromAlias = AddListItem(S_path, foldersFromAlias, FILE_LIST_SEP, Inf)
[00]          	|			else
[00]          	|				ASSERT(0, "Unexpected file type")
[00]          	|			endif
[00]          	|		endfor
[00]          	|	endif
[00]          	|
[00]          	|	AssertOnAndClearRTError()
[04]*         	|	folders = IndexedDir($pathName, -1, 1, FILE_LIST_SEP); err = GetRTError(1)
[00]          	|	folders = folders + foldersFromAlias
[00]*         	|	WAVE/T wFolders = ListToTextWave(folders, FILE_LIST_SEP)
[00]*         	|	for(folder : wFolders)
[00]          	|
[00]          	|		subFolderPathName = GetUniqueSymbolicPath()
[00]          	|
[12]*         	|		NewPath/Q/O $subFolderPathName, folder
[00]*         	|		files = GetAllFilesRecursivelyFromPath(subFolderPathName, extension = extension)
[11]*         	|		KillPath/Z $subFolderPathName
[00]          	|
[00]*         	|		if(!isEmpty(files))
[01]*         	|			allFiles = AddListItem(RemoveEnding(files, FILE_LIST_SEP), allFiles, FILE_LIST_SEP, Inf)
[00]          	|		endif
[00]          	|	endfor
[00]          	|
[00]          	|	return allFiles
[00]          	|End

Review comments
Check Mac behaviour
Fix

 Test finished with no errors
  ? Free wave leak detected (leaked waves: 6) in "ZeroMQPublishingTests#CheckTPPublishing:period_now"
End of test "MIES with Basic"

-> flaky test

Make that a CI failure, upstream issue: free wave leak does not trigger test error byte-physics/igortest#494

Close #2402
Close #1733

MichaelHuth

I think also the recursion in ResolveAlias can be ditched for Windows as shortcuts to shortcuts can not be created by normal means.
Also the line
folders = folders + foldersFromAlias
should use AddListItem
Generally I also think that these filesystem targetting function should not use recursion because that couples stack size to file system depth, that will fail.
Also the function could use a rewrite, such that we directly convert the returned file lists from IndexedFile/IndexedDir to waves and work with waves, also return a text wave.
This also prevents allFiles growing over 2 GB in size.

The function could also use an optional extension where duplicates are removed at the end.

Packages/MIES/MIES_Utilities_File.ipf

t-b · 2025-04-15T15:30:59Z

Document that GetAllFilesRecursivelyFromPath does only resolve symbolic links when the requested extension is ???? or .lnk
Add test with GetAllFilesRecursivelyFromPath where a ".lnk" file points into the woods. Failed on Michael's machine.

t-b · 2025-04-16T11:10:08Z

Also the line
folders = folders + foldersFromAlias
should use AddListItem

This complicates things as you then need to check that foldersFromAlias is not empty as adding an empty element is something different than adding an empty string. But this is also moot as I'm moving to text waves.

MichaelHuth · 2025-04-16T13:08:59Z

@t-b I had some more thoughts: IndexedFile is traversing all files anyway in a folder.

So if we change the extension option of GetAllFilesRecursivelyFromPath to a regex option. Then we change the call of IndexedFile to not use any file extension filter such that it returns all files in the list. And then we apply a GrepList to that list with the regex.

Advantage: For cases like the AB where we want to have .pxp and .uxp we only need one call and one file traversal.

I think the overhead handling a longer list string is ok.

t-b · 2025-04-16T19:10:28Z

So if we change the extension option of GetAllFilesRecursivelyFromPath to a regex option. Then we change the call of IndexedFile to not use any file extension filter such that it returns all files in the list. And then we apply a GrepList to that list with the regex.

Added.

