The European Data Format (EDF) is a simple and flexible format for exchange and storage of multichannel biological and physical signals. It was developed by a few European ‘medical’ engineers who first met at the 1987 international Sleep Congress in Copenhagen. See http://www.edfplus.info/
The original EDF specification has been expanded in several ways. EDF+ supports the addition of annotations and non-continuous recordings. The BioSemi Data Format BDF format uses 24 bits per sample (in stead of the 16 bits per sample in EDF). And BDF+ is an EDF+ like extension of BDF.
This packages supports all these variants.
Both EDF and BDF files consist of an header followed by one or more data records with the recorded signals, either ordinary signals or annotation signals.
This package follows this structure by providing two basic functions: readEdfHeader and readEdfSignals (see the help pages for details)
The examples below are based on the following two files:
CFile an EDF+ file with a continuous recording of 11 ordinary signals and one annotation signal
DFile a BDF+ file with a discontinuous recording of 11 ordinary signals and one annotation signal
Both files are derived from the “test_generator_2” test files from http://www.teuniz.net/edf_bdf_testfiles
libDir <- system.file ("extdata", package="edfReader")
CFile <- paste (libDir, '/edfPlusC.edf', sep='') # a continuously recorded EDF file
DFile <- paste (libDir, '/bdfPlusD.bdf', sep='') # discontinuously recorded BDF fileThe readEdfHeader function returns a list of class ‘ebdfHeader’ with all the data from the EDF or BDF file header. Part of this list is a data frame of class ‘ebdfSHeader’ which contains the signal headers.
A file header can be read with readEdfHeader()
library (edfReader)
CHdr <- readEdfHeader (CFile)
DHdr <- readEdfHeader (DFile) Summaries of the header data can be shown with the S3 summary () and print() functions
CHdr## Patient : X X X X
## RecordingId : Startdate 10-DEC-2009 X X test_generator
## StartTime : 2009-12-10 12:44:02
## Continuous recording : TRUE
## Signal labels : squarewave ramp pulse ECG noise sine 1 Hz sine 8 Hz sine 8.5 Hz sine 15 Hz sine 17 Hz sine 50 Hz EDF Annotationssummary (DHdr)## File name : /Library/Frameworks/R.framework/Versions/3.2/Resources/library/edfReader/extdata/bdfPlusD.bdf
## File type : BDF+
## Version : "255"BIOSEMI
## Patient : X X X X
## RecordingId : Startdate 10-DEC-2009 X X test_generator
## StartTime : 2009-12-10 12:45:54
## Continuous recording : FALSE
## Recording period : 10 sec (= 00:00:10)
## Ordinary signals : 11
## Annotation signals : 1
## Signal labels : squarewave ramp pulse ECG noise sine 1 Hz sine 8 Hz sine 8.5 Hz sine 15 Hz sine 17 Hz sine 50 Hz BDF AnnotationsSummaries of the signal header data can be shown with the S3 print() and summary () functions.
CHdr$sHeader## Signal labels : squarewave ramp pulse ECG noise sine 1 Hz sine 8 Hz sine 8.5 Hz sine 15 Hz sine 17 Hz sine 50 Hz EDF Annotationssummary (DHdr$sHeader)## signal label transducer sampleRate preFilter
## 1 1 squarewave 200
## 2 2 ramp 200
## 3 3 pulse 200
## 4 4 ECG 200
## 5 5 noise 200
## 6 6 sine 1 Hz 200
## 7 7 sine 8 Hz 200
## 8 8 sine 8.5 Hz 200
## 9 9 sine 15 Hz 200
## 10 10 sine 17 Hz 200
## 11 11 sine 50 Hz 200
## 12 12 BDF Annotations NAThe readEdfSignals function with simplify=FALSE returns a list of class ‘ebdfSignals’ with the signals selected from the EDF / BDF file.
The signals in this list are of the following :
ordinary continuous signals
of class ebdfCSignal
ordinary discontinuous signals
of class ebdfFSignal
annotation signals
of class ebdfASignal
The signals in an EDF or BDF file can be read with the readEdfSignals function.
