Key concepts & syntax

Overview

This page introduces some key concepts for using Luna. Although introduced in terms of the lunaC command-line version of Luna, almost all core concepts are applicable in the Python and R versions too. This page contains a lot of detail, covering three main areas:

basic syntax for invoking Luna and specifying inputs and scripts
a list of special variables -- options that can be set to control the behavior of Luna
an overview of the output mechanisms

Prerequisites

Luna is fundamentally a console/command-line package, i.e. there is no point-and-click. Familiarity with the basic Unix/macOS console environment and shell scripting is recommended. The walk-through tutorial contains a brief shell orientation section that outlines some core commands useful when using Luna (or similar command-line tools). Naturally, there is a huge amount of easily accessible online tutorial information to getting started with the command shell too...

Luna syntax

Once installed and in your command path, lunaC is invoked via the luna command, often in the form:

luna sample.lst -o out.db < commands.txt

Here, Luna expects a list of IDs, EDFs (and possibly annotation files) in a sample list file (sample.lst), reads a series of commands (commands.txt) to be applied to each EDF, and writes the output to a lunout database file (out.db).

Types of command line arguments

lunaC expects the first argument to be either 1) an EDF (or EDF+ or EDFZ) file, 2) a sample-list, 3) a plain-text ASCII file or 4) a special command that does not require signal data, e.g. such as --build or --xml. With the exception of command scripts specified by -s, all subsequent arguments can come in any order and are interpreted as follows:

terms containing = are interpreted as variables, with the exception of certain special reserved names that change the behaviour of Luna, e.g. annot or alias, as described below
terms starting with - are interpreted as options, e.g. primarily -o and -s
once an -s option is encountered, all subsequent terms are interpreted as Luna commands rather than command line options; thus, if given, -s (and any subsequent commands) must be the final argument
terms starting with @ are interpreted as parameter files, the contents of which are loaded in to define/set new (special) variables
otherwise, terms that are numbers are interpreted as sample-list row numbers (either a single row, or a range, depending if one or two numbers are specified)
otherwise, that term is assumed to be the ID of a single individual to be analysed from the sample-list
if specifying one or more IDs on the command line, it is best to use the special variable form id (which can handle purely numeric IDs, i.e. interpreting it as an ID rather than than a row number in a sample list )

Help

Luna has a help function that describes the available commands, their parameters and their outputs. Commands are organized by domains, listed by the following command:

luna -h

usage: luna [sample-list|EDF] [n1] [n2] [@parameter-file] [sig=s1,s2] [v1=val1] < command-file

List of domains
---------------

annot      Annotations                 
artifact   Artifacts                   
cfc        Cross-frequency coupling    
cmdline    Command-line options        
epoch      Epochs                      

...

To view the commands within a domain:

luna -h manip

ANON         Strips EDF ID and Start Date headers
COPY         Duplicate one or more EDF channels
FLIP         Flips the polarity of a signal
RECORD-SIZE  Alters the record size and writes a new EDF
REFERENCE    Re-reference signal(s)
RESAMPLE     Resample signal(s)
SIGNALS      Retain/remove specific EDF channels
mV           Converts a signal to mV units
uV           Converts a signal to uV units

To view the parameters and outputs for a given command:

luna -h PSD

PSD : Power spectral density estimation (Welch) (Power spectra)
    : http://zzz.bwh.harvard.edu/luna/ref/power-spectra/#psd

Parameters:
===========

  epoch                           Calculate per-epoch band power
  epoch-spectrum                  Calculate per-epoch power spectra
  max              max=100        Specify maximum frequency for power spectra
  bin              bin=0.5        Specify bin-size for power spectra
  sig              sig=C3,C4      Restrict analysis to these channels
  spectrum                        Calculate power spectra

Outputs:
========

   CH                      Number of epochs
   ------------------------------------------------------------
     NE                    Number of epochs

   B x CH                  Whole-night, per-channel band power
   ------------------------------------------------------------
     PSD                   Power
     RELPSD                Relative power

   CH x F                  Whole-night, per-channel power
   ------------------------------------------------------------
     PSD                   Power

   B x CH x E              Whole-night, per-channel per-epoch band power
   ------------------------------------------------------------
     PSD                   Power
     RELPSD                Relative power

   CH x E x F              Whole-night, per-channel per-epoch power
   ------------------------------------------------------------
   (compressed output)
     PSD                   Power

Note

By convention, all Luna commands should be in CAPITAL LETTERS.

Options

As well as specifying the main input, setting any variables and supplying Luna commands to be processed, the following flags can also appear on the Luna command line.

Primary options:

Option	Description
`-s`	Directly specify Luna commands after `-s`, rather than reading them from a command file; if specified, this option must come last
`-o`	Write all output to a lunout database; if it already exists, it will be overwritten
`-a`	Similar to `-a` except appends to an existing output database rather than overwriting it
`-t`	Write all output as text tables rather than to a database
`@<file>`	Read (special) variables from a parameter file, e.g. `@param.txt`
N	Read only observation N (nth row) from the sample list
N M	Read only observations N to M from the sample list
`id=<id>`	Read only observation with sample list ID matching `<id>` from the sample list, e.g. `id=night001`

Special-case, secondary options:

Option	Description
`--fs`	Specify a sample rate when reading an ASCII (non-EDF) file
`--nr`	Specify the number of records when creating an empty EDF
`--rs`	Specify the record duration (seconds) when creating an empty EDF
`--opt` or `--options`	Only applicable when using a special helper/utility function such as `--psc`; options to be passed to that command come after this

Input

EDFs

Luna can read EDF and EDF+ files. The latter allow for discontinuities (by having an explicit time-track) and provide some support for annotations. After restructuring a file (e.g. removing certain epochs), it will be represented internally in a form that corresponds to an EDF+ (i.e. with gaps/discontinuities). Luna can read a single EDF (rather than a sample list) by specifying a filename (with an .edf or .EDF extension - or alternatively, a compressed .edf.gz):

luna test1.edf < commands.txt

To attach annotations to a single EDF, use annot-file (although sample-lists are generally more convenient to link EDF and annotation files, as described below):

luna test1.edf annot-file=test1.annot < commands.txt

In-memory vs on-disk representations

In this documentation, we often make a distinction between the on-disk EDF and the in-memory (internal) representation of the EDF.

When Luna first "attaches" an EDF, it does not load anything other than the header. Subsequently, Luna uses a lazy-loading approach, whereby it only pulls records from disk when needed. These are cached in memory: if they are needed again, they do not need to be read in afresh.
All commands that manipulate EDFs and the signals therein operate only on the internal EDF. Although we may use language such as "drop a channel from the EDF" we generally do not imply that the original on-disk file has been changed.
The in-memory EDF may differ from the on-disk version, for example, if channels and/or epochs have been dropped or added by SIGNALS, MASK, RESTRUCTURE and other commands. As noted, all Luna commands report on the current, in-memory representation: for example, the original EDF may have 64 channels, but DESC may report fewer (or more) depending if channels have been dropped/added within that particular Luna run.
For command-line Luna, changes made to the in-memory EDF do not persist after that run. For example, the following may report that 6 channels are present:
```
luna my.edf -s DESC 
```
One could subsequently run a command that drops two channels and then calls DESC:
```
luna my.edf -s 'SIGNALS drop=ECG,EMG & DESC'
```
in which case, only 4 channels are reported. However, on running the first command again:
```
luna my.edf -s DESC
```
Luna will report 6 channels again, i.e. as nothing was changed in the original file my.edf. (Note that the Python and R packages differ here, meaning that the same in-memory EDF persists between commands.)

Sample lists

The sample list (sample.lst in the example at the top of this page) file defines a project, i.e. a collection of EDFs and their associated IDs and annotations. Sample lists should contain at least two tab-delimited fields: the subject ID, followed by the EDF file location:

id001   test1.edf
id002   test2.edf

An optional additional column(s) specifies any annotation files (e.g. containing stage information) for that EDF. As in the example below, you can use either absolute or relative file paths:

id001   test1.edf   /data/annots/test1-staging.xml
id002   test2.edf   staging2.xml

Relative paths are evaluated relative to the directory that Luna is run from. On a single system, and if files won't be moved often, it is better to use absolute paths. See below for notes on using relative paths, which can be convenient in some circumstances. Also see the path special variable and the --repath helper function that can be used to quickly search/replace paths in a sample list.

In place of an annotation file, it is possible to specify a folder to be searched (but not recursively) for annotation files (those with extensions .annot, .txt, .tsv, .eannot and .xml):

id001   test1.edf   /data/annots/indiv/id001/

Multiple annotation files (or folders) can be listed as separate tab-delimited fields (i.e. columns 3, 4, 5, etc), or as a comma-delimited list in the third column. If there are no annotation files, you can put a period (.) character. These last two rules allow for a clean three tab-delimited column scheme irrespective of the number of annotation files. This can make sample lists easier to work with (e.g. to load into R as a tab-delimited file with a regular, rectangular structure):

id001   test1.edf   test1.tsv
id002   test2.edf   .
id003   test3.edf   test3.tsv,staging-id003.eannot

Warning

Sample lists must be tab-delimited plain-text/ASCII files, i.e. not containing any special characters or formatting. Use a text-editor (not or word processor) or generate them programmatically (see --build). Also be aware of potential issues that Windows-style line-ending characters can cause.

--build option

Luna's --build option can generate sample-lists automatically, by recursively scanning one or more folders (and their subfolders) to find EDF files (ending .edf, .EDF, or .edf.gz etc) and associated annotation files (e.g. .annot, .xml, or a user-specified alternative). By default, an annotation file is said to be associated with an EDF if it has the same file-name (except for the extension); it is not necessary for it to be in the same folder as the EDF.

