collection of useful utility functions for MarsBaR etc
fname = mars_utils('str2fname', str)
accepts string, attempts return of string for valid filename
The passed string should be without path or extension
tf = mars_utils('is_valid_varname', str)
accepts string, tests if it is a valid variable name
returns 1 for yes.
P = mars_utils('get_img_name', fname, flags);
gets name of image, if image exists, checks for overwrite
returns filename, or empty string if overwrite not wanted
XYZ = mars_utils('e2xyz', els, dims);
takes element numbers in an image (e.g. find(img>5)) and the
dimensions of the image [X Y Z] and returns the 3xN voxel
coordinates corresponding to the N elements
absf = mars_utils('isabspath', path);
Takes path name, and returns flag, 1 if path is absolute on this
system, 0 if relative or empty
mars_utils('graphic_text', strs, [title_str, [, figure_str]])
Displays cell array of text (strs) in SPM graphics window
with optional title (char) title_string. Can also set to display to
other figure window (string or figure handle).
mars_utils('spm_version', [check_global])
Gets SPM version string. Robust version to allow there to be
versions of the spm.m file to not have Contents.m files in the same
directory. If optional flag check_global is zero, does _not_ check
global SPM_VER variable for version, and tries to get directly from
spm.m / Contents.m pairs.
tf = mars_utils('is_swapped_wrong', V)
Deprecated - see version in mars_vol_utils
tf = mars_utils('version_less_than', v1, v2)
Returns 1 if version v1 is lower than version v2.
Versions can be numbers. If strings, versions can contain more than
one '.' character. For example, '0.38.1' is less than '0.39', or
'0.38.2'
$Id$
0001 function varargout=mars_utils(varargin) 0002 % collection of useful utility functions for MarsBaR etc 0003 % 0004 % fname = mars_utils('str2fname', str) 0005 % accepts string, attempts return of string for valid filename 0006 % The passed string should be without path or extension 0007 % 0008 % tf = mars_utils('is_valid_varname', str) 0009 % accepts string, tests if it is a valid variable name 0010 % returns 1 for yes. 0011 % 0012 % P = mars_utils('get_img_name', fname, flags); 0013 % gets name of image, if image exists, checks for overwrite 0014 % returns filename, or empty string if overwrite not wanted 0015 % 0016 % XYZ = mars_utils('e2xyz', els, dims); 0017 % takes element numbers in an image (e.g. find(img>5)) and the 0018 % dimensions of the image [X Y Z] and returns the 3xN voxel 0019 % coordinates corresponding to the N elements 0020 % 0021 % absf = mars_utils('isabspath', path); 0022 % Takes path name, and returns flag, 1 if path is absolute on this 0023 % system, 0 if relative or empty 0024 % 0025 % mars_utils('graphic_text', strs, [title_str, [, figure_str]]) 0026 % Displays cell array of text (strs) in SPM graphics window 0027 % with optional title (char) title_string. Can also set to display to 0028 % other figure window (string or figure handle). 0029 % 0030 % mars_utils('spm_version', [check_global]) 0031 % Gets SPM version string. Robust version to allow there to be 0032 % versions of the spm.m file to not have Contents.m files in the same 0033 % directory. If optional flag check_global is zero, does _not_ check 0034 % global SPM_VER variable for version, and tries to get directly from 0035 % spm.m / Contents.m pairs. 0036 % 0037 % tf = mars_utils('is_swapped_wrong', V) 0038 % Deprecated - see version in mars_vol_utils 0039 % 0040 % tf = mars_utils('version_less_than', v1, v2) 0041 % Returns 1 if version v1 is lower than version v2. 