CSignals <- readEdfSignals (CHdr)
DSignals <- readEdfSignals (DHdr)NOTE In case only one signal was read the list of one will be simplified to this singe object. This can be prevented by using the ‘simplify=FALSE’ parameter. So readEdfSignals (CHdr, signals=7, simplify=FALSE)[[1]] and readEdfSignals (CHdr, signals=7) will return the same object. If required the reading can be restricted to a specific number of signals and/or a particular period.
The signals are then identified by their label, signal number or signal type (‘Ordinary’ or ‘Annotations’).
someCSignalsPeriod <- readEdfSignals (CHdr, signals=c(3, "5", "sine 8.5 Hz"), from=5.1, till=18)
annoDSignalsPeriod <- readEdfSignals (DHdr, signals='Annotations', from=5.1, till=18)Note that the period read will be - apart from rounding errors - [10.1,45). See the section “Samples, time and periods” for details.
NOTE In this case DFile is an BDF file with one annotation signal. So readEdfSignals (DHdr, signals=‘Annotations’) will return the same object as readEdfSignals (DHdr, signals=‘Annotations’, simplify=FALSE)[[‘BDF Annotations’]]
Summaries of the list of signals can be shown with the S3 print() and summary () functions.
someCSignalsPeriod## Continuous recording TRUE
## Recorded period 20
## Recording segment from 5.1 sec (= 00:00:05.1) till 18 sec (= 00:00:18)
## bits per sample 16
## Ordinary signals:
## signal label transducer sampleRate samples preFilter
## 1 3 pulse 200 2580
## 2 5 noise 200 2580
## 3 8 sine 8.5 Hz 200 2580summary (DSignals)## Continuous recording FALSE
## Total recording time 20
## Recorded period 10
## Recording segment whole recording
## bits per sample 24
## Annotation signal:
## signal recordStartAnnotations otherAnnotations
## 1 12 0 1
## Ordinary signals:
## signal label transducer sampleRate samples preFilter
## 1 1 squarewave 200 4000
## 2 2 ramp 200 4000
## 3 3 pulse 200 4000
## 4 4 ECG 200 4000
## 5 5 noise 200 4000
## 6 6 sine 1 Hz 200 4000
## 7 7 sine 8 Hz 200 4000
## 8 8 sine 8.5 Hz 200 4000
## 9 9 sine 15 Hz 200 4000
## 10 10 sine 17 Hz 200 4000
## 11 11 sine 50 Hz 200 4000NOTE In case only one signal was read the list of one will be simplified to this singe object. This can be prevented by using the ‘simplify=FALSE’ parameter. So readEdfSignals (CHdr, signals=7, simplify=FALSE)[[1]] and readEdfSignals (CHdr, signals=7) will return the same object.
Summaries of a continuously recorded ordinary signal can be shown with the S3 print() and summary () functions.
someCSignalsPeriod[[1]]## Signal number 3
## Label pulse
## Continuous recording TRUE
## Recorded period 20 sec (= 00:00:20)
## Recording segment from 5.1 sec (= 00:00:05.1) till 18 sec (= 00:00:18)
## Number of samples 2580
## Sample rate 200
## Transducer
## Range -1000 : 1000 uV
## Prefiltersummary (CSignals$pulse) # a signals has its label as its name## Signal number 3
## Label pulse
## Continuous recording TRUE
## Recorded period 20 sec (= 00:00:20)
## Recording segment whole recording
## Number of samples 4000
## Sample rate 200
## Transducer
## Range -1000 : 1000 uV
## Prefilter
## Signal summary:## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.01526 0.01526 0.01526 2.01500 0.01526 99.99000Ordinary signals that are not continuously recorded can be read in two different ways:
as a ‘continuous’ sequence of samples with ‘NA’ values filling the gaps (use ‘fragments=FALSE’, the default).
The result is of class ebdfCSignal (the same as for a continuously recorded signal).
as a number fragments of continuously recorded parts (use ‘fragments=TRUE’)
The result is of class ebdfFSignal.
The latter method will use a more complex data structure, the first may result in a (much too) huge object.
CDSignals <- readEdfSignals (DHdr, from=5.1, till=18)
FDSignals <- readEdfSignals (DHdr, fragments=TRUE)The objects of class ebdfCSignal are summarised in the same way as continuously recorded signals.
