Commit 1d6bed1e authored by Jay Dubb's avatar Jay Dubb
Browse files

1.28.7 

-- Fix Homer3 not detecting and not offering to convert all .nirs files if even one .snirf exists in a group folder. It should offer to convert to .snirf whichever .nirs files have not been converted to .snirf.
-- Add some improvements to the debug messages in Nirs2Snirf and related functions used to convert .nirs to .snirf
-- Replace convertToStandardPath with filesepStandard for uniformity everywhere possible. Didn't do it everywhere because convertToStandardPath behaves slightly differently in the case of relative path it converts to absolute path whereas filesepStandard does not. So in cases where there might be a relative path which is necessesary I didn't replace with filesepStandard.
parent 4c4a1dec

DataTree/AcquiredData/DataFiles/DataFilesClass.m

+32 −7
Original line number Diff line number Diff line
@@ -7,7 +7,7 @@ classdef DataFilesClass < handle 
        errmsg;

        pathnm;

        config;

        

        nfiles;

    end

    

    methods
@@ -17,6 +17,7 @@ classdef DataFilesClass < handle 
            obj.type = '';

            obj.pathnm = pwd;

            skipconfigfile = false;

            obj.nfiles = 0;

            

            if nargin>0

                obj.pathnm = varargin{1};
@@ -72,9 +73,8 @@ classdef DataFilesClass < handle 
        function findDataSet(obj, type)

            obj.files = mydir([obj.pathnm, '/*.', type]);

            if isempty( obj.files )                

                

                % If there are no .nirs files in current dir, don't give up yet - check

                % the subdirs for .nirs files.

                % If there are no data files in current dir, don't give up yet - check

                % the subdirs for data files.

                dirs = mydir(obj.pathnm);

                for ii=1:length(dirs)

                    if dirs(ii).isdir && ...
@@ -93,9 +93,12 @@ classdef DataFilesClass < handle 
                                foos(jj).name         = [dirs(ii).name, '/', foos(jj).name];

                                foos(jj).map2group    = struct('iGroup',0, 'iSubj',0, 'iRun',0);

                                foos(jj).pathfull     = dirs(ii).pathfull;

                                if ~foos(jj).isdir

                                    obj.nfiles = obj.nfiles+1;

                                end

                            end

                            

                            % Add .nirs file from current subdir to files struct

                            % Add file from current subdir to files struct

                            if isempty(obj.files)

                                obj.files = dirs(ii);

                            else
@@ -109,6 +112,7 @@ classdef DataFilesClass < handle 
                for ii = 1:length(obj.files)

                    obj.files(ii).pathfull = obj.pathnm;

                end

                obj.nfiles = obj.nfiles+length(obj.files);

            end

        end
@@ -152,5 +156,26 @@ classdef DataFilesClass < handle 
            end

        end

       

        

                

        % ----------------------------------------------------------

        function found = ConvertedFrom(obj, src)

            found = zeros(length(src.files), 1);

            for ii = 1:length(src.files)

                if src.files(ii).isdir

                    found(ii) = -1;

                    continue;

                end

                [ps, fs] = fileparts(src.files(ii).name);

                for jj = 1:length(obj.files)

                    [pd, fd] = fileparts(obj.files(jj).name);

                    if strcmp(filesepStandard([ps,'/',fs], 'nameonly'), filesepStandard([pd,'/',fd], 'nameonly'))

                        found(ii) = 1;

                        break;

                    end

                end

            end

        end

        

    end

end

DataTree/AcquiredData/DataFiles/FindFiles.m

+45 −14
Original line number Diff line number Diff line 
function [files, dirnameGroup] = FindFiles(varargin)

function files = FindFiles(varargin)



% Syntax:

%
@@ -62,22 +62,27 @@ while files.isempty() 
    switch fmt

        case {'snirf','.snirf'}

            files = DataFilesClass(dirnameGroup, 'snirf');

            if files.isempty()

                files = DataFilesClass(dirnameGroup, 'nirs');

                if ~files.isempty()

                    if files.config.RegressionTestActive

                        q = 1;

                    else                        

                        msg{1} = sprintf('Homer3 did not find any .snirf files in the current folder but did find .nirs files. ');

                        msg{2} = sprintf('Do you want to convert .nirs files to .snirf format and load them?');

                        q = MenuBox([msg{:}], {'YES','NO'}, 'center');

            filesSrc = DataFilesClass(dirnameGroup, 'nirs');           

            if ~filesSrc.isempty()

                nfolders = length(filesSrc.files)-filesSrc.nfiles;

                if nfolders==0

                    nfolders = 1;

                end

                fprintf('FindFiles: Found %d .nirs data files in %d folders\n', filesSrc.nfiles, nfolders);

            end

            

            % Search for source acquisition files in .nirs format which have not

            % been converted to .snirf. 

            found = files.ConvertedFrom(filesSrc);

            if ~all(found)

                q = GetOptionsForIncompleteDataSet(files, filesSrc);

                if q==2

                    if files.isempty()