MichaelHuth · 2025-04-17T12:31:28Z

Some numbers:

Local drives:

Fast Samsung SSD
•test()
Time: 1751
Number of files: 793393
Files per second 453.108

Regular HDD:
•test()
Time: 7630.9
Number of files: 2.80506e+06
Files per second 367.592

With the new function:

*******************************************************************************************
Function: MIES_Utilities_File.ipf GetAllFilesRecursivelyFromPath; Percent total 99%
*******************************************************************************************
[00]          	|Function/WAVE GetAllFilesRecursivelyFromPath(string pathName, [string regex, variable resolveAliases])
[00]          	|
[00]          	|	string files, subFoldersList, subFilesList, cdf, workPath
[00]          	|	variable err
[00]          	|	variable numFolders, numFiles, needsAliasResolving, i, needsFiltering
[00]          	|
[00]          	|	if(ParamIsDefault(regex))
[00]          	|		regex = ".*"
[00]          	|	else
[00]          	|		ASSERT(IsValidRegexp(regex), "Expected a valid regex")
[00]          	|		needsFiltering = 1
[00]          	|	endif
[00]          	|
[00]          	|	if(ParamIsDefault(resolveAliases))
[00]          	|		resolveAliases = 0
[00]          	|	else
[00]          	|		resolveAliases = !!resolveAliases
[00]          	|	endif
[00]          	|
[00]          	|	Make/FREE/N=(MINIMUM_WAVE_SIZE_LARGE)/T resultFiles
[00]          	|	SetNumberInWaveNote(resultFiles, NOTE_INDEX, 0)
[00]          	|
[00]          	|	Make/FREE/N=(MINIMUM_WAVE_SIZE)/T folders
[00]          	|	SetNumberInWaveNote(folders, NOTE_INDEX, 0)
[00]          	|
[00]          	|	PathInfo $pathName
[00]          	|	ASSERT(V_flag, "Given symbolic path does not exist")
[00]          	|	Make/T/FREE startFolder = {S_path}
[00]          	|	numFolders = ConcatenateWavesWithNoteIndex(folders, startFolder)
[00]          	|
[00]          	|	workPath = GetUniqueSymbolicPath()
[00]          	|
[00]          	|	AssertOnAndClearRTError()
[00]*         	|	for(i = 0; i < numFolders; i += 1)
[00]          	|
[00]*         	|		cdf = folders[i]
[68]*******   	|		NewPath/Q/O/Z $workPath, cdf
[00]          	|
[02]*         	|		subFoldersList = IndexedDir($workPath, -1, 1, FILE_LIST_SEP); err = GetRTError(1)
[00]*         	|		WAVE/T subFolders = ListToTextWave(subFoldersList, FILE_LIST_SEP)
[00]          	|		// add trailing colon
[00]*         	|		Multithread subFolders[] += ":"
[00]          	|
[00]          	|		ConcatenateWavesWithNoteIndex(folders, subFolders)
[00]          	|
[29]***       	|		subFilesList = IndexedFile($workPath, -1, "????", "????", FILE_LIST_SEP); err = GetRTError(1)
[00]*         	|		WAVE/T subFiles = ListToTextWave(subFilesList, FILE_LIST_SEP)
[00]          	|		// make them absolute
[00]*         	|		Multithread subFiles[] = cdf + subFiles[p]
[00]          	|
[00]          	|		if(resolveAliases)
[00]          	|			[WAVE/T filesResolved, WAVE/T foldersResolved] = GetAllFilesAliasHelper(subFiles)
[00]          	|		else
[00]*         	|			WAVE/T filesResolved = subFiles
[00]          	|			WAVE/ZZ/T foldersResolved
[00]          	|		endif
[00]          	|
[00]*         	|		numFiles   = ConcatenateWavesWithNoteIndex(resultFiles, filesResolved)
[00]          	|		numFolders = ConcatenateWavesWithNoteIndex(folders, foldersResolved)
[00]          	|	endfor
[00]          	|
[00]          	|	if(!numFiles)
[00]          	|		return $""
[00]          	|	endif
[00]          	|
[00]          	|	Redimension/N=(numFiles) resultFiles
[00]          	|	Note/K resultFiles
[00]          	|
[00]          	|	if(needsFiltering)
[00]          	|		WAVE/Z/T resultFilesFiltered = GrepTextWave(resultFiles, regex)
[00]          	|	else
[00]          	|		WAVE/T resultFilesFiltered = resultFiles
[00]          	|	endif
[00]          	|
[00]          	|	return resultFilesFiltered
[00]          	|End

Some last bench numbers:

With Igor Pro on SSD:

•test()
Time: 415.755
Number of files: 328419
Files per second 789.9345141884879

The same folder with Total Commander gathering files and sizes: 3.3 s

That is roughly a factor of 125x faster.

t-b · 2025-04-17T14:04:54Z

Jeep, the profiling clearly shows all the work is spent in IP itself.

