Description of phiw

0001 function [phiw, msgstr] = phiw_options(optstr, phiw, cfg_fname)
0002 % options utility routines for phiwave
0003 % FORMAT [phiw msgstr] = phiw_options(optstr, phiw, cfg_fname)
0004 %
0005 % Input [default]
0006 % optstr            - option string: one of
0007 %                     'load' - load options from file
0008 %                     'save' - save options to file
0009 %                     'edit' - GUI interface to edit options
0010 %                     'basedefaults' - return hardcoded factory defaults
0011 %                     'defaults' - return values from default config
0012 %                        file, or hardcoded defaults, if not present
0013 %                     'fill' - fill candidate options from passed new
0014 %                        structure
0015 %                     [Default optstr is 'load']
0016 % phiw              - phiwave options structure [PHI.OPTIONS]
0017 % cfg_fname         - filename for configuration file [GUI]
0018 %
0019 % Output
0020 % phiw              - possible modified phiwave structure
0021 % msgstr            - any relevant messages
0022 %
0023 % $Id: phiw_options.m,v 1.12 2005/06/21 15:19:22 matthewbrett Exp $
0024   
0025 if nargin < 1
0026   optstr = 'load';
0027 end
0028 if nargin < 2
0029   phiw = [];
0030 end
0031 if nargin < 3
0032   cfg_fname = '';
0033 end
0034 if isempty(phiw)
0035   phiw = mars_struct('getifthere', spm('getglobal','PHI'), 'OPTIONS');
0036 end
0037 msgstr = '';
0038 
0039 % fields, and descriptions of fields, in phiw options structure
0040 optfields = {'wt','denoise','structural','display','statistics'}; 
0041 optlabs =  {'Wavelet transform','Denoising','Default structural', ...
0042         'Image display','Statistics'};
0043 
0044 switch lower(optstr)
0045  
0046  % --------------------------------------------------
0047  case 'load'
0048   if isempty(cfg_fname)
0049     [fn, fn2] = phiwave('cfgfile');
0050     if isempty(fn), fn=fn2;end
0051     [p f e] = fileparts(fn);
0052     cfg_fname = spm_get([0 1],[f e], 'Configuration file to load',p);
0053   end
0054   if ~isempty(cfg_fname)
0055     tmp = load(cfg_fname);
0056     if ~isempty(tmp)
0057       if isfield(tmp, 'phiw')
0058     phiw = mars_struct('fillafromb', tmp.phiw, phiw);
0059       end
0060     end
0061   end
0062  
0063   % --------------------------------------------------
0064  case 'save'
0065   if nargin < 3
0066     [fn, fn2] = phiwave('cfgfile');
0067     if isempty(fn), fn=fn2;end
0068     [f p] = uiputfile(fn, 'Configuration file to save');
0069     cfg_fname = fullfile(p, f);
0070   end
0071   if ~isempty(cfg_fname)
0072     try
0073       save(cfg_fname, 'phiw');
0074     catch
0075       warning(['Error saving config to file ' cfg_fname])
0076     end
0077   end
0078   
0079   % --------------------------------------------------
0080  case 'basedefaults'
0081   % hardcoded defaults
0082 
0083   % scales for wavelet image transform
0084   phiw.wt.scales = 4;
0085 
0086   % wavelet
0087   phiw.wt.wavelet = phiw_lemarie(2);
0088   
0089   % wavelet transformed file prefix
0090   phiw.wt.wtprefix = 'wv_';
0091   
0092   % threshold for statistics mask post wt
0093   phiw.statistics.maskthresh = 0.05;
0094   
0095   % whether to write residual images during estimation
0096   phiw.statistics.write_res = 1;
0097   
0098   % wavelet denoising unit
0099   phiw.denoise.thlev = 'quadrant';
0100   
0101   % wavelet denoising type
0102   phiw.denoise.thcalc = 'stein';
0103   
0104   % form of wavelet denoising
0105   phiw.denoise.thapp = 'linear';
0106   
0107   % null hypothesis calculation
0108   phiw.denoise.ncalc = 'n';
0109   
0110   % alpha for t etc Bonferroni etc correction
0111   phiw.denoise.alpha = 0.05;
0112   
0113   % whether to supress variance images from denoising
0114   phiw.denoise.write_err = 0;
0115   
0116   % default structural image for display
0117   phiw.structural.fname = fullfile(spm('Dir'), 'canonical', ...
