function [pipeline] = ft_analysispipeline(cfg, data)

% FT_ANALYSIPIPELINE reconstructs the complete analysis pipeline that was used to create

% the input FieldTrip data structure. The pipeline will be visualized as a flowchart.

% In the future it might be possible to output the complete pipeline as a MATLAB script

% or in a specialized pipeline format like PSOM, JIST, LONI, or Taverna.

%

% Use as

% output = ft_analysispipeline(cfg, data)

%

% The first cfg input contains the settings that apply to the behavior of this

% particular function and the second data input argument can be the output of any

% FieldTrip function, e.g. FT_PREPROCESSING, FT_TIMELOCKANALYSIS, FT_SOURCEANALYSIS,

% FT_FREQSTATISTICS or whatever you like.

%

% Alternatively, for the second data input argument you can also only give the

% configuration of the processed data (for example data.cfg) instead of the full data

% structure.

%

% The configuration options that apply to the behavior of this function are

% cfg.filename = string, filename without the extension

% cfg.filetype = string, can be 'matlab', 'html', 'dot' or 'prov'

% cfg.feedback = string, 'no', 'text', 'gui' or 'yes', whether text and/or

% graphical feedback should be presented (default = 'yes')

% cfg.showinfo = string or cell-array of strings, information to display

% in the GUI boxes, can be any combination of

% 'functionname', 'revision', 'matlabversion',

% 'computername', 'username', 'calltime', 'timeused',

% 'memused', 'workingdir', 'scriptpath' (default =

% 'functionname', only display function name). Can also

% be 'all', show all pipeline. Please note that if you want

% to show a lot of information, this will require a lot

% of screen real estate.

% cfg.remove = cell-array with strings, determines which objects will

% be removed from the configuration prior to writing it to

% file. For readibility of the script, you may want to

% remove the large objectssuch as event structure, trial

% definition, source positions

% cfg.keepremoved = 'yes' or 'no', determines whether removed fields are

% completely removed, or only replaced by a short textual

% description (default = 'no')

%

% This function uses the nested cfg and cfg.previous that are present in

% the data structure. It will use the configuration and the nested previous

% configurations to climb all the way back into the tree. This funtction

% will print a complete MATLAB script to screen (and optionally to file).

% Furthermore, it will show an interactive graphical flowchart

% representation of the steps taken during the pipeline(i). In the flowchart

% you can click on one of the steps to see the configuration details of

% that pipeline(i).

%

% Example use:

% data = ft_timelocksimulation([]);

% data_bl = ft_timelockbaseline([], data);

% data_avg = ft_timelockanalysis([], data_bl);

% ft_analysispipeline([], data_avg)

%

% Note that the nested cfg and cfg.previous in your data might not contain

% all details that are required to reconstruct a complete and valid

% analysis script.

%

% To facilitate data-handling and distributed computing you can use

% cfg.inputfile = ...

% If you specify this, the input data will be read from a *.mat file on disk. The

% file should contain only a single variable, corresponding with the input structure.

%

% See also FT_PREPROCESSING, FT_TIMELOCKANALYSIS, FT_FREQANALYSIS, FT_SOURCEANALYSIS,

% FT_CONNECTIVITYANALYSIS, FT_NETWORKANALYSIS

% Copyright (C) 2014-2023, Robert Oostenveld

%

% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org

% for the documentation and details.

%

% FieldTrip is free software: you can redistribute it and/or modify

% it under the terms of the GNU General Public License as published by

% the Free Software Foundation, either version 3 of the License, or

% (at your option) any later version.

%

% FieldTrip is distributed in the hope that it will be useful,

% but WITHOUT ANY WARRANTY; without even the implied warranty of

% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

% GNU General Public License for more details.

%

% You should have received a copy of the GNU General Public License

% along with FieldTrip. If not, see <http://www.gnu.org/licenses/>.

