Error computing Soundscape Metrics

[laralps]

Hello to all!

My data was collect with SoundTraps as wav files of 96kHz sampling rate and 10-minutes length.
I'm testing computing soundscape metrics in triton for the first time and I don't have much experience with matlab, so I started generating soundscape LTSAs with default settings (1s, 1Hz and 7 days resolution). LTSAs were generated correctly, but when I try to compute soundscape metrics (300s bin size for time, 1hz bin size for frequency, 50% min. seconds/average and single value calibration), I get the following error message:

Unrecognized function or variable 'utFindFiles'.

Error in sm_cmpt_metrics (line 15)
    utFindFiles('*.ltsa', REMORA.sm.cmpt.indir, 0);

Error in sm_cmpt_control (line 136)
    sm_cmpt_metrics;
 
Error while evaluating DestroyedObject Callback.

What can be happening, is it not recognizing the soundscape LTSA files?

Any help is much appreciated!

[marie-r]

Dear laralps, utFindFiles is a Mathworks user contribution for finding files based on their names that I pulled into the detector version of Triton years ago. It is not in the git tracked mainline code, but it is in the logger Remora. You can either add the logger Remora path or copy it into your code. However, if you are planning on integrating your code into Triton, having multiple copies of the same function creates maintenance nightmares and the code and then utFindFiles should be moved into the mainline code and removed from the logger Remora (and anywhere else it might have been copied). As an aside, there are better alternative to utFindFiles these days. I’ve been using findfiles by Azim Jinha that I modified slightly and am attaching here. All my best, Marie From: laralps ***@***.***> Sent: Friday, August 5, 2022 5:36 AM To: MarineBioAcousticsRC/Triton ***@***.***> Cc: Subscribed ***@***.***> Subject: [MarineBioAcousticsRC/Triton] Error computing Soundscape Metrics (Issue #87) Hello to all! My data was collect with SoundTraps as wav files of 96kHz sampling rate and 10-minutes length. I'm testing computing soundscape metrics in triton for the first time and I don't have much experience with matlab, so I started generating soundscape LTSAs with default settings (1s, 1Hz and 7 days resolution). LTSAs were generated correctly, but when I try to compute soundscape metrics (300s bin size for time, 1hz bin size for frequency, 50% min. seconds/average and single value calibration), I get the following error message: Unrecognized function or variable 'utFindFiles'. Error in sm_cmpt_metrics (line 15) utFindFiles('*.ltsa', REMORA.sm.cmpt.indir, 0); Error in sm_cmpt_control (line 136) sm_cmpt_metrics; Error while evaluating DestroyedObject Callback. What can be happening, is it not recognizing the soundscape LTSA files? Any help is much appreciated! — Reply to this email directly, view it on GitHub <#87> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABQB76VTUOANE2EFG7WUPDLVXUDELANCNFSM55V6FR3Q> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> function fileList = findfiles(searchPath,filePattern,patternMode, pathMode, fileList) % FUNCTION files = findfiles(searchPath, filePattern, patternMode, pathMode, fileList) % A case insensitive search to find files with in the folder _searchPath_ % (if specified) whos file name matches the pattern _filePattern_ and add % the results to the list of files in the cell array _fileList_. % % The search can be either a wild-card or regular expression search and is % case insenstive % % % INPUTS (all are optional % searchPath - Default ask user % - directory or string to search can be either a absolute % or relative path. % % filePattern - Default: *.* (All files) % - List of file wildcard file patterns to search % - Wild-card examples % filePattern = '*.xls' % find Excel files % filePattern = {'*.m' *.mat' '*.fig'}; % MATLAB files % % - Regular expression examples (See regexpi help for more) % filePattern = '^[af].*\.xls' % Excel files beginning % % with either A,a,F or f % % patternMode - Default: 'wildcard' % - 'wildcard' for wild-card searches or % - 'regexp' for regular expression searches % % pathMode - Default: 'file' % - 'file' - patten match on file without directories % - 'path' - pattern match on entire path to file % % fileList - list of files (nx1 cell). Default is an empty cell. % % % author: Azim Jinha (2011) % modifications: Marie A Roch (2014) % - stopped translating the filePatterns each time % - added % Test inputs %*** searchPath *** if ~exist('searchPath','var') || isempty(searchPath) || ~exist(searchPath,'dir') searchPath = uigetdir('Select Path to search'); end % *** filePattern *** if ~exist('filePattern','var') || isempty(filePattern), filePattern={'*.*'}; end if ~iscell(filePattern) % if only one file pattern is entered make sure it % is still a cell-string. filePattern = {filePattern}; end % *** patternMode *** if ~exist('patternMode','var')||isempty(patternMode),patternMode = 'wildcard'; end switch lower(patternMode) case 'wildcard' % convert wild-card file patterns to regular expressions fileRegExp=cell(length(filePattern(:))); for i=1:length(filePattern(:)) fileRegExp{i}=regexptranslate(patternMode,filePattern{i}); end % Change patternmode so that recursvie calls do not retranslate. filePattern = fileRegExp; patternMode = 'regexp'; otherwise % assume that the file pattern(s) are regular expressions fileRegExp = filePattern; end % *** pathMode *** if ~exist('pathMode', 'var') || isempty(pathMode), pathMode = 'file'; end % *** fileList *** % test input argument file list if ~exist('fileList','var'),fileList = {}; end % does it exist % is fileList a nx1 cell array if size(fileList,2)>1, fileList = fileList'; end if ~isempty(fileList) && min(size(fileList))>1, error('input fileList should be a nx1 cell array'); end % Perform file search % Get the parent directory contents dirContents = dir(searchPath); if ~isempty(dirContents) % Construct paths newPaths = ... cellfun(@(x) fullfile(searchPath, x), {dirContents.name}, ... 'UniformOutput', false); if size(newPaths, 2) > 1 newPaths = newPaths'; end matched = false(size(dirContents)); % assume none matched for now switch pathMode case 'file' matchOn = {dirContents.name}; case 'path' matchOn = newPaths; otherwise error('Bad pathMode'); end for i=1:length(dirContents) % don't process current/parent/private directories % (anything starting with a .) if ~strncmpi(dirContents(i).name,'.',1) if dirContents(i).isdir fileList = findfiles(newPaths{i}, filePattern, ... patternMode, pathMode, fileList); else for jj=1:length(fileRegExp) matched(i) = ~isempty(regexpi(matchOn{i}, ... fileRegExp{jj})); if matched(i), break; end end end end end fileList = [fileList; newPaths(matched)]; %#ok<AGROW> end % for i=1:length(dirContents) % if ~strncmpi(dirContents(i).name,'.',1) % newPath = fullfile(searchPath,dirContents(i).name); % if dirContents(i).isdir % fileList = findfiles(newPath,filePattern,patternMode,fileList); % else % foundFile=false; % for jj=1:length(fileRegExp) % foundFile = ~isempty(regexpi(dirContents(i).name, ... % fileRegExp{jj})); % if foundFile, break; end % end % if foundFile % fileList{end+1,1} = newPath; %#ok<AGROW> % end % end % end %end

[sfregosi]

Hi Both - do you mind if I "repost" this issue/question and solution to the Bioacoustics Stack Exchange in case others have a similar issue in the future but aren't on GitHub?

[laralps]

thank you Marie! So I will first try to add the logger Remora path.
And sure Selene, please do share this at the Bioacoustics Stack Exchange .