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 will be possible to output the complete pipeline as a MATLAB script
or in a specialized pipeline format (e.g. PSOM, JIST, LONI, 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 input argument you can also only give the configuration
of the processed data (i.e. "data.cfg") instead of the full data.
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' or 'dot'
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).
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