MichaelHuth

See comment.

Packages/MIES/MIES_Utilities_File.ipf

Packages/MIES/MIES_AnalysisBrowser.ipf

t-b · 2025-04-22T21:48:39Z

@MichaelHuth I'm assigning you already although CI is not yet finished.

MichaelHuth

Needs commit compilation fix.

Rest LGTM.

timjarsky · 2025-04-24T02:33:50Z

@t-b when attempting to add a folder, I'm getting:

  !!! Threadsafe assertion FAILED !!!
  Message: "Invalid value"
  Please provide the following information if you contact the MIES developers:
  ################################
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Stacktrace:
  AB_OpenAnalysisBrowser(...)#L2772 [MIES_AnalysisBrowser.ipf]
PGC_SetAndActivateControl(...)#L220 [MIES_ProgrammaticGUIControl.ipf]
AB_ButtonProc_Refresh(...)#L2959 [MIES_AnalysisBrowser.ipf]
AB_AddExperimentEntries(...)#L2688 [MIES_AnalysisBrowser.ipf]
AB_AddFile(...)#L267 [MIES_AnalysisBrowser.ipf]
AB_LoadFile(...)#L401 [MIES_AnalysisBrowser.ipf]
AB_FillListWave(...)#L486 [MIES_AnalysisBrowser.ipf]
EnsureLargeEnoughWave(...)#L68 [MIES_Utilities_WaveHandling.ipf]
FindNextPower(...)#L112 [MIES_Utilities_Numeric.ipf]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Time: 2025-04-23T19:32:36-07:00
  Experiment: Untitled ()
  Igor Pro version: 9.0.6.1 (56565)
  ################################

t-b · 2025-04-24T08:41:16Z

@timjarsky Oops, I'll fix that.

t-b · 2025-04-25T18:33:30Z

@timjarsky Fixed.

There is no reason we can't support it. We have to special case it though.

As we are now using DeleteFile/DeleteFolder we also need to check that the misc settings entry is correct so that these call work.

When we get a filename with a symbolic path for an existing file, we need to return the full path as well. Use S_Path from GetFileFolderInfo for that.

This is not needed.

