function write_v141(obj,filename,create_signature)
%WRITE Write sequence to file.
%   WRITE(seqObj, filename) Write the sequence data to the given
%   filename using the open file format for MR sequences.
%
%   Examples:
%   Write the sequence file to the my_sequences directory, relying on the
%   previous stable file format (v143).
%
%       write_v143(seqObj,'my_sequences/gre.seq')
%
% See also  write, read

if (nargin<3)
    create_signature=true;
end

fid=fopen(filename, 'w');
assert(fid ~= -1, 'Cannot open file: %s', filename);
fprintf(fid, '# Pulseq sequence file\n');
fprintf(fid, '# Created by MATLAB mr toolbox\n\n');

% we always write files in the default current version, which may be
% differen to one, loaded (and stored in the seq object)
[version_major, version_minor, version_revision]=mr.aux.version('output');
fprintf(fid, '[VERSION]\n');
fprintf(fid, 'major %s\n', num2str(1));
fprintf(fid, 'minor %s\n', num2str(4));
fprintf(fid, 'revision %s\n', num2str(1));
fprintf(fid, '\n');

if ~isempty(obj.definitions)
    fprintf(fid, '[DEFINITIONS]\n');
    keys = obj.definitions.keys;
    values = obj.definitions.values;
    for i=1:length(keys)
        fprintf(fid, '%s ', keys{i});
        if (ischar(values{i}))
            fprintf(fid, '%s ', values{i});
        else
            fprintf(fid, '%.9g ', values{i});
        end
        fprintf(fid, '\n');
    end
	fprintf(fid, '\n');
end

fprintf(fid, '# Format of blocks:\n');
fprintf(fid, '# NUM DUR RF  GX  GY  GZ  ADC  EXT\n');
fprintf(fid, '[BLOCKS]\n');
idFormatWidth = length(num2str(length(obj.blockEvents)));
idFormatStr = ['%' num2str(idFormatWidth) 'd'];
for i = 1:length(obj.blockEvents)
    %fprintf(fid,[idFormatStr ' %2d %2d %3d %3d %3d %2d 0\n'],[i obj.blockEvents(i,:)]);
    %fprintf(fid,[idFormatStr ' %2d %2d %3d %3d %3d %2d 0\n'],[i obj.blockEvents{i}]);
    bd=obj.blockDurations(i)/obj.blockDurationRaster;
    bdr=round(bd);
    assert(abs(bdr-bd)<1e-6); % this may still trigger false alarms for very long delays due to the limited accuracy of the double
    fprintf(fid,[idFormatStr ' %3d %3d %3d %3d %3d %2d %2d\n'], ...
            [i bdr obj.blockEvents{i}(2:end)]);
end
fprintf(fid, '\n');

if ~isempty(obj.rfLibrary.keys)
    fprintf(fid, '# Format of RF events:\n');
    fprintf(fid, '# id amplitude mag_id phase_id time_shape_id delay freq phase\n');
    fprintf(fid, '# ..        Hz   ....     ....          ....    us   Hz   rad\n');
    fprintf(fid, '[RF]\n');
    keys = obj.rfLibrary.keys;
    for k = keys
        libData1 = obj.rfLibrary.data(k).array(1:4);
        full_freqPhaseOffset=obj.rfLibrary.data(k).array(9:10)+obj.rfLibrary.data(k).array(7:8)*1e-6*obj.sys.gamma*obj.sys.B0;  % convert freqPPM and phasePPM to fixed offsets
        delay = round(obj.rfLibrary.data(k).array(6)/obj.rfRasterTime)*obj.rfRasterTime*1e6; % a bit of a hack: round the delay
        fprintf(fid, '%d %12g %d %d %d %g %g %g\n', [k libData1 delay full_freqPhaseOffset]);
    end
    fprintf(fid, '\n');
end

arbGradMask = obj.gradLibrary.type == 'g';
trapGradMask = obj.gradLibrary.type == 't';

