add marsbar dependency

Author: Remi-Gau

lib/marsbar-0.44/@mardo/add_contrasts.m

@@ -0,0 +1,172 @@
+function [D,Ic,changef] = add_contrasts(D, C, varargin)
+% method to add contrast definitions to design
+%
+% The function has many different formats
+%
+% FORMAT [D Ic changef] = add_contrasts(D, D2 [,Ic])
+%
+% where D2 is a design. If there is no third argument, all the contrasts in
+% D2 will be added.  If third argument (Ic) is passed, specifies which
+% contrasts in D2 to add. If Ic passed, and empty, or contains the string
+% 'ui', contrasts to add are fetched using the GUI
+%
+% OR
+% FORMAT [D Ic changef] = add_contrasts(D, xCon)
+%
+% where xCon is a structure in SPM contrast format containing contrasts to
+% add.  If there is no third argument, all the contrasts in xCon will be
+% added.  If third argument (Ic) is passed, specifies which contrasts in xCon
+% to add. If Ic passed, and empty, or contains the string 'ui', contrasts to
+% add are fetched using the GUI
+%
+% OR
+% FORMAT [D Ic changef] = add_contrasts(D, stat_struct)
+% where stat_struct has fields
+%      'names',       string, or cell array of strings
+%      'types',       string ('T' or 'F'), or cell array
+%      'set_actions', string ('c', 'X0' or 'iX0') or array
+%                     (see spm_FcUtil)
+%                     (field is optional, defaults to 'c')
+%      'values',      matrix of values
+%
+% OR
+% FORMAT [D Ic changef] = add_contrasts(D, names, types, values)
+% where names, types, values are cell arrays of values, or values
+% (defined as above)
+%
+% OR
+% FORMAT [D Ic  changef] = add_contrasts(D, names, types, set_actions, values)
+% where names, types, set_actions, values are cell arrays of values, or
+% values (defined as above)
+%
+% Returns
+% D       - possibly modified SPM design
+% Ic      - indices of specified contrasts as stored in D
+% changef - 1 if D has changed during call else 0
+%
+% Contrast will not be added if it is already present, but the correct
+% index will be returned in Ic
+%
+% $Id$
+
+if nargin < 2
+  error('Need contrasts to add');
+end
+
+% Get parameters from current design
+SPM  = des_struct(D);
+sX   = SPM.xX.xKXs;
+xCon = SPM.xCon;
+v_f  = verbose(D);
+
+% process inputs
+% The ``C`` variable will hold the xCon structure for the contrasts to add
+if isa(C, 'mardo')        % design
+  C = des_struct(C);
+end
+if isfield(C, 'xCon')     % design structure
+  C = C.xCon;
+end
+if isfield(C, 'STAT')     % xCon structure
+  % parse Ic input
+  if nargin > 2 % There is Ic input
+    Ic_in = varargin{1};
+    if isempty(Ic_in) | strcmp(Ic_in,'ui')
+      D2 = set_contrasts(D, C, 0);
+      Ic_in = ui_get_contrasts(D2,'T&F',Inf,...
+        'Select contrasts to merge','',1);
+    end
+    C = C(Ic_in);
+  end
+else % contrast setting structure or values or cells
+  if ~isstruct(C) % make stat_struct structure if not already passed
+    C = sf_cell_to_conset(C, varargin{:});
+  end
+  % make xCon structure from stat_struct
+  C = sf_conset_to_xcon(C, sX);
+end
+% Initial xCon before adding new contrasts
+xc_len = length(xCon);
+old_xc_len = xc_len;
+% C contains the contrasts to add
+for i=1:length(C)
+  % Update this contrast using our own filtered design
+  c_i  = refresh_con(C(i), sX);
+  if xc_len == 0 % the xCon to add to is empty
+    xCon = c_i;
+    xc_len = 1;
+    Ic(1) = 1;
+    continue
+  end
+  % Check if we have this contrast already
+  Ic(i) = spm_FcUtil('In', c_i, sX, xCon);
+  if Ic(i) == 0
+    xc_len = xc_len+1;
+    xCon(xc_len) = c_i;
+    Ic(i) = xc_len;
+  elseif v_f
+    fprintf('\nContrast %s (type %s) already in xCon\n', ...
+            c_i.name, c_i.STAT);
+  end
+end
+changef =  xc_len ~= old_xc_len;
+if changef
+  SPM.xCon = xCon;
+  D = des_struct(D, SPM);
+end
+return
+
+function xcon_re_entry = refresh_con(xcon_entry, sX)
+% Rebuild contrast structure from our own filtered design
+if isempty(xcon_entry.c)
+    error('Empty c matrix for contrast, crashing because confused')
+end
+xcon_re_entry = spm_FcUtil('Set',...
+        xcon_entry.name,...
+        xcon_entry.STAT,...
+        'c',...
+        xcon_entry.c,...
+        sX);
+
+function C = sf_cell_to_conset(names, types, varargin)
+% makes contrast setting structure from cell input
+if nargin < 3
+  error('Need at least names, statistic types and values');
+end
+C = struct(...
+    'names', names,...
+    'types', types);
+if nargin < 4 % values call
+  values = varargin{1};
+  set_actions = 'c';
+else % contrast types, values call
+  set_actions = deal(varargin{1});
+  values      = deal(varargin{2});
+end
+C = struct(...
+    'names', names,...
+    'types', types,...
+    'set_actions', set_actions,...
+    'values', values);
+return
+
+function C = sf_conset_to_xcon(con_set, sX)
+% make xCon structure from cell or struct setting parameters
+if ~isfield(con_set, 'set_actions')
+  [con_set.set_actions] = deal('c');
+end
+n_e = size(sX.X, 2);
+for c = 1:length(con_set)
+  c1 = con_set(c);
+  if size(c1.values, 1) ~= n_e & ...
+      size(c1.values, 2) == n_e
+      c1.values = c1.values';
+  end
+  C(c) = spm_FcUtil('Set',...
+    c1.names,...
+    c1.types,...
+    c1.set_actions,...
+    c1.values,...
+    sX);
+end
+return