CDSignals[[8]]## Signal number 8
## Label sine 8.5 Hz
## Continuous recording FALSE
## Total recording time 20 sec (= 00:00:20)
## Recorded period 10 sec (= 00:00:10)
## Recording segment from 5.1 sec (= 00:00:05.1) till 18 sec (= 00:00:18)
## Number of samples 2580
## Sample rate 200
## Transducer
## Range -1000 : 1000 uV
## Prefiltersummary (CDSignals$`sine 8.5 Hz`) # note the "`" quotes for a name with spaces.## Signal number 8
## Label sine 8.5 Hz
## Continuous recording FALSE
## Total recording time 20 sec (= 00:00:20)
## Recorded period 10 sec (= 00:00:10)
## Recording segment from 5.1 sec (= 00:00:05.1) till 18 sec (= 00:00:18)
## Number of samples 2580
## Sample rate 200
## Transducer
## Range -1000 : 1000 uV
## Prefilter
## Signal summary:## Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
## -100.000 -70.990 -3.141 -1.537 68.450 100.000 1200Summaries of a not continuously recorded ordinary signal stored in fragments can be shown with the S3 print() and summary () functions.
FDSignals[[8]]## Signal number 8
## Label sine 8.5 Hz
## Continuous recording FALSE
## Total recording time 20 sec (= 00:00:20)
## Recorded period 10 sec (= 00:00:10)
## Recording segment whole recording
## Number of fragments 8
## Sample rate 200
## Transducer
## Range -1000 : 1000 uV
## Prefiltersummary (FDSignals$`sine 8.5 Hz`) ## Signal number 8
## Label sine 8.5 Hz
## Continuous recording FALSE
## Total recording time 20 sec (= 00:00:20)
## Recorded period 10 sec (= 00:00:10)
## Recording segment whole recording
## Number of fragments 8
## Sample rate 200
## Transducer
## Range -1000 : 1000 uV
## Prefilter
## fragment start samples Min. X1st.Qu. Median Mean X3rd.Qu.
## 1 1 0 200 -99.89 -65.24 9.4110000 3.7230000 71.81
## 2 2 3 200 -100.00 -71.81 -9.4110000 -3.7220000 65.24
## 3 3 5 200 -100.00 -71.81 -9.4110000 -3.7220000 65.24
## 4 4 7 200 -100.00 -71.81 -9.4110000 -3.7220000 65.24
## 5 5 10 400 -100.00 -70.71 0.0000596 0.0000596 70.71
## 6 6 13 200 -100.00 -71.81 -9.4110000 -3.7220000 65.24
## 7 7 16 400 -100.00 -70.71 0.0000596 0.0000596 70.71
## 8 8 19 200 -100.00 -71.81 -9.4110000 -3.7220000 65.24
## Max.
## 1 100.00
## 2 99.89
## 3 99.89
## 4 99.89
## 5 100.00
## 6 99.89
## 7 100.00
## 8 99.89
## All fragments:
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## -100.000 -71.810 -3.141 -1.489 69.590 100.000Summaries of an annotation signal (ASignal) can be shown with the S3 print() and summary () functions.
CSignals$`EDF Annotations`## Signal number 12
## Signal label EDF Annotations
## Recorded period 20 sec (= 00:00:20)
## Recording segment whole recording
## Record start annotations 0
## Other annotations 2summary(annoDSignalsPeriod)## Signal number 12
## Signal label BDF Annotations
## Recorded period 10 sec (= 00:00:10)
## Recording segment from 5.1 sec (= 00:00:05.1) till 18 sec (= 00:00:18)
## Record start annotations 0
## Other annotations 0The “Record start annotations = 0” indicates that the record start annotations were not included, i.e. readEdfSignals was used with the parameter recordStartTimes = FALSE.
‘Other annotations’ shows the number of ‘real’ annotations.
As usual, a recording starts at time 0 with sample 1.
Consequently sample n will be at time (n-1)/sRate, where sRate denotes the sample rate.
Apart from rounding errors, a from - till period in readEdfSignals will be the period [from,till), i.e. starting at from and up to be but not including till.
This may sound strange, but this convention has the following properties
the sample rate can be defined as the total number of samples divided by the total time
or, more precise, any period which is a multiple of the sample period sPeriod will always contain the same number of samples
i.e. for any t ≥ 0, [t, t+n*sPeriod) will always contain n samples
for any number of adjacent periods, the total number of samples will be always the sum of the samples in the individual periods.
the first sample will be ceiling(from*sRate) + 1
the last sample will be ceiling(till*sRate)
with from=t and till=t, the empty set [t,t) corresponds to [ceiling(tsRate) + 1, ceiling(tsRate)] which is also empty.
