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Manipulations

Commands to alter basic properties of the EDF and the signals therein

Command Description
SIGNALS Retain/remove specific EDF channels
RENAME Rename channels
COPY Duplicate one or more EDF channels
RESAMPLE Resample signal(s)
ENFORCE-SR Require a particular sample rate
REFERENCE Re-reference signals
CANONICAL Generate canonical signals
MINMAX Set digital/physical min/max across channels
uV Rescale units to uV
mV Rescale units to mV
FLIP Flip polarity of signal
ZC Mean-center signal
ROBUST-NORM Robust normalisation
EDF Force EDF (versus EDF+) state
TIME-TRACK Add a time-track to an EDF
RECORD-SIZE Change EDF record size
ALIGN Realign EDF records, annotations and epochs
ANON Strip ID information from EDF header
SET-HEADERS Directly specify certain EDF headers
SET-VAR Directly specify Luna variables
RECTIFY Rectify a signal
REVERSE Reverse a signal

SIGNALS

The command requires one of two options: either keep or drop. Each expects a comma-delimited list of channel names (or aliases), which are either retained or removed from the in-memory dataset.

Parameters

Option Example Description
drop drop=EMG,ECG Drop channels EMG and ECG
keep keep=C3,C4 Drop all channels except C3 and C4

Outputs

Other than modifying the in-memory representation of the EDF, there is no further output (except some notes written to the log).

Example

For an EDF with 6 signals, including EMG, EOG-L and EOG-R, this command would drop these three signals:

luna s.lst -s "SIGNALS drop=EMG,EOG-L,EOG-R & DESC"
as shown by the relevant lines in the output from DESC:
Number of signals : 3
Signals           : EEG1[256] EEG2[256] EEG3[256]
In contrast, the keep option with the same arguments:
luna s.lst -s "SIGNALS keep=EMG,EOG-L,EOG-R & DESC"
yields the expected output:
Number of signals : 3
Signals           : EOG-L[256] EOG-R[256] EMG[256]

RENAME

Renames channels

This command can rename channels within the context of evaluating a Luna script. In this way, it differs from using signal aliases (which can only be specified when first initiating Luna, and will be fixed for all individuals), as this command can use variables (which may be individual-specific).

Parameters

Parameter Example Description
sig C3,C4 List of channels to duplicate
new C3_LM,C4_LM List of new labels (same size as sig)

Note that you cannot use an existing channel label as a new label.

Output

No formal output, other than changing the labels of channels in the internal EDF

Example

In its simplest form, if we have a channel named THOR_RES, for example, we can rename to some other label -- here just using XX -- using RENAME, and then use that new label in other commands:

luna s.lst -s ' RENAME sig=THOR_RES new=XX & STATS sig=XX '

Note that this also adds an alias internally, so that THOR_RES can still be used as a label (e.g. with the sig option of a command), but the output will be labelled with the primary term XX.

As noted above, this provides similar functionality as using a signal alias:

luna s.lst "alias=XX|THOR_RES" -s ' STATS sig=XX '

The primary difference is that RENAME accepts (individual-specific) variables as arguments, i.e. which can allow different individuals to have different assignments (with sig and/or new). For example, in this toy example, we change THOR_RES and ABDO_RES (all present in the three individuals in the tutorial dataset to different labels. If we have a tab-delimited file that defines these variables for each individual:

cat ch.txt
ID  CHS
nsrr01  XX,YY
nsrr02  AA,BB
nsrr03  CC,DD

Now, the command

luna s.lst vars=ch.txt \
     -s ' DESC & RENAME sig=THOR_RES,ABDO_RES new=${CHS} & DESC ' 

will use RENAME to swap those two channels to the other specified values: e.g. showing extracts from the DESC output for the three individuals: in all cases, the first DESC command gives the same:

Signals : SaO2[1] PR[1] EEG_sec_[125] ECG[250] EMG[125] EOG_L_[50]
          EOG_R_[50] EEG[125] AIRFLOW[10] THOR_RES[10] ABDO_RES[10] POSITION[1]
          LIGHT[1] OX_STAT[1]
whereas the second DESC varies between the three individuals as expected:
Signals : SaO2[1] PR[1] EEG_sec_[125] ECG[250] EMG[125] EOG_L_[50]
          EOG_R_[50] EEG[125] AIRFLOW[10] XX[10] YY[10] POSITION[1]
          LIGHT[1] OX_STAT[1]

