Initial commit

.gitignore

@@ -0,0 +1,9 @@
+.DS_Store
+/.build
+/Packages
+xcuserdata/
+DerivedData/
+.swiftpm/configuration/registries.json
+.swiftpm/xcode/package.xcworkspace/contents.xcworkspacedata
+.netrc
+*.class

Package.resolved

@@ -0,0 +1,24 @@
+{
+  "originHash" : "bf0b92ec2751ab82eed76f0b5f4c42d45557a303569895153367fd1d19d1045a",
+  "pins" : [
+    {
+      "identity" : "swift-algorithms",
+      "kind" : "remoteSourceControl",
+      "location" : "https://github.com/apple/swift-algorithms",
+      "state" : {
+        "revision" : "f6919dfc309e7f1b56224378b11e28bab5bccc42",
+        "version" : "1.2.0"
+      }
+    },
+    {
+      "identity" : "swift-numerics",
+      "kind" : "remoteSourceControl",
+      "location" : "https://github.com/apple/swift-numerics.git",
+      "state" : {
+        "revision" : "0a5bc04095a675662cf24757cc0640aa2204253b",
+        "version" : "1.0.2"
+      }
+    }
+  ],
+  "version" : 3
+}

Package.swift

@@ -0,0 +1,33 @@
+// swift-tools-version: 6.0
+// The swift-tools-version declares the minimum version of Swift required to build this package.
+
+import PackageDescription
+
+let package = Package(
+    name: "EcgSynKit",
+    products: [
+        // Products define the executables and libraries a package produces, making them visible to other packages.
+        .library(
+            name: "EcgSynKit",
+            targets: ["EcgSynKit"]),
+    ],
+    dependencies: [
+        .package(url: "https://github.com/apple/swift-algorithms", from: "1.2.0"),
+        // .package(url: "https://github.com/AudioKit/KissFFT.git", from: "1.0.0")
+        .package(path: "./KissFFT/")
+    ],
+    targets: [
+        // Targets are the basic building blocks of a package, defining a module or a test suite.
+        // Targets can depend on other targets in this package and products from dependencies.
+        .target(
+          name: "EcgSynKit",
+          dependencies: [
+            .product(name: "Algorithms", package: "swift-algorithms"),
+            .product(name: "KissFFT", package: "kissfft")
+          ]),
+        .testTarget(
+            name: "EcgSynKitTests",
+            dependencies: ["EcgSynKit"]
+        ),
+    ]
+)