The header data encompass the following:
str (CHdr, max.level=1)## List of 16
## $ fileName : chr "/Library/Frameworks/R.framework/Versions/3.2/Resources/library/edfReader/extdata/edfPlusC.edf"
## $ fileType : chr "EDF"
## $ version : chr "0"
## $ patient : chr "X X X X"
## $ recordingId : chr "Startdate 10-DEC-2009 X X test_generator"
## $ startTime : POSIXlt[1:1], format: "2009-12-10 12:44:02"
## $ headerLength : int 3328
## $ reserved : chr "EDF+C"
## $ nRecords : int 20
## $ recordDuration: num 1
## $ nSignals : int 12
## $ recordedPeriod: num 20
## $ sampleBits : num 16
## $ isPlus : logi TRUE
## $ isContinuous : logi TRUE
## $ sHeaders :Classes 'ebdfSHeaders' and 'data.frame': 12 obs. of 15 variables:
## - attr(*, "class")= chr "ebdfHeader"The fields version, patient, recordingId, startTime, headerLength, reserved, nRecords, recordDuration, and nSignals are from the file header. The others are derived, but see below for sHeaders.
The signal header data encompass the following:
str (CHdr$sHeader, max.level=1)## Classes 'ebdfSHeaders' and 'data.frame': 12 obs. of 15 variables:
## $ label : chr "squarewave" "ramp" "pulse" "ECG" ...
## $ transducerType : chr "" "" "" "" ...
## $ physicalDim : chr "uV" "uV" "uV" "uV" ...
## $ physicalMin : num -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 ...
## $ physicalMax : num 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 ...
## $ digitalMin : int -32768 -32768 -32768 -32768 -32768 -32768 -32768 -32768 -32768 -32768 ...
## $ digitalMax : int 32767 32767 32767 32767 32767 32767 32767 32767 32767 32767 ...
## $ preFilter : chr "" "" "" "" ...
## $ samplesPerRecord: int 200 200 200 200 200 200 200 200 200 200 ...
## $ reserved : chr "" "" "" "" ...
## $ gain : num 0.0305 0.0305 0.0305 0.0305 0.0305 ...
## $ offset : num 0.0153 0.0153 0.0153 0.0153 0.0153 ...
## $ sRate : num 200 200 200 200 200 200 200 200 200 200 ...
## $ isAnnotation : logi FALSE FALSE FALSE FALSE FALSE FALSE ...
## $ sLength : int 4000 4000 4000 4000 4000 4000 4000 4000 4000 4000 ...The fields label, transducerType, physicalDim, physicalMin, physicalMax, digitalMin, digitalMax, preFilter, samplesPerRecord, and reserved are from the file header. The others are derived. Gain and offset are used to map the digital sample values to the range of physical values.
For annotation signals the only relevant fields are “label” which must have the value “EDF Annotations” (or “BDF Annotations”) and “samplesPerRecord”.
The data for ordinary signal objects of class ebdfCSignal encompass the following:
str(CSignals$pulse, max.level=1) ## List of 15
## $ signalNumber : int 3
## $ label : chr "pulse"
## $ isContinuous : logi TRUE
## $ from : num 0
## $ till : num Inf
## $ start : num 0
## $ fromSample : num 1
## $ transducerType: chr ""
## $ sampleBits : num 16
## $ sRate : num 200
## $ range : chr "-1000 : 1000 uV"
## $ preFilter : chr ""
## $ signal : num [1:4000] 99.9924 99.9924 99.9924 99.9924 0.0153 ...
## $ recordedPeriod: num 20
## $ totalPeriod : num 20
## - attr(*, "class")= chr "ebdfCSignal"The attributes signalNumber, label, isContinuous, transducerType, sampleBits, sRate, range, preFilter, recordedPeriod and totalPeriod are (derived) from the header data.
For a continuously recorded signal the totalPeriod is equal to the recordedPeriod.
The attributes from and till contain the values of the corresponding actual readEdfSignals parameters. The default values are 0 and Inf.