Signals  : SaO2[1] PR[1] EEG_sec_[125] ECG[250] EMG[125] EOG_L_[50]
           EOG_R_[50] EEG[125] AIRFLOW[10] AA[10] BB[10] POSITION[1]
           LIGHT[1] OX_STAT[1]
and
Signal   : SaO2[1] PR[1] EEG_sec_[125] ECG[250] EMG[125] EOG_L_[50]
           EOG_R_[50] EEG[125] AIRFLOW[10] CC[10] DD[10] POSITION[1]
           LIGHT[1] OX_STAT[1]

Another difference is that using a signal aliases allows a many-to-one mapping, whereas RENAME requires a one-to-one mapping of labels. That is, "alias=XX|AA|BB|CC" will map either AA, BB or CC to XX (i.e. where an individual EDF may have none, one or multiple of these labels). In contrast, RENAME must use the single, primary label in the sig option. However, there is nothing stopping combined use of signal aliases and the RENAME command, i.e. to achieve a many-to-many mapping of labels: e.g.

luna s.lst vars=ch.txt "alias=XX|AA|BB|CC" \
     -s ' RENAME sig=XX new=${CHS} & WRITE edf-dir=edfs/ ' 

This effectively uses XX as an intermediate (mapped to from either AA, BB or CC) and will then write to the new EDF a label as defined in ch.txt. Of course, an alternative would be to also supply individual-specific labels for both sig and new in the vars.txt file, e.g. if it had two columns defining OLD and NEW variables/columns:

luna s.lst vars=ch.txt \
     -s ' RENAME sig=${OLD} new=${NEW} & WRITE edf-dir=edfs/ '  

COPY

Duplicates one or more EDF channels

Because some Luna commands modify a channel (e.g. FILTER), it can be desirable to first make a copy of the original channel. New channels are written out with the WRITE command.

Although multiple signals can be duplicated at the same time (i.e. will all be given the same tag), only data channels (i.e. not EDF Annotation channels in EDF+) are duplicated.

Parameters

Parameter Example Description
sig sig=C3,C4 List of channels to duplicate
tag tag=DELTA A required option, this is added to make the new channel name, e.g. C3 becomes C3_DELTA

Output

One or more new channels are created in the in-memory representation of the EDF. Aside from a note in the log, there is no formal (destrat-based) output for this command.

Example

To extract one channel (EEG) from an original EDF, and then duplicate it:

luna s.lst 2 sig=EEG -s 'DESC & COPY sig=EEG tag=V2 & DESC'

As expected, the first DESC output shows a single channel:

EDF filename      : edfs/learn-nsrr02.edf
ID                : nsrr02
Clock time        : 21:18:06 - 07:15:36
Duration          : 09:57:30
# signals         : 1
Signals           : EEG[125]

After the COPY command has been executed, there are now two channels: EEG and EEG_V2:

EDF filename      : edfs/learn-nsrr02.edf
ID                : nsrr02
Clock time        : 21:18:06 - 07:15:36
Duration          : 09:57:30
# signals         : 2
Signals           : EEG[125] EEG_V2[125]

RESAMPLE

Changes the sampling rate of a signal

Uses functions from libsamplerate to upsample or downsample signals. Within a maximum upsampling/downsampling of 256, there are no constraints on the new sample rate (i.e. the ratio of old and new sample rates need not be a rational number).

Parameters

Parameter Example Description
sig sig=C3,C4 Signal list
sr sr=100 New sampling rate (Hz)

Output

No output other than a message to the log (and altering the in-memory signal).

Example

To create a new EDF with the EEG channel resampled to 100 Hz:

luna s.lst -s 'RESAMPLE sig=EEG sr=100 & WRITE edf-tag=resample edf-dir=edfs/ sample-list=s2.lst'

ENFORCE-SR

Drop signals that do not conform to a given EDF record size, or min/max sample rate

To enable clean EDF record-size conversion, this command first drops any signals which would not be able to be represented by an N-second record size. For example, a signal with a sample rate of 125 Hz cannot be represented in the EDF block/record structure if each block is only 0.5 seconds. Such signals will be dropped (based on dur) from the internal EDF representation. This command can be used prior to a RECORD-SIZE command.

Further, this command can optionally drop signals with a sample rate below or above a given range (using sr).

Parameters

Parameter Example Description
dur dur=1 Proposed EDF record size (seconds), which may differ from the current value
sr sr=100,200 Optionally, drop signals with rates below 100 Hz or above 200 Hz

Output

No output other than a message to the log (and altering the in-memory signal).

