Commit a7167cdd authored by jayd1860's avatar jayd1860
Browse files

v1.15.1 

-- Fix bugs in DeleteSnirfFiles and related functions to use absolute paths without having to change current working directory. This is following the new work flow which alloows multiple groups to be loaded into Homer3 from last commit.
-- Fix bugs in demo_snirf and demo_snirf_readfile and refine demo_snirf_readfile to display clearly all fields using new SnirfClass.Info() method and the new Utils/pretty_print_struct.m function.
-- Update README and generate new snirf_homer3.
-- Small tweaks to unit test display of groupResults file paths.
parent 32d4a574

DataTree/AcquiredData/DataFiles/DeleteSnirfFiles.m

+26 −0
Original line number Diff line number Diff line 
function DeleteSnirfFiles(dirname, snirffiles0)



% Syntax:

%

%   DeleteSnirfFiles()

%   DeleteSnirfFiles(dirname)

%   DeleteSnirfFiles(dirname, snirffiles0)

%

% Description:

%   

%   Delete all .snirf files in group folder. The group folder is same

%   concept as in Homer3 so DeleteSnirfFiles will find all .snirf data 

%   acquisition files in folder dirname. If dirname is not supplied it'll 

%   treat the current working directory as the group folder. If snirffiles0

%   if supplied it'll delete.

%

% Examples:

%

%   1. Delete all .snirf files in the Homer3 Examples directory

%

%       DeleteSnirfFiles('C:\jdubb\workspaces\Homer3\DataTree\AcquiredData\Snirf\Examples')

%

%   2. Delete all .snirf files in the current group folder

%

%       DeleteSnirfFiles()

%

%



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

    dirname = pwd;

end

DataTree/AcquiredData/Snirf/Examples/demo_snirf.m

+7 −10
Original line number Diff line number Diff line
@@ -10,13 +10,13 @@ function demo_snirf() 
%



% Find the Homer3 Examples folder and cd to it

[~, currdir] = findexamplesdir(); 

examplesDir = findexamplesdir(); 



% Delete any previously generated .snirf files to make sure to start from scratch

DeleteSnirfFiles('standalone');

DeleteSnirfFiles(examplesDir, 'standalone');



% Start with .nirs files

nirsfiles = mydir('./*.nirs');

nirsfiles = mydir([examplesDir, '*.nirs']);



fprintf('\n')
@@ -24,9 +24,10 @@ fprintf('\n') 
for ii=1:length(nirsfiles)

    

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

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

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

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

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

    pname = convertToStandardPath(pname);

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

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

    

    % Compare the saved and loaded SnirfClass objects, using overloaded == operator 

    if snirf_saved == snirf_loaded
@@ -36,7 +37,3 @@ for ii=1:length(nirsfiles) 
    end

    fprintf('\n');

end
 


% Return to original folder

cd(currdir);

DataTree/AcquiredData/Snirf/Examples/demo_snirf_readfile.m

+109 −62
Original line number Diff line number Diff line 
function snirf = demo_snirf_readfile(fname)



% Syntax: 

%

%   snirf = demo_snirf_readfile() 

%

% Description:

%

%   Demo of how to read individual SNIRF fields using SnirfClass methods.

%  

% Examples:

% 

%   In each example, make sure the standard Examples .snirf files are there

%   by first running demo_snirf (only once), then call this function.

%

%       demo_snirf

%

%   1. Read and print data from default .snirf file 

%

%       snirf = demo_snirf_readfile();

%

%   2. Read and print data from named files

%

%       snirf = demo_snirf_readfile('Simple_Probe.snirf');

%       snirf = demo_snirf_readfile('FingerTapping_run3_tdmlproc.snirf');

%       snirf = demo_snirf_readfile('neuro_run01.snirf');

%      

%



REPLACE_CODE_WITH_SNIRF_INFO_METHOD = true;



if nargin==0

    fname = 'neuro_run01.snirf';

end

[rootdirexamples, currdir] = findexamplesdir(); 

fnamefullpath = findfile(rootdirexamples, fname, currdir);



rootdirexamples = findexamplesdir(); 

fnamefullpath = findfile(rootdirexamples, fname);

if isempty(fnamefullpath)

    return;

end



%%%%% This is the actual demo showing how to read a .snirf file on the command line
@@ -26,45 +44,69 @@ fnamefullpath = findfile(rootdirexamples, fname, currdir); 
snirf = SnirfClass();



% Use the SnirfClass LoadYYYY method to load whichever field you want 

fprintf('This is a demo of how to load data from a SNIRF file and convert it to .nirs style data.\n');

fprintf('========================================================================================\n');

fprintf('Displaying data from %s\n\n', fnamefullpath);