For example, given these two folders:

ls edfs/

f1.edf f2.edf f3.edf

and

ls xmls/

f1.xml f2.xml f3.xml

The command

luna --build edfs xmls > s.lst

will scan these two folders, matching f1.edf with f1.xml, etc, to generate a sample-list (written to standard output) with three entries:

cat s.lst

f1   edfs/f1.edf   xmls/f1.xml
f2   edfs/f2.edf   xmls/f2.xml
f3   edfs/f3.edf   xmls/f3.xml

Note that you can specify any number of folders for --build to search, and each folder can contain EDFs, annotation files or both.

By default, Luna looks at the filename of the EDF to determine the ID (i.e. what will be placed in the first column of the sample list). Alternatively, you can instruct --build to use the identifier in the EDF header (i.e. which may or may not be the same as the filename of the EDF) to be the sample list ID, by adding the option:

 -edfid

In general, we advise equating the EDF filenames with IDs is better, as this tends to encourage better alignment between the other files associated with that individual/recording.

Matching across folders

If the EDFs and the XML annotations were in the same folder (say mydata), the following would still work as intended:

luna --build mydata > s.lst

Alternatively, different folders might contain distinct EDFs but that have similar file names. For example, we may have two subjects in two folders:

ls subj1 subj2

subj1:
night1.edf  night1.xml  night2.edf  night2.xml

subj2:
night1.edf  night1.xml  night2.edf  night2.xml

In this scenario, we would not not want to associate subj1/night1.edf with subj2/night1.edf or sub2/night1.xml (which --build would do by default, based on the root of the filenames). Here, adding the option -nospan instructs Luna not to span folders when associating files:

luna --build subj1 subj2 -nospan -edfid > s.lst

s1night1    subj1/night1.edf    subj1/night1.xml
s1night2    subj1/night2.edf    subj1/night2.xml
s2night1    subj2/night1.edf    subj2/night1.xml
s2night2    subj2/night2.edf    subj2/night2.xml

In this example, the IDs (s1night1, etc) come from the EDF headers as we used the -edfid option. If the IDs weren't unique, Luna will print a warning message about dulplicates. That is, every row of a sample-list should have a unique ID.

Annotation extensions

To specify special extensions for annotation files (i.e. other than .annot, .xml etc), add the -ext option: e.g. to match on .dat files:

luna --build mydata -ext=dat > s.lst

By default, --build will match potential annotation files based on .xml, .annot, .eannot, .txt and .tsv extensions. You can specify a comma-delimited list of multiple extensions with -ext.

It can be convenient to specify extensions if annotation files have a regular naming scheme but do not match the EDF files identically. For example, many NSRR files have EDF and annotation files in the form:

file1.edf     file1-nsrr.xml
file2.edf     file2-nsrr.xml

To associate these files, add the full tag and extension:

luna --build mydata -ext=-nsrr.xml > s.lst

i.e. this matches file1[.edf] with file1[-nsrr.xml].

Absolute and relative paths

Whether or not the resulting sample-list uses relative or absolute paths depends on how you specify the search folders on the command line:

luna --build edfs xmls

f1  edfs/f1.edf xmls/f1.xml
f2  edfs/f2.edf xmls/f2.xml
f3  edfs/f3.edf xmls/f3.xml

versus

luna --build /Users/mary/proj1/edfs /Users/mary/proj1/xmls

f1  /Users/mary/proj1/edfs/f1.edf   /Users/mary/proj1/xmls/f1.xml
f2  /Users/mary/proj1/edfs/f2.edf   /Users/mary/proj1/xmls/f2.xml
f3  /Users/mary/proj1/edfs/f3.edf   /Users/mary/proj1/xmls/f3.xml

Command files

Command files or scripts (i.e. commands.txt in the example at the top of this page), contain one or more Luna commands. This can be more flexible, convenient (and reproducible) than placing all commands after the -s argument.

Some conventions:

new commands should start on a new line
lines that begin with one or more spaces are assumed to be continuations of the same command, meaning that commands can be spread over several lines
blank lines are skipped
all text after a % character on a line is treated as a comment and skipped

Say we wished to EPOCH an EDF and apply power spectral density estimation via the PSD command for a channel named EEG, outputting spectra for each epoch. For a sample-list s.lst and output file out.db, we might write:

luna s.lst -o out.db -s ' EPOCH & PSD epoch sig=EEG '

Note that we place the command string in single quotes, as otherwise the & character would be interpreted by most shells, to mean that the job should be run in the background. In general, putting any command-line script after -s in single quotes is advised. (Single versus double quotes has implications for how you want variables to be interpret, as shell variables versus Luna variables, as described below.)

Alternatively, we could place the following in a plain-text file called commands.txt (or anything else, there are no limitations on the file name or extension):

EPOCH 
PSD epoch sig=EEG

and run it as follows:

luna s.lst -o out.db < commands.txt

Alternatively, we would achieve the same outcome using a more verbose script, with ample comments and spreading commands and options over multiple lines:

% This is a new command file
% v1.0, 5-Feb-19
% First epoch the data, default epoch duration is 30 seconds

EPOCH

% Power spectral density estimation for the EEG channel
% Note the we start lines after PSD with spaces (otherwise, they
% would be interpreted as new commands)

PSD
  epoch     % produce per-epoch level output 
  sig=EEG   % only apply this command to channels named EEG

Multi-line statements using -s

It is also possible to specify multiline scripts with the -s option. First, different commands can be separated by & or new lines:

luna s.lst -o out.db id=person1 -s ' HEADERS & SEGMENTS '

is the same as

luna s.lst -o out.db id=person1 \
  -s ' HEADERS
       SEGMENTS '

and is also the same as

luna s.lst \
  -o out.db \
  id=person1 \
  -s ' HEADERS
       SEGMENTS '

where \ is the shell line-continuation character. Note, it is not needed between HEADERS and SEGMENTS as the Luna script is quoted; also note that & is not needed as the commands are on different lines.

Second, a single command command can be split onto multiple lines when using -s, by using the \ line continuation symbol (which, as with the shell, must be the last character on that line, no trailing spaces): -s ' HEADERS \ signals SEGMENTS ' This can be convenient if the command has a very long option list.

Note, you don't want or need to put a \ between different quoted Luna commands: if you did, then -s ' HEADERS \ SEGMENTS ' would be read as -s ' HEADERS SEGMENTS ' i.e. without the implicit &. In this case, you could choose to write -s ' HEADERS \ & SEGMENTS ' although this is unnecessary when the following achieves the same result: -s ' HEADERS SEGMENTS ' that is, internally, this is passed to Luna as -s ' HEADERS & SEGMENTS '

Variables

In a command file, a Luna variable var is denoted by the following syntax:

${var}

Building on the previous section's example script, we could modify it to allow different epoch durations and channel names:

EPOCH len=${l}
PSD epoch sig=${s}

When running Luna on this command file, it would then be necessary to specify a value for the variables l and s, e.g.:

luna s.lst l=20 s=EEG < commands.txt

which will then perform the spectral analyses using 20-second epochs. If l or s were not specified, Luna would give an error.

Using variables can make command files more generic by reducing the need to make minor edits across different projects. For example, consider one project that labels stage N2 sleep NREM2 and has EEG channels C3-M2 and C4-M1, whereas another project uses Stage2 with EEG channel EEG1 only. In this scenario, we could still use a single command file:

EPOCH
MASK ifnot=${nrem2}
PSD sig=${eeg}

but then invoke Luna with project-specific values for these variables (spaces added for clarity):

luna proj1.lst nrem=N2      eeg=C3-M2,C4-M1  -o out1.db < commands.txt

luna proj2.lst nrem=Stage2  eeg=EEG1         -o out2.db < commands.txt

Hint

Using project-specific parameter files as described below can further simplify working with multiple projects.

Within-script variable assignment

It is also possible to define (or redefine) variables within a command script, using the following syntax:

${var=xyz}

which sets ${var} equal to the string xyz; this variable can subsequently be used as above, e.g.:

PSD sig=${var}

You can also use the append syntax with the += operator which generates a comma-delimited string, for example:

${var=a}
${var+=b}
${var+=c,d}

would result in ${var} equalling a,b,c,d. This is used primarily in the context of the CANONICAL command.

It is also possible to use previously defined variables in a variable definition:

${z=${var}_v2}

would set ${z} equal to xyz_v2. Note, it is not possible to use arithmetic expressions in variable definitions: in command scripts, all variables are treated as simple text strings. The following would not work therefore:

${a=2}          
${b=${a}+1}  % NO!!  i.e. sets ${b} to string '2+1' rather than '3'

Using variables on the command-line

If using variables on the command line, i.e. after -s or piping in from echo, etc, rather than using a separate command file, you will need to make sure the shell does not interpret the $ as a shell variable. For example, if using bash, then use single quotes instead of double quotes. That is, this will not work:

 luna s.lst -s "EPOCH & STATS sig=${eeg}"

as the shell will try to expand the variable ${eeg} before passing it to Luna. In this instance, using single quotes to stop the bash shell from expanding the variable will achieve the desired effect:

 luna s.lst -s 'EPOCH & STATS sig=${eeg}'

That is, in the second scenario, Luna "sees" ${eeg} as the sig option for STATS, and so figures out what replacement is desired (e.g. that might be based on data from a vars file, or from a default built-in definition, as is the case for ${eeg}). In contrast, in the first (double-quote) scenario, the shell (and not Luna) will attempt to figure out what the ${eeg} variable means: unless otherwise specified, ${eeg} will not be defined by the shell/prior script, and so Luna will simply see nothing instead of ${eeg}, i.e. sig=.

Inside a command/script, Luna variables have the form ${l}, whereas when setting that variable on the command line, one just writes l=20, for example. Instead of a fixed value (20), one can also set a Luna variable to equal a shell variable, which might even have the same name. Rather than setting l to a fixed value of 20, it would also be possible to use a shell variable to set the Luna variable l - and the shell variable might even have the same name (l):

luna s.lst l=${l} s=EEG -s ' EPOCH len=${l} '

In the above, the first ${l} is the shell variable l, whereas the second ${l} is the Luna variable l.

