function job = spm_rewrite_job(job)
% Rewrite a batch job for SPM12
%__________________________________________________________________________
% Copyright (C) 2012-2017 Wellcome Trust Centre for Neuroimaging

% $Id: spm_rewrite_job.m 7063 2017-04-19 10:49:44Z guillaume $


try
    job.spatial.preproc.data;
    fprintf('Conversion Segment -> Old Segment\n');                     %-#
    job = struct('tools', struct('oldseg', job.spatial.preproc));
    if ~spm_existfile(spm_file(job.tools.oldseg.opts.tpm{1},'number',''))
        fprintf('You might have to manually update the tissue probability maps in Old Segment to:\n');
        TPM = spm_get_defaults('old.preproc.tpm');
        fprintf('    %s\n',TPM{:});
    end
end

try
    job.spatial.normalise.est.subj(1).source ;
    fprintf('Conversion Normalise:Est -> Old Normalise:Est\n');         %-#
    job = struct('tools', struct('oldnorm', job.spatial.normalise));
    if ~spm_existfile(spm_file(job.tools.oldnorm.est.eoptions.template{1},'number',''))
        fprintf('You might have to manually update the template image in Old Normalise:Est.\n');
    end
end

try
    job.spatial.normalise.write.subj(1).matname;
    fprintf('Conversion Normalise:Write -> Old Normalise:Write\n');     %-#
    job = struct('tools', struct('oldnorm', job.spatial.normalise));
end

try
    job.spatial.normalise.estwrite.subj(1).source;
    fprintf('Conversion Normalise:EstWrite -> Old Normalise:EstWrite\n');%-#
    job = struct('tools', struct('oldnorm', job.spatial.normalise));
    if ~spm_existfile(spm_file(job.tools.oldnorm.estwrite.eoptions.template{1},'number',''))
        fprintf('You might have to manually update the template image in Old Normalise:EstWrite.\n');
    end
end

try
    job.tools.preproc8;
    fprintf('Conversion Tools:New Segment -> Spatial:Segment\n');       %-#
    job = struct('spatial',struct('preproc',job.tools.preproc8));
    if ~spm_existfile(spm_file(job.spatial.preproc.tissue(1).tpm{1},'number',''))
        fprintf('You might have to manually update the tissue probability maps in Segment to:\n');
        fprintf('    %s\n',fullfile(spm('dir'),'tpm','TPM.nii'));
    end
    if numel(job.spatial.preproc.warp.reg) == 1
        job.spatial.preproc.warp = rmfield(job.spatial.preproc.warp,'reg');
    end
end

try
    for i=1:numel(job.stats.con.consess)
        try
            con = job.stats.con.consess{i}.tcon.convec;
            job.stats.con.consess{i}.tcon = rmfield(job.stats.con.consess{i}.tcon,'convec');
            job.stats.con.consess{i}.tcon.weights = con;
        end
        try
            con = job.stats.con.consess{i}.fcon.convec;
            job.stats.con.consess{i}.fcon = rmfield(job.stats.con.consess{i}.fcon,'convec');
            job.stats.con.consess{i}.fcon.weights = con;
        end
        try
            job.stats.con.consess{i}.fcon.weights{1};
            fprintf('Conversion to new syntax: Contrast Manager:F-contrast\n'); %-#
            try
                con = cat(1,job.stats.con.consess{i}.fcon.weights{:});
            catch
                fprintf('Error concatenating F-contrast vectors.\n');   %-#
            end
            job.stats.con.consess{i}.fcon.weights = con;
        end
    end
end

try
    if isequal(job.stats.results.print, false) || isequal(job.stats.results.print, 'no')
        job.stats.results.export = {};
        job.stats.results = rmfield(job.stats.results,'print');
    end
    if isequal(job.stats.results.print, true) || isequal(job.stats.results.print, 'yes')
        job.stats.results.print = spm_get_defaults('ui.print');
    end
    try, N = numel(job.stats.results.export)+1; catch, N = 1; end
    if strcmp(job.stats.results.print,'nidm')
        job.stats.results.export{N}.nidm = struct;
    else
        job.stats.results.export{N}.(job.stats.results.print) = true;
    end
    job.stats.results = rmfield(job.stats.results,'print');
end
try
    fn = char(fieldnames(job.stats.results.write));
    if ismember(fn,{'tspm','binary','nary'})
        try, N = numel(job.stats.results.export)+1; catch, N = 1; end
        job.stats.results.export{N}.(fn) = job.stats.results.write.(fn);
    end
    job.stats.results = rmfield(job.stats.results,'write');
end