0118                    ['avg152T1' mars_veropts('template_ext')]);
0119   
0120   % range for structural (empty means set from image range)
0121   phiw.structural.range = [];
0122   
0123   % name of default activation colormap for display routines
0124   phiw.display.cmapname = 'flow.lut';
0125   
0126   % proportion of displayed color intensity for activation image
0127   phiw.display.actprop = 0.5;
0128   
0129   % transform for slice display routine
0130   phiw.display.transform = 'axial';
0131   
0132   % default slices to display (mm)
0133   phiw.display.slices = -60:6:78;
0134 
0135   % --------------------------------------------------
0136  case 'edit'
0137   
0138   % Edit defaults.  See 'basedefaults' option for other defaults
0139   defarea = cfg_fname;  % third arg is defaults area, if specified
0140   if isempty(defarea)
0141     % get defaults area
0142     [Finter,Fgraph,CmdLine] = spm('FnUIsetup','Phiwave Defaults');
0143     % fields, and descriptions of fields, in phiw options structure
0144     optfields = {'wt','statistics', 'denoise','structural','display'}; 
0145     optlabs =  {'Wavelet transform', 'Statistics', 'Denoising', ...
0146         'Default structural', 'Image display'};
0147         
0148     defarea = char(...
0149       spm_input('Defaults area', '+1', 'm',{optlabs{:} 'Quit'},...
0150         {optfields{:} 'quit'},length(optfields)+1));
0151   end
0152   
0153   oldphiw = phiw;
0154   switch defarea
0155    case 'quit'
0156     return
0157    case 'wt'
0158     % scales for analysis
0159     phiw.wt.scales = spm_input('Scales for analysis',  ...
0160                    '+1', 'e', phiw.wt.scales, ...
0161                    1);
0162     
0163     % wavelet transform
0164     wlabs =  {'Battle-Lemarie', 'Daubechies'};
0165     wtypes = {'phiw_lemarie', 'phiw_daub'};
0166     tmp = oldphiw.wt;
0167     tmp.wavelet = class(tmp.wavelet);
0168     phiw.wt = getdefs(...
0169     phiw.wt,...
0170     tmp,...
0171     'wavelet',...
0172     'Wavelet',...
0173     wtypes,...
0174     wlabs);
0175     switch phiw.wt.wavelet
0176      case 'phiw_lemarie'
0177       wv = phiw_lemarie;
0178       d_d = spm_input('Divisor for image width', '+1', 'e', 2);
0179       wv = dim_div(wv, d_d);
0180      case 'phiw_daub'
0181       wv = phiw_daub;
0182       n_c = spm_input('Number of coefficients', '+1', 'e', 4);
0183       wv = num_coeffs(wv, n_c);
0184     end
0185     phiw.wt.wavelet = wv;
0186 
0187     % wavelet transform prefix
0188     phiw.wt.wtprefix = spm_input('WT image prefix', '+1', 's', ...
0189                   phiw.wt.wtprefix);
0190      
0191     
0192 
0193    case 'statistics'
0194     % statistics / estimation defaults
0195     
0196     % In-brain mask definition threshold for WT brain mask
0197     phiw.statistics.maskthresh = spm_input('Threshold for WT brain mask', '+1', ...
0198                        'e', ...
0199                        phiw.statistics.maskthresh, ...
0200                        1);
0201     
0202 
0203     % Whether to write out residual images
0204     phiw.statistics.write_res = spm_input('Write residual images?', '+1', ...
0205                       'b', 'Yes|No', [1 0], ...
0206                       2 - phiw.statistics.write_res*-1);
0207 
0208    case 'denoise'
0209     % denoising defaults
0210 
0211     % denoising threshold calculation
0212     phiw.denoise = getdefs(...
0213     phiw.denoise,...
0214     oldphiw.denoise,...
0215     'thcalc',...
0216     'Threshold calculation',...
0217     {'visu','sure','stein','bonf','fdr','hoch'},...
0218     ['MinMax|SURE|Stein|Bonferroni|FDR|Hoch']); ...
0219        
0220     % denoising block level
0221     phiw.denoise = getdefs(...
0222     phiw.denoise,...
0223     oldphiw.denoise,...
0224     'thlev',...
0225     'Threshold level',...
0226     {'image','level','quadrant'},...
0227     ['Image|Level|Quadrant']);
0228     
0229        
0230     % denoising threshold application
0231     if strmatch('sure', phiw.denoise.thcalc)
0232       phiw.denoise.thapp = 'soft';
0233     else
0234       vals = {'soft','hard'};
0235       labs = 'Soft|Hard';
0236       if strcmp(phiw.denoise.thcalc, 'stein')
0237     vals = {vals{:},'linear'};
0238     labs = [labs '|Linear'];
0239       end
0240       phiw.denoise = getdefs(...
0241       phiw.denoise,...
0242       oldphiw.denoise,...
0243       'thapp',...
0244       'Thresholding method',...
0245       vals,...
0246       labs);
0247     end
0248 
0249     % p value thresholding methods
0250     if any(strcmp(phiw.denoise.thcalc,...
0251        {'bonf','hoch','fdr'}))
0252       
0253       % denoising null hypothesis calculation
0254       phiw.denoise = getdefs(...
0255       phiw.denoise,...
0256       oldphiw.denoise,...
0257       'ncalc',...
0258       'Estimate of Ho coefficient no',...