REFERENCE

Re-references signals with respect to one or more other signals

Parameters

Parameter Example Description
sig sig=C3,C4 Signal(s) to re-reference
ref ref=A1,A2 Signal(s) to provide the reference
pairwise Perform pairwise re-referencing between sig and ref (see below)

Both sig and ref are required parameters. If more than one channel is given as the reference (in a comma-delimited list), the average of those channels is used as the reference value. Alternatively, if the pairwise option is also specified, then sig and ref should be of the same length. In this case, rather than average multiple ref channels, the command would do a pairwise referencing:

Given the above sig and ref values in the table above: without the pairwise option, the two channels would be calculated as:

  -->  C3 - (A1+A2)/2
       C4 - (A1+A2)/2
With pairwise:
  ---> C3 - A1
       C4 - A2

Output

No output, other than a note to the log. In memory, the updated sig channels will contain the re-referenced values.

MINMAX

Set digitial and physical minimum and maximum values in the EDF header to be equal across multiple channels. This can be necessary to enable other software to be able to work with an EDF, by making it better conform to the EDF specification. Signals specified here must be comparable, e.g. all EEG and EOG with a common amplifier and ADC, and so are expected to have similar scaling and sensitivity (unit/bit) in the EDF.

Parameters

Parameter Example Description
sig sig=C3,C4 Signals (two or more) to set group min/max values

Output

No formal output is given. The channels are rescaled internally. Any subsequent commands (i.e. including WRITE to write a new EDF) will therefore based based on these new header values.

Example

Here we have an EDF with channels C3, C4, F3, F4, O1, O2, A1 and A2. The HEADERS command shows that the channels have different physical min/max values, and therefore different SENS values (scaling of micro-volts per bit in the EDF):

luna id01.edf -o out.db -s HEADERS
destrat out.db +HEADERS -r CH
ID        CH  DMAX   DMIN    PDIM  PMAX    PMIN     SENS    SR   TYPE
id01.edf  F3  32767  -32768  uV    1574.8  -3276.8  0.07403 500  EEG
id01.edf  F4  32767  -32768  uV    1720.9  -3276.8  0.07626 500  EEG
id01.edf  C3  32767  -32768  uV    3276.7  -3276.8  0.1     500  EEG
id01.edf  C4  32767  -32768  uV    2034.5  -3276.8  0.08104 500  EEG
id01.edf  O1  32767  -32768  uV    3276.7  -3276.8  0.1     500  EEG
id01.edf  O2  32767  -32768  uV    3276.7  -3276.8  0.1     500  EEG
id01.edf  A1  32767  -32768  uV    3238.6  -3276.8  0.09941 500  EEG
id01.edf  A2  32767  -32768  uV    3255.3  -3276.8  0.09967 500  EEG

After running the MINMAX command, we see that the SENS values are now set to be equal across all channels. This command will not fundamentally change the underlying signal data, only the scaling in the EDF header.

luna id01.edf -o out.db -s 'MINMAX & HEADERS'
ID        CH  DMAX   DMIN    PDIM  PMAX    PMIN     SENS  SR   TYPE
id01.edf  F3  32767  -32768  uV    3276.7  -3276.8  0.1   500  EEG
id01.edf  F4  32767  -32768  uV    3276.7  -3276.8  0.1   500  EEG
id01.edf  C3  32767  -32768  uV    3276.7  -3276.8  0.1   500  EEG
id01.edf  C4  32767  -32768  uV    3276.7  -3276.8  0.1   500  EEG
id01.edf  O1  32767  -32768  uV    3276.7  -3276.8  0.1   500  EEG
id01.edf  O2  32767  -32768  uV    3276.7  -3276.8  0.1   500  EEG
id01.edf  A1  32767  -32768  uV    3276.7  -3276.8  0.1   500  EEG
id01.edf  A2  32767  -32768  uV    3276.7  -3276.8  0.1   500  EEG

Note, if the EDF contained other signals that you did not want included in the MINMAX procedure (e.g. respiratory channels, which have different scaling from EEG channels), you would need to add sig after MINMAX to specify, e.g. only the EEG channels. This command will skip any EDF+ Annotation channels automatically.

uV

Converts a signal to uV units

Checks the unit (physical dimension) field of the EDF header for either V, mV or uV and rescales the signal appropriately. If the header specifies some other unit, or none, then no action is taken.

Parameters

Parameter Example Description
sig sig=C3,C4 Signal(s) to convert

If sig is not specified, this command is applied to all channels.

