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FAQ and trouble-shooting

Although not necessarily asked with respect to Luna, here are some frequently asked questions:

What?

Luna is a C/C++ library focused on the analysis of large numbers of sleep studies encoded as EDFs. This is a free, open-source project. Currently, there is a command-line tool (lunaC) and an extension library for R (lunaR).

Which?

The current version is the beta-release v0.25.5 (31-March-2021). Use luna -v to display the specific build date/time.

Where?

Luna is developed at the Brigham & Women's Hospital and Harvard Medical School, Boston, MA, United States.

Who?

Luna was primarily developed by Shaun Purcell, with input from a number of colleagues:

  • Shyamal Agarwal for work on automating the build distribution -- and onging work on the to-be-released web-based NSRR Automated Pipeline (NAP) built around Luna
  • Nataliia Kozhemiako for input into multiple EEG analytic components and the revised artifact detection workflows
  • Alexander Kent for testing and feedback
  • Susan Redline and her team developing the National Sleep Research Resource
  • Dennis Dean for sharing his original SpectralTrainFig code-base
  • Sara Mariani and Charmaine Demanuele for input on several EEG and ECG analysis components

Interested to contribute (either as a colleague or as a job)? Please contact me.

How?

Luna development is indirectly supported via a number of NIH grants: NHLBI R01HL146339 (PI Purcell), NHLBI R21HL145492 (PI Purcell), NIMH R03 MH108908 (PI Purcell), as well as NHLBI R35HL135818 (PI Redline) and NHLBI R24HL114473 (PI Redline).

Why?

This is a good question and deserves a longer answer... The primary aim of Luna was to provide a platform for 1) adopting some of the elegant methods and models that have emerged from animal and lab-based cognitive neuroscience studies over the past decade or so, and 2) for applying them in the context of large (albeit sometimes noisy) epidemiological studies with polysomnography.

As a relative newcomer to sleep research (my personal background is primarily in psychiatric genetics), the development of Luna has tracked with my (still steep) learning curve, in how to think about sleep signal data. Because of this, I adopted the tools I was most familiar with (namely C/C++ and R), rather than the ubiquitous "in-house Matlab script". In developing Luna though, I've been constantly reminded of how powerful Matlab and its associated toolboxes are for working with electrophysiological signal data. I can also appreciate that working with Luna's particular instantiations of specific methods may be unnecessarily restrictive for some.

So, why wouldn't I just use Matlab? There was, from my perspective, still an unmet need for tools to work with sleep data in thousands of individuals, such as from the NSRR. In my (limited) experience of seeing how others approached sleep data, it seemed clear that although the substantive core of a particular analysis (e.g. power spectral density estimation) could be efficiently and flexibly implemented in a single Matlab command (i.e. pwelch() or similar), a lot of the scaffolding around these one or two central functions (i.e. most of the "work" from a practical perspective) was more often than not a tangle of brittle, error-prone and undocumented scripting. Although not a perfect solution even for our own work, Luna represents a modest step in the direction of building more robust and scalable analysis tools.

I had originally conceived of Luna just as my own personal library of functions that would assist me in my sleep research. However, I decided to document and distribute this code for a number of reasons:

  • to make the tool better: documenting and distributing code has intrinsic value, as this process tends to make the underlying tool better, even if it will only ever be used by yourself or a very small number of people.

  • accessibility and transparency: the sleep field is unfortunately replete with black box proprietary software and file formats which can be limiting; making things open-source lets others see what you've done, and use it without restriction.

  • community: others can build upon your work; in genetics, for example, I developed a tool PLINK, which has been quite widely-used. Since it was first developed (in 2007), however, there have been considerable advances in the scale of data, and in the types of analytic approaches taken. Being an open-source tool, others were able to very significantly augment and even rewrite it, to produce an order-of-magnitude more powerful tool, whilst at the same time maintaining the pipelines and community experience that had been built over more than a decade with PLINK.

For both larger and smaller projects, I'd strongly recommend the document/distribute model whenever practically possible.

