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Outputs

Commands to rewrite EDFs and signals/annotations in other text-based formats

Command Description
WRITE Write a new EDF file
MATRIX Dump signals (and annotations) to a file
DUMP-RECORDS Dump annotations and signals, by EDF record
RECS Dump basic information on EDF record structure
SEGMENTS Dump (discontinuous EDF+) intervals
SEDF Generate a "summary EDF"

WRITE

Save a (modified) EDF file to disk

Writes a new EDF to disk, that will reflect any manipulation, filtering, or masking, etc, that has been applied.

Parameters
Parameter Example Description
sig sig=C3 Signal to output (only one)
edf-dir edf-dir=edfs/ Set folder where new EDFs should be written
edf-tag edf-tag=v2 Add a tag to each new EDF filename
sample-list sample-list=v2.lst Name of the new sample-list
Output

No formal output, other than a message to the log and one or more new EDFs.

Example

To write a set of new EDFs that (for example) have been masked, filtered and retaining only one signal, given the commands in a file, say cmd.txt as follows:

EPOCH                       % Epoch the signals

MASK epoch=1-10             % Set to retain only the first 10 epochs

RESTRUCTURE                 % Apply the above mask 

SIGNALS keep=EEG            % Only retain the EEG signal

FILTER bandpass=0.5,4.5     % Apply a bandpass filter to the signal
       ripple=0.01
       tw=0.5 

WRITE edf-dir=newx/         % Write new EDFs, to the folder newx/
      edf-tag=v2            % add a 'v2' tag to each EDF
      sample-list=newx.lst  % create a new sample list pointing to the new EDFs

Running this set of commands:

luna s.lst < cmd.txt

will produce a new folder newx with three new EDFs:

ls newx
learn-nsrr01-v2.edf learn-nsrr02-v2.edf learn-nsrr03-v2.edf

That is, the new EDF filenames have a -v2 tag added. The folder (which must be specified with a / character in the edf-dir argument) will be created if it does not exist. In addition, Luna creates a new sample-list called newx.lst, that points to these new EDFs:

cat newx.lst 
nsrr01        newx/learn-nsrr01-v2.edf
nsrr02        newx/learn-nsrr02-v2.edf
nsrr03        newx/learn-nsrr03-v2.edf

Note that Luna appends each item to this list, and so you may want to delete it before running the command, if it already exists.

We can use the new sample list to check the properties of the new set of EDFs:

luna newx.lst -s DESC

As expected, we do in fact see that the EDFs are now only 10 epochs in length and contain only a single channel: (here, showing output only for the first EDF):

EDF filename      : newx/learn-nsrr01-v2.edf
ID                : nsrr01
Clock time        : 21:58:17 - 22:03:17
Duration          : 00:05:00
# signals         : 1
# EDF annotations : 1
Signals           : EEG[125]

Finally, to check the filtering, we can use the MATRIX command to dump the raw signals to a file. First from the original EDF (for the first 10 epochs only):

luna s.lst 1 -s "MASK epoch=1-10 & RE & MATRIX sig=EEG file=old.txt"
luna newx.lst 1 -s "MATRIX file=new.txt"

In R

o <- scan("old.txt",skip=1)
n <- scan("new.txt",skip=1)
plot( o[1:1000] , type="l" ) 
lines( n[1:1000] , col="blue" ) 

../img/write.png

MATRIX

Dumps signal information to a file

For one or more signals of similar sampling rates, this command generates a text file containing the raw signal data.

Parameters
Parameter Example Description
file file=signals.txt Required parameter, to specify the filename for the output
sig sig=C3,C4 Restrict output to these signals/channels
hms hms Add a clock-time column in hh:mm:ss format
hms2 hms2 Add a clock-time column in hh:mm:ss:microsecond format
annot annot=X,Y Add columns with values 1/0 to indicate the presence/absence of that annotation
min min Minimal output to show only signal information (no headers or lead columns)
Output

All output is written to a text file as specified by the file parameter. For example:

ID    E   S   SP   T           EOG-L      EOG-R     EMG       EEG      
id01  1   0   0    0           -6.07448   4.18193   31.044    0.763126  
id01  1   0   1    0.00390625  -0.030525  2.83883   52.7778   11.5079   
id01  1   0   2    0.0078125   7.23443    2.22833   45.3297   23.0464   
id01  1   0   3    0.0117188   11.569     2.10623   23.4127   29.4567   
id01  1   0   4    0.015625    12.9731    2.16728   8.82173   31.2882  
id01  1   0   5    0.0195312   12.79      2.22833   -4.73138  30.7387  
id01  1   0   6    0.0234375   12.1795    2.28938   -13.6447  29.6398  
id01  1   0   7    0.0273438   11.6911    2.22833   -14.1331  28.663   
id01  1   0   8    0.03125     11.3858    2.22833   -11.8742  28.0525  
id01  1   0   9    0.0351562   11.2027    2.16728   -13.4615  27.6862  
... cont'd ...