% Load the SNIRF fields into empty snirf class object, one at a time 

snirf.LoadMetaDataTags(fnamefullpath);

snirf.LoadData(fnamefullpath);

snirf.LoadProbe(fnamefullpath);

snirf.LoadStim(fnamefullpath);

snirf.LoadAux(fnamefullpath);



% Read meta data tags from file

fprintf('Read metaDataTags from %s.\n', fnamefullpath);

snirf.LoadMetaDataTags(fnamefullpath,'/nirs');

% The SnirfClass.Info() method replaces the code in the else statement below. It is essentially 

% the same code adapted to work from within the class. We keep the else statement around for 

% easy viewing of code showing how to load, extract and display SnirfClass data

if REPLACE_CODE_WITH_SNIRF_INFO_METHOD



    snirf.Info();



else 

    

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    % Load meta data tags from file and extract the tag names and values for display

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    fprintf('    MetaDataTags:\n');

    tags = snirf.GetMetaDataTags();

    for ii=1:length(tags)

    fprintf('metaDataTag(%d): {key = ''%s'', value = ''%s''}\n', ii, tags(ii).key, tags(ii).value);

        fprintf('        Meta data tag #%d: {''%s'', ''%s''}\n', ii, tags(ii).key, tags(ii).value);

    end

    fprintf('\n');

    

% Read data matrix

fprintf('Read data field from %s and extract data matrix.\n', fnamefullpath);

snirf.LoadData(fnamefullpath,'/nirs');

    

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    % Load data from file and extract .nirs-style d and ml matrices for display

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    fprintf('    Data (.nirs-style display):\n');

    for ii=1:length(snirf.data)

        

        % Display data matrix dimensions and data type

        d = snirf.data(ii).GetDataMatrix();

    s = '';

    for jj=1:ndims(d)

        if jj==1

            s = num2str(size(d,jj));

        else

            s = sprintf('%sx%s', s, num2str(size(d,jj)));

        end

    end    

    fprintf('d: %s %s\n', s, class(d));

        pretty_print_struct(d, 8, 1);

        

        % Display meas list dimensions and data type

        ml = snirf.data(ii).GetMeasList();

        pretty_print_struct(ml, 8, 1);

        

    end

    fprintf('\n');

    

    

% Load Probe and extract .nirs-style SD structure

fprintf('Extract SD structure from %s.\n', fnamefullpath);

snirf.LoadProbe(fnamefullpath,'/nirs');

SD = snirf.Get_SD()

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    % Load probe and extract .nirs-style SD structure

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    fprintf('    Probe (.nirs-style display):\n');

    SD = snirf.GetSDG();

    pretty_print_struct(SD, 8, 1);

    fprintf('\n');

    

    

% Read meta stims from file

fprintf('Read stim data from %s.\n', fnamefullpath);

snirf.LoadStim(fnamefullpath,'/nirs');

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    % Load stim from file and extract it for display

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    fprintf('    Stim (.snirf-style display):\n');

    for ii=1:length(snirf.stim)

        fprintf('        stim(%d): {name = ''%s'', data = [', ii, snirf.stim(ii).name);

        for jj=1:size(snirf.stim(ii).data,1)
@@ -79,6 +121,11 @@ end 
    fprintf('\n');

    

    

%%%%% Return to original folder

cd(currdir);

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    % Load aux from file and extract nirs-style data for display

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    fprintf('    Aux (.nirs-style display):\n');

    aux = snirf.GetAuxiliary();

    pretty_print_struct(aux, 8, 1);

    

end

DataTree/AcquiredData/Snirf/Examples/findexamplesdir.m

+2 −5
Original line number Diff line number Diff line 
function [rootdirexamples, currdir] = findexamplesdir()

function rootdirexamples = findexamplesdir()



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

rootdirexamples = [rootdir, '/Examples/'];

rootdirexamples(rootdirexamples=='\') = '/';

currdir = pwd;

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

DataTree/AcquiredData/Snirf/Examples/findfile.m

+2 −3
Original line number Diff line number Diff line 
function fnamefullpath = findfile(rootdirexamples, fname, currdir)

function fnamefullpath = findfile(rootdirexamples, fname)



fnamefullpath = [rootdirexamples, fname];

if ~exist(fname, 'file')

if ~exist(fnamefullpath, 'file')

    msg = sprintf('%s does not exist. You first have to generate it by running demo_snirf\n', fnamefullpath);

    MenuBox(msg, 'OK');

    fnamefullpath = '';

    cd(currdir);

    return;

end

CRA Git | Maintained and supported by SUSTech CRA and CCSE