%

% $Id$

% these are used by the ft_preamble/ft_postamble function and scripts

ft_revision = '$Id$';

ft_nargin = nargin;

ft_nargout = nargout;

% callinfo feedback is highly annoying in this recursive function

% do this here, otherwise ft_defaults will override our setting

if ~isfield(cfg, 'showcallinfo'), cfg.showcallinfo = 'no'; end

% do the general setup of the function

ft_defaults

ft_preamble init

ft_preamble debug

ft_preamble loadvar data

ft_preamble provenance data

% the ft_abort variable is set to true or false in ft_preamble_init

if ft_abort

return

end

% set the defaults

cfg.filename = ft_getopt(cfg, 'filename');

cfg.showinfo = ft_getopt(cfg, 'showinfo', {'functionname'});

cfg.keepremoved = ft_getopt(cfg, 'keepremoved', 'no');

cfg.feedback = ft_getopt(cfg, 'feedback', 'text');

cfg.prune = ft_getopt(cfg, 'prune', 'yes');

cfg.filetype = ft_getopt(cfg, 'filetype');

cfg.fontsize = ft_getopt(cfg, 'fontsize', 10);

if isempty(cfg.filetype) && ~isempty(cfg.filename)

[p, f, x] = fileparts(cfg.filename);

switch x

case '.m'

cfg.filetype = 'matlab';

case '.html'

cfg.filetype = 'html';

case '.dot'

cfg.filetype = 'dot';

case '.prov.jsonld'

cfg.filetype = 'prov';

otherwise

ft_error('cannot determine filetype');

end

end

if ~isfield(cfg, 'remove')

% this is the default list of configuration elements to be removed. These

% elements would be very large to print and make the script difficult to

% read. To get a correctly behaving script, you may have to change this.

cfg.remove = {

'sgncmb'

'channelcmb'

'event'

'trl'

'trlold'

'artfctdef.eog.trl'

'artfctdef.jump.trl'

'artfctdef.muscle.trl'

'pos'

'inside'

'outside'

'sourcemodel.pos'

'sourcemodel.inside'

'sourcemodel.outside'

'vol.bnd.pos'

'vol.bnd.tri'

'headmodel.bnd.pos'

'headmodel.bnd.tri'

};

elseif ~iscell(cfg.remove)

cfg.remove = {cfg.remove};

end

if strcmp(cfg.showinfo, 'all')

cfg.showinfo = {

'functionname'

'revision'

'matlabversion'

'computername'

'architecture'

'username'

'calltime'

'timeused'

'memused'

'workingdir'

'scriptpath'

};

end

if ~isfield(cfg, 'showinfo')

cfg.showinfo = {'functionname'};

elseif ~iscell(cfg.showinfo)

cfg.showinfo = {cfg.showinfo};

end

if ~isfield(data, 'cfg')

% assume that the user only passed the cfg instead of a complete data structure

data = struct('cfg', data);

end

% walk the tree, gather information about each node

ft_progress('init', cfg.feedback, 'parsing provenance...');

pipeline = walktree(data.cfg);

ft_progress('close');

% convert the cell-array into a structure array

for i=1:length(pipeline)

tmp(i) = pipeline{i};

end

pipeline = tmp;

if istrue(cfg.prune)

% prune the double occurences

[dummy, indx] = unique({pipeline.this});

pipeline = pipeline(sort(indx));

end

% start at the end of the tree and determine the level of each of the parents

hasparent = false(size(pipeline));

haschild = false(size(pipeline));

for i=1:length(pipeline)

hasparent(i) = ~isempty(pipeline(i).parent);

haschild(i) = any(strcmp(pipeline(i).this, [pipeline.parent]));

end

% construct a matrix with all pipeline steps

width = zeros(size(pipeline));

height = zeros(size(pipeline));

level = 1;

% the items without children start at height 1

sel = find(~haschild);

while ~isempty(sel)

height(sel) = level;

% find the parents of the items at this level

sel = match_str({pipeline.this}, [pipeline(sel).parent]);

% the parents should be at least one level higher

height(sel) = level + 1;