Here, the first five columns are:

  • ID: individual/EDF ID
  • E: epoch number
  • S: elapsed time in seconds (integer)
  • SP: sample point in the EDF record
  • T: elapsed time in seconds

The subsequent columns represent the channels in the EDF (or those specified by the sig parameter).

If the min (or minimal) parameter is specified, then the header and the first five columns are omitted.

If the hms parameter is specified, then an additional column HMS is added, which is the clock-time in hh:mm:ss format. If hms2 is specified instead of hms, this field is printed with micro-second resolution.

If the annot parameter is specified, additional columns are added with the same names as the annotations specified, e.g. annot=X,Y will add two columns X and Y. For each sample point, these columns will have a 0 or 1 value to indicate whether or not that annotation was present at that point.

DUMP-RECORDS

Writes detailed annotation and signal data to standard output

This command is unlikely to be of great utility to most users. It dumps detailed information about the signals and annotations to stdout.

Parameters
Parameter Example Description
no-signals no-signals Do not show signal data
no-annots no-annots Do not show annotation information
Output

All output is sent to the console (stdout) and so can be redirected, etc. Output is organized by EDF record, e.g.:

Record 1 of 40920 total (30 retained)
followed by Luna annotation information:
Generic Annotations-----------------------
wake    wake    0.00->30.00     wake[flag]=.
and then any EDF+ annotations:
EDF Annotations--------------------------
Signal 15 EDF Annotations
<0||(time-stamp, secs)>
Signals are then displayed, organized by record (in this instance, 1 second); the first signal SaO2 has a sample rate of 1 Hz, and so there is only one entry per record:
s = 0
interval = 0-999999999999
RECORD-DUMP     SaO2    rec=0   1/1     0       0       95.115587
Likewise for the second signal PR:
s = 1
interval = 0-999999999999
RECORD-DUMP     PR      rec=0   1/1     0       0       74.222934
In this example, the third signal (s=2) is EEG(sec), which has a sample rate of 125Hz (and so 125 entries here):
s = 2
interval = 0-999999999999
RECORD-DUMP     EEG(sec)        rec=0   1/125   0       0       -0.49019608
RECORD-DUMP     EEG(sec)        rec=0   2/125   8000000000      0.008   1.4705882
RECORD-DUMP     EEG(sec)        rec=0   3/125   16000000000     0.016   6.372549
RECORD-DUMP     EEG(sec)        rec=0   4/125   24000000000     0.024   3.4313725
RECORD-DUMP     EEG(sec)        rec=0   5/125   32000000000     0.032   -10.294118
RECORD-DUMP     EEG(sec)        rec=0   6/125   40000000000     0.04    -8.3333333
RECORD-DUMP     EEG(sec)        rec=0   7/125   48000000000     0.048   1.4705882
RECORD-DUMP     EEG(sec)        rec=0   8/125   56000000000     0.056   -0.49019608
RECORD-DUMP     EEG(sec)        rec=0   9/125   64000000000     0.064   -0.49019608
RECORD-DUMP     EEG(sec)        rec=0   10/125  72000000000     0.072   7.3529412
RECORD-DUMP     EEG(sec)        rec=0   11/125  80000000000     0.08    11.27451
... cont'd ...
The columns for signals are

  • a standard RECORD-DUMP
  • signal name
  • record number (starting at 0)
  • the sample point per record (e.g. 1/125, 2/125, etc)
  • the starting time for that sample point in time units
  • time in seconds
  • the value of the signal

For most purposes, the MATRIX command will likely be an easier route to achieve direct access to the signals in an EDF. (In fact, this command was in large part only added to assist in debugging during Luna development, but is described here for completeness.)

RECS

Dumps basic information about record structure to standard output

Parameters

None.

Output

Text written to the log/console; this command does not generate any output through Luna's standard output mechanism.

Example

Taking the first tutorial EDF (where EDF is one second):

luna s.lst 1 -s SUMMARY
Rec. dur. (s)  : 1

we extract a subset of the data (epochs 5 through 8, defaulting to 30-second epochs) and then call the RECS command:

luna s.lst 1 -s 'MASK epoch=5-8 & RECS'

The output (to the console) is as follows (abridged):

RECS    nsrr01  1   121 120/40920   120.00->121.00   5;120.00->150.00
RECS    nsrr01  2   122 120/40920   121.00->122.00   5;120.00->150.00
RECS    nsrr01  3   123 120/40920   122.00->123.00   5;120.00->150.00
RECS    nsrr01  4   124 120/40920   123.00->124.00   5;120.00->150.00
RECS    nsrr01  5   125 120/40920   124.00->125.00   5;120.00->150.00

...

