Commit 9fb39d61 authored by Jay's avatar Jay
Browse files

v1.20.0 

-- When SNIRF format (or any other supported file format) changes and old .snirf don't load properly, but .nirs files exist in the same subject folder then offer to delete or move the .snirf in order to regenerate the .snirf from .nirs files.

-- Add textLineWidth parameter to MenuBox.m in order to allow explicit control over the width of the menu box window and override the automatic calculation of the width.

-- Rename DeleteSnirfFiles.m to DeleteDataFiles.m which is a more general utility for any format and which allows the options of moving instead of deleting files or restoring the old files back to their active names (e.g., <filename>.snirf.old to <filename>.snirf) for debugging purposes
parent 529848ce

DataTree/AcquiredData/DataFiles/DeleteDataFiles.m

0 → 100644
+101 −0
Original line number Diff line number Diff line 
function DeleteDataFiles(varargin)



% Syntax:

%

%   DeleteDataFiles()

%   DeleteDataFiles(dirname)

%   DeleteDataFiles(dirname, datafiles0)

%   DeleteDataFiles(dirname, format)

%   DeleteDataFiles(dirname, datafiles0, options)

%   DeleteDataFiles(dirname, format, options)

%

% Description:

%   

%   Delete all .<format extension> files in group folder. DeleteDataFiles will find all 

%   .<format extension> data acquisition files in the group folder. If dirname is not supplied it'll 

%   treat the current working directory as the group folder. 

%

% Examples:

%

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

%

%       DeleteDataFiles('C:\jdubb\workspaces\Homer3\DataTree\AcquiredData\Snirf\Examples', '.snirf')

%

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

%

%       DeleteDataFiles(pwd, '.nirs)

%

%



global supportedFormats

if isempty(supportedFormats)

    supportedFormats = {

    '.snirf',0;

    '.nirs',0;

    };

end





% Set argument defaults

dirname = convertToStandardPath(pwd);

format = supportedFormats{1};

datafiles0 = [];

options = 'delete';





% Parse arguments

if nargin==1

    dirname = convertToStandardPath(varargin{1});

elseif nargin==2

    dirname = convertToStandardPath(varargin{1});

    if ischar(varargin{2})

        format = varargin{2};

    else

        datafiles0 = varargin{2};

    end

elseif nargin==3

    dirname = convertToStandardPath(varargin{1});

    if ischar(varargin{2})

        format = varargin{2};

    else

        datafiles0 = varargin{2};

    end

    options = varargin{3};

end

if isempty(datafiles0)

    datafiles0 = DataFilesClass(dirname, format, 'standalone').files;

end





% Get final list of data files

datafiles = mydir(dirname);

if iscell(datafiles0)

    for ii=1:length(datafiles0)

        datafiles(ii) = mydir([dirname, datafiles0{ii}]);

    end

elseif ischar(datafiles0)

    datafiles = mydir([dirname, datafiles0]);

elseif isa(datafiles0, 'FileClass')

    datafiles = datafiles0;

end





% Delete data files

for ii=1:length(datafiles)

    if datafiles(ii).isdir

        continue;

    end

    if strcmp(options, 'delete')

        fprintf('Deleting %s\n', [datafiles(ii).pathfull, '/', datafiles(ii).name]);

        delete([datafiles(ii).pathfull, '/', datafiles(ii).name]);

    elseif strcmp(options, 'move')

        fprintf('Moving %s to %s\n', [datafiles(ii).pathfull, '/', datafiles(ii).name], [datafiles(ii).pathfull, '/', datafiles(ii).name, '.old']);

        movefile([datafiles(ii).pathfull, '/', datafiles(ii).name], [datafiles(ii).pathfull, '/', datafiles(ii).name, '.old']);

    elseif strcmp(options, 'restore')

        [pname, fname] = fileparts(datafiles(ii).name);

        fprintf('Restoring %s to %s\n', [datafiles(ii).pathfull, '/', datafiles(ii).name], [datafiles(ii).pathfull, '/', pname, '/', fname]);

        movefile([datafiles(ii).pathfull, '/', datafiles(ii).name], [datafiles(ii).pathfull, '/', pname, '/', fname]);

    end

    pause(0.25);

end

DataTree/AcquiredData/DataFiles/DeleteSnirfFiles.m

deleted100644 → 0
+0 −57
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

dirname = convertToStandardPath(dirname);



if ~exist('snirffiles0','var')

    snirffiles0 = DataFilesClass(dirname, '.snirf', 'standalone').files;

end



snirffiles = mydir(dirname);

if iscell(snirffiles0)