% continue with the next level

level = level + 1;

end

for i=1:max(height)

sel = find(height==i);

width(sel) = 1:length(sel);

end

for i=1:length(pipeline)

pipeline(i).position = [height(i) width(i)];

end

% sort according to a decreasing level, i.e. the last pipeline(i) at the end

[dummy, indx] = sortrows(-[height(:) width(:)]);

pipeline = pipeline(indx);

if isempty(cfg.filename)

pipeline2matlabfigure(cfg, pipeline);

else

switch cfg.filetype

case 'matlab'

pipeline2matlabscript(cfg, pipeline);

case 'dot'

pipeline2dotfile(cfg, pipeline);

case 'html'

pipeline2htmlfile(cfg, pipeline);

case 'prov'

pipeline2provfile(cfg, pipeline);

otherwise

ft_error('unsupported filetype');

end

end

% do the general cleanup and bookkeeping at the end of the function

ft_postamble debug

ft_postamble previous data

ft_postamble provenance

ft_postamble savefig

if isempty(cfg.filename)

% add a menu to the figure, note that the menu makes FT_ANALYSISPIPELINE recursive

menu_fieldtrip(gcf, cfg);

end

% do not return an output variable if not requested

if ~ft_nargout

clear pipeline

end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% SUBFUNCTION for recursive walking along the cfg.previous.previous info

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function info = walktree(cfg)

if isempty(cfg) || (isstruct(cfg) && numel(fieldnames(cfg))==0)

info = [];

return

end

this = getnode(cfg);

% parse all previous steps

if isfield(cfg, 'previous') && ~isempty(cfg.previous) && iscell(cfg.previous)

previous = cellfun(@walktree, cfg.previous, 'UniformOutput', false);

if iscell(previous{1})

previous = cat(2, previous{:});

end

elseif isfield(cfg, 'previous') && ~isempty(cfg.previous) && isstruct(cfg.previous)

previous = walktree(cfg.previous);

elseif isfield(cfg, 'previous') && ~isempty(cfg.previous)

ft_error('unexpected content in cfg.previous');

else

previous = {};

end

% parse the side branches, such as cfg.headmodel and cfg.layout

fn = fieldnames(cfg);

branch = {};

for i=1:numel(fn)

if isstruct(cfg.(fn{i})) && isfield(cfg.(fn{i}), 'cfg')

branch = [walktree(cfg.(fn{i}).cfg) branch];

this.parent{end+1} = branch{1}.this; % the start of the branch is a parent to this element

end

end

ft_progress(rand(1), 'parsing provenance for %s\n', this.name); % FIXME no percentage complete known

drawnow

% the order of the output elements matters for the recursion

info = [{this} branch previous];

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% SUBFUNCTION for gathering the information about each pipeline

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function node = getnode(cfg)

[p, f, x] = myfileparts(getvalue(cfg, 'version.name'));

node.cfg = cfg;

node.name = f;

node.id = getvalue(cfg, 'version.id');

node.this = ft_hash(cfg);

if isfield(cfg, 'previous') && ~isempty(cfg.previous) && iscell(cfg.previous)

% skip the entries that are empty

cfg.previous = cfg.previous(~cellfun(@isempty, cfg.previous));

node.parent = cellfun(@ft_hash, cfg.previous, 'UniformOutput', false);

elseif isfield(cfg, 'previous') && ~isempty(cfg.previous) && isstruct(cfg.previous)

node.parent = {ft_hash(cfg.previous)};

elseif isfield(cfg, 'previous') && ~isempty(cfg.previous)

ft_error('unexpected content in cfg.previous');

else

node.parent = {};

end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% SUBFUNCTION

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function v = getvalue(s, f)

if issubfield(s, f)

v = getsubfield(s, f);

else

v = 'unknown';

end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% SUBFUNCTION

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function [p, f, x] = myfileparts(filename)

if ispc

filename(filename=='/') = filesep;

else

filename(filename=='\') = filesep;

end

[p, f, x] = fileparts(filename);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% SUBFUNCTION

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function varargout = button(h, eventdata, handles, varargin)

pos = get(get(gcbo, 'CurrentAxes'), 'CurrentPoint');

x = pos(1,1);

y = pos(1,2);

pipeline = guidata(h);

for i=1:numel(pipeline)

if (x >= pipeline(i).x(1) && x <= pipeline(i).x(2) && y >= pipeline(i).y(1) && y <= pipeline(i).y(3))

cfg = pipeline(i).cfg;

if isfield(cfg, 'previous')

cfg = rmfield(cfg, 'previous');

end

% use a helper function to remove uninteresting fields

cfg = removefields(cfg, ignorefields('pipeline'), 'recursive', true);