Output

No output, other than updating the in-memory signal.

mV

Converts a signal to mV units

Checks the unit (physical dimension) field of the EDF header for either V, mV or uV and rescales the signal appropriately. If the header specifies some of unit, or none, then no action is taken.

Parameters

Parameter Example Description
sig sig=C3,C4 Signal(s) to convert

If sig is not specified, this command is applied to all channels.

Output

No output, other than updating the in-memory signal.

TIME-TRACK

Adds a time-track, which implicitly converts an EDF into an EDF+

This command is only used internally, currently.

FLIP

Flips the polarity of a signal

Multiplies every sample value of a signal by -1.

Parameters

Parameter Example Description
sig sig=C3,C4 Signals to flip

Output

No output, other than a message to the log and an updated in-memory signal.

Example

This next command takes the first 10 epochs of the C3 signal, outputs the original signal to a file (f1), then flips the signal, and re-outputs it (to f2):

luna me.lst sig=C3 -s 'EPOCH & MASK epoch=1-10 & \
                       RESTRUCTURE & MATRIX file=f1 & \
                       FLIP & MATRIX file=f2'

Note

In the above, we used the end-of-line \ character (with no trailing whitespace) to continue the command on multiple lines, as many shells allow.

Comparing the original signals (looking at just the first 10 rows of output) ...

head f1
ID       E   S   SP T             C3
id001    1   0   0  0             3.43407
id001    1   0   1  0.00390625    2.06044
id001    1   0   2  0.0078125    -0.0763126
id001    1   0   3  0.0117188    -1.60256
id001    1   0   4  0.015625     -2.21306
id001    1   0   5  0.0195312    -2.21306
id001    1   0   6  0.0234375    -2.21306
id001    1   0   7  0.0273438    -2.06044
id001    1   0   8  0.03125      -2.06044

... to the new signals, we see the values have been flipped, albeit not as exactly as one might expect. (This is due to the encoding used by EDFs; see the note below for more details).

head f2
ID       E   S   SP T             C3
id001    1   0   0  0            -3.43865
id001    1   0   1  0.00390625   -2.06244
id001    1   0   2  0.0078125     0.0728122
id001    1   0   3  0.0117188     1.59799
id001    1   0   4  0.015625      2.20806
id001    1   0   5  0.0195312     2.20806
id001    1   0   6  0.0234375     2.20806
id001    1   0   7  0.0273438     2.05909
id001    1   0   8  0.03125       2.05909

Floating point accuracy

EDFs store data as 2-byte integers: in contrast, floating point numbers as used in Luna typically take up 4 or 8 bytes in memory. This relatively low resolution of EDF introduces slight numerical differences so that the values are clearly different from -1 times the original: i.e. 3.43407 is not minus -3.43865. As noted in the EDF spec, practically this limit on resolution is not a real issue for most biosignals, if they are recorded with sensible physical and digital min/max values to reflect the dynamic range of the signal.

ZC

Mean-center a signal

Subtracts the mean from a signal, either based on the entire duration or performed epoch-by-epoch. The latter may be more appropriate if there are large changes in the scale/mean of the signal across the recording.

Parameters

Parameter Example Description
sig C3,C4 Signals to flip
epoch Perform mean-centering epoch-by-epoch

Output

No output, other than a message to the log and an updated in-memory signal.

Example

Consider the SpO2 signal,

luna s.lst -s 'STATS sig=SpO2'
which has a mean as follows:
MEAN   94.1955

First adding the ZC command:

luna s.lst -s 'ZC sig=SpO2 & STATS sig=SpO2'
we now see the mean is (effectively) zero:
MEAN   -0.000734802

Note that, due to EDF's 16-bit floating-point accuracy, the mean will not be numerically exactly 0.00 (i.e. as internally, the signal is written back to the internal, in-memory EDF at the end of the ZC command, before being re-read by STATS).

ROBUST-NORM

Standardizes a signal using a robust approach

Normalizes a signal, using as measures of central tendency and spread the median and an estimate of the SD based on the inter-quartile range ( 0.7413 times IQR ). Additionally, this command can winsorize a signal (and optiomally re-normalize after winsorization, to ensure (non-robust) mean/SD of 0/1). This can be performed either on the whole signal, or epoch-by-epoch.

Parameters

Parameter Example Description
sig C3,C4 Signals to flip
epoch Perform mean-centering epoch-by-epoch
center 'F' Perform median-centering (default: true )
scale 'F' Perform rescaling (default: true )
winsor 0.05 Winsorize the signal, e.g at 5th percentile (default: none)
second-norm Perform a second round of normalization after winsorization (default: no)

Output

No output, other than a message to the log and an updated in-memory signal.