We used to always perform alias/shortcut handling even when we only look for certain file suffixes. But we only have to try following these if they can be part of the returned list. So for the common case of Windows OS and a extension which does not match .lnk we can skip the alias resolving. When we do have aliases we also first call GetFileFolderInfo and only if we have an alias ResolveAlias again, skipping another GetFileFolderInfo for the case when the pointed to file is not an alias. This allows to gather 100k files on a 1Gb/s network link in under 60s. ```igorpro Function Dostuff() Newpath/O testPath "Y:" beginfunctionProfiling(testTime = 50000) string result = getAllfilesRecursivelyFromPath("testPath", extension = ".mp3") endfunctionProfiling() printf "Number of files: %d\r", ItemsInList(result, "|") End ``` gives ``` Total time: 54.4173, Time in Function code: 54.3973 (100%) Top function percentages: Function MIES_Utilities_File.ipf GetAllFilesRecursivelyFromPath: 99% Annotated Top Functions: ******************************************************************************************* Function: MIES_Utilities_File.ipf MIES_Utilities_File.ipf#GetAllFilesRecursivelyFromPath; Percent total 99% ******************************************************************************************* [00] |Function/S GetAllFilesRecursivelyFromPath(string pathName, [string extension]) [00] | [00] | string fileOrPath, folders, subFolderPathName, fileName [00] | string files, allFilesList [00] | string allFiles = "" [00]* | string foldersFromAlias = "" [00] | variable err, isWindows [00] | [00] |#ifdef WINDOWS [00] | isWindows = 1 [00] |#endif [00] | [01]* | PathInfo $pathName [00] | ASSERT(V_flag, "Given symbolic path does not exist") [00] | [00] | if(ParamIsDefault(extension)) [00] | extension = "????" [00] | endif [00] | [00] | AssertOnAndClearRTError() [70]******* | allFilesList = IndexedFile($pathName, -1, extension, "????", FILE_LIST_SEP); err = GetRTError(1) [00] | [00]* | if(isWindows && cmpstr(extension, "????") && cmpstr(extension, ".lnk")) [00] | allFiles = AddPrefixToEachListItem(S_path, allFilesList, sep = FILE_LIST_SEP) [00] | else [00] | // try to resolve aliases/shortcuts when we can have them [00] | WAVE/T allFilesInDir = ListToTextWave(allFilesList, FILE_LIST_SEP) [00] | for(fileName : allFilesInDir) [00] | [00] | GetFileFolderInfo/P=$pathName/Q/Z fileName [00] | [00] | if(V_Flag != 0) [00] | // error querying file [00] | continue [00] | endif [00] | [00] | if(V_IsAliasShortcut) [00] | fileOrPath = ResolveAlias(fileName, pathName = pathName) [00] | [00] | // redo the check [00] | GetFileFolderInfo/P=$pathName/Q/Z fileOrPath [00] | [00] | if(V_Flag != 0) [00] | // error querying file/folder pointed to by alias [00] | continue [00] | endif [00] | endif [00] | [00] | if(V_isFile) [00] | allFiles = AddListItem(S_path, allFiles, FILE_LIST_SEP, Inf) [00] | elseif(V_isFolder) [00] | foldersFromAlias = AddListItem(S_path, foldersFromAlias, FILE_LIST_SEP, Inf) [00] | else [00] | ASSERT(0, "Unexpected file type") [00] | endif [00] | endfor [00] | endif [00] | [00] | AssertOnAndClearRTError() [04]* | folders = IndexedDir($pathName, -1, 1, FILE_LIST_SEP); err = GetRTError(1) [00] | folders = folders + foldersFromAlias [00]* | WAVE/T wFolders = ListToTextWave(folders, FILE_LIST_SEP) [00]* | for(folder : wFolders) [00] | [00] | subFolderPathName = GetUniqueSymbolicPath() [00] | [12]* | NewPath/Q/O $subFolderPathName, folder [00]* | files = GetAllFilesRecursivelyFromPath(subFolderPathName, extension = extension) [11]* | KillPath/Z $subFolderPathName [00] | [00]* | if(!isEmpty(files)) [01]* | allFiles = AddListItem(RemoveEnding(files, FILE_LIST_SEP), allFiles, FILE_LIST_SEP, Inf) [00] | endif [00] | endfor [00] | [00] | return allFiles [00] |End ``` Close #2402

We don't need to look at the minimum wave size when the requested index already fits. We now also ensure that we double the wave sizes so that we should end up always with a power of two when we started with one.

t-b · 2025-04-25T23:02:18Z

@timjarsky I think it might be beneficial to have this in the next release 2.9 as well.

timjarsky · 2025-04-26T00:42:53Z

@t-b Sure. Here are the latest profiling results from adding folder 105 to the analysis browser

Total time: 506.613, Time in Function code: 453.053 (89.4%)
Top function percentages:
Function MIES_Utilities_File.ipf AskUserForExistingFolder: 84%

Annotated Top Functions:

*******************************************************************************************
Function: MIES_Utilities_File.ipf AskUserForExistingFolder; Percent total 84%
*******************************************************************************************
[00]          	|Function/S AskUserForExistingFolder(string baseFolder)
[00]          	|
[00]          	|	string symbPath, selectedFolder
[00]          	|
[00]*         	|	symbPath = GetUniqueSymbolicPath()
[00]          	|
[00]*         	|	NewPath/O/Q/Z $symbPath, baseFolder
[00]          	|	// preset next undirected NewPath/Open call using the contents of a
[00]          	|	// *symbolic* folder
[00]*         	|	PathInfo/S $symbPath
[00]          	|
[00]          	|	// let the user choose a folder, starts in $baseFolder if supplied
[84]********  	|	NewPath/O/Q/Z $symbPath
[00]*         	|	if(V_flag == -1)
[00]          	|		return ""
[00]          	|	endif
[00]*         	|	PathInfo $symbPath
[00]          	|	selectedFolder = S_path
[00]*         	|	KillPath/Z $symbPath
[00]          	|
[00]          	|	return selectedFolder
[00]          	|End