Best practice

At least when using bash as a shell, single quotes after -s is the most likely best practice. If you want to pass in shell variables to Luna, use the form:

luna s.lst x=${x} -s ' COMMAND option=${x} '

To make the distinction between shell and Luna variables clear, assuming shell variable ${x} the above is equivalent to:

luna s.lst y=${x} -s ' COMMAND option=${y} '

which is also equivalent to

luna s.lst -s " COMMAND option=${x} "

(although this latter form is not advised as it arguably blurs the distinction between shell and Luna variables)

Conditional blocks

There are two ways to specify conditional blocks: the IF command, and [[ blocks. The preferred mechanism is IF because it a) is clearer to read, and b) it is sensitive to variables that are defined dynamically (i.e. during execution of the script).

`IF`/`FI` commands

Within a command file, you can execute only certain parts of the code depending on the value of a variable. Specifically,

empty, 0, or values starting with N or F (i.e. no or false) all evaluate to false / null
all other values evaluate to true (non-null)

The commands here will only be evaluated if ${x} is non-null:

IF x

 ... some commands ....
 ... some commands ....

FI

The term ENDIF can be used instead of FI. Here, the commands within that block will be executed here:

luna s.lst x=T < cmd.txt

but not here:

luna s.lst x=F < cmd.txt

or here:

luna s.lst < cmd.txt

Importantly, IF is responsive to variables defined within the script:

${x=T}

... other commands ....

IF x

 ... some commands ....
 ... some commands ....

FI

This can be useful if the variable is dynamically set by the script (e.g. from the CONTAINS command).

`[[` blocks

This syntax is supported for historical reasons only: using the IF command is preferred.

Within a command file, you can define blocks that are only executed if a variable is set to a non-null value, e.g. 1.

Importantly, these blocks are evaluated when first reading the script: this means they are not sensitive to variables defined on-the-fly (i.e. within a script, unlike the IF command.

If the variable is null (undefined or 0) those blocks are skipped. This uses the following double-bracket syntax:

EPOCH len=${l}

[[var

  SIGSTATS sig=${eeg} mask th=${thresholds}

]]var

PSD sig=${eeg}

If ${var} is null, then all text (i.e. including any other variable definitions and conditional statements as well as commands) will be skipped, up until the end of the block (here ]]var). In this example, the SIGSTATS command will only be executed if ${var} has been set to a non-null value:

luna my.edf var=1 < cmd.txt

Note how the variable var is referenced without the usual ${} syntax when paired with [[ or ]]. Also note that every block opening (e.g. [[var) requires a matching block closing (e.g. ]]var). Luna will give an error if it encounters a block closing without having first encountered a closing.

It is possible to set nested conditional blocks:

% commands here always executed

[[a

 % commands here only executed if ${a} is non-null

 [[b
   % commands here only executed if both ${a} and ${b} are non-null
 ]]b

 % commands here only executed if ${a} is non-null

]]a

% commands here always executed

Sequence expansion

Luna scripts support a simple convenience feature to specify regularly-structured sequences of items, for places where Luna is expecting a comma-delimited list of entries (e.g. for sig or annot etc). This is done using the form [x][y] where x and y are of the form:

a single value, e.g. ch-
a comma-delimited list, e.g. a,b,c
an n:m integer numeric sequence, e.g. 1:3 (which implies 1,2,3)

The two lists are expanded as follows:

[a][1:3] = a1,a2,a3
[a][x,y,z] = ax,ay,az
[a,b,c][1:3] = a1,a2,a3,b1,b2,b3,c1,c2,c3

These can also accept variables. For example, the command:

HILBERT sig=${eeg} f=11,15

will add a new channel for every channel in ${eeg} with a default suffix _ht_mag, e.g. C3_ht_mag, C4_ht_mag, etc, reflecting the instantaneous magnitude (envelope) from the filter-Hilbert transform.

If one wants to subsequently refer to the whole group of these new channels, you can write [${eeg}][_ht_mag], i.e. which expands to C3_ht_mag,C4_ht_mag etc.

Similarly, it can sometimes be convenient to automatically specify a series of channels, e.g for the output of ICA, where new channels are created as ICA1, ICA2, etc. Use the form [root][1:3] to obtain a comma-delimited list root1,root2,root3. For example:

PSD sig=[ICA][1:5]

is identical to

PSD sig=ICA1,ICA2,ICA3,ICA4,ICA5

As above, this can be combined with a variables to specify the number of components:

PSD sig=[ICA][1:${k}]

luna s.lst k=10 < cmd.txt

Individual variables

As well as run-level variables that are common to all individuals/EDFs processed, you can assign values on an individual-by-individual basis, using values stored in a text file - here called vars files.

For example, the following vars file defines three variables ${var1}, ${var2} and ${var3} for the tutorial individuals:

ID       var1    var2       var3
nsrr01   22      EEG1,EEG2  T
nsrr02   12      EEG1       F
nsrr03   98      .          T

A vars file should:

be a ASCII, plain-text file (no special characters, etc)
have a header row that includes the column ID in the first field
be tab-delimited, with the same number of columns on each row

Variables can be given any valid name: i.e. they do not need to be var1, var2, etc, but they should not include special characters and they are case-sensitive. You then include these variables by setting the vars special variable to point to the file(s). If the above file is named indiv.dat:

luna s.lst vars=indiv.dat < my-commands.txt

You can have multiple vars statements, or pass vars a comma-delimited list of multiple files to include.

If the command script contained references to ${var1}, etc, they would be substituted as appropriate for each individual. For example, all the EDFs had channels EEG1 and EEG2, the following command would run the PSD command 1) for both, 2) only for EEG1, and 3) neither, for the first, second and third individual respectively:

PSD sig=${var2}

The log summaizes any attached variables for each individual: e.g. for the first individual (var1, etc are listed at the end):

 variables:
  airflow=AIRFLOW | ecg=ECG | eeg=EEG(sec),EEG | effort=THOR_RES,A...
  emg=EMG | eog=EOG(L),EOG... | hr=PR | id=nsrr01 | light=LIGHT
  oxygen=SaO2,OX_STAT | position=POSITION | var1=22 | var2=EEG1,EEG2 | var3=T

The other automatic variables listed above (airflow, etc) derive from Luna's automatic assignment (aka guessing) of channel types. The VARS command dumps list of which variables are defined for each individual.

You can add the special variable verbose=T to make the console print out the variables in full (i.e. above we see the default reduced format).

Individual-ID substitution

One special variable is the ^ symbol (or, equivalently, ${id}), which denotes the ID (from the sample-list) of the current observation, which is automatically set for each EDF processed. This can be useful to point to individual-specific files as inputs or outputs.

For example, below we use a combination of a project-specific variable p and the special individual-ID ^ variable with the EPOCH-ANNOT command:

...
EPOCH-ANNOT file=/path/to/${p}/data/^.eannot 
...

With the above script, one might then issue commands such as:

luna proj1.lst p=proj1 -o out1.db < commands.txt

luna proj2.lst p=proj2 -o out2.db < commands.txt

and (assuming both projects had IDs id0001, id0002, etc) Luna would look to the correct places to attach the epoch-annotations, e.g.:

/path/to/proj1/data/id0001.eannot
/path/to/proj1/data/id0002.eannot
/path/to/proj1/data/id0003.eannot
...

or

/path/to/proj2/data/id0001.eannot
/path/to/proj2/data/id0002.eannot
/path/to/proj2/data/id0003.eannot
...

When using a command such as as WRITE or WRITE-ANNOTS, you will almost always want to use ^: e.g.

 WRITE-ANNOTS file=annots/^-v2.annot

would generate a file annots/id0001-v2.annot for an individual with ID id0001.

Parameter files

As well as defining variables, other command-line options control aspects of Luna's behavior, as tabulated below. These are called special variables, which might be needed for any analysis of an entire project. For example, to set the search path for files from a sample list, one might use:

luna s.lst path=/home/joe/data/edfs/ -o out1.db < commands.txt

i.e. if the sample list just had the relative path p1/id1.edf, adding the above path would make Luna search for /home/joe/data/edfs/p1/id1.edf instead.

Rather than having to retype such things on every Luna command line, it can be convenient to wrap them up in a parameter file, which is included with a special @ syntax, as follows:

luna s.lst @param.txt -o out.db < commands.txt

where param.txt (which can be called any legal filename) is a plain-text file that includes (possibly among other things) the line:

path    /home/joe/data/edfs

Arguments in param.txt are inserted as though they were explicitly typed on the command line. Note that whereas the command line expects key=value pairs, parameter files use a tab to delimit the key (variable name) and value. Thus, parameter files should contain exactly two tab-delimited columns on every row. As a larger example:

alias   EEG|C3-M2|C3|EEG1
sig EEG
annot-folder    /path/to/my/annots/
path    /path/to/my/data/
sr  256
sample  project-name
nrem1   "Stage 1 sleep|1"
nrem2   "Stage 2 sleep|2"
nrem3   "Stage 3 sleep|3"
nrem4   "Stage 4 sleep|4"
rem     "REM sleep|5"
wake    "Wake|0"
excl    "Arousal resulting from respiratory effort|Arousal (ARO RES)","Arousal|Arousal ()","ASDA arousal|Arousal (ASDA)","Limb movement - left|Limb Movement (Left)","Periodic leg movement - left|PLM (Left)","Respiratory artifact|Respiratory artifact","Respiratory effort related arousal|RERA","Spontaneous arousal|Arousal (ARO SPONT)","Unscored|9","Unsure|Unsure"

Note that the use of quotes is necessary when the annotation (e.g. Stage 2 sleep|2) contains spaces (or commas or the special | character).

In the above example, we define an alias (EEG) which is specified to be the only channel loaded (via the sig option). As well as setting the annot-folder and path folders, this parameter file also defines a number of other variables that might be used in command scripts. For example, ${sr} might be the sampling rate; ${nrem1}, ${nrem2}, etc, specify the annotation labels used for sleep stages; the comma-delimited list in ${excl} might define a list of exclusionary annotations, e.g. to be used with MASK:

MASK if=${excl}

Annotations

The standard EDF format does not allow for any additional annotations, i.e. labels that typically describe events in the data, such as sleep stages, artifacts, or other scored features (e.g. spindles). The EDF+ format has some limited support for annotations but is awkward to work with: although Luna can read EDF+ annotations, these are not the preferred mode.