RECS    nsrr01  115 235 120/40920   234.00->235.00   8;210.00->240.00
RECS    nsrr01  116 236 120/40920   235.00->236.00   8;210.00->240.00
RECS    nsrr01  117 237 120/40920   236.00->237.00   8;210.00->240.00
RECS    nsrr01  118 238 120/40920   237.00->238.00   8;210.00->240.00
RECS    nsrr01  119 239 120/40920   238.00->239.00   8;210.00->240.00
RECS    nsrr01  120 240 120/40920   239.00->240.00   8;210.00->240.00

The columns are:

  • RECS command label
  • current EDF ID
  • record number with respect to current in-memory EDF representation (always starts 1)
  • record number with respect to original EDF file (starting 121, i.e. the start of the fifth epoch)
  • number of records in the current in-memory EDF / total number of records in the on-file EDF
  • start and stop of this record (in seconds)
  • (for epoched data) the epoch number (e.g. 5-8) that record belongs to, and the epoch start/stop (seconds)

Four 30-second epochs (5,6,7 and 8) implies 120 seconds; the start/stop times correspond to this, as expected: 240-121+1 = 120.

SEGMENTS

Reports the number of contiguous segments in an EDF/EDF+

Identifies and reports on the contiguous segments in a file; this is primarily of use for EDF+ files with discontinuous signal data. Internally, Luna represents signal data as equivalent to an EDF+ after any masks that remove epochs have been applied; therefore, the SEGMENTS command can also be used in this context too.

Parameters

None.

Output

Basic EDF header information (strata: none)

Variable Description
NR Number of segments

Per-segment information (strata: SEG)

Variable Description
START Segment start (seconds)
STOP Segment stop (seconds)
START_HMS Segment start (hh:mm:ss)
STOP_HMS Segment stop (hh:mm:ss)
DUR_HR Segment duration (hours)
DUR_MIN Segment duration (minutes)
DUR_SEC Segment duration (seconds)
Example

Taking the first tutorial EDF, which is a continuous EDF file:

luna s.lst 1 -s SEGMENTS

We'd expect just a single segement to be reported, and this is indeed what we see:

destrat out.db +SEGMENTS
ID  NSEGS
nsrr01  1
That 'segment' spans the entire length of the recording:
destrat out.db +SEGMENTS -r SEG
ID      SEG  DUR_HR   DUR_MIN  DUR_SEC  START  START_HMS  STOP   STOP_HMS
nsrr01  1    11.3667  682      40920     0     21.58.17   40920  09.20.17

In contrast, if we break up the data (e.g. using the MASK command, then the data are implicitly represnted as a discontinuous EDF+ after restructuring:

luna s.lst 1 -t out -s 'MASK epoch=9-12,22-23,70-74 & RE & SEGMENTS'

Hint

Note, purely to illustrate different options, here we used Luna's -t output option rather than -o

Now the SEGMENT command shows the expected three segments:

cat out/nsrr01/SEGMENTS.txt

ID  NSEGS
nsrr01  3
with the correponding times:
cat out/nsrr01/SEGMENTS-SEG.txt 
ID     SEG  DUR_HR     DUR_MIN  DUR_SEC  START  START_HMS  STOP  STOP_HMS
nsrr01 1    0.0333333  2        120      240    22.02.17   360   22.04.17
nsrr01 2    0.0166667  1        60       630    22.08.47   690   22.09.47
nsrr01 3    0.0416667  2.5      150      2070   22.32.47   2220  22.35.17

SEDF

Generates a summary-EDF and writes it to disk

For data channels only (i.e. not any EDF+ annotation channels), the SEDF command creates a "summary" EDF

Option Description
sig Signals to output (if not given, all signals)
sedf-dir Directory for SEDFs (if not working directory)

This creates an EDF in which contains epoch-level summary statistics of the original EDF. That is, if the original EDF has 1000 30-second epochs, the SEDF will comprise only 1000 records, where each record has a duration of 30 seconds, and contains only a single value. For a given channel, e.g. CZ, the SEDF will contain three new channels, depending on the type of that channel. For a channel called XYZ in the original:

  • for oscillatory signals (e.g. EEG, EMG, etc), the three Hjorth parameters: XYZ_H1, XYZ_H2 and XYZ_H3
  • for other signals (e.g. light or heart rate, etc), the mean, min and max: XYZ_M, XYZ_L, XYZ_U

The idea is that this SEDF file is an effective thumbnail for the EDF, which can be quickly loaded and rendered, e.g. by a viewer application.