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Helpers

Miscellaneous functions designed to help with Luna workflows

Command Description
--build Generate a sample list automatically
--repath Change root filepaths in a sample list
--merge Merge (concatenate) multiple EDFs
--xml View NSRR XML annotation files
--xml2 View NSRR XML annotation files (verbose)
`--otsu Calculate thresholds based on Otsu's method (external data)
`OTSU Calculate thresholds based on Otsu's method (internal channel)

--build

Automatically compile a sample list

to be added

Parameters

Parameter Example Description
-nsrr Assume NSRR file names
-ext Include this extension

Output

A sample list written to the standard output stream.

Example

to be added

--repath

Swap out file paths in a sample list

Reads a sample list from standard input, and (ignoring the first ID column) changes the starting path. This can be useful if you have moved the EDFs, and so need a new path. Alternatively, if you are working with files mounted via a network drive, or from a Docker container, then the paths may be different from the local paths.

This command accepts . as the first argument, meaning always append the second argument if (and only if) the sample list has a relative path.

Parameters

Parameter Example Description
first arg /old/path/ Part of sample list to be replaced ( or .)
second arg /new/path/ Replacement

Output

x A new sample list written to the standard output stream.

Example

If the working folder have changed from Users/js7/data to home/jsmith/cfs/, for example. The original sample list (4 files from CFS):

cat s.lst
cfs-800002  /Users/js7/data/cfs-800002.edf  /Users/js7/data/cfs-800002.xml
cfs-800010  /Users/js7/data/cfs-800010.edf  /Users/js7/data/cfs-800010.xml
cfs-800011  /Users/js7/data/cfs-800011.edf  /Users/js7/data/cfs-800011.xml
cfs-800017  /Users/js7/data/cfs-800017.edf  /Users/js7/data/cfs-800017.xml

Using repath to fix the sample list:

luna --repath /Users/js7/data /home/jsmith/cfs < s.lst > s2.lst
cat s2.lst
cfs-800002  /home/jsmith/cfs/cfs-800002.edf /home/jsmith/cfs/cfs-800002.xml
cfs-800010  /home/jsmith/cfs/cfs-800010.edf /home/jsmith/cfs/cfs-800010.xml
cfs-800011  /home/jsmith/cfs/cfs-800011.edf /home/jsmith/cfs/cfs-800011.xml
cfs-800017  /home/jsmith/cfs/cfs-800017.edf /home/jsmith/cfs/cfs-800017.xml

--merge

Create a single EDF from multiple partial EDFs

Some systems may export EDFs in small segments (e.g. each 1 hour or 5 minutes in duration). The --merge command can take these and create a single EDF for analysis.

Future versions of this command will be able to merge "horizontally" (i.e. EDFs with different channels) as well as handling overlapping regions and/or gaps. As it stands, this command only provides a simple way to concatenate multiple EDFs that must have identical header structures (in terms of the number of channels, their labels and samples rates). That is, currently we assume that all segments specified are contiguous, and without gaps. They do not need to be of similar duration, however.

Parameters

Parameter Example Description
id id001 ID to be specified in the resulting EDF's header
edf merged.edf Filename for the resulting EDF
sample-list s.lst Write the resulting ID/EDF pair to a sample list
* f1.edf f2.edf ... Two or more EDFs to be merged

Output

No output other than message to the log and writing a new, merged EDF (and optionally, writing to a sample list).

Example

echo "id=id01 edf=id01.edf sample-list=s.lst data/*.edf" | luna --merge

This command will read all the EDFs in the folder data/ and attempt to concatenate them, and save a new EDF called id01.edf. The resulting EDF will have the start time set to the earliest start time/date observed in the whole set. EDFs will be concatenated (as a single, continuous EDF) in the order in which they are specified on the command line. Therefore, be careful if using wildcards as per the above example (i.e. if ordered files are listed as block1.edf, block10.edf, block11.edf, ..., block2.edf). In this example, use, e.g. block01.edf, block02.edf, etc to ensure correct sorting.

--xml

Dump XML annotation files

Also see --xml2

to be added

Parameters

to be added

Output

to be added

Example

to be added

--xml2

Dump any XML file

Also see --xml

to be added

Parameters

to be added

Output

to be added

Example

to be added

--build

Automatically compile a sample list

See here for details.

Parameters

Parameter Example Description
-nsrr Assume NSRR file names
-ext Include this extension

Output

A sample list written to standard output.

--otsu

Derive Otsu optimal binary threshold for values from an external file

to be added

OTSU

Derive Otsu optimal binary threshold for values from an internal EDF channel

to be added

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