EDF+ annotations

EDF+ annotations are limited by record size, and hard to generate or edit without altering the original EDF+ file. For many practical applications, where the annotations reflect derived features of the sleep time series data, it is simpler to keep the signal data and the annotation information separate.

As well as EDF+ Annotations, Luna accepts various other types of annotation file that typically describe events in the EDF, which are specified in the sample-list and associated with the EDF. Luna accepts the following annotation formats:

Format	Description
.annot	Generic Luna annotation format (`.txt` and `.tsv` extensions are also valid)
.eannot	Simple epoch-level annotation files (can also be loaded via the `EPOCH-ANNOT` command)
EDF+	EDF+ Annotation channels
XML	XML format used by the National Sleep Research Resource to distribute sleep staging, and information on manually-scored arousals, movements and artifacts

Dates

By default, all dates are assumed to be in European (day-month-year) format (following from the use of EDF as the primary input format). This extends to annotation (e.g. .annot) files. The special variables read-mdy-annot-dates and read-mdy-edf-dates allow for non-European (month-day-year) format dates to be read from files -- either in annotations or EDF headers -- if set to true (T). Currently, all outputs are in European format, and any other commands (e.g. to specify the EDF header via SET-HEADERS) still assumes European date format.

Ranges

Given a sample list, by default Luna will iterate through all EDFs in that list. To restrict analyses to a single EDF, you can specify it directly on the command line, either by its ID or by the number that is its position in the sample list. For the sample list used in the tutorial, for example, if this is called s.lst:

nsrr01  edfs/learn-nsrr01.edf   edfs/learn-nsrr01-profusion.xml
nsrr02  edfs/learn-nsrr02.edf   edfs/learn-nsrr02-profusion.xml
nsrr03  edfs/learn-nsrr03.edf   edfs/learn-nsrr03-profusion.xml

you could analyze only nsrr02 by either

luna s.lst nsrr02 < commands.txt

or

luna s.lst 2 < commands.txt

To operate on a range of subjects within a sample list, just give two numbers: e.g.

luna large.lst 50 100 < commands.txt

The above would analyze from the 50th to the 100th EDFs in the large.lst project sample list. This can be useful if using Luna on a cluster, to parallelize processing via batch submission, for example.

The special variables id and skip (also include and exclude ID list files) can alternatively be used to control which individuals are analysed from a sample list.

Note

If a number is given after the sample list, it is always interpreted as the position in the sample list, not an ID. In other words, best not to use pure numbers as IDs in the sample list if possible. If the IDs are numeric, you can always us id

lune s.lst id=22 -o out.db < cmd.txt

i.e. this will look for an EDF with the ID (first column in s.lst) that matches the ID 22 (nb. matching is for a string, so 022 != 22)

EDFZs

As described in this vignette, to save disk space (and sometimes speed up analysis), Luna can read and write compressed EDF files, using the BGZF library. EDFZ files must be created by Luna's WRITE command, with the edfz parameter option added. For example, taking the first tutorial EDF, we can write it out as an EDFZ:

luna s.lst 1 -s ' WRITE edfz edf-dir=z/ edf-tag=compressed sample-list=z.lst '

If the original EDF wasfile.edf, this creates two files z/file-compressed.edfz and z/file-compressed.edfz.idx (along with a sample list z.lst that points to them). As well as .edfz, the extension .edf.gz (paired with a .edf.gz.idx file) is supported - this latter form is preferrable as utilities such as gunzip may expect to see a final .gz extension.

In the above example, we see a reduction in disk space:

ls -lh z

    21M  z/learn-nsrr01-compressed.edfz
   528K  z/learn-nsrr01-compressed.edfz.idx

In contrast, the original EDF is almost three times the size:

    59M  edfs/learn-nsrr01.edf

Although for a single PSG this saving is negligible, across thousands of studies, savings can become more significant.

Although EDFZ files must be created by a special Luna command, they can be read (i.e. decompressed) as any other gzip file. The following standard Unix/Mac gunzip command decompresses an EDFZ to a standard EDF:

cat file.edfz | gunzip > file.edf

See information on the WRITE command's edfz option for more details.

Hint

Although compression as an EDFZ is lossless (i.e. all information is preserved), there may be small differences between the original EDF and an uncompressed EDFZ simply due to floating point accuracy of the EDF format. This is not specific to EDFZ files per se -- it also applies to standard EDFs generated by the WRITE command.

Plain-text input

Luna can read signals from ASCII-formatted, tab-delimited plain-text files as well as EDFs. Consider if we had a file signals.txt with 15,360 rows and three columns (i.e. three signals):

head signals.txt

 4.18192918193   9.73748473748  6.33394383394
 3.93772893773   6.74603174603  6.94444444444
 3.44932844933   4.12087912088  7.09706959707
 2.41147741148   2.28937728938  6.33394383394
 0.21367521367   1.12942612943  5.72344322344
-3.02197802198  -0.27472527472  4.96031746032
-6.74603174603  -2.53357753358  3.89194139194
-9.43223443223  -4.91452991453  3.12881562882
-9.92063492063  -6.86813186813  2.67094017094
-8.45543345543  -8.15018315018  1.75518925519

If Luna finds the option --fs (specifying a sample rate) on the command line, it will interpret the first argument to be a text file (rather than a sample list or an EDF). In this instance, the sample rate is set to 256 Hz (and so, implies 15,360/256 = 60 seconds of signal).

luna signals.txt --fs=256 -s DESC

Processing: signals.txt [ #1 ]
  reading 3 signals, 60 seconds (15360 samples 256 Hz) from signals.txt
 ..................................................................

EDF filename      : signals.txt
ID                : signals.txt
Clock time        : 00.00.00 - 00.01.00
Duration          : 00.01.00
# signals         : 3
Signals           : S1[256] S2[256] S3[256]

Here, we see the recording is of the expected length (1 minute). If combined with the WRITE command, one can use Luna to convert a text file into an EDF.

The new signals are, by default, labelled S1, S2, etc. If the --chs option is specified on the command-line, different channel labels can be assigned:

luna signals.txt --fs=256 --chs=Cz,Fz,Pz -s DESC

Signals           : Cz[256] Fz[256] Pz[256]

Alternatively, if the first row of the text file starts with a # symbol, Luna assumes this is a comma-delimited list of channel labels:

#EEG1,EEG2,EEG3

Signals           : EEG1[256] EEG2[256] EEG3[256]

Warning

If both a header row and --ch are specified, the values in --chs will be used. If the number of channels specified by either --chs or the header does not match the number of columns in the file, Luna may give an error, as it expects the total number of sample points read to be a multiple of the number of channels and the sampling rate. In other words, internally, Luna will structure the data as an EDF with a 1-second record size, and therefore any input must contain an integer number of seconds.

Naturally, if a different/incorrect sampling rate is given, Luna will assume the recording is of a different length (subject to the constraint above about integer number of seconds being required): e.g.

luna signals.txt --fs=128 -s DESC

Duration          : 00.02.00

Additionally, all channels must have the same sample rate when being input as ASCII.

Raw data and EDF comparisons

As a simple demonstration of converting between ASCII and EDF formats (and also to show the relative speed and filesize benefits of EDF), here we'll generate random signals for 4 channels for a 10 hour recording at 256 Hz using awk:

echo | awk '{for (i=0;i<256*60*60*10;i++) print rand(),rand(),rand(),rand()}' OFS="\t" > i.txt

Whereas R takes about 25 seconds to read these data (using a vanilla call to read.delim()), Luna takes about 7 seconds:

luna i.txt --fs=256 -s DESC

reading 4 signals, 36000 seconds (9216000 samples 256 Hz) from i.txt

ID                : i.txt
Clock time        : 00.00.00 - 10.00.00
Duration          : 10:00:00  36000 sec
# signals         : 4
Signals           : S1[256] S2[256] S3[256] S4[256]

We can convert to an EDF, i.edf:

luna i.txt --fs=256 -s WRITE edf=i

Luna now reads the EDF in approximately 0.1 seconds:

luna i.edf -s READ

(we've added the READ to force Luna to load all the signal data from EDF)

In terms of file size, whereas i.txt is 316M, the corresponding i.edf is only 70M, i.e. one fifth the file size.

Empty EDFs

Rather than reading data from a file, it is possible to specify an empty or "virtual" EDF. This will have a fixed duration and sample rate, but initially no channel/signal data. This can be convenient when using certain commands that do not require signal data, e.g. the SIMUL or OVERLAP commands.

To create an empty EDF, specify . (period character) as the sample-list/filename along with --nr and --rs to give the number of records (nr) and the EDF record size (rs) respectively. Luna will create an EDF of this duration (i.e. with headers speciying the length of the recording) but with no signals, i.e. a collection of empty records.

Time points

Internally, Luna encodes time in time-points where 1 unit is 10^-9 seconds (stored internally as uint64_t types). A handful of outputs from some commands use this format (rather than in seconds, clock-time or sample-points). For a given EDF, time-points start at 0, corresponding to the start of the EDF. One consequence is that Luna cannot represent any event that occurs before the EDF start. (If this becomes an issue, it is always possible to work with EDF+D files that have a sufficiently early EDF start, but then the first signal records starting at some later point, i.e. which would be after initial annotations.)

Channel location files

Some commands that work with hdEEG data require a channel location map - a "clocs" file. Locations should be in Cartesian X, Y, Z format.

Four tab-delimited columns
First column is channel name
Second to fourth columns are X, Y and Z coordinates

Internally, all coordinates are converted to spherical coordinates on a unit sphere, so any scaling can be used.

Here is an example file: https://zzz.bwh.harvard.edu/dist/luna/clocs/clocs64.

If a clocs file is not specified but a particular command requires one, Luna will use a default map, applicable for typical 64-channel applications (matching the example file above).

