.TH PARSESCP 1 "8 March 2014" "WFDB 10.5.23" "WFDB Applications Guide"
.SH NAME
parsescp \- parse SCP-ECG, optionally save in PhysioBank-compatible format
.SH SYNOPSIS
\fBparsescp [ \fIoptions\fR ... ]
.SH DESCRIPTION
\fBparsescp\fR converts SCP-ECG output produced by SpaceLabs/Burdick ECG carts
into more easily usable formats. It was written in 2000 and has been used to
convert about a million ECGs collected at Boston's Beth Israel Deaconess Medical
Center since then. \fBparsescp\fR can also be used to create deidentified
SCP-ECG files, although it does not perform this function by default.
.PP
\fIOptions\fR include:
.TP
\fB-a\fR
Anonymize: copy standard input to standard output, removing protected health
information (PHI). This option suppresses all other output.
.TP
\fB-b\fR
Show baselines (residuals after template subtraction).
.TP
\fB-f\fR
Force the input to be parsed even if it contains CRC errors.
.TP
\fB-h\fR
Print a usage summary.
.TP
\fB-l\fR
Low-pass filter (smooth) the output waveforms.
.TP
\fB-o\fR \fIrecord\fR
Set the record name (default: \fBecg\fR) for output files.
.TP
\fB-s\fR \fIN\fR
Shift templates by \fIN\fR samples before adding them to the baselines.
.TP
\fB-S\fR \fIN\fR
Skip parsing of SCP-ECG section \fIN\fR.
.TP
\fB-t\fR
Show templates; suppress baselines (complement of \fB-b\fR option).
.TP
\fB-v\fR
Verbose mode: print a very detailed analysis of the SCP-ECG input, and write
\fIrecord\fR.txt (specify \fIrecord\fR using \fB-o\fR).
.TP
\fB-w\fR
Create a PhysioBank-compatible record (specify the record name using \fB-o\fR).
.TP
\fB-x\fR
Show a hexadecimal data dump (implies \fB-v\fR).
.TP
\fB-z\fR
Suppress final transients and zero-mean the ECGs.
.PP
Unless the \fB-a\fR option is used, this program produces at least these three
files:
.TP
\fIrecord\fB.des\fR
(text) description (age, sex, recording bandwidth, measurements, diagnoses)
.TP
\fIrecord\fB.ecg\fR (binary) reconstructed ECGs (see comments in
\fBparsescp.c\fR, the \fBparsescp\fR source file, for format)
.TP
\fIrecord\fB.key\fR
(text) patient's name and ID (medical record number)
.PP
If invoked with the \fB-v\fR option, \fBparsescp\fR produces:
.TP
\fIrecord\fB.txt\fR
(text) reconstructed ECGs
.PP
With \fB-v\fR, \fBparsescp\fR also writes a (very) detailed analysis of the
contents of the SCP-ECG input on the standard output.
.PP
If \fBparsescp\fR was compiled with the WFDB library, and if it is invoked with
the \fB-w\fR option, it also produces a pair of PhysioBank-compatible output
files:
.TP
\fIrecord\fB.dat\fR
(binary) signal file containing 12 continuous leads
.TP
\fIrecord\fB.hea
(text) header file describing \fIrecord\fB.dat\fB
.SS Supported SCP versions
.PP
This program was written using AAMI SCP-1999 (\fIStandard communications
protocol for computer-assisted electrocardiography\fR, 25 October 1999 draft)
as a reference for SCP format. It has been tested only with SCP records
produced by SpaceLabs/Burdick ECG carts (these produce second-difference
encoded data with reference beat subtraction using a single reference beat,
Huffman encoded using the SCP standard Huffman table). Amplitude (unencoded)
data and first-difference encoded data should be readable using this program,
but these formats have not been tested. Use of custom Huffman tables is
recognized but not otherwise supported. Use of multiple reference beats is
recognized but not otherwise supported.
.SS ECG signals in Spacelabs/Burdick SCP-ECG files
.PP
Spacelabs/Burdick ECG carts of the type for which this program was designed
record 2 of the 3 Einthoven leads and all 6 precordial leads simultaneously for
10 seconds, at 500 samples per second per lead, with 16-bit precision over a
range of +/-32.767 mV. Thus the sampling interval is 2 ms, and the amplitude
resolution is 5 microvolts (5000 nanovolts) per ADC unit.
.PP
Note that although the SCP standard specifies how to record the sampling
frequency and amplitude resolution in SCP-ECG files, the Spacelabs/Burdick
carts don't do this, so \fBparsescp\fR assumes the sampling frequency and
resolution above. \fBparsescp\fR will need modification in order to convert
ECGs with other sampling frequencies or resolutions correctly.
.SS ECG signals in parsescp's output files
.PP
This program derives the third Einthoven lead and the three augmented leads
using the standard relationships among the leads:
.br
III = II - I
.br
aVR = -(I + II)/2
.br
aVL = II/2 - III
.br
aVF = I/2 + III
.PP
In all of its output formats, \fBparsescp\fR represents the samples of each
signal as a sequence of unscaled integers, exactly as they appear in the
original SCP-ECG input file. Thus, in the \fB.ecg\fR, \fB.txt\fR, and
\fB.dat\fR output files, the unit of amplitude is equivalent to 5 microvolts
(5000 nanovolts), as in the SCP input. If the recording is shorter than 10
seconds, or if a signal is missing and cannot be reconstructed from the
relationships above, each missing sample is assigned a special value
(WFDB_INVALID_SAMPLE, or -32768).