This does now not use recursion anymore, so the supported file system depth is independent of the IP stack depth. It also returns a text wave.

t-b assigned timjarsky and MichaelHuth Apr 14, 2025

t-b requested review from timjarsky and MichaelHuth as code owners April 14, 2025 18:08

t-b unassigned timjarsky Apr 14, 2025

t-b force-pushed the bugfix/2403-speedup-get-all-files-recursively branch from e10465a to 7d13220 Compare April 14, 2025 18:10

t-b mentioned this pull request Apr 14, 2025

AnalysisBrowser: Make it faster #2092

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t-b force-pushed the bugfix/2403-speedup-get-all-files-recursively branch from 7d13220 to adeb219 Compare April 16, 2025 19:11

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t-b force-pushed the bugfix/2403-speedup-get-all-files-recursively branch from 9880c9b to 30b61e7 Compare April 22, 2025 21:45

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t-b force-pushed the bugfix/2403-speedup-get-all-files-recursively branch from bfb875d to bd592d9 Compare April 25, 2025 18:33

t-b assigned timjarsky and unassigned t-b Apr 25, 2025

t-b added 8 commits April 26, 2025 01:00

Tests: Add some for FindNextPower

7fda0e5

FindNextPower: Handle zero for the limit gracefully

f82b985

There is no reason we can't support it. We have to special case it though.

Tests: Add some for ResolveAlias

1d51512

As we are now using DeleteFile/DeleteFolder we also need to check that the misc settings entry is correct so that these call work.

ResolveAlias: Return full path in all cases

46aba20

When we get a filename with a symbolic path for an existing file, we need to return the full path as well. Use S_Path from GetFileFolderInfo for that.

ResolveAlias: Avoid recursion

d82d899

This is not needed.

ConcatenateWavesWithNoteIndex: Add it

d9b94ff

EnsureLargeEnoughWave: Avoid resizing when not needed

602d37c

We don't need to look at the minimum wave size when the requested index already fits. We now also ensure that we double the wave sizes so that we should end up always with a power of two when we started with one.

t-b force-pushed the bugfix/2403-speedup-get-all-files-recursively branch from bd592d9 to 8e5aa1a Compare April 25, 2025 23:00

timjarsky approved these changes Apr 26, 2025

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timjarsky previously approved these changes Apr 26, 2025

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t-b mentioned this pull request Apr 28, 2025

Prepare release 2.9 #2412

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2 tasks

t-b assigned t-b and unassigned timjarsky Apr 29, 2025

GetAllFilesRecursivelyFromPath: Rework it completely

2436f40

This does now not use recursion anymore, so the supported file system depth is independent of the IP stack depth. It also returns a text wave.

t-b dismissed timjarsky’s stale review via 2436f40 April 30, 2025 09:56

t-b force-pushed the bugfix/2403-speedup-get-all-files-recursively branch from 8e5aa1a to 2436f40 Compare April 30, 2025 09:56

t-b enabled auto-merge April 30, 2025 17:57

t-b disabled auto-merge May 1, 2025 10:18

t-b merged commit c918064 into main May 1, 2025
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t-b deleted the bugfix/2403-speedup-get-all-files-recursively branch May 1, 2025 10:18

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GetAllFilesRecursivelyFromPath: Speed it up with custom extension #2403

GetAllFilesRecursivelyFromPath: Speed it up with custom extension #2403

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GetAllFilesRecursivelyFromPath: Speed it up with custom extension #2403

GetAllFilesRecursivelyFromPath: Speed it up with custom extension #2403

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t-b commented Apr 15, 2025 •

edited

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MichaelHuth commented Apr 17, 2025 •

edited

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