Sources/EcgSynKit/EcgSynKit.swift

@@ -0,0 +1,186 @@
+import Algorithms
+import Foundation
+import KissFFT
+
+struct Parameters {
+    /// The number of beats to simulate.
+    let numBeats: Int = 256
+
+    /// The ECG sampling frequency in Hz.
+    let sfEcg: Int = 256
+
+    /// The internal sampling frequency in Hz.
+    var sfInternal: Int = 512
+
+    /// The mean heart rate in beats per minute.
+    let hrMean: Double = 60.0
+
+    /// The standard deviation of the heart rate.
+    let hrStd: Double = 1.0
+
+    /// The ratio of power between low and high frequencies.
+    let lfhfRatio: Double = 0.5
+
+    /// The ECT amplitude in mV.
+    let amplitude: Double = 1.4
+
+    /// RNG seed value.
+    let seed: Int = 0
+
+    /// Amplitude of the noise.
+    let aNoise: Double = 0.0
+
+    /// The angle of each attractor (P, Q, R, S, T) around the limit cycle, in radians.
+    let theta: [Double] = [-60, -15, 0, 15, 90].map { $0 * .pi / 180 }
+
+    /// Widths of the attractors (P, Q, R, S, T).
+    let a: [Double] = [1.2, -5, 30, -7.5, 0.75]
+
+    /// The position of attractors (P, Q, R, S, T) above or below the z=0 plane.
+    let b: [Double] = [0.25, 0.1, 0.1, 0.1, 0.4]
+
+    /// Mayer wave frequency in Hz.
+    let flo = 0.1
+
+    /// flo standard deviation.
+    let flostd = 0.01
+
+    /// Respiratory rate frequency in Hz.
+    let fhi = 0.25
+
+    /// fhi standard deviation.
+    let fhistd = 0.01
+}
+
+/// Compute fft or inverse (based on sign) of vector data, where [i] is real and [i+1] is imaginary, i starts
+/// from 0.
+func fft(data: inout [Double], isign: Int) {
+    let isign = Double(isign)
+    let n = data.count
+
+    var j = 0
+    for i in stride(from: 0, to: n, by: 2) {
+        if j > i {
+            data.swapAt(j, i)
+            data.swapAt(j + 1, i + 1)
+        }
+        var m = n / 2
+        while m >= 2, j >= m {
+            j -= m
+            m /= 2
+        }
+        j += m
+    }
+
+    var mmax = 2
+    while mmax < n {
+        let istep = 2 * mmax
+        let theta = isign * (2.0 * .pi / Double(mmax))
+        let wtemp = sin(0.5 * theta)
+        let wpr = -2.0 * wtemp * wtemp
+        let wpi = sin(theta)
+        var wr = 1.0
+        var wi = 0.0
+
+        for m in stride(from: 0, to: mmax, by: 2) {
+            for i in stride(from: m, to: n, by: istep) {
+                let j = i + mmax
+                let tempr = wr * data[j] - wi * data[j + 1]
+                let tempi = wr * data[j + 1] + wi * data[j]
+                data[j] = data[i] - tempr
+                data[j + 1] = data[i + 1] - tempi
+                data[i] += tempr
+                data[i + 1] += tempi
+            }
+            let wrtemp = wr
+            wr = wr * wpr - wi * wpi + wr
+            wi = wi * wpr + wrtemp * wpi + wi
+        }
+        mmax = istep
+    }
+}
+
+func rrprocess(params: Parameters, nrr: Int) -> [Double] {
+    let w1 = 2.0 * .pi * params.flo
+    let w2 = 2.0 * .pi * params.fhi
+    let c1 = 2.0 * .pi * params.flostd
+    let c2 = 2.0 * .pi * params.fhistd
+
+    let sig2 = 1.0
+    let sig1 = params.lfhfRatio
+
+    let rrmean = 60.0 / params.hrMean
+    let rrstd = 60.0 * params.hrStd / (params.hrMean * params.hrMean)
+
+    let sf = Double(params.sfInternal)
+    let df = sf / Double(nrr)
+
+    var swc = (0 ..< nrr / 2 + 1).map {
+        let w = df * Double($0) * 2.0 * .pi
+        let dw1 = w - w1
+        let dw2 = w - w2
+        let hw = sig1 * exp(-dw1 * dw1 / (2.0 * c1 * c1)) / sqrt(2.0 * .pi * c1 * c1)
+            + sig2 * exp(-dw2 * dw2 / (2.0 * c2 * c2)) / sqrt(2.0 * .pi * c2 * c2)
+
+        let sw = (sf / 2.0) * sqrt(hw)
+
+        let ph = 2.0 * .pi * Double.random(in: 0.0 ..< 1.0)
+        return kiss_fft_cpx(r: sw * cos(ph), i: sw * sin(ph))
+    }
+    swc[0].i = 0.0
+    swc[nrr / 2].i = 0.0
+
+    let fft = kiss_fftr_alloc(Int32(nrr), 1, nil, nil)
+
+    let outptr = UnsafeMutablePointer<Double>.allocate(capacity: nrr)
+    kiss_fftri(fft, swc, outptr)
+
+    var rr = (0 ..< nrr).map { outptr[$0] * (1.0 / Double(nrr)) }
+    outptr.deallocate()
+
+    let xstd = stdev(rr)
+    let ratio = rrstd / xstd
+
+    for i in 0 ..< nrr {
+        rr[i] = rr[i] * ratio + rrmean
+    }
+
+    return rr
+}
+
+func stdev(_ data: [Double]) -> Double {
+    let n = Double(data.count)
+    let mean = data.reduce(0.0, +) / n
+    return sqrt(data.lazy.map { ($0 - mean) * ($0 - mean) }.reduce(0.0, +) / (n - 1))
+}
+
+func compute(params: Parameters) {
+    // adjust extrema parameters for mean heart rate
+    let hrFact = sqrt(params.hrMean / 60)
+    let hrFact2 = sqrt(hrFact)
+
+    let bi = params.b.map { $0 * hrFact }
+
+    /// XXX: Discrepancy here between Java/C and Matlab, the former uses 1.0 for ti[4] adjustment.
+    let ti = zip([hrFact2, hrFact, 1, hrFact, hrFact2], params.theta).map(*)
+
+    let ai = params.a
+
+    let x0 = SIMD3<Double>(1.0, 0.0, 0.04) // XXX: Convert to init from vector3d
+    let rseed = params.seed
+
+    // calculate time scales
+    let h = 1.0 / Double(params.sfInternal)
+    let tstep = 1.0 / Double(params.sfEcg)
+
+    // calculate length of the RR time series
+    let rrmean = (60.0 / params.hrMean)
+
+    let numRr = Int(pow(2.0, ceil(log2(Double(params.numBeats * params.sfInternal) * rrmean))))
+
+    var rr = [Double](repeating: 0.0, count: numRr)
+
+    // TODO: check sfInternal is integer multple of sfEcg
+
+    // define frequency parameters for rr process
+}

