function reorient = spm_cfg_reorient
% SPM Configuration file for Reorient Images
%__________________________________________________________________________
% Copyright (C) 2006-2015 Wellcome Trust Centre for Neuroimaging

% Volkmar Glauche
% $Id: spm_cfg_reorient.m 6952 2016-11-25 16:03:13Z guillaume $


%--------------------------------------------------------------------------
% srcfiles Images to reorient
%--------------------------------------------------------------------------
srcfiles         = cfg_files;
srcfiles.tag     = 'srcfiles';
srcfiles.name    = 'Images to reorient';
srcfiles.help    = {'Select images to reorient.'};
srcfiles.filter  = 'image';
srcfiles.ufilter = '.*';
srcfiles.num     = [0 Inf];

%--------------------------------------------------------------------------
% transF Reorientation File (e.g. as saved from spm_ov_reorient)
%--------------------------------------------------------------------------
transF         = cfg_files;
transF.tag     = 'transF';
transF.name    = 'Saved reorientation matrix';
transF.help    = {['Select mat file containing saved reorientation ' ...
    '(e.g. after using reorient from Display or Check Reg and saving ' ...
    'when prompted).']};
transF.filter  = 'mat';
transF.ufilter = 'reorient';
transF.num     = [1 1];

%--------------------------------------------------------------------------
% transM Reorientation Matrix
%--------------------------------------------------------------------------
transM         = cfg_entry;
transM.tag     = 'transM';
transM.name    = 'Reorientation Matrix';
transM.help    = {
                  'Enter a valid 4x4 matrix for reorientation.'
                  ''
                  'Example: This will L-R flip the images.'
                  ''
                  '   -1 0 0 0; 0 1 0 0; 0 0 1 0; 0 0 0 1'
}';
transM.strtype = 'r';
transM.num     = [4 4];

%--------------------------------------------------------------------------
% transprm Reorientation Parameters
%--------------------------------------------------------------------------
transprm         = cfg_entry;
transprm.tag     = 'transprm';
transprm.name    = 'Reorientation Parameters';
transprm.help    = {
                    'Enter 12 reorientation parameters.'
                    'P(1)  - x translation'
                    'P(2)  - y translation'
                    'P(3)  - z translation'
                    'P(4)  - x rotation about - {pitch} (radians)'
                    'P(5)  - y rotation about - {roll}  (radians)'
                    'P(6)  - z rotation about - {yaw}   (radians)'
                    'P(7)  - x scaling'
                    'P(8)  - y scaling'
                    'P(9)  - z scaling'
                    'P(10) - x affine'
                    'P(11) - y affine'
                    'P(12) - z affine'
                    'Parameters are entered as listed above and then processed by spm_matrix.'
                    ''
                    'Example: This will L-R flip the images (extra spaces are inserted between each group for illustration purposes).'
                    ''
                    '   0 0 0   0 0 0   -1 1 1   0 0 0'
                    ''
}';
transprm.strtype = 'r';
transprm.num     = [1 12];

%--------------------------------------------------------------------------
% transform Reorient by
%--------------------------------------------------------------------------
transform         = cfg_choice;
transform.tag     = 'transform';
transform.name    = 'Reorient by';
transform.val     = {transM};
transform.help    = {'Specify reorientation parameters - 12 parameters, a 4x4 transformation matrix or a saved mat file (containing the matrix). The resulting transformation will be left-multiplied to the voxel-to-world transformation of each image and the new transformation will be written to the image header.'};
transform.values  = {transM transprm transF};

%--------------------------------------------------------------------------
% prefix Filename Prefix
%--------------------------------------------------------------------------
prefix         = cfg_entry;
prefix.tag     = 'prefix';
prefix.name    = 'Filename Prefix';
prefix.help    = {['Specify the string to be prepended to the filenames ' ...
                   'of the reoriented image file(s). If this is left ' ...
                   'empty, the original files will be overwritten.']};
prefix.strtype = 's';
prefix.num     = [0 Inf];
% This should not be hardcoded here
prefix.val     = {''};
% Final solution: defaults setting
% prefix.def     = @(val)spm_get_defaults('reorient.prefix', val{:});
% The following 3 lines should go into spm_defaults.m
% % Reorient defaults
% %=======================================================================
% defaults.reorient.prefix = ''; % Output filename prefix ('' == overwrite)

%--------------------------------------------------------------------------
% reorient Reorient Images
%--------------------------------------------------------------------------
reorient      = cfg_exbranch;
reorient.tag  = 'reorient';
reorient.name = 'Reorient Images';
reorient.val  = {srcfiles transform prefix};
reorient.help = {
    'Reorient images given a set of parameters.'
    'The reorientation parameters can be given either as a 4x4 matrix or as parameters as defined for spm_matrix.m. The new image orientation will be computed by PRE-multiplying the original orientation matrix with the supplied matrix.'
    }';
reorient.prog = @spm_run_reorient;
reorient.vout = @vout;


%==========================================================================
function dep = vout(job)
dep            = cfg_dep;
dep.sname      = 'Reoriented Images';
dep.src_output = substruct('.','files');
dep.tgt_spec   = cfg_findspec({{'filter','image','strtype','e'}});