Example

Consider the SpO2 signal,

luna s.lst -s 'STATS sig=SpO2'
which has a mean as follows:
MEAN   94.1955
and is also very highly skewed:
SKEW   -8.02593

If, for some reason, one wanted to normalize this measure, we can use ROBUST-NORM, also adding winsor=0.05 to winsorize the signal at the 5th (and 95th) percentiles:

luna s.lst -s 'ROBUST-NORM sig=SpO2 winsor=0.05 & STATS sig=SpO2'

From the subsequent STATS output, we can see the mean and SD are closer to 0 and 1 respectively, and (due to the winsorization), the signal is also much less skewed:

MEAN    -0.80652
SKEW    -0.4575
SD      2.05714
Here, the mean and SD are still quite different from 0 and 1 - which naturally reflects the fact that we used robust measures of central tendency and spread (median and IQR-based estimate of the SD) rather than the typical mean and SD. If we look at the percentiles from the STATS command, we see the median (P50) is effectively 0 (save for numerical rounding):
P01 -5.39593
P02 -5.39593
P05 -5.39593
P10 -4.04687
P20 -2.69795
P30 -1.3489
P40 -1.3489
P50 -9.67455e-05
P60 -9.67455e-05
P70 -9.67455e-05
P80 1.48381
P90 1.48381
P95 2.83286
P98 2.83286
P99 2.83286
This above also shows the impact of winsoriation, e.g. P01, P02 and P05 are all identical now.

If for some reason it is important to further rescale the signal to have mean and SD of 0 and 1 more precisely, then add the option second-norm to ROBUST-NORM. This results in the following mean and SD:

MEAN   -5.44263e-06
SD     0.999983

EDF

Sets/forces EDF status for a EDF+

This command downcasts an EDF+ to a standard EDF file. This means that

  • any EDF Annotations channels will be dropped

  • if the file is a EDF+D (i.e. a potentially discontinuous EDF), then it is converted to a standard EDF if it is actually continuous (i.e. is a EDF+D but does not actually contain any gaps)

  • if the force option is given, then the conversion to EDF is done even if the EDF+D actually contains gaps.

Parameters

Parameter Description
force Change a EDF+D to EDF even if it actually contains gaps

Output

No output other than changing the internal status of the EDF

Example

to be added

RECORD-SIZE

Alters the record size of an EDF

This command changes the low-level encoding of data in an EDF, which is something that you should not normally need to change. Often, EDFs have a record size (i.e. the size of the blocks in which the data are stored) of 1 second or so. Why might you want to change this?

  • as the smallest EPOCH size is limited by the EDF record size, if the EDF record size is relatively large (e.g. 10 seconds), it will not be possible to specify smaller epochs (e.g. 5 seconds).

  • if the EDF record size is very small (e.g. 100 milliseconds), this can reduce performance when reading the EDF from disk

There are a number of points that should be borne in mind:

  • no subsequent commands can be issued after a RECORD-SIZE command; rather, a new EDF will be written to disk
  • you should ensure that the new record size contains an integer number of samples for all signals
  • currently, you can only change the record size of EDF, not EDF+ files
  • as only whole records are written to disk, the final part of an EDF (that is shorter than the new record size) may be truncated

Parameters

Parameter Example Description
dur dur=1 New EDF record/block size
edf-dir edf-dir=edfs/ Folder for writing new EDFs
edf-tag edf-tag=rec1 Tag added to new EDFs
sample-list sample-list=s2.lst Generate a sample-list pointing to the new EDFs

That is, while RECORD-SIZE itself only takes dur as the single option, one must also specify all options for WRITE, as RECORD-SIZE automatically triggers WRITE after changing the record size of the in-memory representation. (That is, as always, the original EDF file is left untouched.)

Output

No output, other than message to the log and an updated in-memory signal.

Example

Focusing only on the signals PR and EEG in the first tutorial EDF, we see that this EDF has a record size of 1 second:

luna s.lst 1 sig=PR,EEG -s "SUMMARY" 
# signals      : 2
# records      : 40920
Duration       : 1

That is, the EDF has 40,920 records, each of duration 1 second. Looking at the two signals, because the record duration is 1 second, this implies a sample rate of 1 Hz and 125 Hz respectively for PR and EEG.

Signal 1 : [PR]
       # samples per record : 1
...
Signal 2 : [EEG]
       # samples per record : 125
...