Tests/EcgSynKitTests/EcgSynKitTests.swift

@@ -0,0 +1,14 @@
+import Testing
+@testable import EcgSynKit
+@testable import KissFFT
+
+@Test func fftTest ()  {
+    // Write your test here and use APIs like `#expect(...)` to check expected conditions.
+    let p = Parameters()
+
+
+    let rr = rrprocess(params: p, nrr: 131072)
+    //fft(data: &a, isign: -1)
+    //print("out: \(rr)")
+
+}

ecgsyn-1.0.0/C/index.html

@@ -0,0 +1,11 @@
+<html>
+<head><title>Index of /static/published-projects/ecgsyn/1.0.0/C/</title></head>
+<body>
+<h1>Index of /static/published-projects/ecgsyn/1.0.0/C/</h1><hr><pre><a href="../">../</a>
+<a href="linux/">linux/</a>                                             12-Apr-2019 17:35                   -
+<a href="solaris/">solaris/</a>                                           12-Apr-2019 17:35                   -
+<a href="src/">src/</a>                                               12-Apr-2019 17:35                   -
+<a href="windows/">windows/</a>                                           12-Apr-2019 17:35                   -
+<a href="index.shtml">index.shtml</a>                                        12-Apr-2019 17:35                4274
+</pre><hr></body>
+</html>