lib/marsbar-0.44/@mardo/adjusted_data.m

@@ -0,0 +1,33 @@
+function Ya = adjusted_data(D, Ic)
+% Return adjusted data for estimated design and contrast no
+% FORMAT Ya = adjusted_data(D, Ic)
+% 
+% D      - Estimated marsbar design
+% Ic     - Contrast number to adjust for
+% 
+% Outputs
+% Ya     - Adjusted data, N by M, where N is number of time points
+%          and M is number of regions in estimated marsbar design
+% 
+% e.g
+% E = estimate(D, Y);
+% [E Ic] = add_contrasts(E, 'task', 'T', [1 0 0]);
+% Ya = adjusted_data(E, Ic);
+% 
+% Matthew Brett
+
+if nargin < 2
+  error('Need contrast number');
+end
+if nargin < 3
+  r_no = 1;
+end
+Ya = [];
+if ~is_mars_estimated(D)
+  error('Need a MarsBaR estimated design');
+end
+
+SPM   = des_struct(D);
+B = betas(D);
+xCon = get_contrasts(D);
+Ya = spm_FcUtil('Yc', xCon(Ic),SPM.xX.xKXs, B);

lib/marsbar-0.44/@mardo/betas.m

@@ -0,0 +1,10 @@
+function r = betas(o)
+% method to get estimated betas
+% 
+% $Id$
+
+if ~is_mars_estimated(o)
+  error('No betas, model not estimated');
+end
+SPM = des_struct(o);
+r   = SPM.betas;

lib/marsbar-0.44/@mardo/block_mean_cols.m

@@ -0,0 +1,9 @@
+function bmrs = block_mean_rows(D)
+% method returns rows for means for blocks in design
+% 
+% $Id$
+
+bmrs = [];
+SPM =  des_struct(D);
+bmrs = SPM.xX.iB;   
+  

