v.15 (32d4a574) · Commits · github_fork / Homer3

DataTree/AcquiredData/DataFiles/DataFilesClass.m

+19 −13

Original line number	Diff line number	Diff line
		@@ -19,14 +19,19 @@ classdef DataFilesClass < handle
		skipconfigfile = false;

		if nargin>0
		obj.type = varargin{1};
		obj.pathnm = varargin{1};
		end
		obj.pathnm = convertToStandardPath(obj.pathnm);

		if nargin>1
		obj.type = varargin{2};
		if obj.type(1)=='.'
		obj.type(1)='';
		end
		end
		obj.errmsg = {};

		if nargin>1
		if nargin>2
		if strcmp(varargin{2}, 'standalone')
		skipconfigfile = true;
		end
		@@ -44,13 +49,12 @@ classdef DataFilesClass < handle
		else
		obj.config.RegressionTestActive=false;
		end
		foo = mydir(obj.pathnm);
		if ~isempty(foo) && ~foo(1).isdir
		obj.files = foo;
		end

		if nargin==0
		return;
		end

		obj.files = mydir(obj.pathnm);
		GetDataSet(obj);
		end

		@@ -60,27 +64,25 @@ classdef DataFilesClass < handle
		if exist(obj.pathnm, 'dir')~=7
		error(sprintf('Invalid subject folder: ''%s''', obj.pathnm));
		end
		cd(obj.pathnm);
		obj.findDataSet(obj.type);
		end


		% ----------------------------------------------------
		function findDataSet(obj, type)
		obj.files = mydir(['./*.', 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.
		dirs = mydir();
		dirs = mydir(obj.pathnm);
		for ii=1:length(dirs)
		if dirs(ii).isdir && ...
		~strcmp(dirs(ii).name,'.') && ...
		~strcmp(dirs(ii).name,'..') && ...
		~strcmp(dirs(ii).name,'hide')
		dirs(ii).idx = length(obj.files)+1;
		cd(dirs(ii).name);
		foos = mydir(['./*.', type]);
		foos = mydir([obj.pathnm, dirs(ii).name, '/*.', type]);
		nfoos = length(foos);
		if nfoos>0
		for jj=1:nfoos
		@@ -90,6 +92,7 @@ classdef DataFilesClass < handle
		foos(jj).filename = foos(jj).name;
		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;
		end

		% Add .nirs file from current subdir to files struct
		@@ -100,9 +103,12 @@ classdef DataFilesClass < handle
		end
		obj.files(end+1:end+nfoos) = foos;
		end
		cd('../');
		end
		end
		else
		for ii=1:length(obj.files)
		obj.files(ii).pathfull = obj.pathnm;
		end
		end
		end

DataTree/AcquiredData/DataFiles/DeleteSnirfFiles.m

+12 −7

Original line number	Diff line number	Diff line
		function DeleteSnirfFiles(snirffiles0)
		function DeleteSnirfFiles(dirname, snirffiles0)

		if ~exist('dirname','var')
		dirname = pwd;
		end
		dirname = convertToStandardPath(dirname);

		if ~exist('snirffiles0','var')
		snirffiles0 = DataFilesClass('.snirf','standalone').files;
		snirffiles0 = DataFilesClass(dirname, '.snirf', 'standalone').files;
		end

		snirffiles = mydir('');
		snirffiles = mydir(dirname);
		if iscell(snirffiles0)
		for ii=1:length(snirffiles0)
		snirffiles(ii) = mydir(snirffiles0{ii});
		snirffiles(ii) = mydir([dirname, snirffiles0{ii}]);
		end
		elseif ischar(snirffiles0)
		snirffiles = mydir(snirffiles0);
		snirffiles = mydir([dirname, snirffiles0]);
		elseif isa(snirffiles0, 'FileClass')
		snirffiles = snirffiles0;
		end
		@@ -19,8 +24,8 @@ for ii=1:length(snirffiles)
		if snirffiles(ii).isdir
		continue;
		end
		fprintf('Deleting %s\n', [snirffiles(ii).pathfull, '/', snirffiles(ii).filename]);
		delete([snirffiles(ii).pathfull, '/', snirffiles(ii).filename]);
		fprintf('Deleting %s\n', [snirffiles(ii).pathfull, '/', snirffiles(ii).name]);
		delete([snirffiles(ii).pathfull, '/', snirffiles(ii).name]);
		pause(0.25);
		end