0259       {'n','pplot'},...
0260       ['Raw no|PPlot']);
0261       
0262       % alpha for t etc Bonferroni correction
0263       phiw.denoise.alpha = spm_input('Alpha level', '+1', 'r', ...
0264                  phiw.denoise.alpha,1,[0 1]);
0265     else
0266       phiw.denoise.ncalc = 'n';
0267     end
0268 
0269     % Whether to write out variance image from denoising
0270     phiw.denoise.write_err = spm_input('Write denoised variance?', '+1', ...
0271                        'b', 'Yes|No', [1 0], ...
0272                        2 - phiw.denoise.write_err*-1);
0273     
0274     % display stuff - default structural scan
0275    case 'structural'
0276     phiw.structural.fname = spm_get(1, mars_veropts('get_img_ext'),...
0277                     'Default structural image', ...
0278                     fileparts(phiw.structural.fname));
0279     
0280     % intensity range for structural
0281     [mx mn] = slover('volmaxmin', spm_vol(phiw.structural.fname));
0282     phiw.structural.range = spm_input('Img range for structural','+1', ...
0283                       'e', [mn mx], 2);
0284     
0285     % display stuff - color overlays
0286    case 'display'
0287      % name of colormap for display routines
0288      cmap = [];
0289      ypos = spm_input('!NextPos');
0290      while isempty(cmap)
0291        cmapname = spm_input('Name of activation colormap', ypos,'s', ...
0292                 phiw.display.cmapname);
0293        [cmap str] = slover('getcmap', cmapname);
0294        if isempty(cmap)
0295      disp(str);
0296        end
0297      end
0298      phiw.display.cmapname = cmapname;
0299      
0300      % proportion of displayed color intensity for activation image
0301      phiw.display.actprop = spm_input('Activation colour intensity', '+1', 'r', ...
0302                   phiw.display.actprop,1,[0 1]);
0303      
0304      phiw.display.transform = lower(spm_input('Image orientation', '+1','b',...
0305                       ['Axial|Coronal|Sagittal'], [],1));
0306      ypos = spm_input('!NextPos'); sflg = 0;
0307      while ~sflg
0308        sflg=1;
0309        slstr = spm_input('Slices to display (mm)', ypos, 's', ...
0310              sprintf('%0.0f:%0.0f:%0.0f',...
0311                  min(phiw.display.slices),...
0312                  mean(diff(phiw.display.slices)),...
0313                  max(phiw.display.slices)));
0314        eval(['phiw.display.slices = ' slstr ';'], 'sflg=0;');
0315      end
0316 
0317      % statistics - not currently used
0318    case 'statistics'
0319      phiw.statistics.maskthresh = spm_input('WT mask threshold', '+1', 'r', ...
0320                   phiw.statistics.maskthresh,1,[0 1]);
0321      
0322    otherwise 
0323     error('Unknown defaults area')
0324   end
0325 
0326   % Offer a rollback
0327   if spm_input('Accept these settings', '+1', 'b','Yes|No',[0 1],1)
0328     phiw = oldphiw;
0329   end
0330   
0331   % --------------------------------------------------
0332  case 'defaults'                             %-get phiwave defaults
0333   pwdefs = [];
0334   msgstr = 'base defaults';
0335   cfgfile = phiwave('cfgfile');
0336   if ~isempty(cfgfile);
0337     tmp = load(cfgfile);
0338     if isfield(tmp, 'phiw')
0339       pwdefs = tmp.phiw;
0340       msgstr = cfgfile;
0341     else
0342       warning(...
0343       ['File ' cfgfile ' does not contain valid config settings'],...
0344       'Did not load phiwave config file');
0345     end
0346   end
0347   phiw = mars_struct('fillafromb', ...
0348              pwdefs, phiw_options('basedefaults'));
0349   
0350    % --------------------------------------------------
0351  case 'fill'                             %-fill from template
0352   phiw = mars_struct('fillafromb', phiw, cfg_fname);
0353   
0354  otherwise
0355   error('Don''t recognize options action string')
0356 end
0357 return
0358 
0359 % ---------------------------------------------
0360 % Subfunctions
0361 % ---------------------------------------------
0362 
0363 function s = getdefs(s, defval, fieldn, prompt, vals, labels)
0364 % sets field in structure given values, labels, etc
0365     
0366 if isstruct(defval)
0367   defval = getfield(defval, fieldn);  
0368 end
0369 
0370 if ischar(defval)
0371   defind = find(strcmp(defval,vals));
0372 else
0373   defind = find(defval == vals);
0374 end
0375 
0376 v = spm_input(prompt, '+1', 'm', labels, vals, defind);
0377 if iscell(v) & ischar(defval)
0378   v = char(v);
0379 end
0380   
0381 s = setfield(s,fieldn,v);
0382 
0383 return
phiw_options

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SUBFUNCTIONS

SOURCE CODE