Acknowledgments

Luna uses a number of excellent open-source components, in particular:

  • FFTW library

  • SQLite embedded database

  • R Project for Statistical Computing

  • Chapters and example code from Mike X Cohen's fabulously clear and practical book: Analyzing neural time series data

  • Lees, J. M. and J. Park (1995): Multiple-taper spectral analysis: A stand-alone C-subroutine: Computers & Geology: 21, 199

  • Laurent Condat (2013) A Direct Algorithm for 1-D Total Variation Denoising . IEEE Signal Processing Letters, 20:11.

  • Multi-scale entropy (MSE) algorithm by Madalena Costa et al. (Costa M., Goldberger A.L., Peng C.-K. Multiscale entropy analysis of biological signals. Phys Rev E 2005;71:021906.)

Trouble-shooting

Windows line endings

MS Windows uses carriage return (CR) and line feed (LF) characters to denote the end of a line, whereas UNIX-like systems (including Mac) use LF alone. The file command on UNIX-like systems will indicate if this is the case.

file *.txt
foo.txt:     ASCII text, with CRLF line terminators
bar.txt:     ASCII text

Use a utility such as unix2dos to convert these files. Otherwise, use the tool tr available on most systems:

tr -d '\r' < infile.txt > outfile.txt

Spaces and special characters in labels

Luna will automatically convert spaces channel and annotation labels to a different character (underscore, _), to facilitate working in a command line (or R) environment with these labels. See here.

By default, spaces are converted to underscores (unless keep-spaces=T), as are special characters (unless sanitize=F). Special characters in this context are:

 (space) - + / \ * < > = & ^ ! @ # $ % ( )
The following are not converted, as they are already treated as special delimiters by Luna:
 " ' | ,

That is, by default the label EEG C3-M2 will become EEG_C3_M2. This facilitates working with channels as variable names in subsequent applications: e.g. TRANS commands, or for processing output in R, for example, if variable/columns are labelled by the CH name. Despite the convention of using labels such as EEG C3-M2 in the EDF specification, this is not convenient for automated processing of data, thus Luna's approach to a) allow those names as inputs, but also b) by default, change them on-the-fly.

As Luna parses command files by whitespace, it is necessary to handle spaces in labels explicitly. If you've turned off the above options (keep-spaces=T and sanitize=F) then you have to explicitly place quotes around labels with spaces: e.g.

STATS sig="THOR RES",SpO2
Otherwise, the command would be parsed as sig=THOR (which would not match any channel) a and RES,SpO2 (which would be ignored).

If you are using the -s option to specify a commands directly as arguments to Luna, you can quote the term with a space in it; this assumes the entire expression will be in single-quotes (which it should be, to avoid the shell interpreting characters such as &, $, etc):

luna s.lst -o out.db -s ' EPOCH & MASK if="REM sleep|5" '

Similarly, if masking on an annotation with a space, you need to put quotes around it. For example, the NSRR annotation for REM sleep has spaces and special characters, REM sleep|5. Therefore, in a command file use:

MASK if="REM sleep|5" 

Alternatively, you can alias or remap labels as they are initially read by Luna, to control more explicitly any renaming meaning that Luna does not have to do this automatically. For example, to change a signal REF X1 to simply REF, one can set an signal alias in a parameter file:

 alias     REF|"REF X1"

Note how we put REF X1 in quotes, to assist the parsing of this term. All subequent commands can now reference REF instead of REF X1.

Paralleling the use of alias for channels, you can use the remap option for annotations:

remap     REM|"REM sleep|5"
Again, note the use of quotes around REM sleep|5 as both spaces and | are special characters (here, | is used to delimit different annotations that would be mapped to the same term, e.g.:
remap     REM|"REM sleep|5"|R|Stage_REM|"Stage REM"|5
i.e. the above maps five different labels to REM; to make it clearer, below we add spaces to show the different terms:
       REM   <-  REM sleep|5     or     R     or     Stage_REM     or     Stage REM      or     5

In general, we suggest you use aliases and remapping if Luna's defaults don't work, but try to use sensible channel labels and annotation names whenever possible.

Advice on channel names

Try to keep channel names to simple alphanumeric characters combined with the underscore character to delimit terms. Although Luna will accept spaces and characters such as + - * % ( ) ., etc, in channel names, we advise against them if you wish to use destrat and other tools such as R to process results downstream.