Special variables

Special variables (options that control Luna's behavior) are tabulated below. For command-line Luna, these should be placed after the samlpe-list/EDF (first argument) but before any -s command; otherwise, in general the order typically doesn't matter. All special variables must be assigned (=) an explicit value. Often this will simply be T meaning true to turn on that option. For example, this is incorrect as Luna would assume that force-edf is an ID in the s.lst sample list:

luna s.lst force-edf < cmd.txt

The correct format is:

luna s.lst force-edf=T < cmd.txt

i.e. Luna uses the presence of the key=value form to let it know this is not an ID.

Controlling inputs

Special Variable	Description
`id`	Only analyse these IDs from the sample list, e.g. `id=study-001` or `id=p1,p3`
`skip`	Skip these IDs from the sample list, e.g. `skip=study-001` or `skip=p1,p3`
`vars`	Specify a file with individual-level variables/values
`ids`	Specify a file of remapped IDs
`exclude`	Specify a file of IDs to exclude from analysis
`include`	Specify a file of IDs to include from analysis
`path`	Set search path for files in sample lists
`preload`	Preload the entire EDF if `T`
`order-signals`	Force EDF signals to be in alphabetical order
`fix-edf`	Attempt to correct truncated/over-long EDFs if `T`
`force-edf`	Skip EDF annotations and time-track from any EDF+, and force as a continuous EDF if `T`
`read-mdy-annot-dates`	Assume US-style month-day-year dates when reading all annotation files if `T`
`read-mdy-edf-dates`	Assume US-style month-day-year dates when reading the EDF start date if `T`

Controlling outputs

Special Variable	Description
`silent`	Runs Luna silently if `T`
`verbose`	Runs Luna in verbose mode if `T`
`tt-prepend`	Add value to start of text-table file names (equiv. `tt-prefix`)
`tt-append`	Add value to end of text-table file names (equiv. `tt-suffix`)
`compressed`	Y/N to force all `-t` text-table output to compressed (Y) or not (N)

Signals and EDF headers

Special Variable	Description
`sig`	Include this signal(s) in analysis
`anon`	Anonymize EDF headers
`starttime`	Set EDF start time
`startdate`	Set EDF start date
`wildcard`	Set individual ID wildcard character (default is `^`)

Annotations

Special Variable	Description
`annot-file`	Specify annotations to attach on the command line
`annots`	(Or `annot`). Load only this (comma-delimited) list of annotation classes (rather than all)
`tab-only`	Only allow tabs (vs tabs and spaces) as delimiters in `.annot` files
`annot-keyval`	Set key=value delimiter for annotation meta-date (default: `=`)
`align-annots`	(Advanced) Align these annotations (comma-delimited list) to EDF record start, assuming 1 second records
`class-inst-delimiter`	Specify character to delimit annotation classes and instances (default: `:`)
`combine-annots`	Character to use when combining classes and instance IDs (default: '_' )
`annot-whitelist`	Read only these annotations
`annot-unmapped`	Read only these annotations
`annot-remap`	Read only these annotations

`sec-dp`	Set number of decimal places for annotation time outputs (default: 3)
`add-ellipsis`	For `WRITE-ANNOTS` of `.annot`only, set zero-duration events to have `...` stop fields
`annot-segment`	Label for segment annotation from `SEGMENTS annot` (default: `segment`)
`annot-gap`	Label for gap annotation from `SEGMENTS annot` (default: `gap`)

`skip-annots`	(Or `skip-all-annots`). Same as `skip-sl-annots=T` and `skip-edf-annots=T` combined (default: F)
`skip-sl-annots`	Skip annotation files specified in the sample list (default: F)
`skip-edf-annots`	Skip EDF Annotations tracks from any EDF+ (default: F)
`inst-hms`	Assign missing annotation instance IDs based on time
`force-inst-hms`	Always assign annotation instance IDs based on time
`annot-remap`	Set automatic remapping of stages (default: `T`)
`nsrr-remap`	Set extra NSRR remapping of annotations (default: `F`)
`edf-annot-class`	Read these EDF+ (comma-delimited) labels as classes (default: `N1,N2,N3,R,W,?,arousal,LM,NR`)
`edf-annot-class-all`	Read all EDF+ labels as classes (default: `F`)

Annotation meta-data

Special Variable	Description
`annot-meta-default-num`	Set default annotation meta-data type to numeric if present/`T`
`num-atype`	Set these meta-data keys to numeric type, e.g. `num-atype=dur,amp,frq`
`int-atype`	As above, for integer type
`txt-atype`	As above, for string (text) type
`bool-atype`	As anove, for boolean (T/F) type
`annot-meta-delim1`	Set meta-data delimiter 1 (default `;`, e.g. `a=1;b=2` )
`annot-meta-delim2`	Set meta-data delimiter 2 (default `\|`, e.g. `a=1\|b=2` )
`annot-keyval`	Set key=value delimiter for annotation meta-date (default `=`)

Remapping channel/annotation labels

Special Variable	Description
`alias`	Specify a channel alias
`remap`	Specify an annotation remapping (cf. channel aliases)
`sanitize`	Change special character labels to `_` if this is set to `T`
`upper`	Set all channel labels to uppercase if set to `T`
`spaces`	Alternate character for space substitution in channel/annotation names
`keep-spaces`	Retain spaces in channel/annotation names if set to true
`keep-channel-spaces`	Retain spaces in channel names if set to true
`keep-annot-spaces`	Retain spaces in annotation names if set to true
`retain-case`	Keep signal label case when it (case-insensitive) matches primary alias

Epochs and sleep staging

Special Variable	Description
`epoch-len`	Specify the default epoch duration
`no-epoch-check`	Do not enforce epoch check for .eannot files
`epoch-check`	Set tolerance value for epoch check (default: 5)
`assume-pm-start`	Force morning times (after X am) to be X pm
`assume-stage-duration`	Assume zero-duration stage labels are of epoch-length
`ss-prefix`	Set stage annotation prefix (for reading in stage data)
`ss-pops`	Same as `ss-prefix=p`
`ss-soap`	Same as `ss-prefix=s`

Misc

Special Variable	Description
power bands (various)	Change default power bands (delta, theta, etc.)
`srand`	Set the seed of the random number generator to this fixed value, e.g. `srand=123456`
`ch-exact`	Add an exact match for a channel type
`ch-match`	Add a partial match for a channel type
`ch-clear`	Clear all channel type mappings

Any other variables specified on the command line or a parameter file are interpreted as typical variables, that can be used in scripts: e.g.

luna s.lst xyz=123 < cmd.txt

will set ${xyz} to 123 if used in scripts. Special variables (i.e. those tabulated above) are reserved names and cannot be used in scripts.

Specifying special variable values

Variables (special or otherwise) always need to be explicitly assigned a value: e.g.

luna s.lst keep-spaces=T < cmd.txt

rather than just

luna s.lst keep-spaces < cmd.txt

as in the second case, keep-spaces would be interpreted as an ID to be matched in the sample list s.lst. (In this sense, the syntax varies from command line options, e.g. one can write PSD dB versus having to explicitly write PSD dB=T.)

For variables that expect true/false values:

matches are case-insenstive
values of 1 or starting with T (true) or Y (yes) are all interpreted as true
all other values are interpreted as false; for clarity, 0, F or N should be used in practice

Special variables can be assigned values on the command line, or via an @-included parameter file.

Signal lists

To restrict analyses to a subset of signals/channels in an EDF, use the sig option either on the command line

luna s.lst sig=EEG,ECG,EMG -s DESC

or in a parameter file as separate lines

sig EEG
sig ECG
sig EMG

or as a comma-delimited list

sig EEG,ECG,EMG

Note

These options (when used on the command line, or via a parameter file) mean that only these channels are loaded from the EDF, i.e. it is as though the other channels do not exist from Luna's perspective. (One minor but virtuous side effect is that this can speed up reading an EDF, if one knows that only a subset of channels is needed.)

This is different from the using the sig option to modify the behavior of an individual Luna command: in this latter case, it is only that particular command that is restricted to those signals/channels, and so other channels are still part of the in-memory EDF and available for subsequent processing. For example:

...
FILTER bandpass=0.3,35 ripple=0.01 tw=0.2 sig=C3 
STATS sig=C3,EMG,ECG
...

Note

The terms signals and channels are used interchangeably throughout this documentation.

sig and EDF+

The sig special option cannot be used with EDF+ files.

The sig option works with the alias options also. For example, if the original EDF label is CH_X001 but an alias has been defined to convert it to EEG, we can use that aliased form in the sig statement:

luna s.lst sig="EEG,EMG,ECG" alias="EEG|CH_X001" -s DESC

That is, we've relabeled CH_X001 as EEG and used sig to select it; the output from DESC reads:

Signals           : EEG EMG ECG

Restrictions for channel names

Channel names should not have any of the following characters: comma, tab, new-line, pipe (|). Moreover, there are advantages in not using any special characters (e.g. space, parentheses, asterisks, etc) or characters that are common logical or arithmetic operators, e.g. minus, plus signs, etc. Avoiding such characters makes it easier to specify channels on the command line and in scripts.

Avoding special characters in channel labels can also make processing output easier, i.e. if you use destrat to produce a table that uses channel labels as variable (column) names.

In general, it is desirable to restrict channel labels to alphanumeric characters and the underscore character as a separator. See this FAQ. You can also use Luna aliases to make better channel names.