% use a helper function to remove too large fields

cfg.checksize = 3000;

cfg = ft_checkconfig(cfg, 'checksize', 'yes');

cfg = rmfield(cfg, 'checksize');

script = printstruct('cfg', cfg);

uidisplaytext(script, pipeline(i).name);

break;

end

end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% SUBFUNCTION

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function pipeline2matlabfigure(cfg, pipeline)

fprintf('plotting pipeline as MATLAB figure\n');

layout = cell(numel(pipeline), numel(pipeline));

for i=1:length(pipeline)

% get the vertical and horizontal position in integer values

% high numbers are towards the begin, low numbers are towards the end of the pipeline

v = pipeline(i).position(1);

h = pipeline(i).position(2);

layout{v,h} = pipeline(i).this;

end

% remove the empty columns

maxheight = max(sum(~cellfun(@isempty, layout),1));

maxwidth = max(sum(~cellfun(@isempty, layout),2));

layout = layout(1:maxheight,1:maxwidth);

fig = figure;

hold on

axis manual; % the axis should not change during the contruction of the arrows, otherwise the arrowheads will be distorted

set(gca, 'Units', 'normalized'); % use normalized units

set(gcf, 'ToolBar', 'none');

axis([0 1 0 1])

axis off;

axis tight;

for i=1:numel(pipeline)

label = makelabel(pipeline(i), cfg.showinfo);

% dublicate backslashes to escape tex interpreter (in case of windows filenames)

label = strrep(label, '\', '\\');

label = strrep(label, '{\\bf', '{\bf'); % undo for bold formatting

% escape underscores

label = strrep(label, '_', '\_');

% strip blank line if present and not needed

if strcmp(label{end}, '')

label(end) = [];

end

% compute width and height of each box, note that axis Units are set to Normalized

boxsize = 1./[maxwidth+1 maxheight+3];

% create the 4 corners for our patch, close the patch by returning to the start point

x = ([0 1 1 0 0]-0.5) .* boxsize(1);

y = ([0 0 1 1 0]-0.5) .* boxsize(2);

% position the patch

location = pipeline(i).position([2 1]);

location(1) = (location(1)-0.5)/maxwidth;

location(2) = (location(2)-0.5)/maxheight;

% the location specifies the center of the patch

x = x + location(1);

y = y + location(2);

p = patch(x', y', 0);

set(p, 'Facecolor', [1 1 0.6])

pipeline(i).x = x;

pipeline(i).y = y;

guidata(fig, pipeline);

if length(label)==1

textloc = location;

l = text(textloc(1), textloc(2), label);

set(l, 'HorizontalAlignment', 'center');

set(l, 'VerticalAlignment', 'middle');

set(l, 'fontUnits', 'points');

set(l, 'fontSize', cfg.fontsize);

set(l, 'interpreter', 'tex');

else

textloc = location;

textloc(1) = textloc(1)-boxsize(1)/2;

textloc(2) = textloc(2)+boxsize(2)/2;

l = text(textloc(1), textloc(2), label);

set(l, 'HorizontalAlignment', 'left');

set(l, 'VerticalAlignment', 'top');

set(l, 'fontUnits', 'points');

set(l, 'fontSize', cfg.fontsize);

set(l, 'interpreter', 'tex');

end

% draw an arrow if appropriate

n = length(pipeline(i).parent);

for j=1:n

[parentlocation(2), parentlocation(1)] = ind2sub([maxheight, maxwidth], find(strcmp(layout(:), pipeline(i).parent{j}), 1, 'first'));

% parentlocation = info(find(strcmp({pipeline.this}, analysis.parent{j}), 1, 'first')).position;

parentlocation(1) = (parentlocation(1)-0.5)/maxwidth;

parentlocation(2) = (parentlocation(2)-0.5)/maxheight;

base = parentlocation + [0 -0.5].*boxsize;

if false % n>1

% distribute the inputs evenly over the box

rel = 2*(j+n-1)/(n-1)-1; % relative location between -1.0 and 1.0

rel = rel*(n-1)/(n+3); % compress the relative location

tip = location + [0 0.5].*boxsize + [rel 0].*boxsize/2;

else

% put it in the centre

tip = location + [0 0.5].*boxsize;

end

arrow(base, tip, 'length', 8, 'lineWidth', 1);

end

end % for numel(info)

set(fig, 'WindowButtonUpFcn', @button);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% SUBFUNCTION