    for ii=1:length(snirffiles0)

        snirffiles(ii) = mydir([dirname, snirffiles0{ii}]);

    end

elseif ischar(snirffiles0)

    snirffiles = mydir([dirname, snirffiles0]);

elseif isa(snirffiles0, 'FileClass')

    snirffiles = snirffiles0;

end



for ii=1:length(snirffiles)

    if snirffiles(ii).isdir

        continue;

    end

    fprintf('Deleting %s\n', [snirffiles(ii).pathfull, '/', snirffiles(ii).name]);

    delete([snirffiles(ii).pathfull, '/', snirffiles(ii).name]);

    pause(0.25);

end

DataTree/AcquiredData/DataFiles/FindFiles.m

+1 −1
Original line number Diff line number Diff line
@@ -65,7 +65,7 @@ while files.isempty() 
                        q = MenuBox([msg{:}], {'YES','NO'}, 'center');

                    end

                    if q==2

                        files = DataFilesClass(dirnameGroup);

                        files = [];

                        return;

                    end

                end

DataTree/AcquiredData/Snirf/Examples/demo_snirf.m

+1 −1
Original line number Diff line number Diff line
@@ -13,7 +13,7 @@ function demo_snirf() 
examplesDir = findexamplesdir(); 



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

DeleteSnirfFiles(examplesDir, 'standalone');

DeleteDataFiles(examplesDir, '.snirf');



% Start with .nirs files

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

DataTree/DataTreeClass.m

+64 −5
Original line number Diff line number Diff line
@@ -67,6 +67,7 @@ classdef DataTreeClass < handle 
            obj.SetCurrElem(1,1,1);

            

            obj.warningflag = 0;

            

        end
@@ -79,12 +80,68 @@ classdef DataTreeClass < handle 
        

        

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

        function status = SelectOptionsWhenLoadFails(obj, ~)

        function status = FoundDataFilesInOtherFormat(obj, dataInit)            

            global supportedFormats

            status = false;

            k = [];



            format0 = dataInit.type;

            

            % Find index of another file format to try

            for ii = 1:length(supportedFormats)

                if ~isempty(findstr(dataInit.type, supportedFormats{ii,1}))

                   k = ii;

                   break;

                end

            end

            if isempty(k)

                return;

            end

            if k<length(supportedFormats) && k>1

                k = k-1;

            elseif k<length(supportedFormats)

                k = k+1;

            else

                k = [];

            end

            if ~isempty(k)

                dataInit = FindFiles(obj.dirnameGroup, supportedFormats{k});

                if isempty(dataInit) || dataInit.isempty()

                    return;

                end

            else

                dataInit = [];

            end

            

            if ~isempty(dataInit)

                msg{1} = sprintf('Could not load any of the .%s files in the group folder but did find .%s files. ', format0, dataInit.type);

                msg{3} = sprintf('Do you want to rename the .%s files to names with a .old extension, delete them or cancel? ', format0);

                msg{2} = sprintf('NOTE: Renaming or deleting the .%s files will allow Homer3 to regenerate them from .%s file later.', ...

                    format0, dataInit.type);

                q = MenuBox([msg{:}], {'Rename (Recommended)','Delete','CANCEL'}, [], 90);

                if q==1

                    DeleteDataFiles(obj.dirnameGroup, format0, 'move')

                    status = true;

                elseif q==2

                    DeleteDataFiles(obj.dirnameGroup, format0)

                    status = true;

                end

            end            

        end



        

        

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

        function status = SelectOptionsWhenLoadFails(obj)

            status = -1;

    

            %             msg{1} = sprintf('Could not load any of the requested files in the group folder %s. ', obj.dirnameGroup);

            %             msg{2} = sprintf('Do you want to select another group folder?');

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

                        

            msg{1} = sprintf('Could not load any of the requested files in the group folder %s. ', obj.dirnameGroup);

            msg{2} = sprintf('Do you want to select another group folder?');

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

            q = MenuBox([msg{:}], {'YES','NO'}, [], 110);

            if q==2

                obj.logger.Write(sprintf('Skipping group folder %s...\n', obj.dirnameGroup));

                obj.dirnameGroup = 0;
@@ -122,7 +179,9 @@ classdef DataTreeClass < handle 
                    

                    obj.LoadGroup(procStreamCfgFile);

                    if length(obj.groups) < iGnew

                        if SelectOptionsWhenLoadFails(obj, dataInit)<0

                        if obj.FoundDataFilesInOtherFormat(dataInit) 

                            continue;

                        elseif obj.SelectOptionsWhenLoadFails()<0

                            break;

                        end

                    end

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