Ordering signals

Setting order-signals to true (T, Y or 1) will ensure that EDF channels are loaded in alpha-numeric order: e.g.

luna s.lst 1 -s DESC

Signals           : C3[128] C4[128] A1[128] A2[128] LOC[128] ROC[128]
                    ECG2[256] ECG1[256] LEFT_LEG1[256] LEFT_LEG2[256] RIGHT_LEG1[256] RIGHT_LEG2[256]
                    EMG1[256] EMG2[256] EMG3[256] AIRFLOW[32] THOR_EFFORT[32] ABDO_EFFORT[32]
                    SNORE[256] SUM[32] POSITION[1] OX_STATUS[1] PULSE[1] SpO2[1]
                    NASAL_PRES[64] PlethWV[128] Light[1024] HRate[1024]

In contrast, with ordering:

luna s.lst 1 order-signals=T -s DESC

Signals           : A1[128] A2[128] ABDO_EFFORT[32] AIRFLOW[32] C3[128] C4[128]
                    ECG1[256] ECG2[256] EMG1[256] EMG2[256] EMG3[256] HRate[1024]
                    LEFT_LEG1[256] LEFT_LEG2[256] LOC[128] Light[1024] NASAL_PRES[64] OX_STATUS[1]
                    POSITION[1] PULSE[1] PlethWV[128] RIGHT_LEG1[256] RIGHT_LEG2[256] ROC[128]
                    SNORE[256] SUM[32] SpO2[1] THOR_EFFORT[32]

This can be useful when wanting to harmonize EDFs, i.e. to ensure that the SIGNALS output of HEADERS is not trivially different due only to different ordering. One other context where this can matter is for commands that output pairwise channel combinations: typically this is done according to the order of the EDF header, and so whereas one EDF might output CH1 as C3 and CH2 as F3, for example, another may output these reversed (if the EDF order differs). Having a fixed order can make it easier to combine outputs (i.e. without having to double-enter all outputs).

Preloading

By default, Luna performs lazy loading of EDFs, meaning it only pulls a record when it is needed. On first attaching an EDF, only the header is loaded from disk, which is always very quick. One exception is for EDF+D channels: on first attaching a file, Luna must scan all records in order to be able to build the timeline for the recording. If the file is large and contains a large number of records, this can take a non-trivial amount of time.

Further, by default Luna uses random-access reading, i.e. skipping to a record within the EDF and only reading that record, one record at a time. The performance of this type of random access approach can vary depending on the operating system and file system. For example, modern solid state drives (SSDs) typically do not incur any penalty for randomly accessing a file, even if the entire file is to be read from disk. In contrast, hard disk drives (HDDs) often perform better when streaming sequentially across a large file. Further, network-attached storage may incur different costs for random versus sequential access of data.

If performance is slow, especially for EDF+D files, it can be useful to set preload=T which means that the entire file is read in a single, sequential pass, which is often quicker (especially as, in practice, many commands will end up pulling all records from disk anyway).

The default is not to preload data, as quite a few commands don't actually need to read any signal data from the EDF (e.g. reporting headers, working with annotations, or in the context of using the Luna library as part of an interacrive viewer, as in lunapi's scope(), etc).

Search paths

As noted above, when parsing sample-lists Luna can use either absolute or relative paths for EDFs and annotation file-names. To use the same project on different computers, it is often convenient to hard-code absolute path names, i.e.

id001   /home/joe/edfs/proj1/edf1.edf
id002   /home/joe/edfs/proj1/edf2.edf
id003   /home/joe/edfs/proj1b/edf3.edf

as this means that you can run Luna from any folder and it will still know where to look for the EDFs. Alternatively, the path option (either on the command line, or in a parameter file) lets you write a sample list in relative terms:

id001   proj1/edf1.edf
id002   proj1/edf2.edf
id003   proj1b/edf3.edf

One would then give the path separately, which will be added as a prefix to all relative paths in the sample list:

luna s.lst path=/home/joe/edfs < commands.txt

(i.e. otherwise Luna would not be able to find the EDFs unless it was run from the /home/joe/edfs/ folder directly.)

This can also be convenient if the project is moved, i.e. if /home/joe/edfs/ becomes /home/mary/projects/, then you only need change the path rather than recreate the sample list:

luna s.lst path=/home/mary/projects/ < commands.txt

Aliases

Aliases are different names for channels/signals in an EDF. Aliases can be useful if different EDFs in a project have different labels for the same channel, e.g. C3, C3-M1 and C3-A1. Alternatively, aliases can be useful if a channel has a long unwieldy name, perhaps that contains spaces or other special characters.

Aliases can be specified either on the command line:

luna s.lst alias="C3|C3-M1|C3-A1" -s STATS sig=C3

or in a parameter file:

alias   C3|C3-M1|C3-A1

where the format is a series of |-delimited labels, with the first being the primary alias, or canonical channel label.
When specifying channels, one can either use the original EDF terms (e.g. C3-M1) or the primary alias (C3). That is, even if the EDF only has a channel C3-M1, it will still be included in any analysis that requires C3. Similarly, in all output (including new EDFs generated via the WRITE command), the canonical channel labels (primary aliases) will be swapped in whenever needed (i.e. to C3 here). It is not necessary that the canonical form exists in any of the project's EDFs: it could be an new label you wish to apply to this group of differently-named but otherwise identical channels.

Note

Because most shell scripts interpret | as a special control character (pipe), we use quotes when specifying alias on the command line, i.e. alias="C3|C3-M1|C3-A1". This also implies that channel names should not contain | characters.

Remapping annotations

The remap option operates in the same way as the alias option, except for annotation labels instead of channel names. For example, to change an annotation REMS to REM, add the following:

luna s.lst remap="REM|REMS" < cmd.txt

As with aliases, you can specify multiple, |-delimited remappings, i.e. in a many-to-one fashion. Likewise, you can put these in a parameter file rather than write these out on the command line. This will also be easier if you annotations have spaces and special characters; you'll still need to use quotes if the labels have spaces: e.g.

remap      REM|REMS|"REM Sleep"|"Rapid eye movement sleep"

This will remap any of the three forms listed to the primary label: REM.

Automatic annotation remappings

Note that Luna by defaults add in some default annotaton remappings for sleep stages, e.g. turning Stage NREM1 to N1, etc, so that the HYPNO, SOAP and POPS commands know which labels to expect. This can be disabled by setting annot-remap=F. It is also possible to turn on some more mappings for common NSRR labels (e.g. arousals, apnea, etc) by adding nsrr-remap=T. Note that the order of annot-remap and nsrr-remap will matter (as annot-remap turns off all annotation remappings.

Spaces in channel and annotation names

BY default, Luna swaps all spaces in channel or annotation names with an underscore (_) character, and will also trim any leading or trailing space/underscore characters. You can change the character swapped in by setting the special variable spaces

luna s.lst spaces=/ < cmd.txt

Note: if the desired character would cause problems with the shell (e.g. an * character), then you can instead put these assignments in a parameter file, e.g. param.txt:

spaces     *

luna s.lst @param.txt < cmd.txt

As an aside: we do not recommend swapping in special characters into channel and annotation labels: the point of the spaces option is to make these labels easier to interact with in a typical command-line environment.

To turn off this functionality, set keep-spaces=T. To turn it off for only channel labels use keep-channel-spaces=T. To turn it off for only annotation labels use keep-annot-spaces=T.

Any aliases and remappings will be matched to both the pre-translated (i.e. with spaces present) and post-translated (i.e. with spaces potentially swapped out).

Channel types

Based on the channel label, Luna will attempt to classify the type of channel and automatically assign corresponding variables (e.g. ${eeg} and ${emg}). The current channel types are listed below:

Type	Variable	Description
`IGNORE`	`${ignore}`	Flag to ignore these channels
`REF`	`${ref}`	Mastoid EEG reference
`IC`	`${ic}`	Independent components
`EOG`	`${eog}`	Electrooculogram
`ECG`	`${ecg}`	Electrocardiogram
`EMG`	`${emg}`	Electromyogram (chin)
`LEG`	`${leg}`	Leg EMG
`AIRFLOW`	`${airflow}`	Nasal or oral airflow
`EFFORT`	`${effort}`	Respiratory effort indicators (e.g. chest belts)
`OXYGEN`	`${oxygen}`	Oxygen saturation (e.g. pulse oximetry)
`POSITION`	`${position}`	Position
`LIGHT`	`${light}`	Light channel
`SNORE`	`${snore}`	Snore channel
`HR`	`${hr}`	Heart rate/pulse
`GENERIC`	`${generic}`	Generic channel (i.e. unknown) type
`EEG`	`${eeg}`	Any EEG channel

Types are assigned based on channel names, as defined here, and are set up for typical PSG and sleep EEG studies, but can be altered by the user:

Setting ch-clear=Y will clear the current list of type definitions
ch-match can add a partial match to the list of type definitions. Partial matches are case insensitive and do not need to fully match the channel label, e.g. eeg will match EEG1, EEG A, and eeg_Cz.
ch-exact can add an exact match to the list of type definitions. Exact matches are case sensitive and do need to fully match the channel label, e.g. eeg will only match eeg and not EEG1, eeg1, etc.

Both ch-match and ch-exact expect a comma-delimited list of definitions, where each definition is a pipe-delimited list of a) the type, and b) one or more matches. For example, this assigns A1 and A2 as partial matches for the type EEG:

ch-match="EEG|A1|A2"

This example does as above, but additionally assigns EKG1 to the type ECG:

ch-match="EEG|A1|A2,ECG|EKG1"

As with channel aliases, these are better placed in an include file, e.g. if the text file called param param contains (two tab-delimited columns):

ch-match    EEG|A1|A2
ch-match    ECG|EKG1

then they will be included here:

luna s.lst @param < cmd.txt

When determining channel type, Luna will attempt to match exact matches first, and then partial matches. Furthermore, within each class of match, Luna will try to match types in the order as listed in the table above (i.e. IGNORE first, then EOG, etc, until EEG).

Whenever new channels are added within a Luna run (e.g. via ICA or COPY), a new type label will be assigned as appropriate, and the corresponding variables (e.g. ${ic} or ${eeg}) will be updated.

Exclude lists

To skip one or more EDFs in a project, you can create an exclude list: a plain-text file with one ID per row. You can then use the exclude option to point to this file, either on the command line:

luna s.lst exclude=skip.txt -s DESC

or by specifying it in a parameter file

exclude skip.txt

These individuals/EDFs will be skipped in all analyses.

Include lists

Using the include keyword, this is similar to exclude-lists except this means that only individuals in the specified file will be included, everybody else will be excluded. You cannot specify an include list and exclude list together.