DataTree/AcquiredData/DataFiles/FileClass.m

+30 −7

Original line number	Diff line number	Diff line
		@@ -49,6 +49,12 @@ classdef FileClass < matlab.mixin.Copyable
		else
		return;
		end
		if strcmp(file_struct.name,'.')
		return;
		end
		if strcmp(file_struct.name,'..')
		return;
		end

		% Copy all fields of file_struct that exist in this class to this object.
		fields = propnames(file_struct);
		@@ -64,11 +70,7 @@ classdef FileClass < matlab.mixin.Copyable
		obj.subjdiridx = 0;
		obj.filename = obj.name;
		obj.map2group = struct('iSubj',0,'iRun',0);
		if obj.isdir
		obj.pathfull = fileparts(fileparts(fullpath(obj.name)));
		else
		obj.pathfull = fileparts(fullpath(obj.name));
		end
		obj.err = 0; % Assume file is not loadable
		end


		@@ -119,7 +121,12 @@ classdef FileClass < matlab.mixin.Copyable

		% -----------------------------------------------------------
		function [groupName, subjName, runName] = ExtractNames(obj)
		[~, groupName] = fileparts(pwd);
		if obj.pathfull(end)=='/' \|\| obj.pathfull(end)=='\'
		groupPath = obj.pathfull(1:end-1);
		else
		groupPath = obj.pathfull;
		end
		[~, groupName] = fileparts(groupPath);
		subjName = '';
		runName = '';

		@@ -134,7 +141,9 @@ classdef FileClass < matlab.mixin.Copyable
		return;
		end

		%%%% obj is a data file
		%%%% obj is a data file representing single run
		% [~, fname, ext] = fileparts(obj.name);
		% runName = [fname, ext];
		runName = obj.name;

		% Determine subject name from filename
		@@ -185,6 +194,20 @@ classdef FileClass < matlab.mixin.Copyable
		end
		end


		% -----------------------------------------------------------
		function b = IsEmpty(obj)
		b = true;
		if isempty(obj.name)
		return;
		end
		if obj.err ~= 0
		return;
		end
		b = false;
		end


		end

		end
		No newline at end of file

DataTree/AcquiredData/DataFiles/FindFiles.m

+19 −31

Original line number	Diff line number	Diff line
		@@ -3,9 +3,8 @@ function [files, dirnameGroup] = FindFiles(varargin)
		% Syntax:
		%
		% [files, dirnameGroup] = FindFiles()
		% [files, dirnameGroup] = FindFiles(fmt)
		% [files, dirnameGroup] = FindFiles(fmt, dirnameGroup)
		% [files, dirnameGroup] = FindFiles(fmt, dirnameGroup, handles)
		% [files, dirnameGroup] = FindFiles(dirnameGroup)
		% [files, dirnameGroup] = FindFiles(dirnameGroup, fmt)
		%
		% Descrition:
		%
		@@ -13,15 +12,8 @@ function [files, dirnameGroup] = FindFiles(varargin)
		%
		% Examples:
		%
		% Call FindFiles standalone
		%
		% files = FindFiles('.nirs', 'c:\users\public\group');
		% files = FindFiles('.snirf');
		%
		% Call FindFiles in a GUI context:
		%
		% files = FindFiles('.nirs');
		% files = FindFiles('.snirf');
		% files = FindFiles('c:\users\public\group1');
		% files = FindFiles('c:\users\public\group1','.snirf');


		global maingui
		@@ -37,13 +29,14 @@ supportedFormats = {
		% First get all the argument there are to get using the 7 possible syntax
		% calls
		if nargin==1
		fmt = varargin{1};
		dirnameGroup = varargin{1};
		elseif nargin==2
		fmt = varargin{1};
		dirnameGroup = varargin{2};
		elseif nargin==3
		fmt = varargin{1};
		dirnameGroup = varargin{2};
		dirnameGroup = varargin{1};
		fmt = varargin{2};
		end

		if ~exist('dirnameGroup','var') \|\| isempty(dirnameGroup)
		dirnameGroup = pwd;
		end

		if ~exist('fmt','var') \|\| isempty(fmt)
		@@ -54,20 +47,15 @@ if ~exist('fmt','var') \|\| isempty(fmt)
		end
		end

		if ~exist('dirnameGroup','var') \|\| isempty(dirnameGroup)
		dirnameGroup = pwd;
		end