                        files = [];

                        return;

                    end

                    return;

                end

                Nirs2Snirf(dirnameGroup);

                Nirs2Snirf(dirnameGroup, filesSrc.files(~found));

                files = DataFilesClass(dirnameGroup, 'snirf');

            end

        case {'snirfonly'}
@@ -127,3 +132,29 @@ while files.isempty() 
end







% ----------------------------------------------------------------------------

function  q = GetOptionsForIncompleteDataSet(files, filesSrc)

if files.config.RegressionTestActive

    q = 1;

elseif  files.isempty()

    msg{1} = sprintf('Homer3 did not find any .snirf files in the current folder but did find %d .nirs files. ', filesSrc.nfiles);

    msg{2} = sprintf('Do you want to convert .nirs files to .snirf format and load them?');

    q = MenuBox([msg{:}], {'YES','NO'}, 'center');

else

    if files.nfiles>1

        s = 'have';

    else

        s = 'has';

    end

    if filesSrc.nfiles-files.nfiles>1

        msg{1} = sprintf('Homer3 found %d .nirs files which have not been converted to .snirf format and %d that %s. ', filesSrc.nfiles-files.nfiles, files.nfiles, s);

        msg{2} = sprintf('Do you want to convert the remaining %d .nirs files to .snirf format?', filesSrc.nfiles-files.nfiles);

    else

        msg{1} = sprintf('Homer3 found %d .nirs file which has not been converted to .snirf format and %d that %s. ', filesSrc.nfiles-files.nfiles, files.nfiles, s);

        msg{2} = sprintf('Do you want to convert the remaining .nirs file to .snirf format?');

    end

    q = MenuBox([msg{:}], {'YES','NO'}, 'center');

end

DataTree/AcquiredData/DataFiles/Nirs2Snirf.m

+15 −7
Original line number Diff line number Diff line
@@ -16,7 +16,7 @@ DEBUG=false; 
snirf = SnirfClass().empty();



if ~exist('dirname','var') || isempty(dirname)

    dirname = convertToStandardPath(pwd);

    dirname = filesepStandard(pwd);

end

if ~exist('nirsfiles0','var') || isempty(nirsfiles0)

    nirsfiles0 = DataFilesClass(dirname,'nirs').files;
@@ -39,16 +39,22 @@ elseif isa(nirsfiles0, 'FileClass') 
    nirsfiles = nirsfiles0;

end



h = waitbar_improved(0,'Converting .nirs files to .snirf ...');

fprintf('\n');



h = waitbar_improved(0, sprintf('Converting %d .nirs files to .snirf ...', length(nirsfiles)));

for ii=1:length(nirsfiles)

    if nirsfiles(ii).isdir

        continue;

    end

    [pname, fname, ext] = fileparts([nirsfiles(ii).pathfull, '/', nirsfiles(ii).name]);

    fprintf('Converting %s to %s\n', [pname,'/',fname,ext], [pname,'/',fname,'.snirf']);

    

    src = filesepStandard([pname,'/',fname, ext]);

    dst = filesepStandard([pname,'/',fname,'.snirf'], 'nameonly');

    

    fprintf('Converting %s to %s\n', src, dst);

    waitbar_improved(ii/length(nirsfiles), h, sprintf('Converting %s to SNIRF: %d of %d', nirsfiles(ii).name, ii, length(nirsfiles)));



    nirs = load([pname,'/',fname,ext],'-mat');

    nirs = load(src,'-mat');

    

    if DEBUG==false

        snirf(ii) = SnirfClass(nirs);
@@ -56,9 +62,11 @@ for ii=1:length(nirsfiles) 
        snirf(ii) = SnirfClass(nirs, ntimebases);

    end

    

    snirf(ii).Save([pname,'/',fname,'.snirf']);

    snirf(ii).Save(dst);

    if replace

        delete([pname,'/',fname,ext]);

        delete(src);

    end

end

close(h);



fprintf('\n');

DataTree/AcquiredData/Snirf/Examples/demo_snirf.m

+1 −1
Original line number Diff line number Diff line
@@ -25,7 +25,7 @@ for ii=1:length(nirsfiles) 
    

    % Convert sample .nirs file to SNIRF file (*.snirf) 

    [pname,fname,ext] = fileparts([examplesDir, nirsfiles(ii).name]);

    pname = convertToStandardPath(pname);

    pname = filesepStandard(pname);

    fprintf('Converting %s to %s\n', [pname, fname, ext], [pname, fname, '.snirf']);

    [snirf_saved, snirf_loaded] = snirf_load_save([pname, nirsfiles(ii).name]);

DataTree/AcquiredData/Snirf/Examples/findexamplesdir.m

+1 −1
Original line number Diff line number Diff line 
function rootdirexamples = findexamplesdir()



rootdir = fileparts(which('SnirfClass.m'));

rootdirexamples = convertToStandardPath([rootdir, '/Examples/']);
 
rootdirexamples = filesepStandard([rootdir, '/Examples/']);

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