Swapping IDs

The ids special variable takes a file (e.g. ids=file.txt), for which each row should have exactly two tab-delimited fields refleting the observed (original) ID in the first column, and the new ID in the second column: e.g.

id1 newid1
id2 newid2

Luna swaps the original ID (as supplied from the sample list) to the new value, if it is encountered.

Anonymize EDF headers

Adding anon=T will wipe the EDF headers (the EDF header Patient ID, Recording Information and Start date fields will be set to their default null values as per the EDF spec.) This is similar to the ANON command except this is performed before any annotations are attached. This will influence how dates are interpreted in any annotation files that use dates, therefore. In contrast, the ANON command allows a greater degree of flexibility in terms of which fields are wiped.

Set EDF start time

This special variable sets the EDF start time (header) value to the specified string, e.g. starttime=20.30.05. This should use EDF spec. for the values: i.e. 8 characters, 24-hour times, hh.mm.ss format with period (.) delimiters. Unlike the SET-HEADERS command, this change is made on first attaching the EDF, before any annotations are attached: annotation times will therefore reflect these changes, depending on whether they use relative or absolute values, etc.

Set EDF start date

This special variable sets the EDF start date (header) value to the specified string, e.g. startdate=25.12.00. This should use EDF spec. for the values: i.e. 8 characters, dd.mm.yy format with period (.) delimiters. Dates cannot be before 01.01.85 which is the null date as per EDF spec. Unlike the SET-HEADERS command, this change is made on first attaching the EDF, before any annotations are attached: annotation times will therefore reflect these changes, depending on whether they use relative or absolute values, etc.

Attaching annotations

To attach an annotation file without having to edit the sample-list, you can use the annot-file (or equivalently annot-files, annots-file or annots-files) option.

luna s.lst 1 annot-file=path/to/file.annot < cmd.txt

This will be most useful when working with a single EDF - especially as the ^ special character for individual ID is not translated on the shell command line. To use annot-file (or any other special variable) in a programmatic manner, one can use shell variables, e.g. within a loop, where here ${id} is a shell variable, e.g.:

for id in `cut -f1 s.lst`
do
luna data/${id}.edf annot-file=data/${id}.annot -o out/${id}.db < cmd.txt
done

Note that the above scenario would be better approached by simply using a sample list that links EDFs and annotations (although this implies all output in a single database all.db), i.e.:

luna s.lst -o all.db < cmd.txt

Selecting annotations

To only load certain annotation classes use the annot (or equivalently annots) option. For example, the following only loads classes labeled wake and artifact1:

luna s.lst annots=wake,artifact1 < commands.txt

To specify this in a parameter file:

annot          wake,artifact1

This can be useful if the sample-list otherwise specifies that many annotations are loaded by default (e.g. by pointing to an annotation folder for that individual/EDF).

EDF+ annotations

Unless skip-edf-annot=T or skip-annots=T are set, Luna will read any EDF Annotations channels present in EDF+ files and treat them as standard annotations (i.e. as if they were read from an .annot or XML file).

As EDF+ annotations can often contain notes, Luna does not assign a class to each unique annotation: rather, all annotations are assigned to the edf_annot class, with the instance ID set the the value in the EDF+. This behavior can be changed by setting the special variable edf-annot-class-all=T. Alternatively, a subset of EDF+ annotations can be set to classes, and everything else pooled under the edf_annot class, with edf-annot-class=X,Y,Z option. By default, the following special values are treated this way (after annotation remapping, unless annot-remap=F to handle variation in stage labels): N1,N2,N3,R,W,?,arousal,LM,NR

Other annotation options

The skip-all-annots option (yes/no) indicates whether to skip loading all annotations (default no):

skip-all-annots    Y

The skip-edf-annots option (yes/no) indicates whether to skip loading EDF annotations tracks (default no):

skip-edf-annots    1

Epochs and sleep staging

The epoch-len command can be used to specify a default epoch duration (in seconds) different from 30, which will be used when attaching .eannot files specified in the sample-list (i.e. to calculate the implied number of epochs in the EDF).

epoch-len   20

Stage annotations

Unless annot-remap=F, Luna will attempt to map a set of "typical" stage labels (e.g. Stage N1, Stage NREM1, NREM1, etc) to a standard set of labels: the five main stages are:

  N1  N2  N3  R   W

and L is a lights-on epoch and ? is unknown/missing.

If working with other sets of stage labels (e.g. from manual scoring as well as POPS, etc) it can be useful to distinguish them by a prefix. The ss-prefix special variable can achieve this, e.g. by ss-prefix=p will change the above to

  pN1  pN2  pN3  pR  pW

Commands such as HYPNO that depend on these labels will then use those values if they exist, instead of the standard ones.

Also, when reading stage labels from an annotation file, the assume-stage-duration=T will change zero-duration labels to be of epoch length. (Sometimes an annotation file does not explicitly specify the duration/end of each stage, and so (if each annotation is indeed one epoch), this can be convenient.)

Fix truncated EDFs

Some exporters generate EDFs that do not have a complete final EDF record; alternatively, file transfer may result in a truncated file. For example, if the EDF record size is 1 second, but the total recording length is, say, 20000.5 seconds, and so the last 0.5 seconds does not constitute a full record, but something is nonetheless written to disk (i.e. the EDF shoule either be 20,000 or 20,001 seconds, in this case).

For these cases, where there is a small difference (typically < 1 record fewer than expected), you can add the fix-edf=T option to the command line. For example, here is an error encountered with a real EDF as found in the wild:

luna s.lst -s DESC

Processing: id_XXXXXX [ #1 ]
 uniqifying Resp/Abd1-Gnd to Resp/Abd1-Gnd.1

 error : corrupt EDF: expecting 288820320 but observed 288817152 bytes
 details:
   header size ( = 256 + # signals * 256 ) = 5120
   num signals = 19
   record size = 7600
   number of records = 38002
   implied EDF size from header = 5120 + 7600 * 38002 = 288820320

   assuming header correct, implies the file has -0.416842 records too many
   (where one record is 1 seconds)

Luna then goes on to give the following suggestion - but stressing the point that it is only an assumption that the data are truncated (i.e. and otherwise okay). (That is, there could be other reasons why the EDF size does not match that expected based on the EDF headers.)

 IF you're confident about the remaining data you can add the option:

    luna s.lst fix-edf=T ... 

  to attempt to fix this.  This may be appropriate under some circumstances, e.g.
  if just the last one or two records were clipped.  However, if other EDF header
  information is incorrect (e.g. number of signals, sample rates), then you'll be
  dealing with GIGO... so be sure to carefully check all signals for expected properties;
  really you should try to determine why the EDF was invalid in the first instance, though

Re-running but with the fix-edf=T option added:

luna s.lst fix-edf=T -s DESC

allows Luna to proceed (with a warning)

  assuming header correct, implies the file has -0.416842 records too many
  (where one record is 1 seconds)

  attempting to fix this, ...
    changing the header number of records from 38002 to 38001 ... good luck!

 duration: 10.33.21 | 38001 secs ( clocktime 20.38.43 - 07.12.03 )

 signals: 19 (of 19) selected in a standard EDF file:
  F3-Ref | F4-Ref | C3-Ref | C4-Ref | O1-Ref | O2-Ref | A1-Ref | A2-Ref
  ...

In other words, proceed with care if you find yourself having to use this option...

Force evening start time

By default, Luna assumes a 24-hour clock format, and so a start time in the EDF of 8:00 means 8am and not 8pm. If you suspect an EDF has used a 12-hour time format instead (which does not properly specify whether it is AM or PM), you can set the variable assume-pm-start=X, meaning that Luna will assume a 12-hour clock but convert all times between X AM and noon to X PM. For example:

 assume-pm-start=4

means that EDF header start times of 04:00, or 5:30 will be converted to 16:00 and 17:30 respectively. However, 1:30 will remain as 01:30. That is, this function works on the assumption of "typical" bedtimes being in the late evening or very early morning. If the EDFs use 24-hour notation correctly, then you should have no reason to use this option.

Spectral power bands

The following special variables can be changed on the command line or via a parameter file:

Band name	Definition
`slow`	Slow power band (default 0.5-1 Hz)
`delta`	Delta power band (default 1-4 Hz)
`theta`	Theta power band (default 4-8 Hz)
`alpha`	Alpha power band (default 8-12 Hz)
`sigma`	Sigma power band (default 12-15 Hz)
`beta`	Beta power band (default 15-30 Hz)
`gamma`	Gamma power band (default 30-50 Hz)
`total`	Total power band, denominator for relative power (default 0.5-50 Hz)

For example, to change the definition of sigma power to 11 to 15 Hz (instead of 12 to 15 Hz):

luna s.lst sigma=11-15 -s "PSD sig=C3,C4"

Output

Logs

Luna writes a log to the standard error (stderr) stream, i.e. the console, that reports the progress of a given command. This will display the version of Luna, the date and time the command was initiated, and the input commands. For each EDF processed, Luna will then list the ID along with some basic information about the EDF, its attached annotations and the commands applied to that EDF. Any error messages will be sent to the stderr also.

luna s.lst 1 -o out.db -s HEADERS

===================================================================
+++ luna | v0.99, 04-Dec-2023 | starting 04-Dec-2023 12:24:49 +++
===================================================================
input(s): s.lst
output  : out.db
commands: c1    HEADERS 

___________________________________________________________________
Processing: nsrr01 [ #1 ]
 duration 11.22.00, 40920s | time 21.58.17 - 09.20.17 | date 01.01.85

 signals: 14 (of 14) selected in a standard EDF file
  SaO2 | PR | EEG_sec | ECG | EMG | EOG_L | EOG_R | EEG
  AIRFLOW | THOR_RES | ABDO_RES | POSITION | LIGHT | OX_STAT

 annotations:
  Arousal (x194) | Hypopnea (x361) | N1 (x109) | N2 (x523)
  N3 (x17) | Obstructive_Apnea (x37) | R (x238) | SpO2_artifact (x59)
  SpO2_desaturation (x254) | W (x477)

 variables:
  airflow=AIRFLOW | ecg=ECG | eeg=EEG_sec,EEG | effort=THOR_RES,A...
  emg=EMG | eog=EOG_L,EOG_R | hr=PR | id=nsrr01 | light=LIGHT
  oxygen=SaO2,OX_STAT | position=POSITION
 ..................................................................
 CMD #1: HEADERS
   options: sig=*