if any(arbGradMask)
    fprintf(fid, '# Format of arbitrary gradients:\n');
    fprintf(fid, '#   time_shape_id of 0 means default timing (stepping with grad_raster starting at 1/2 of grad_raster)\n');
    fprintf(fid, '# id amplitude amp_shape_id time_shape_id delay\n'); % do we need delay ???
    fprintf(fid, '# ..      Hz/m       ..         ..          us\n');
    fprintf(fid, '[GRADIENTS]\n');
    keys = obj.gradLibrary.keys;
    for k = keys(arbGradMask)
        if obj.gradLibrary.data(k).array(5)<0
            error("Current sequence contains arbitrary gradients with oversampling, which are not compatible with the format 1.4.1");
        end
        fprintf(fid, '%d %12g %d %d %d\n', ...
                [k obj.gradLibrary.data(k).array([1 4 5]) ...
                 round(obj.gradLibrary.data(k).array(6)*1e6)]);
    end
    fprintf(fid, '\n');
end

if any(trapGradMask)
    fprintf(fid, '# Format of trapezoid gradients:\n');
    fprintf(fid, '# id amplitude rise flat fall delay\n');
    fprintf(fid, '# ..      Hz/m   us   us   us    us\n');
    fprintf(fid, '[TRAP]\n');
    keys = obj.gradLibrary.keys;
    for k = keys(trapGradMask)
        data = obj.gradLibrary.data(k).array;
        data(2:end) = round(1e6*data(2:end));
        fprintf(fid, '%2d %12g %3d %4d %3d %3d\n', [k data]);
    end
    fprintf(fid, '\n');
end

if ~isempty(obj.adcLibrary.keys)
    fprintf(fid, '# Format of ADC events:\n');
    fprintf(fid, '# id num dwell delay freq phase\n');
    fprintf(fid, '# ..  ..    ns    us   Hz   rad\n');
    fprintf(fid, '[ADC]\n');
    keys = obj.adcLibrary.keys;
    for k = keys
        data = [obj.adcLibrary.data(k).array(1:3) obj.adcLibrary.data(k).array(6:7)+obj.adcLibrary.data(k).array(4:5)*1e-6*obj.sys.gamma*obj.sys.B0].*[1 1e9 1e6 1 1]; % convert freqPPM and phasePPM to fixed offsets
        fprintf(fid, '%d %d %.0f %.0f %g %g\n', [k data]);
    end
    fprintf(fid, '\n');
end

%if ~isempty(obj.delayLibrary.keys)
%    fprintf(fid, '# Format of delays:\n');
%    fprintf(fid, '# id delay (us)\n');
%    fprintf(fid, '[DELAYS]\n');
%    keys = obj.delayLibrary.keys;
%    for k = keys
%        fprintf(fid, '%d %d\n', ...
%                [k round(1e6*obj.delayLibrary.data(k).array)]);
%    end
%    fprintf(fid, '\n');
%end

if ~isempty(obj.extensionLibrary.keys)
    fprintf(fid, '# Format of extension lists:\n');
    fprintf(fid, '# id type ref next_id\n');
    fprintf(fid, '# next_id of 0 terminates the list\n');
    fprintf(fid, '# Extension list is followed by extension specifications\n');
    fprintf(fid, '[EXTENSIONS]\n');
    keys = obj.extensionLibrary.keys;
    for k = keys
        fprintf(fid, '%d %d %d %d\n', ...
                [k round(obj.extensionLibrary.data(k).array)]);
    end
    fprintf(fid, '\n');
end

if ~isempty(obj.trigLibrary.keys)
    fprintf(fid, '# Extension specification for digital output and input triggers:\n');
    fprintf(fid, '# id type channel delay (us) duration (us)\n');
%     fprintf(fid, 'extension TRIGGERS 1\n'); % fixme: extension ID 1 is hardcoded here for triggers
    fprintf(fid, ['extension TRIGGERS ',num2str(obj.getExtensionTypeID('TRIGGERS')),'\n']);

    keys = obj.trigLibrary.keys;
    for k = keys
        fprintf(fid, '%d %d %d %d %d\n', ...
                [k round(obj.trigLibrary.data(k).array.*[1 1 1e6 1e6])]);
    end
    fprintf(fid, '\n');
end