try
    job.stats.results.conspec(1).mask.thresh;
    for i=1:numel(job.stats.results.conspec)
        if isempty(job.stats.results.conspec(i).mask)
            job.stats.results.conspec(i).mask = struct('none',1);
        else
            job.stats.results.conspec(i).mask = struct('contrast',job.stats.results.conspec(i).mask);
        end
    end
end

try
    D = job.dcm.fmri;
    job.dcm.spec.fmri = D;    
    job.dcm = rmfield(job.dcm,'fmri');
end

try
    D = job.dcm.meeg;
    job.dcm.spec.meeg = D;
    job.dcm = rmfield(job.dcm,'meeg');
end

try
    D = job.dcm.spec.fmri.estimate.dcmmat;
    for i=1:numel(D)
        job.dcm.estimate.dcms.subj(i).dcmmat = cellstr(D(i));
    end
    job.dcm.estimate.output.separate = struct([]);
    job.dcm.estimate.est_type = 3;  
    if isfield(job.dcm.spec.fmri,'estimate') && isfield(job.dcm.spec.fmri.estimate,'analysis')
        job.dcm.estimate.fmri.analysis = job.dcm.fmri.estimate.analysis;
    end
    
    % Prune
    job.dcm.spec.fmri = rmfield(job.dcm.spec.fmri,'estimate');
    if isempty(fieldnames(job.dcm.spec.fmri))
        job.dcm.spec = rmfield(job.dcm.spec,'fmri');
    end
    if isempty(fieldnames(job.dcm.spec))
        job.dcm = rmfield(job.dcm,'spec');
    end
end

try
    job.stats.bms.bms_dcm;
    job = struct('dcm',struct('bms',struct('inference',job.stats.bms.bms_dcm)));
    for i=1:numel(job.dcm.bms.inference.sess_dcm)
        job.dcm.bms.inference.sess_dcm{i}.dcmmat = job.dcm.bms.inference.sess_dcm{i}.mod_dcm;
        job.dcm.bms.inference.sess_dcm{i} = rmfield(job.dcm.bms.inference.sess_dcm{i},'mod_dcm');
    end
end

try
    job.tools.sendmail;
    job = struct('util', job.tools);
end

try
    job.util.spm_surf;
    job = struct('util', struct('render', struct('extract',job.util.spm_surf)));
end

try
    job.util.dicom;
    job.util = struct('import', job.util);
end
try
    job.util.minc;
    job.util = struct('import', job.util);
end
try
    job.util.ecat;
    job.util = struct('import', job.util);
end

try
    job.tools.fieldmap;
    opts = {'presubphasemag','realimag','phasemag','precalcfieldmap'};
    imgs{1} = {'phase','magnitude'};
    imgs{2} = {'shortreal','shortimag','longreal','longimag'};
    imgs{3} = {'shortphase','shortmag','longphase','longmag'};
    imgs{4} = {'precalcfieldmap','magfieldmap'};
    for j=1:numel(opts)
        try
            job.tools.fieldmap.(opts{j});
            job.tools.fieldmap = struct('calculatevdm',job.tools.fieldmap.(opts{j}));
            for i=1:numel(job.tools.fieldmap.calculatevdm.subj)
                for k=1:numel(imgs{j})
                    job.tools.fieldmap.calculatevdm.subj(i).data.(opts{j}).(imgs{j}{k}) = job.tools.fieldmap.calculatevdm.subj(i).(imgs{j}{k});
                end
            end
            job.tools.fieldmap.calculatevdm.subj = rmfield(job.tools.fieldmap.calculatevdm.subj,imgs{j});
        end
    end
end

try
    if numel(job.tools.longit) > 1
        ws = warning('off','backtrace');
        warning('Only converting first item of the "Longitudinal Registration" module.');
        warning(ws);
    end
    job.tools.longit = job.tools.longit{1};
end

try
    util = char(fieldnames(job.util));
    if ismember(util, {'cdir','md','deletefiles','movefile'})
        ws = warning('off','backtrace');
        warning(['spm.util.%s was DEPRECATED in SPM8 and has now been REMOVED.\n' ...
            'Please update your batches to use BasicIO instead.'],util);
        warning(ws);
        %job = struct([]);
    end
end