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= Documentation: Functions for reading and writing data files =

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'''IN CONSTRUCTION'''

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== Location of Data Files ==
The data that we record (using the BrainVision Recorder) is stored in raw format
in a subdirectory of EEG_RAW_DIR (global variable). The naming scheme for
the subdirectories is Subject_yy_mm_dd, e.g., Gabriel_02_11_24. One data set
in BrainVision generic data format consists for three files: (1) a binary data 
file, extension .eeg, (2) a header file holding information on the settings of the recording
as sampling rate, used channels, etc., extension .vhdr, and (3) a marker file, extension
.vmrk. Data we receive in other formats from other labs are stored in a subdirectory
of EEG_IMPORT_DIR.

Preprocessed data is stored in matlab format in a subdirectory of EEG_MAT_DIR.
The name of this subdirectory should be the same as that of the raw data. Typically
the data is stored in a version which is just downsampled and in a version which
is filtered and downsampled for display purpose. The former fi
le is called like the
original data, and the latter has the appendix _display. Each matlab file should
include the variables cnt, mrk and mnt, see Section [[2.1]].


== Loading Data which is in the Original Generic Data Format ==


For the EEG experiments, that we record at our lab, we store data in "preprocessed"
formats see [[Sec. 2.2]]. One version is just downsampled, which can also be done when
reading the original data (using readGenericEEG). But loading the preprocessed data
(using eegfile_loadMatlab) has the advantage that the markers are already brought to
a nice format. If you want to load data in this convenient way, see [[Sec. 2.4]]. Otherwise
read on in this section.

{{{#!highlight matlab
cnt = readGenericEEG(file, [clab, fs, from, maxlen]);
}}}

This function can be used to load data which is in BrainVision's generic data format.
So far it is quite constrained to take only specific variants of the general generic data
format. Data must be multiplexed and in the binary format INT16. (To read data in
binary format float there is the function readGenericEEG_float: should be integrated
in one function?) To determine the available channels or the length of the data use
the function readGenericHeader.

||file || is taken relative to EEG_RAW_DIR, unless it starts with the character '/'. (Under Windows the condition for an absolute pathname is that the second character is a ':'.) ||
||clab || labels of the channels to be loaded.||
||fs || sampling rate to which the original data are to be downsampled. The default value is 100. This works only when fs is a divisor of the original sampling rate. To read data in the original sampling rate use 'raw'.||
||from ||is the start in msec from which data is to be read.||
||maxlen || is the maximum length of data in msec to be read.||

Output:

||cnt || struct of continous EEG data, as described in [[Section 2.1.]]||

See also: eegfile_loadMatlab, readGenericHeader, readGenericMarkers.

{{{#!highlight matlab
[clab, scale, fs, endian, len] = readGenericHeader(file);
}}}

This function is used by readGenericEEG. It can also be called directly to determine
the original sampling rate, the length of the signals and the recorded channels.

||file||is the name of the header file (without the extension .vhdr). The same applies as for read readGenericEEG.||

Output:


||clab || cell array of electrode labels.||
||scale ||vector specifying the scaling factor for each channel by which each sample value (in INT16 format) has to be multiplied to obtain the µV value.||
||fs|| sampling rate in which the signals are stored.||
||endian ||big ('b') or little ('l') endian byte order.||
||len|| length of the EEG signals in seconds.||


{{{#!highlight matlab
Mrk = readGenerikMarkers(file, [outputStructArray]);
}}}

This function reads all markers of BrainVision's generic data format. If you are only
interested in 'Stimulus' and 'Response' markers, readMarkerTable is your friend. Note:
this function returns the markers in the original sampling rate. In contrast, readMarkerTable returns markers by default resampled to 100 Hz.


||file || is the name of the header file (without the extension .vmrk). The same applies as for readGenericEEG.||
|| outputStructArray || specifies the output format, default 1. If false the output is a struct of arrays, not a struct array. ||

Output:

||Mrk|| struct array of markers with fields type, desc, pos, length, chan, time which are defined in the BrainVision generic data format, see the comment lines in any *.vmrk marker file. ||
|| fs || sampling rate, as read from the corresponding header file. ||

See also: readMarkerTable, readGenericHeader.