if ~isempty(obj.labelsetLibrary.keys) || ~isempty(obj.labelincLibrary.keys)
    lbls=mr.getSupportedLabels();

    if ~isempty(obj.labelsetLibrary.keys)
       fprintf(fid, '# Extension specification for setting labels:\n');
        fprintf(fid, '# id set labelstring\n');
        tid=obj.getExtensionTypeID('LABELSET');
        fprintf(fid, ['extension LABELSET ',num2str(tid),'\n']);
        keys = obj.labelsetLibrary.keys;
        for k = keys
                fprintf(fid, '%d %d %s\n', ...
                    k, obj.labelsetLibrary.data(k).array(1),lbls{obj.labelsetLibrary.data(k).array(2)});
        end
        fprintf(fid, '\n');
    end
    if ~isempty(obj.labelincLibrary.keys)
        fprintf(fid, '# Extension specification for increasing labels:\n');
        fprintf(fid, '# id inc labelstring\n');
        tid=obj.getExtensionTypeID('LABELINC');
        fprintf(fid, ['extension LABELINC ',num2str(tid),'\n']);
        lbls=mr.getSupportedLabels();
        keys = obj.labelincLibrary.keys;
        for k = keys
                fprintf(fid, '%d %d %s\n', ...
                    k, obj.labelincLibrary.data(k).array(1),lbls{obj.labelincLibrary.data(k).array(2)});
        end
        fprintf(fid, '\n');
    end
end

if ~isempty(obj.softDelayLibrary.keys)
    warning('WARNING! The sequence in memory uses ''soft delay'' extension, which is incompatible with the file format v1.4.1. The produced Pulseq file is only partially valid and may fail to load or operate in some cases');
end

if ~isempty(obj.rotationLibrary.keys)
    error('WARNING! The sequence in memory uses the ''rotations'' extension, which is incompatible with the file format v1.4.1. The produced Pulseq file is likely to be invalid and would probably fail to operate');
end

if ~isempty(obj.shapeLibrary.keys)
    fprintf(fid, '# Sequence Shapes\n');
    fprintf(fid, '[SHAPES]\n\n');
    keys = obj.shapeLibrary.keys;
    for k = keys
        shape_dat = obj.shapeLibrary.data(k).array;
        fprintf(fid, 'shape_id %d\n', k);
        fprintf(fid, 'num_samples %d\n', shape_dat(1));
        fprintf(fid, '%.9g\n', shape_dat(2:end));
        fprintf(fid, '\n');
    end
end

fclose(fid);

if create_signature
    % sign the file (this version with re/loading the file is a factor 2 faster than the sprintf() based one that kept a memory-copy of the data written)

    % re-open and read in the file
    fid=fopen(filename, 'r');
    buf=fread(fid);
    fclose(fid);

    % calculate the digest
    if mr.aux.isOctave()
      md5hash=hash('MD5',char(buf(:)')); % Octave-specific function
    else
      md5hash=md5_java(buf); % Matlab Java hack
    end
    %fprintf('%s\n',md5hash);

    % store the signature in the object
    obj.signatureType='md5';
    obj.signatureFile='text';
    obj.signatureValue=md5hash;

    % re-open the file for appending
    fid=fopen(filename, 'a');
    fprintf(fid, '\n[SIGNATURE]\n'); % the preceding new line BELONGS to the signature (and needs to be sripped away to recalculate the signature)
    fprintf(fid, '# This is the hash of the Pulseq file, calculated right before the [SIGNATURE] section was added\n');
    fprintf(fid, '# It can be reproduced/verified with md5sum if the file trimmed to the position right above [SIGNATURE]\n');
    fprintf(fid, '# The new line character preceding [SIGNATURE] BELONGS to the signature (and needs to be sripped away for recalculating/verification)\n');
    fprintf(fid, 'Type md5\n');
    fprintf(fid, 'Hash %s\n', md5hash);
    fclose(fid);
end

end

function out=md5_java(buf)
    import java.security.*;
    import java.math.*;
    import java.lang.String;

    md = MessageDigest.getInstance('MD5');
    hash = md.digest(double(buf));
    bi = BigInteger(1, hash);

    out=char(String.format('%032x', bi));
end