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function label = makelabel(pipeline, showinfo)

% create the text information to display

label = {};

for k = 1:numel(showinfo)

switch showinfo{k}

case 'functionname'

% label{end+1} = ['{\bf ' pipeline(i).name '}'];

label{end+1} = pipeline.name;

if k == 1 % add blank line if function name is on top, looks nice

label{end+1} = '';

end

case 'revision'

if isfield(pipeline.cfg, 'version') && isfield(pipeline.cfg.version, 'id')

label{end+1} = pipeline.cfg.version.id;

else

label{end+1} = '<revision unknown>';

end

case 'matlabversion'

if isfield(pipeline.cfg, 'callinfo') && isfield(pipeline.cfg.callinfo, 'matlab')

label{end+1} = ['MATLAB ' pipeline.cfg.callinfo.matlab];

else

label{end+1} = '<MATLAB version unknown>';

end

case 'computername'

if isfield(pipeline.cfg, 'callinfo') && isfield(pipeline.cfg.callinfo, 'hostname')

label{end+1} = ['Hostname: ' pipeline.cfg.callinfo.hostname];

else

label{end+1} = '<hostname unknown>';

end

case 'architecture'

if isfield(pipeline.cfg, 'callinfo') && isfield(pipeline.cfg.callinfo, 'hostname')

label{end+1} = ['Architecture: ' pipeline.cfg.callinfo.computer];

else

label{end+1} = '<architecture unknown>';

end

case 'username'

if isfield(pipeline.cfg, 'callinfo') && isfield(pipeline.cfg.callinfo, 'user')

label{end+1} = ['Username: ' pipeline.cfg.callinfo.user];

else

label{end+1} = '<username unknown>';

end

case 'calltime'

if isfield(pipeline.cfg, 'callinfo') && isfield(pipeline.cfg.callinfo, 'calltime')

label{end+1} = ['Function called at ' datestr(pipeline.cfg.callinfo.calltime)];

else

label{end+1} = '<function call time unknown>';

end

case 'timeused'

if isfield(pipeline.cfg, 'callinfo') && isfield(pipeline.cfg.callinfo, 'proctime')

label{end+1} = sprintf('Function call required %d seconds', round(pipeline.cfg.callinfo.proctime));

else

label{end+1} = '<processing time unknown>';

end

case 'memused'

if isfield(pipeline.cfg, 'callinfo') && isfield(pipeline.cfg.callinfo, 'procmem')

label{end+1} = sprintf('Function call required %d MB', round(pipeline.cfg.callinfo.procmem/1024/1024));

else

label{end+1} = '<memory requirement unknown>';

end

case 'workingdir'

if isfield(pipeline.cfg, 'callinfo') && isfield(pipeline.cfg.callinfo, 'pwd')

label{end+1} = sprintf('Working directory was %s', pipeline.cfg.callinfo.pwd);

else

label{end+1} = '<working directory unknown>';

end

case 'scriptpath'

if isfield(pipeline.cfg, 'version') && isfield(pipeline.cfg.version, 'name')

label{end+1} = sprintf('Full path to script was %s', pipeline.cfg.version.name);

else

label{end+1} = '<script path unknown>';

end

end

end % for numel(showinfo)

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% SUBFUNCTION

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function pipeline2matlabscript(cfg, pipeline)