To generate a new EDF (which contains only these two signals) with an altered record size (in this example, 50 seconds):

luna s.lst 1 sig=PR,EEG -s "RECORD-SIZE dur=50 edf-tag=r50" 

(Note that setting a 50-second record size would be unusual, this is done here purely for illustrative purposes.) After running this command, you'll see the following messages in the log:

 saved new EDF, edfs/learn-nsrr01-r50.edf
 **warning: the PROBLEM flag was set, skipping to next EDF...

The warning message is expected, this is just Luna's way of ensuring that no further commands can be run after RECORD-SIZE command. Running SUMMARY on the new EDF, we see that the record size has been changed:

luna edfs/learn-nsrr01-r50.edf -s SUMMARY
# records      : 818
Duration       : 50
...
Signal 1 : [PR]
       # samples per record : 50
...
Signal 2 : [EEG]
       # samples per record : 6250
...

That is, instead of 40,920 records of 1 second we have 818 records of 50 seconds. Correspondingly, there are now 50 times the number of samples per record compared to the original EDF (the sample rate in Hz is obviously the same as before).

Note

Because 40,920 is not evenly divisible by 50, the last 20 seconds has been truncated (i.e. the log will indicate a total duration of 11:21:40 instead of the original 11:22:00).

ALIGN

Alters the EDF record structure to perfectly align records with annotations and epochs

This is a rather specialized command to fix certain issues that can arise when working with EDFs and epoch-defining annotations when the annotations are not "aligned" with EDF records.

Consider the following (which occurs in the NSRR National Children's Hospital dataset):

  • all EDFs start on a clock-time with an exact, integer number of seconds (i.e. EDF spec. does not allow otherwise), e.g. 23.03.07

  • sample rate is 256 Hz for all EEG channels, and the EDF record size is 4 seconds

  • annotations that define sleep stages are all in exactly 30-second epochs, but they start at a fractional offset:

    Stage   Onset (elapsed seconds from EDF start)
    N1      4110.9609375 
    N2      4140.9609375 
    N2      4170.9609375 
    

This means that annotations and EDF records not in exact temporal alignment. In theory, there is of course absolutely nothing wrong per se with this. In practice, it can make some Luna commands, or more generally, working with EDFs (that have a fixed block size) a little challenging. That is, the EDF record is an atomic unit: one must either write a whole record, or none of it, when constructing a new EDF. If epochs only partially span EDF records, this naturally poses problems when thinking about how to write a new EDF that is structured by those epochs, i.e. only NREM sleep epochs, etc.

Here we break this down three distinct issues, only the third of which is more challenging and requires the ALIGN command.

Offsets for EDF annotations

Specifically, when counting epochs, by default Luna starts at 0 seconds elapsed (i.e. the EDF start) and proceeds forwards: 0-30, 30-60, etc. If sleep stages start at some different offset (other than starting at 0 or a multiple of 30 seconds) this means that some Luna-defined epochs may contain more than one implied stage. For example, consider that sleep stages start at 4 seconds past the EDF start:

      Elapsed seconds from EDF start:
      0000000000 1111111111 2222222222 3333333333 4444444444 5555555555 666...
      0123456789 0123456789 0123456789 0123456789 0123456789 0123456789 012...

Luna: |---epoch 1----------------------|
                                       |---epoch 2----------------------|

Actual:   |---epoch 1-(W)------------------|
                                           |---epoch 2-(N1)------------------|

As in the above example, the second Luna epoch (30-60) will span two distinct annotations, which is clearly a mistake. This means that commands that use sleep stages will report (in this example) a missing (?) annotation, as there is a conflict in that epoch 2 has both a wake (W) and N1 (N1) annotation. Luna will also flag in the log that conflicts were found, e.g.:

 CMD #1: HYPNO
   options: sig=*
  set epochs to default 30 seconds, 1186 epochs
  *** found 37 epoch(s) of 1186 with conflicting spanning annotations
  *** check that epochs and annotations align as intended
  *** see EPOCH 'align' or 'offset' options
and write CONF variable to the standard output.