lib/marsbar-0.44/@mardo/block_means.m

@@ -0,0 +1,20 @@
+function bms = block_means(D)
+% method returns means for blocks in design
+% 
+% Inputs
+% D        - design object
+%
+% Outputs
+% bms      - means over block.  Returns B x N matrix
+%            where B is number of blocks, and N is number
+%            of ROIs 
+%
+% $Id$
+
+Y = data(D);
+if isempty(Y)
+  error('Design does not yet have data');
+end
+bms = summary_block_means(data(D));
+
+

lib/marsbar-0.44/@mardo/cd_images.m

@@ -0,0 +1,63 @@
+function D = cd_images(D, newpath, byteswap)
+% method for changing path to image files in design
+% FORMAT D = cd_images(D, newpath [, byteswap])
+%
+% Synopsis
+% D = cd_images(D); % get new path from GUI
+% D = cd_images(D, '/new/root/path'); 
+% D = cd_images(D, '/new/root/path', 1); % force byteswap
+% D = cd_images(D, '/new/root/path', 1); % prevent byteswap  
+%  
+% D          - mardo design
+% newpath    - path to replace common path of files in analysis [GUI]
+% byteswap   - whether to indicate byte swapping in vol structs 
+%              [determined from images by default]
+%             
+% $Id$
+  
+if nargin < 2
+  newpath = spm_get(-1, '', 'New directory root for files');
+end
+if nargin < 3
+  byteswap=[];
+end
+
+% get images
+if ~has_images(D)
+  warning('Design does not contain images');
+  return
+end
+VY = get_images(D);
+
+% now change directory
+newpath = spm_get('cpath', newpath);
+if filesep == '\', other_filesep='/';else other_filesep='\';end
+n = length(VY);
+strout = strvcat(VY(:).fname);
+msk    = diff(strout+0)~=0; % common path
+d1     = min(find(sum(msk,1))); 
+d1     = max([find(strout(1,1:d1) == other_filesep | strout(1,1:d1) == filesep) 0]);
+ffnames = strout(:,d1+1:end); % common path removed
+tmp = ffnames == other_filesep; % filesep exchanged for this platform
+ffnames(tmp) = filesep;
+nfnames = cellstr(...
+    strcat(repmat(newpath,n,1),filesep,ffnames));
+[VY(:).fname] = deal(nfnames{:});
+
+% do the files exist here then?
+if ~exist(nfnames{1}, 'file')
+  error(['Cannot find first file here: ' nfnames{1}]);
+end
+if isempty(byteswap) 
+  byteswap = mars_vol_utils('is_swapped_wrong', VY(1));
+end
+
+% do byteswap as necessary
+if byteswap
+  VY = mars_vol_utils('byte_swap', VY);
+  if verbose(D)
+    disp('Images vols byteswapped');
+  end
+end    
+
+D = set_images(D, VY);

lib/marsbar-0.44/@mardo/contrasts.m

@@ -0,0 +1,11 @@
+function r = contrasts(o, xcon)
+% method to get or set contrasts
+% 
+% $Id$
+  
+if nargin < 2
+  r = get_contrasts(o);
+else
+  % Always refreshes the contrasts for safety
+  r = set_contrasts(o, xcon);
+end

lib/marsbar-0.44/@mardo/data.m

@@ -0,0 +1,10 @@
+function r = data(o, Y)
+% method to get or set data object 
+% 
+% $Id$
+  
+if nargin < 2
+  r = get_data(o);
+else
+  r = set_data(o, Y);
+end

lib/marsbar-0.44/@mardo/des_struct.m

@@ -0,0 +1,11 @@
+function res = des_struct(obj, Struct)
+% get/set method for des_struct field
+%
+% $Id$
+  
+if nargin > 1
+  obj.des_struct = Struct;
+  res = obj;
+else
+  res = obj.des_struct;
+end

lib/marsbar-0.44/@mardo/descrip.m

@@ -0,0 +1,11 @@
+function strs = descrip(D)
+% method gets cell string description of design
+%
+% $Id$ 
+  
+SPM = des_struct(D);
+strs = {'Not specified'};
+if ~isfield(SPM, 'xsDes');
+  return
+end
+strs = mars_struct('celldisp', SPM.xsDes);