Info

As as v0.26, Luna will automatically sanitize (replace the above type of special characters with underscores) channel and annotation labels (unless you set sanitize=F).

For any output that is stratified by channel (CH), you may wish to create a dataset where each channel corresponds to a column/variable in the output. Without sanitization of labels, if a variable name is, for example, SIGMA, then using a command like

destrat out1.db -c CH > my-file.txt 

may create variables with names such as SIGMA.CH.C3-M2 or SIGMA.CH.EEG(2). When loaded into R, this may lead to variable names that are harder to work with (i.e. these characters are swapped to . or you need to quote variable/list names, etc). For example, if you output with channels are row stratifiers:

destrat out1.db -r CH > my-file.txt 

but subsequently use an R command such as dcast (from the reshape2 or data.table packages) to generate a data frame where channels correspond to columns, you'll end up with variable names such as d$C3-M2 which can make life difficult (i.e. R would complain that M2 doesn't exist, as the - is interpreted as a minus, so you'd need to write d$"C3-M2", or find other work-arounds, etc).

To avoid this, use aliases.

PS. for other reasons, always good advice to avoid special characters in IDs too... just stick to alpha-numeric characters and underscores. In particular, the ^ character which is the reserved symbol (meaning, within a script, "swap in the ID").

Variables and special characters when using -s

When writing Luna script on the command line, i.e. directly after -s (rather than having Luna read in a script from a file or pipe), it may be necessary to handle special characters that the shell (assuming a bash shell here) might try to interpret different. For example, & would mean to run the prior command in the background; * would be expanded to match all files in the current directory, etc.

The easiest way to handle most scenarios is to use single-quotes around all Luna commands, in this example, to avoid & or | being interpreted as special characters by the shell, e.g.:

 luna s.lst -s 'EPOCH & STATS sig=EEG1|EEG & ANNOTS' 

By using single-quotes, this tells the shell not to interpret the characters there in any way. As such, the input to Luna will be what you'd expect, i.e. the text written as is above.

One possbile exception is if you want to include shell variables in a Luna script. It is important to understand this distinction between shell variables and Luna variables, as they have similar syntax (${var}). However, these are distinct entities, even if they share the same label.

To set a shell variable, e.g. on the shell command line:

eeg=XYZ

If there was a channel named XYZ, you use the following Luna commands:

luna s.lst -s STATS sig=${eeg}
or
luna s.lst -s "STATS sig=${eeg}"
In both cases, ${eeg} will be replaced with XYZ before Luna even sees any input/commands.

In contrast, the following would produce different behavior:

luna s.lst -s 'STATS sig=${eeg}'
as now the shell does not try to expand the shell variable ${eeg} (because it is enclosed within single quotes). Rather, now, Luna will read ${eeg} and interpret it as a Luna variable. (In this case, ${eeg} is a special Luna variable that is expanded to all channels that have a label matching typical EEG channel names.)

If you did want to pass a shell variable into a script using -s, the best way is to define it explicitly prior to the -s script. Say we have a shell variable ${v}:

luna s.lst v=${v} -s 'STATS sig=${v}'
The initial assignment sets a Luna variable (that happens to be called v) equal to the shell variable v; then within the script, it is the Luna variable that is used. To make this clearer, we could give a different label to the Luna variable, but the behavior would be identical:
luna s.lst w=${v} -s 'STATS sig=${w}'
Note that even if the shell variable ${s} exists, the following would not work:
luna s.lst -s 'STATS sig=${s}'
as there is no Luna variable named ${s}. (The example above with ${eeg} was a special case of a pre-populated Luna variable.)

String literals

One or two Luna commands expect single quotes to define string literals: e.g. if using eval expressions, such as c('a','b','c') to define a vector of characters a, b and c. If already using single quotes after the -s command, it will not work to use additional single quotes in expressions such as this. For this special scenario (that likely will not often arise), either 1) place the commands in a separate file rather than use the -s function, or 2) utilize the fact that { an } can stand in for single quotes in this context: e.g. c( {a}, {b}, {c} ) is interpreted identically to the above expression.

EDF+ support for long integers and floats

As noted here, the EDF+ spec allows for a logarithmic transformation which can be helpful to represent floating-point data with a large dynamic range. This is not currently implemented in Luna.

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