The solution to this is simply to supply an offset to the epoch command, which can either be done manually:

luna s.lst -s 'EPOCH offset=4 & HYPNO`
or automatically with respect to a set of annotations (i.e. making the offset equal to the start of the first of these annotions encountered):
luna s.lst -s 'EPOCH align=N1,N2,N3,R,W,? & HYPNO'

EDF record size and epoch duration

Another issue arises when epochs may span EDF records only partially. The core data structure (of EDF, and internally of Luna) is a block/record based system: the underlying data must correspond to whole records. If epochs span partial EDF records, this presents a problem if we want to restructure the data, e.g. remove W epochs and write a new EDF

In the above example, with an EDF record duration of 4 seconds, one cannot straightforwardly output a new EDF on an epoch-by-epoch basis, as for 30 second epochs), an epoch is not perfectly divisible by 4. In Luna, this can be fixed by using the RECORD-SIZE command to change the EDF record size, e.g. to 1 second say. Now, Luna would be outputting only whole EDF records (i.e. 30 times 1 second) rather than having to worry about a partial record (i.e. 7 times 4 seconds, plus an additional two seconds, which would be half an EDF record).

Fractional offsets

Finally, a more tedious issue arises if the annotations/epochs start at arbitray, fractional time points within an EDF. In the example above, we, for example, an annotation starting:

   N1      4110.9609375
In this example, with a sample rate of 256 Hz, this offset corresponds exactly to 246 (= 0.9609375 * 256 ) samples past the start of each second. Although one solution would be to have a very short EDF record sizes (i.e. the length of one sample, 1/256 seconds), this may for technical reasons make data access suboptimal for many readers; further, we consdier the more general case, where the offset is not even exactly aligned with a sample point.

The ALIGN command attempts to handle this issue, by creating a new EDF in which the epochs are perfectly aligned to EDF records.

One specifies a list of annotations that will define epochs: these annotations must be a) non-overlapping, and b) an exact multiple of the EDF record size. i.e. if we have changed the above data to have 1 second records, then we can specify 30-second epochs. The ALIGN command then finds all sample points within an annotation that fits completely within the observed duration (i.e. only ‘complete’ annotations, to skip those spans discontinuities/borders) and maps these into a new set of records (e.g. 30 new 1 second records) for each annotation (i.e. which may be mapping fractionally across original records). The end result is a new EDF with in which annotations, epochs & EDF records are all aligned.

To make this concrete: consider (for ease of presentation) a 5 Hz signal and an EDF record size of 1 second:

    RECORD   SAMPLE    TIME
    1        1         0.0
    1        2         0.2
    1        3         0.4
    1        4         0.6
    1        5         0.8

    2        1         1.0
    2        2         1.2
    2        3         1.4
    2        4         1.6
    2        5         1.8

    3        1         2.0
    3        2         2.2
    3        3         2.4
    3        4         2.6
    3        5         2.8

Also for simplicity of presentation, assume here we have 1 second epoch (rather than 30 seconds)

If we were to have epoch-defining annotations starting with an offset of 0.25 seconds, (e.g. 0.25 - 1.25, 1.25 - 2.25, etc.) The challenge would be, for example: how to extract those epochs into a new EDF. Naturally, this involves changing the internal structure of the EDF.

We first collect all the new data-points, making new 5-sample EDF records from the new data, starting at the first point after 0.25 seconds:

    RECORD   SAMPLE    TIME           NEW RECORD  SAMPLE    TIME 
    1        1         0.0      xxx
    1        2         0.2      xxx
    1        3         0.4      --->      1       1         0.0 
    1        4         0.6      --->      1       2         0.2 
    1        5         0.8      --->      1       3         0.2 
    2        1         1.0      --->      1       4         0.6
    2        2         1.2      --->      1       5         0.8

    2        3         1.4      --->      2       1         1.0
    2        4         1.6      --->      2       2         1.2
    2        5         1.8      --->      2       3         1.4
    3        1         2.0      --->      2       4         1.6
    3        2         2.2      --->      2       5         1.8
    3        3         2.4      xxx          
    3        4         2.6      xxx          
    3        5         2.8      xxx       

If the signal were 100 Hz, we can obviously select an exact sample point (the 25th) in an EDF record to correspond to an offset of 0.25 seconds. In the case of our hypothetical 5 Hz signal, as above, we have to select the closest next signal, so there will be a slight shift in the timings of signals. If this matters, you can first resample all signals to align to the new offset perfectly.

Parameters

Main arguments

Parameter Example Description
align align=N1,N2,N3,R,W,? Annotations to align epochs by
annot-out annot-out=annots/^.annot Write (realigned) annotations

Other arguments as required by the WRITE command

Parameter Description
edf-tag New EDF tag
edf-dir New EDF directory

Output

The ALIGN command forces a WRITE of the EDF; also, annotation files can be output, with the annotations correctly altered to specify onset relative to the new EDF start.