0042 % Versions can be numbers. If strings, versions can contain more than 0043 % one '.' character. For example, '0.38.1' is less than '0.39', or 0044 % '0.38.2' 0045 % 0046 % $Id$ 0047 0048 if nargin < 1 0049 error('Need action'); 0050 end 0051 Action = lower(varargin{1}); 0052 0053 switch(Action) 0054 0055 %======================================================================= 0056 case 'str2fname' %-string to file name 0057 %======================================================================= 0058 if nargin < 2 0059 error('Need to specify string'); 0060 end 0061 str = varargin{2}; 0062 % forbidden chars in file name 0063 badchars = unique([filesep '/\ :;.''"~*?<>|&']); 0064 0065 tmp = find(ismember(str, badchars)); 0066 if ~isempty(tmp) 0067 str(tmp) = '_'; 0068 dt = diff(tmp); 0069 if ~isempty(dt) 0070 str(tmp(dt==1))=[]; 0071 end 0072 end 0073 varargout={str}; 0074 0075 %======================================================================= 0076 case 'is_valid_varname' %- tests if string is valid variable name 0077 %======================================================================= 0078 if nargin < 2 0079 error('Need to specify string'); 0080 end 0081 str = varargin{2}; 0082 try 0083 eval([str '= [];']); 0084 varargout={1}; 0085 catch 0086 varargout = {0}; 0087 end 0088 0089 %======================================================================= 0090 case 'get_img_name' %-gets name of image, checks for overwrite 0091 %======================================================================= 0092 if nargin < 2 0093 fname = ''; 0094 else 0095 fname = varargin{2}; 0096 end 0097 if nargin < 3 0098 flags = ''; 0099 else 0100 flags = varargin{3}; 0101 end 0102 if isempty(flags) 0103 flags = 'k'; 0104 end 0105 0106 varargout = {''}; 0107 fdir = spm_get(-1, '', 'Directory to save image'); 0108 fname = spm_input('Image filename', '+1', 's', fname); 0109 if isempty(fname), return, end 0110 0111 % set img extension and make absolute path 0112 [pn fn ext] = fileparts(fname); 0113 out_ext = mars_veropts('pref_img_out_ext'); 0114 fname = fullfile(fdir, [fn out_ext]); 0115 fname = spm_get('cpath', fname); 0116 0117 if any(flags == 'k') && exist(fname, 'file') 0118 if ~spm_input(['Overwrite ' fn], '+1', ... 0119 'b','Yes|No',[1 0], 1) 0120 return 0121 end 0122 end 0123 varargout = {fname}; 0124 0125 %======================================================================= 0126 case 'e2xyz' %-returns XYZ voxel coordinates for element numbers 0127 %======================================================================= 0128 if nargin < 2 0129 error('Need element numbers'); 0130 end 0131 if nargin < 3 0132 error('Need image dimensions'); 0133 end 0134 els = varargin{2}; 0135 dim = varargin{3}; 0136 if size(els, 2) == 1, els = els'; end 0137 nz = els-1; 0138 pl_sz = dim(1)*dim(2); 0139 Z = floor(nz / pl_sz); 0140 nz = nz - Z*pl_sz; 0141 Y = floor(nz / dim(1)); 0142 X = nz - Y*dim(1); 0143 XYZ = [X; Y; Z] +1; 0144 varargout = {XYZ}; 0145 0146 %======================================================================= 0147 case 'isabspath' % Returns 1 for absolute path, 0 if relative (or empty) 0148 %======================================================================= 0149 if nargin < 2 0150 error('Need path to test'); 0151 end 0152 pn = varargin{2}; 0153 switch (spm_platform('filesys')) 0154 case 'unx' 0155 if (~isempty(pn) && pn(1)=='/'), absf=1; else, absf=0; end 0156 case 'win' 0157 if (length(pn)>1 && pn(2)==':'), absf=1; else, absf=0; end 0158 otherwise 0159 error('isabspath not coded for this filesystem'); 0160 end 0161 varargout = {absf}; 0162 0163 %======================================================================= 0164 case 'graphic_text' % Displays text in SPM figure window 0165 %======================================================================= 0166 if nargin < 2, error('Need text to show'); else S = varargin{2}; end 0167 if ischar(S), S = cellstr(S); end 0168 if nargin < 3, TTitle = ''; else TTitle = varargin{3}; end 0169 if nargin < 4, F = []; else, F=varargin{4}; end 0170 if isempty(F), F='Graphics'; end 0171 if ischar(F), F = spm_figure('GetWin', F); end 0172 if isempty(F), F = spm_figure('GetWin', 'Graphics'); end 0173 0174 FS = spm('FontSizes'); 0175 PF = spm_platform('fonts'); 0176 0177 spm_figure('clear', F); 0178 figure(F); 0179 hAxes = axes('Position',[0.028,0.05,0.85,0.85],... 