{{{#!highlight matlab
mrk = readMarkerTable(file, [fs=100, markerTypes, flag]);
}}}

This function reads all 'Stimulus' and 'Response' markers from the header file. For
reading markers of other types you can use readAlternativeMarker. See also readMarkerTableArtifacts for reading the marker file of an artifact measurement (with annotated artifacts), and readSegmentBorders. A general function that reads all marker information of the BrainVision generic data format is readGenericMarkers.

||file||is the name of the header file (without the extension .vmrk). The same applies as for readGenericEEG.||
||fs|| sampling rate for the returned marker structure. The default value is 100.||
||markerTypes ||read only markers of this type, default {'Stimulus','Response'}.||
||flag|| a vector of the same length as markerTypes which defines the sign of the marker values (in the type-of-event field toe of the returned marker structure). The default is [1 -1], i.e., stimulus markers give positive marker numbers and response markers give negative marker numbers. ||

Output:

||mrk|| struct of EEG marker, as described in [[Section 2.1]]||


== Saving and Loading EEG Data in Matlab Format ==

{{{#!highlight matlab
[dat, mrk, mnt] = eegfile_loadMatlab(file, [opt]);
[var1, var2, ...] = eegfile_loadMatlab(file, opt);
}}}

This function loads EEG data, that was stored using eegfile_saveMatlab. It can also concat a series of such files.

||file|| name of data file, or cell array of file names. In the latter case all files are concatenated. Each file name is taken relative to opt.path (see below), unless it starts with the character '/'. (Under Windows the condition for an absolute pathname is that the second character is a ':').||

The options struct or property/value list (see [[Section A.2]]) can have the following properties:


||.clab|| Channel labels (cell array of strings) for loading a subset of all channels. Default 'ALL' means all available channels. See function chanind for valid formats. In case opt.clab is not 'ALL' the electrode montage mnt is adapted automatically.||
||.vars|| Variables (cell array of strings) which are to be loaded, default 'dat','mrk','mnt'. The names 'dat', 'cnt' and 'epo' are treated equally and all match the data structure.||
||.path|| In case file does not include an absolute path, opt.path is prepended to file. Default EEG_MAT_DIR (global variable).||

Output:

||dat|| structure of continuous or epoched signals||
||mrk|| marker structure||
||mnt|| electrode montage structure||
||varx|| variables as requested by opt.vars.||

Example:

{{{#!highlight matlab
>> file= 'Gabriel_03_05_21/selfpaced2sGabriel';
>> [cnt,mrk,mnt]= eegfile_loadMatlab(file);
>> %% or just to load variables 'mrk' and 'mnt':
>> [mrk,mnt]= eegfile_loadMatlab(file, {'mrk','mnt'});
>> %% or to load only some central channels
>> [cnt, mnt]= eegfile_loadMatlab(file, 'clab','C5-6', 'vars',{'cnt','mnt'});
}}}


{{{#!highlight matlab
eegfile_saveMatlab(file, dat, mrk, mnt, [opt]);
}}}

This functions saves (potentially preprocessed) EEG data along with structures defining markers and a display montage. Optionally additional variable can also be stored.

||
file|| is the name of the file. The same applies as for eegfile_loadMatlab.||
||dat|| structure of EEG data, may be continuous or epoched.||
||mrk|| marker structure||
||mnt|| electrode montage structure||

The options struct or property/value list (see [[Section A.2]]) can have the following
properties:

||.path|| In case file does not include an absolute path, opt.path is prepended to file. Default EEG_MAT_DIR (global variable).||
||.channelwise|| If true, signals are saved channelwise. This is an advantage for big files, because it allows to load selected channels.||
||.format|| 'double', 'float', 'int16', or 'auto' (default). In 'auto' mode, the function tries to find a lossless conversion of the signals to INT16 (see property .resolution_list). If this is possible .format is set to 'INT16', otherwise it is set to 'DOUBLE'.||
||.resolution|| Resolution of signals, when saving in format INT16. (Signals are divided by this factor before saving.) The resolution may be selected for each channel individually, or globally for all channels. In the 'auto' mode, the function tries to find for each channel a lossless conversion to INT16 (see property .resolution_list). For all other channels the resolution producing least information loss is chosen (under the resolutions that avoid clipping). Possible values: (1) 'auto' (default), (2) numerical scalar, or (3) numerical vector of length 'number of channels' (i.e., length(dat.clab)).||
||.resolution_list|| Vector of numerical values. These values are tested as resolutions to see whether lossless conversion to INT16 is possible. Default [1 0.5 0.1].||
||vars|| Additional variables that should be stored. opt.vars must be a cell array with a variable name / variable value structure, e.g., {'Mrk',Mrk, 'blah',blah} when Mrk and blah are the variables to be stored.||

== Exporting Data to the Generic Data Format ==

{{{#!highlight matlab
writeGenericData(dat, [mrk, scale]);
}}}

||dat|| structure of continuous or epoched EEG data.||
||mrk || struct of EEG marker, as described in [[Section 2.1.]]||
||scale|| scaling factor used in the generic data format to bring data from the INT16 range -32768 to 32767 to µV values. This is implemented as a division by the scaling factor before saving the signals. Individual scaling factors may be specified for each channel in a vector, or a global scaling as scalar, default is 0.1 (i.e., signal range is -3276.8 to 3276.7 µV). Use scale= max(abs(cnt.x))'/32768 to achive best resolution (least information loss in INT16 conversion) without clipping. ||