		% Check files data set for errors. If there are no valid
		% nirs files don't attempt to load them.
		files = DataFilesClass();
		while files.isempty()
		cd(dirnameGroup)
		switch fmt
		case {'snirf','.snirf'}
		files = DataFilesClass('snirf');
		files = DataFilesClass(dirnameGroup, 'snirf');
		if files.isempty()
		files = DataFilesClass('nirs');
		files = DataFilesClass(dirnameGroup, 'nirs');
		if ~files.isempty()
		if files.config.RegressionTestActive
		q = 1;
		@@ -77,25 +65,25 @@ while files.isempty()
		q = MenuBox([msg{:}], {'YES','NO'}, 'center');
		end
		if q==2
		files = DataFilesClass();
		files = DataFilesClass(dirnameGroup);
		return;
		end
		end
		Nirs2Snirf();
		files = DataFilesClass('snirf');
		Nirs2Snirf(dirnameGroup);
		files = DataFilesClass(dirnameGroup, 'snirf');
		end
		case {'nirs','.nirs'}
		files = DataFilesClass('nirs');
		files = DataFilesClass(dirnameGroup, 'nirs');
		otherwise
		q = menu(sprintf('Homer3 only supports file formats: {%s}. Please choose one.', cell2str(supportedFormats(:,1))), ...
		'OK','CANCEL');
		if q==2
		files = DataFilesClass();
		files = DataFilesClass(dirnameGroup);
		return;
		else
		selection = checkboxinputdlg(supportedFormats(:,1), 'Select Supported File Format');
		if isempty(selection)
		files = DataFilesClass();
		files = DataFilesClass(dirnameGroup);
		return;
		end
		fmt = supportedFormats{selection,1};

DataTree/AcquiredData/DataFiles/Nirs2Snirf.m

+11 −8

Original line number	Diff line number	Diff line
		function [snirf, nirsfiles] = Nirs2Snirf(nirsfiles0, replace, ntimebases)
		function [snirf, nirsfiles] = Nirs2Snirf(dirname, nirsfiles0, replace, ntimebases)
		%
		% Syntax:
		% snirf = Nirs2Snirf(nirsfiles)
		% snirf = Nirs2Snirf(nirsfiles, replace)
		% snirf = Nirs2Snirf(nirsfiles, replace, ntimebases)
		% snirf = Nirs2Snirf(dirname, nirsfiles)
		% snirf = Nirs2Snirf(dirname, nirsfiles, replace)
		% snirf = Nirs2Snirf(dirname, nirsfiles, replace, ntimebases)
		%
		% Description:
		% Convert all .nirs files in the current folder to .snirf
		% Convert all .nirs files in the folder dirname to .snirf
		%
		%
		%
		@@ -15,8 +15,11 @@ DEBUG=false;

		snirf = SnirfClass().empty();

		if ~exist('dirname','var') \|\| isempty(dirname)
		dirname = convertToStandardPath(pwd);
		end
		if ~exist('nirsfiles0','var') \|\| isempty(nirsfiles0)
		nirsfiles0 = DataFilesClass('nirs').files;
		nirsfiles0 = DataFilesClass(dirname,'nirs').files;
		end
		if ~exist('replace','var') \|\| isempty(replace)
		replace = false;
		@@ -25,7 +28,7 @@ if ~exist('ntimebases','var') \|\| isempty(ntimebases)
		ntimebases = 1;
		end

		nirsfiles = mydir('');
		nirsfiles = mydir(dirname);
		if iscell(nirsfiles0)
		for ii=1:length(nirsfiles0)
		nirsfiles(ii) = mydir(nirsfiles0{ii});
		@@ -41,7 +44,7 @@ for ii=1:length(nirsfiles)
		if nirsfiles(ii).isdir
		continue;
		end
		[pname,fname,ext] = fileparts([nirsfiles(ii).pathfull, '/', nirsfiles(ii).filename]);
		[pname,fname,ext] = fileparts([nirsfiles(ii).pathfull, '/', nirsfiles(ii).name]);
		fprintf('Converting %s to %s\n', [pname,'/',fname,ext], [pname,'/',fname,'.snirf']);
		waitbar_improved(ii/length(nirsfiles), h, sprintf('Converting %s to SNIRF: %d of %d', nirsfiles(ii).name, ii, length(nirsfiles)));

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