ecgsyn-1.0.0/C/index.shtml

@@ -0,0 +1,114 @@
+<!--#set var="TITLE" value="Compiling and using the C version of ECGSYN"-->
+<!--#include virtual="/head.shtml"-->
+
+
+
+<h2>Compiling ECGSYN</h2>
+
+<p>
+Sources for the C version of <a href="../">ECGSYN</a> are <a
+href="src/">here</a>.  Note, however, that two additional files are required in
+order to compile ECGSYN.  These files (<tt>dfour1.c</tt> and <tt>ran1.c</tt>)
+are those included in <a href="http://www.nr.com" target="other">Numerical
+Recipes in C</a>.  Before attempting to compile ECGSYN, obtain these two files
+from Numerical Recipes in C and place them in the same directory as the other
+sources.  (These files are not provided here because they cannot be freely
+redistributed.)
+
+<p>
+If you cannot obtain <tt>dfour1.c</tt> and <tt>ran1.c</tt>, several
+alternatives are available, including ready-to-run executable versions of
+ECGSYN for <a href="linux/">GNU/Linux</a>, <a href="solaris/">Solaris</a>, and
+<a href="windows/">MS-Windows</a>, as well as <a
+href="../Matlab/">Matlab/Octave</a> and <a href="../Java/">Java</a>
+implementations of ECGSYN.
+
+<p>
+On most platforms, including GNU/Linux, MacOS X, and Unix, compile ECGSYN
+by typing
+<pre>
+    make
+</pre>
+in a terminal window.  This will also work under MS-Windows if you have
+installed the free <a href="http://www.cygwin.com" target="other">Cygwin/gcc
+development toolkit</a>.  If you wish to use another compiler under MS-Windows,
+you are on your own.
+
+
+<h2>Running ECGSYN</h2>
+
+<p>
+The executable version is named <tt>ecgsyn</tt> (or, under MS-Windows,
+<tt>ecgsyn.exe</tt>).  Once you have this file, move it into any directory in
+your PATH and run it by typing
+<pre>
+    ecgsyn
+</pre>
+in a terminal window.  You may add options (switches) to the '<tt>ecgsyn</tt>'
+command; the option '<tt>$</tt>', as in
+<pre>
+    ecgsyn $
+</pre>
+starts ECGSYN in interactive mode, as shown below:
+
+<pre>
+    >> ecgsyn $
+    ECGSYN: A program for generating a realistic synthetic ECG
+    Copyright (c) 2003 by Patrick McSharry & Gari Clifford. All rights reserved.
+     
+    O Name of output data file                 "ecgsyn.dat"
+    n Approximate number of heart beats        256
+    s ECG sampling frequency [Hz]              256
+    S Internal Sampling frequency [Hz]         256
+    a Amplitude of additive uniform noise [mV] 0
+    h Heart rate mean [bpm]                    60
+    H Heart rate standard deviation [bpm]      1
+    f Low frequency [Hz]                       0.1
+    F High frequency [Hz]                      0.25
+    v Low frequency standard deviation [Hz]    0.01
+    V High frequency standard deviation [Hz]   0.01
+    q LF/HF ratio                              0.5
+    R Seed                                     1
+    (Type ? for Help)
+    ->
+</pre>
+
+<p>
+At the prompt, you can then type <tt>?</tt> for help, or simply specify each
+parameter that you want to change by typing the corresponding option letter (in
+the first column above) followed by a space and the new value, then
+&lt;enter&gt;.  To review the current settings, enter a blank line.  After you
+have modified all the parameters you want, type = followed by &lt;enter&gt; to
+run the program. You may also specify the parameters in a file called
+<tt>ecgsyn.opt</tt>, which is automatically read (if it exists) the next time
+you run the program.
+
+<p>
+Any of the options can also be entered directly on the command line, by
+prefixing the option letter with '<tt>-</tt>', as in:
+<pre>
+    ecgsyn -h 80 -n 100
+</pre>
+(which would create output at a mean heart rate of 80 bpm, lasting for about
+100 beats).
+
+<p>
+The source files <tt>opt.c</tt> and <tt>opt.h</tt> provide the option
+interpreter for ECGSYN; they were written by James Theiler.  For additional
+information, and for the most recent version of <tt>opt</tt>, see
+<a href="http://nis-www.lanl.gov/~jt/Software/"
+target="other"><tt>http://nis-www.lanl.gov/~jt/Software/</tt></a>.
+
+
+<h2>Interpreting ECGSYN's output</h2>
+
+<p>
+Unless you have changed the name of the output file with the '<tt>O</tt>'
+parameter, you will find the synthetic ECG written to a text file called
+<tt>ecgsyn.dat</tt>.  Click <a href="../sample-output/">here</a> for a sample
+of ECGSYN output and for a description of the format of this file.
+
+<hr>
+<!--#include virtual="/footer.shtml"-->
+</body>
+</html>