The attributes start and fromSample contains the sample time and number for the first sample in the from-till period. They are calculated as follows: from = max (0, from)
fromSample = ceiling (sRate * from) + 1 start = (fromSample - 1) / sRate
The signal attribute contains the sample data from the EDF / BDF data records. If read with the readEdfSignals parameter physical=TRUE, the default, the digital sample values are mapped to physical values. With physical=FALSE, signals contains the digital sample values.
The physical values are calculated as follows:
physicalValue = a * digitalValue + b,
with: a = (physicalMax - physicalMin) / (digitalMax - digitalMin)
b = physicalMax - a* digitalMax
The data for ordinary signal objects of class ebdfFSignal encompass the following:
str(FDSignals$`sine 8.5 Hz`, max.level=1) ## List of 15
## $ signalNumber : int 8
## $ label : chr "sine 8.5 Hz"
## $ isContinuous : logi FALSE
## $ from : num 0
## $ till : num Inf
## $ start : num 0
## $ fromSample : num 1
## $ transducerType: chr ""
## $ sampleBits : num 24
## $ sRate : num 200
## $ range : chr "-1000 : 1000 uV"
## $ preFilter : chr ""
## $ fragments :List of 8
## $ recordedPeriod: num 10
## $ totalPeriod : num 20
## - attr(*, "class")= chr "ebdfFSignal"For the attributes signalNumber, label, isContinuous, from, till, start, fromSample, transducerType, sampleBits, sRate, range, preFilter, recordedPeriod and totalPeriod see the previous section.
For a not continuously recorded signal the total period equals the start of the last data record plus its duration.
The fragments attribute contains the list of recorded fragments.
The data of a signal fragment in objects of class ebdfFSignal encompass the following:
str(FDSignals$`sine 8.5 Hz`$fragments[[1]], max.level=1) ## List of 3
## $ start : num 0
## $ fromSample: num 1
## $ signal : num [1:200] 26.4 50.9 71.8 87.6 97.2 ...The fromSample contains the sample number of the first sample in this fragment (as if it were a continuous recording). The start attribute the sample time for this sample.
The signal contains the fragment’s sample values. These may be physical values (the default) or digital values (see above).
The data for annotation signal objects of class ebdfASignal encompass the following:
str(CSignals$`EDF Annotations`, max.level=1) ## List of 8
## $ signalNumber : int 12
## $ label : chr "EDF Annotations"
## $ isContinuous : logi TRUE
## $ from : num 0
## $ till : num Inf
## $ annotations :'data.frame': 2 obs. of 5 variables:
## $ recordedPeriod: num 20
## $ totalPeriod : num 20
## - attr(*, "class")= chr "ebdfASignal"For the attributes signalNumber, label, isContinuous, from, till, recordedPeriod and totalPeriod see the section for objects of class ebdfCSignal.
The annotations attribute contains a data frame with the individual annotations.
The data for a single annotation encompass the following:
str(CSignals$`EDF Annotations`$annotations, max.level=1) ## 'data.frame': 2 obs. of 5 variables:
## $ record : int 1 2
## $ onset : num 0 600
## $ duration : num NA NA
## $ isRecordStart: logi FALSE FALSE
## $ annotations : chr "RECORD START" "REC STOP"The record attribute refers to the data record that contains the annotation.
The onset attribute contains the time of the annotation relative to the start of the recording.
The duration attribute contains the duration of the annotated event.
The isRecordStart indicates whether or not this annotation is the first one in a data record (and indicates the start time of the recording in that record).
The annotations attribute contains one or more annotations associated with the onset and duration.
This package has used code from
edf.R version 0.3 (27-11-2013),
copied from Fabian Feschet’s web link ‘feschet.fr/?p=11’ (has been removed)”
the work of Henelius Andreas as of July 2015,
https://github.com/bwrc/edf
Specification of EDF
http://www.edfplus.info/specs/edf.html
Specification of EDF+
http://www.edfplus.info/specs/edfplus.html
Specification of EDF++
http://195.154.67.227/en/contribute/edf/
Specification of BDF
see ‘Which file format does BioSemi use’ at
http://www.biosemi.com/faq/file_format.htm
Specification of BDF+ http://www.teuniz.net/edfbrowser/bdfplus%20format%20description.html
Other useful EDF related sources can be found at:
http://www.edfplus.info/downloads/