[p, f, x] = fileparts(cfg.filename);

filename = fullfile(p, [f '.m']);

fprintf('exporting MATLAB script to file ''%s''\n', filename);

varname = {};

varhash = {};

for i=1:length(pipeline)

varname{end+1} = sprintf('variable_%d_%d', pipeline(i).position(1), pipeline(i).position(2));

varhash{end+1} = pipeline(i).this;

end

for i=1:length(pipeline)

pipeline(i).inputvar = {};

pipeline(i).outputvar = varname{strcmp(varhash, pipeline(i).this)};

for j=1:length(pipeline(i).parent)

pipeline(i).inputvar{j} = varname{strcmp(varhash, pipeline(i).parent{j})};

end

end

sep = sprintf('\n\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n\n');

script = sep;

for i=1:length(pipeline)

thiscfg = pipeline(i).cfg;

if isfield(thiscfg, 'previous')

thiscfg = rmfield(thiscfg, 'previous');

end

cfgstr = printstruct('cfg', thiscfg);

if ~isempty(pipeline(i).inputvar)

inputvar = sprintf(', %s', pipeline(i).inputvar{:});

else

inputvar = '';

end

cmd = sprintf('\n%s = %s(cfg%s);', pipeline(i).outputvar, pipeline(i).name, inputvar);

script = cat(2, script, cfgstr, cmd, sep);

end

% write the complete script to file

fid = fopen(filename, 'wb');

fprintf(fid, '%s', script);

fclose(fid);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% SUBFUNCTION

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function pipeline2dotfile(cfg, pipeline)

[p, f, x] = fileparts(cfg.filename);

filename = fullfile(p, [f '.dot']);

fprintf('exporting DOT file to ''%s''\n', filename);

% write the complete script to file

fid = fopen(filename, 'wb');

fprintf(fid, 'digraph {\n');

varhash = {pipeline.this};

for i=1:length(pipeline)

for j=1:length(pipeline(i).parent)

fprintf(fid, '%d -> %d\n', find(strcmp(varhash, pipeline(i).parent{j})), i);

end

end

for i=1:length(pipeline)

label = makelabel(pipeline(i), cfg.showinfo);

if numel(label)>2

% left justified

label = sprintf('%s\\l', label{:});

label = label(1:end-2);

else

% centered

label = sprintf('%s\\n', label{:});

label = label(1:end-2);

end

fprintf(fid, '%d [label="%s",shape=box,fontsize=%d,URL="http://www.fieldtriptoolbox.org/reference/%s"]\n', i, label, cfg.fontsize, pipeline(i).name);

end

fprintf(fid, '}\n');

fclose(fid);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% SUBFUNCTION

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function pipeline2htmlfile(cfg, pipeline)

[p, f, x] = fileparts(cfg.filename);

filename = fullfile(p, [f '.html']);

fprintf('exporting HTML file to ''%s''\n', filename);

html = '';

totalproctime = 0;

ft_progress('init', cfg.feedback, 'serialising cfg-structures...');

for k = 1:numel(pipeline)

ft_progress(k/numel(pipeline), 'serialising cfg-structure %d from %d', k, numel(pipeline));

% strip away the cfg.previous fields, and all data-like fields

tmpcfg = removefields(pipeline(k).cfg, ignorefields('html'));

usercfg = [];

% record the usercfg and proctime if present

if isfield(tmpcfg, 'callinfo')

if isfield(tmpcfg.callinfo, 'usercfg')

usercfg = removefields(tmpcfg.callinfo.usercfg, ignorefields('html'));

% avoid processing usercfg twice

tmpcfg.callinfo = rmfield(tmpcfg.callinfo, 'usercfg');

end

if isfield(tmpcfg.callinfo, 'proctime')

totalproctime = totalproctime + tmpcfg.callinfo.proctime;

end

end

html = [html sprintf('nodes["%s"] = {"id": "%s", "name": "%s", "cfg": "%s", "usercfg": "%s", "parentIds": [',...

pipeline(k).this, pipeline(k).this, pipeline(k).name, escapestruct(tmpcfg), escapestruct(usercfg))];

if ~isempty(pipeline(k).parent)

for j = 1:numel(pipeline(k).parent)

html = [html '"' pipeline(k).parent{j} '"'];

if j < numel(pipeline(k).parent)

html = [html ','];

end

end

end

html = [html sprintf(']};\n')];

if k == numel(pipeline)

% we are at the single leaf node

html = [html sprintf('var leafId = "%s";\n', pipeline(k).this)];

end

end

ft_progress('close');

html = [html(1:end-2) newline];