.PP
The \fB-l\fR and \fB-z\fR options modify the input values as noted above; if
neither option is used, the output sample values are numerically identical to
the input sample values.
.PP
The \fB.ecg\fR file contains selected and rearranged segments of the signals in
the commonly-used layout of twelve 2.5 second segments arranged in groups of 4
above a continuous 10-second lead II. Each sample is represented as a
big-endian 16-bit two's complement signed integer. The file begins with a
512-byte prolog containing the record name and recording date and time, which
are HIPAA-defined protected health information (PHI) unless the input SCP-ECG
has been deidentified. The prolog is followed by four "traces", each
representing the same 10-second interval. The first three of these traces are
made by concatenating 2.5 second segments (1250 samples) of each of the 12
leads, in this order:
.br
( I aVR V1 V4)
.br
( II aVL V2 V5)
.br
(III aVF V3 V6)
.br
The fourth trace is a continuous 10-second segment (5000 samples) of lead II.
.PP
The optional \fB.txt\fR and \fB.dat\fR files contain the ECG signals only (no
metadata, and no PHI). The signals appear in the standard order:
.br
I, II, III, aVR, aVF, aVL, V1, V2, V3, V4, V5, V6
.br
.PP
In the \fB.txt\fR file, each line begins with a sample number (0 to 4999)
and is followed by a sample from each of the 12 leads, in order. Each
sample is represented as a base 10 numeral, with spaces inserted
between samples so that the columns line up. Thus the sample numbers
are in column 0, samples of lead I are in column 1, those of lead II
are in column 2, etc.
.PP
In the \fB.dat\fR file, the first 24 bytes contain the first sample of each
signal, in the standard order as for the \fB.txt\fR file. As in the \fB.ecg\fR
file, each sample is represented as a big-endian 16-bit two's complement
signed integer. The next 24 bytes contain the second sample of each signal,
etc.
.SS Other output files
.PP
The \fB.des\fR file contains a variety of information extracted from the SCP-ECG
input file, in human-readable form. It does not contain the ECG signals
themselves, or the patient's name or medical record number. Note
that \fB.des\fR files made from SCP-ECG files that have not been anonymized will
generally contain HIPAA-defined PHI (protected health information) such as
the recording date and the patient's age (even if over 90).
.PP
The \fB.key\fR file contains the recording date and time, the patient's name,
and the medical record number, if recorded in the input file.
.PP
The \fB.hea\fR file, if generated, contains metadata (information about the
corresponding \fB.dat\fR file) only; it does not contain any PHI, even if the
input was not anonymized. Age and sex are recorded in the \fB.hea\fR file if
present in the input file, except that ages of 90 and more are recorded
as 90. The recording date and time are not recorded in the \fB.hea\fR file.
.SS Using parsescp to create deidentified SCP-ECG files
.PP
The SCP-ECG standard defines how to record a variety of information
that includes elements defined by HIPAA as PHI (protected health information).
These include the patient's name, medical record number, birth day and month,
recording day and month, and (if the age is over 90) birth year and age.
.PP
If invoked with the \fB-a\fR option, \fBparsescp\fR reads the input SCP-ECG
file and writes an anonymized (deidentified) version of it to the standard
output. For example:
.br
\fBparsescp -a <12345678.scp >anonymous.scp\fR
.br
In this case, none of the other output files are produced.
.PP
\fBparsescp\fR removes all of the PHI as well as names of physicians and
technicians, names of hospitals or clinics, and room numbers, replacing them
with 'xxx'. It changes all dates to January 1, and if the age is over 90, it
resets the age to 90 and the birth year to 90 years before the recording year.
Finally, it recalculates the SCP-ECG CRCs so that the output is still a valid
SCP-ECG file. Note that the original input file is not modified.
.PP
Note that \fBparsescp\fR does not deidentify other types of data (including its
own \fB.des\fR and \fB.key\fR files); it can only deidentify SCP-ECG files.
.SH ENVIRONMENT
.PP
It may be necessary to set and export the shell variable \fBWFDB\fR (see
\fBsetwfdb\fR(1)).
.SS Examples
.br
\fBparsescp -o 12345 <12345.scp\fR
.br
The command above converts an SCP-ECG file named \fB12345.scp\fR into a set of
three files (\fB12345.des\fR, \fB12345.ecg\fR, and \fB12345.key\fR), as
described above. The argument following \fB-o\fR need not match the name of
the input file as in this example, but such a choice may reduce opportunities
for confusion.
.br
\fBparsescp -o 12345 -w <12345.scp\fR
.br
Same as the first example, but this command also creates a PhysioBank-compatible
record named \fB12345\fR (consisting of two files named \fB12345.dat\fR
and \fB12345.hea\fR).
.br
\fBparsescp -a <12345.scp >a001.scp\fR
.br
The final example reads its input (\fB12345.scp\fR), removes all PHI, and writes
the deidentified data to a new SCP-ECG file (\fBa001.scp\fR).
.PP
Note that none of these commands modify the original input file
(\fB12345.scp\fR).
.SH SEE ALSO
\fBrdsamp\fR(1), \fBsetwfdb\fR(1), \fBxform\fR(1), \fBsignal\fR(5)
.SH AUTHOR
George B. Moody (george@mit.edu) and Edna S. Moody
.SH SOURCE
http://www.physionet.org/physiotools/wfdb/convert/parsescp.c