___________________________________________________________________
...processed 1 EDFs, done.
...processed 1 command set(s),  all of which passed
-------------------------------------------------------------------
+++ luna | finishing 04-Dec-2023 12:24:49                       +++
===================================================================

Output verbosity

The special variables verbose and silent control the level of console output.

luna s.lst 1 verbose=T -o out.db -s HEADERS

===================================================================
+++ luna | v0.99, 04-Dec-2023 | starting 04-Dec-2023 12:25:41 +++
===================================================================
input(s): s.lst
output  : out.db
commands: c1    HEADERS 

___________________________________________________________________
Processing: nsrr01 [ #1 ]
 duration 11.22.00, 40920s | time 21.58.17 - 09.20.17 | date 01.01.85
  40920 records, each of 1 second(s)

 signals: 14 (of 14) selected in a standard EDF file
  SaO2 | PR | EEG_sec | ECG | EMG | EOG_L | EOG_R | EEG
  AIRFLOW | THOR_RES | ABDO_RES | POSITION | LIGHT | OX_STAT

 annotations:
  [Arousal] 194 instance(s) (from edfs/learn-nsrr01-profusion.xml)
  [Hypopnea] 361 instance(s) (from edfs/learn-nsrr01-profusion.xml)
  [N1] 109 instance(s) (from edfs/learn-nsrr01-profusion.xml)
  [N2] 523 instance(s) (from edfs/learn-nsrr01-profusion.xml)
  [N3] 17 instance(s) (from edfs/learn-nsrr01-profusion.xml)
  [Obstructive_Apnea] 37 instance(s) (from edfs/learn-nsrr01-profusion.xml)
  [R] 238 instance(s) (from edfs/learn-nsrr01-profusion.xml)
  [SpO2_artifact] 59 instance(s) (from edfs/learn-nsrr01-profusion.xml)
  [SpO2_desaturation] 254 instance(s) (from edfs/learn-nsrr01-profusion.xml)
  [W] 477 instance(s) (from edfs/learn-nsrr01-profusion.xml)

 variables:
  airflow=AIRFLOW
  ecg=ECG
  eeg=EEG_sec,EEG
  effort=THOR_RES,ABDO_RES
  emg=EMG
  eog=EOG_L,EOG_R
  hr=PR
  id=nsrr01
  light=LIGHT
  oxygen=SaO2,OX_STAT
  position=POSITION

 ..................................................................
 CMD #1: HEADERS
   options: sig=*

___________________________________________________________________
...processed 1 EDFs, done.
...processed 1 command set(s),  all of which passed
-------------------------------------------------------------------
+++ luna | finishing 04-Dec-2023 12:25:41                       +++
===================================================================

As expected, when running with silent=T, Luna doesn't generate any output to the (standard error) console:

luna s.lst 1 silent=T -o out.db -s HEADERS

Default text output

Beyond the log information described above, if no database option is specified (with -o or -a) then, by default, all primary output goes to stdout, i.e. the console/terminal, and will be interleaved with the logging information. That is, here output refers to the information produced by individual Luna commands, rather than the log information per se.

This is typically not very useful. You can redirect the output to a separate file, say out.txt:

luna s.lst < commands.txt > out.txt

Whilst a few commands such as DESC or SUMMARY produce their own format of output (simple text formatted for human reading), most commands adopt the same output framework, such that the same information can be channeled to either a text file (described here), a database (described next) or even an object in R if using the Luna R extension library.

Using the HEADERS command as an example on the first EDF in the tutorial dataset:

luna s.lst nsrr01 sig=ECG,EMG  -s HEADERS > out.txt

The out.txt file contains the following:

nsrr01  HEADERS .   .   NS  2
nsrr01  HEADERS .   .   NR  40920
nsrr01  HEADERS .   .   REC.DUR 1
nsrr01  HEADERS .   .   TOT.DUR.SEC 40920
nsrr01  HEADERS .   .   TOT.DUR.HMS 11.22.00
nsrr01  HEADERS .   .   EDF_ID      
nsrr01  HEADERS .   .   START_TIME  21.58.17
nsrr01  HEADERS .   .   START_DATE  01.01.85
nsrr01  HEADERS CH/ECG  .   SR      250
nsrr01  HEADERS CH/ECG  .   PDIM        mV
nsrr01  HEADERS CH/ECG  .   PMIN        -1.25
nsrr01  HEADERS CH/ECG  .   PMAX        1.25
nsrr01  HEADERS CH/ECG  .   DMIN        -128
nsrr01  HEADERS CH/ECG  .   DMAX        127
nsrr01  HEADERS CH/EMG  .   SR      125
nsrr01  HEADERS CH/EMG  .   PDIM        uV
nsrr01  HEADERS CH/EMG  .   PMIN        -31.5
nsrr01  HEADERS CH/EMG  .   PMAX        31.5
nsrr01  HEADERS CH/EMG  .   DMIN        -128
nsrr01  HEADERS CH/EMG  .   DMAX        127

Each row is one value for one variable from one command. In this case, only the HEADERS command was performed. The six tab-delimited columns are:

Individual/EDF ID
Command name
Any stratifying factors (or . if not)
Any epoch/interval time factors (or . if not)
Variable name
Value

Stratifying factors mean that the same variable is repeated in different contexts: for example, for different channels in the same EDF. This is represented above by the factor (channel, CH) and the two levels (ECG and EMG). Given that SR is the sample rate for a channel, we can see that the ECG channel has a sample rate of 250 Hz, whereas the EMG has a sample rate of 125 Hz, for example. The first variables, e.g. NR and NS do not have any stratifying factors (. in columns 3 and 4) as these are general properties of the entire EDF, and so only occur once.

This format is primarily used for debugging or in some other very focused cases. Although it is relatively easy to parse, in general you'll want to use Luna's text-tables or lunout databases, described next.

Text-tables

Text-table output format creates a folder for every individual/EDF analysed, containing one plain-text file (tab-delimited, rectangular file with a header row) for every output strata of every command performed.

Text-table output mode is engaged by adding -t to the command line, followed by the name of a root folder (this will be created if it does not exist). For example:

luna s.lst -t out1 -s 'MASK ifnot=NREM2 & RE & PSD spectrum sig=EEG'

will create a folder out1/. Applied to the tutorial data, this would create the following three subfolders, each named by the ID of the individual/EDF:

ls out1/

 nsrr01  nsrr02  nsrr03

Each subfolder will typically contain a set of identical files, reflecting the analyses that were performed:

ls out1/nsrr01

 MASK-EPOCH_MASK.txt  PSD-B,CH.txt  PSD-CH.txt  PSD-F,CH.txt  RE.txt

Certain commands that tend to generate very large output files (e.g. PSD epoch-spectrum) will generate compressed (gzipped) output files by default (with extension .txt.gz). To force all output files to be compressed, set the compressed special variable to true (Y or 1):

luna s.lst -t out1 compressed=Y < s.lst

Alternatively, to set all output files to not be compressed, set compressed to false (N or 0).

Known issues

Please see this page for some current known issues with the initial implementation of the -t flag.

lunout databases

This is the primary mode of output for most Luna commands. Here we run the same command as in the previous section but instead using a lunout database to collect the output, with -o:

luna s.lst nsrr01 sig=ECG,EMG -o out.db -s HEADERS

This generates a file out.db (actually an SQLite database) which is not designed to be directly displayed in the terminal via a text-editor or spreadsheet. Rather, it is an intermediate form, from which various text-files can be extracted in a variety of formats. See this page for information on how to work with output databases, using either destrat or lunaR.

By default, Luna will overwrite an existing database; use -a instead of -o to append to an existing database.

Naming

We don't actually use this name throughout most of the documentation as a) it is the implicit default in most cases, and b) it is an ugly-sounding name, but we couldn't come up with anything better ;-). So, when referring to an output database generically, this means the same as a lunout database.

Which should I use: text-tables or data-bases?

Advantages of the database output format is that all information (potentially from multiple people) is contained in a single place, and can be queried with destrat. Databases can also be loaded directly into R, using ldb(). Disadvantages are 1) for very large projects or output files, performance can suffer, and 2) to export into other software (other than R via lunaR), you first need to extract the information as an intermediate text file. Text-table mode (-t) effectively is the same as dumping (via destrat) all possible tables from a given database; for certain types of large output files, this can be advantageous. The disadvantage of text-table mode is that results are not automatically compiled across individuals: if your project contains 100 individuals, you'll have 100 separate subfolders, each with the same text-table files. The lunaR package provides the function ltxttab() that can help by automatically compiling output across different individuals/subfolders.

In general, use text-table mode to improve performance and avoid duplicating information for commands that generate very large output files (e.g. PSD epoch-spectrum for EDFs with many channels; typically, one is less interested in combining this type of output across different individuals in any case). See the tutorials for examples of using both formats.

Caches

Caches are an advanced, internal feature, to be used to share information between different Luna commands within the same single dataset, in particular the PREDICT command.

New EDFs

Luna can output new EDFs (or EDF+ files, or compressed EDFs) after manipulating signals, masking epochs, etc, via the WRITE command.

Annotations

Some commands, such as WRITE-ANNOTS, can produce .annot files containing interval-based annotations. Other commands (e.g. SPINDLES) may generate annotations internally, which can be used by subsequent commands; to output those annotations, use WRITE-ANNOTS.

Misc text-file dumps

Some commands produce flat-file text output distinct from the usual output mechanism (via the database or text-tables, as described above), for example MATRIX or ICA. These outputs can often be quite large files.