% load the skeleton and put in the html code

thispath = fileparts(mfilename('fullpath'));

htmlfile = fileread([thispath '/private/pipeline-skeleton.html']);

timestamp = [datestr(now(), 'ddd') ' ' datestr(now())];

proctimestr = print_tim(totalproctime);

htmlfile = strrep(htmlfile, '${TIMESTAMP}', timestamp);

htmlfile = strrep(htmlfile, '${PIPELINE}', html);

htmlfile = strrep(htmlfile, '${USER}', getusername());

htmlfile = strrep(htmlfile, '${PROCTIME}', proctimestr);

% write the file

fid = fopen(filename, 'w');

fwrite(fid, htmlfile, 'uchar');

fclose(fid);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% SUBFUNCTION

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function pipeline2provfile(cfg, pipeline)

% this tries to follow http://bids.neuroimaging.io/bep028

[p, f, x] = fileparts(cfg.filename);

filename = fullfile(p, [f '.prov.jsonld']);

fprintf('exporting provenance to ''%s''\n', filename);

prov = [];

prov.context = 'https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json';

prov.BIDSProvVersion = 'dev';

prov.Records.Software{1}.Id = char(java.util.UUID.randomUUID.toString);

prov.Records.Software{1}.RRID = 'RRID:SCR_004849';

prov.Records.Software{1}.Label = 'FieldTrip';

prov.Records.Software{1}.Type = 'Software';

prov.Records.Software{1}.Version = ft_version;

prov.Records.Activities = {};

prov.Records.Entities = {};

% these are used to make random 32-character hexadecimal numbers

hexchar = '0123456789abcdef';

for i=1:numel(pipeline)

% extend the provenance with one activity and one entity

prov.Records.Activities{end+1} = struct();

prov.Records.Entities{end+1} = struct();

if ~isempty(pipeline(i).this)

pipeline(i).this = ['data_' pipeline(i).this];

end

for j=1:numel(pipeline(i).parent)

pipeline(i).parent{j} = ['data_' pipeline(i).parent{j}];

end

% append this activity to the provenance

prov.Records.Activities{end}.Id = hexchar(randi(16, 1, 32));

prov.Records.Activities{end}.Label = pipeline(i).name;

prov.Records.Activities{end}.Used = pipeline(i).parent;

prov.Records.Activities{end}.AssociatedWith = prov.Records.Software{1}.Id;

cfg = rmfield(pipeline(i).cfg, 'previous');

cmd = 'cfg = []; ';

cmd = [cmd strrep(printstruct('cfg', cfg), newline, ' ')];

cmd = [cmd ' ' pipeline(i).name '(cfg, '];

if ~isempty(pipeline(i).parent)

for j=1:numel(pipeline(i).parent)

cmd = [cmd pipeline(i).parent{j} ', '];

end

end

cmd = cmd(1:end-2); % remove the last ', '

cmd = [cmd ');'];

prov.Records.Activities{end}.Command = cmd;

% append this entity to the provenance

prov.Records.Entities{end}.Id = pipeline(i).this;

prov.Records.Entities{end}.Label = 'data';

prov.Records.Entities{end}.GeneratedBy = prov.Records.Activities{end}.Id;

end

% write the file

ft_write_json(filename, prov);

% there is one JSON field that needs to be renamed

fid = fopen(filename, 'rt');

str = fread(fid, [1 inf], 'char=>char');

fclose(fid);

str = strrep(str, '"context"', '"@context"');

fid = fopen(filename, 'w');

fwrite(fid, str);

fclose(fid);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% SUBFUNCTION

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function cfghtml = escapestruct(tmpcfg)

% convert the cfg structure to a suitable string (escape newlines and quotes)

% strip away big numeric fields

if isstruct(tmpcfg)

fields = fieldnames(tmpcfg);

for k = 1:numel(fields)

if isnumeric(tmpcfg.(fields{k})) && numel(tmpcfg.(fields{k})) > 400

tmpcfg.(fields{k}) = '[numeric data of &gt;400 elements stripped]';

end

end

end

cfghtml = strrep(printstruct('cfg', tmpcfg), '\', '\\');

cfghtml = strrep(cfghtml, sprintf('\r'), '\r');

cfghtml = strrep(cfghtml, sprintf('\n'), '\n');

cfghtml = strrep(cfghtml, sprintf('\t'), '\t');

cfghtml = strrep(cfghtml, '"', '\"');