Example

to be added

ANON

Sets the in memory EDF header fields Patient ID and Start Date fields to missing (a . character). If a new EDF is generated with the WRITE command, it will have those fields blanked. As with all Luna commands, this does not alter the original EDF.

Note

This command does not alter the ID specified in the sample-list (i.e. the first column). That ID, which is used to track all output, etc, is distinct from the EDF header Patient ID field, and may or may not be similar.

Parameters

No parameters.

Output

No output other than message to the log, and altering the in-memory representation of the EDF header.

Example

A typical EDF with identifying information in the header (showing only relevant rows from the SUMMARY output):

luna my.edf -s "SUMMARY" | head 
EDF filename   : my.edf
Patient ID     : id00001
Recording info : 
Start date     : 07.06.16
Start time     : 23:07:56

... (cont'd) ...

Here we see how the ANON command effectively wipes this information:

luna my.edf -s "ANON & SUMMARY" | head 
EDF filename   : my.edf
Patient ID     : .
Recording info : 
Start date     : .
Start time     : 23:07:56

This next command takes all EDFs in a project (defined by s.lst) and creates a set of new EDFs with the WRITE command (in the folder edfs/, and with the new sample list s2.lst) that are identical except they have the Patient ID and Start Date fields set to missing:

luna s.lst -s "ANON & WRITE edf-dir=edfs/ edf-tag=anon sample-list=s2.lst" 

SET-HEADERS

Directly specify certain EDF header values

Note that EDF header fields which relate to the size/structure of the actual data (i.e. sample rate, EDF header size, physical min/max, etc) cannot be changed in this way - i.e. for those changes, use the relevant data-modifying command, e.g. RESAMPLE, RECORD-SIZE, MINMAX, etc). That is, these options only modify the header and nothing else.

Parameters

Primary headers

Parameter Example Description
id id001 EDF patient ID (max 80 chars)
recording-info EDF recording information field (max 80 chars)
start-date EDF start date (max 8 characters; no format imposed)
start-time EDF start time (max 8 characters; no format imposed)

Channel-specific headers

Parameter Example Description
sig ${eeg} Specify the channel(s) to modify
transducer Set the transducer field for specified channels (max 80 chars)
physical-dimension Set the physical dimension (units) for specified channels (max 8 chars)
unit Same as physical-dimensions
prefiltering Set the prefiltering field for specified channels (max 80 chars)

Output

This command only modifies the in-memory representation of the EDF. Use WRITE to save any changes.

e.g. to fix the start date, and add transducer types for the EEGs (here using Luna's automatic specification of common EEG channel names):

luna file1.edf -s 'SET-HEADERS start-date=08.08.21 sig=${eeg} transducer=Ag/AgCl & WRITE edf-tag=edit '
will generate a new EDF file1-edit.edf with the above fields fixed.

SET-VAR

Directly specify Luna variables

This can be useful if one wants to include individual-level variables when defining a script variable. If it isn't clear why you'd want to do this, then there is no need to worry about using this command.

Parameters

This command takes only a single option, which will be given as the variable name. The argument is the variable value.

Parameter Example Description
any valid variable name v=100 Sets this variable (e.g. v) to the value 100

Output

None, other than a message to the console log.

Example

Sets an individual-level variable var to the text string val:

luna s.lst -s 'SET-VAR var=val`

RECTIFY

Rectifies a signal

This commands sets all values of an EDF signal to their absolute values. It is primarily designed for use working with other functions such as HILBERT and PEAKS, to build up larger processing procedures.

Parameters

Parameter Example Description
sig C3,C4 Signals to be rectified (or all, if this is absent)

Output

None.

Example

As toy example, here rectifying a signal with positive and negative values (an EEG):

luna s.lst 1 -o out.db \
     -s ' TAG run/1 & STATS sig=EEG
        & RECTIFY sig=EEG
        & TAG run/2 & STATS sig=EEG ' 
Before:
destrat out.db +STATS -r CH run/1 -v MIN MAX | behead

      ID   nsrr01
      CH   EEG
     run   1
     MAX   125
     MIN   -124.019607843137
After:
destrat out.db +STATS -r CH run/2 -v MIN MAX | behead
      ID   nsrr01
      CH   EEG
     run   2
     MAX   125
     MIN   0.490196078431372

REVERSE

Reverse a signal

This command is primarily designed for evaluated other time-domain/phase-based methods, e.g. to provide a sanity-check by completely reversing a signal in the time-domain.

Parameters

Parameter Example Description
sig C3,C4 Signals to be reversed (or all, if this is absent)

Output

None.

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