0180 'DefaultTextInterpreter','none',... 0181 'Units','Points','Visible','off'); 0182 AxPos = get(hAxes,'Position'); set(hAxes,'YLim',[0,AxPos(4)]) 0183 0184 dy = FS(10)*1.2; y0 = floor(AxPos(4)) -dy; y = y0; 0185 0186 text(-0.03,y0,TTitle,'FontSize',FS(14),'FontWeight','bold'); 0187 y = y0 - FS(14); 0188 0189 %-Loop over lines of text 0190 %------------------------ 0191 for i = 1:prod(size(S)) 0192 d = S{i}; 0193 0194 %-For some reason, '|' characters cause a CR. 0195 d = strrep(d,'|','I'); 0196 h = text(0,y,d,'FontName',PF.courier,'FontSize',FS(10)); 0197 y = y - dy; 0198 end 0199 0200 %======================================================================= 0201 case 'spm_version' % Robust get for SPM version string 0202 %======================================================================= 0203 % The problem we are trying to solve here is how to take account of the 0204 % unusual situation of the spm.m file _not_ being in the same directory 0205 % as the Contents.m file. SPM8 raises an error, SPM5 and probably 0206 % previous just returns 'SPM'. We raise an error always. 0207 0208 try 0209 ver = spm('ver'); 0210 catch 0211 err = lasterr; 0212 if strcmp('Undefined', err(1:length('Undefined'))) 0213 error('Marsbar needs SPM on the matlab path') 0214 end 0215 error(lasterr) 0216 end 0217 % If version find failed, for SPM5, routine returns 'SPM' 0218 str = ['Can''t obtain SPM Revision information. Is spm.m in the same' ... 0219 ' directory as Contents.m?']; 0220 if strcmp(ver, 'SPM') 0221 error(str) 0222 end 0223 varargout = {ver}; 0224 0225 %======================================================================= 0226 case 'is_swapped_wrong' % Returns 1 for if vol is incorrectly swapped 0227 %======================================================================= 0228 warning(... 0229 sprintf(['mars_utils version of ''is_swapped_wrong'' deprecated\n',... 0230 'Please use same function in mars_vol_utils'])); 0231 varargout = {mars_vol_utils(varargin{:})}; 0232 0233 %======================================================================= 0234 case 'version_less_than' % Returns 1 for if first version less than last 0235 %======================================================================= 0236 0237 if nargin < 3 0238 error('Need two version strings to compare'); 0239 end 0240 varargout{1} = sf_ver_lt(varargin{2:3}); 0241 0242 otherwise 0243 error([Action ' is too strange']); 0244 end 0245 return 0246 0247 % Subfunctions 0248 0249 function tf = sf_ver_lt(v1, v2) 0250 % Returns 1 if version string v1 is lower than v2 0251 vs = {v1, v2}; 0252 for v = 1:2 0253 ns = vs{v}; 0254 if ~ischar(ns), ns = num2str(ns); end 0255 ns = sf_str_to_nums(ns); 0256 cmp_mat(v, 1:length(ns)) = ns; 0257 end 0258 dp = diff(cmp_mat) * -1; 0259 for i = 1:length(dp) 0260 if dp(i)<0, tf = 1; return, end 0261 if dp(i)>0, tf = 0; return, end 0262 end 0263 tf = 0; 0264 return 0265 0266 function ns = sf_str_to_nums(str) 0267 str = str(ismember(str, '0123456789.')); 0268 str = ['.' str '.']; 0269 ps = find(str == '.'); 0270 ns = []; 0271 for p = 2:length(ps) 0272 s = str(ps(p-1)+1:ps(p)-1); 0273 ns = [ns str2num(s)]; 0274 end 0275 return