ecgsyn-1.0.0/C/linux/HEADER.shtml

@@ -0,0 +1,10 @@
+<!--#set var="TITLE" value="ECGSYN for GNU/Linux"-->
+<!--#include virtual="/head.shtml"-->
+
+
+<p>
+The executable <tt>ecgsyn</tt> file in this directory was compiled from
+these <a href="../src/">ECGSYN sources</a> with gcc 2.96 under Red Hat
+Linux 7.2.  It is known to work under Red Hat Linux 7.1, 7.2, 7.3, 8, and 9,
+and may also work under other versions of GNU/Linux.
+

ecgsyn-1.0.0/C/linux/index.html

@@ -0,0 +1,8 @@
+<html>
+<head><title>Index of /static/published-projects/ecgsyn/1.0.0/C/linux/</title></head>
+<body>
+<h1>Index of /static/published-projects/ecgsyn/1.0.0/C/linux/</h1><hr><pre><a href="../">../</a>
+<a href="HEADER.shtml">HEADER.shtml</a>                                       12-Apr-2019 17:35                 371
+<a href="ecgsyn">ecgsyn</a>                                             12-Apr-2019 17:35               46457
+</pre><hr></body>
+</html>

ecgsyn-1.0.0/C/solaris/HEADER.shtml

@@ -0,0 +1,9 @@
+<!--#set var="TITLE" value="ECGSYN for Solaris"-->
+<!--#include virtual="/head.shtml"-->
+
+
+<p>
+The executable <tt>ecgsyn</tt> file in this directory was compiled from
+these <a href="../src/">ECGSYN sources</a> with gcc 3.1 under SunOS 5.8
+(Solaris 8).
+

ecgsyn-1.0.0/C/solaris/index.html

@@ -0,0 +1,8 @@
+<html>
+<head><title>Index of /static/published-projects/ecgsyn/1.0.0/C/solaris/</title></head>
+<body>
+<h1>Index of /static/published-projects/ecgsyn/1.0.0/C/solaris/</h1><hr><pre><a href="../">../</a>
+<a href="HEADER.shtml">HEADER.shtml</a>                                       12-Apr-2019 17:35                 253
+<a href="ecgsyn">ecgsyn</a>                                             12-Apr-2019 17:35               43854
+</pre><hr></body>
+</html>

ecgsyn-1.0.0/C/src/00README

@@ -0,0 +1,116 @@
+ECGSYN: A program for generating a realistic synthetic ECG
+Copyright (C) 2003 by Patrick McSharry & Gari Clifford. All rights reserved.
+
+
+Compiling ECGSYN
+================
+
+This directory contains sources for the C version of ECGSYN.  Note, however,
+that two additional files are required in order to compile ECGSYN.  These
+files (dfour1.c and ran1.c) are those included in Numerical Recipes in C
+(http://www.nr.com/).  Before attempting to compile ECGSYN, obtain these
+two files from Numerical Recipes in C and place them in this directory.
+(These files are missing from this directory because they cannot be freely
+redistributed.)
+
+If you cannot obtain dfour1.c and ran1.c, several alternatives are available,
+including ready-to-run executable versions of ECGSYN for GNU/Linux, Solaris,
+and MS-Windows (see the directory above this one), as well as Matlab/Octave
+and Java implementations of ECGSYN.  See http://www.physionet.org/ for details.
+
+On most platforms, including GNU/Linux, MacOS X, and Unix, compile ECGSYN
+by typing
+	make
+in a terminal window.  This will also work under MS-Windows if you have
+installed the free Cygwin/gcc development toolkit (http://www.cygwin.com/).
+If you wish to use another compiler under MS-Windows, you are on your own.
+
+
+Running ECGSYN
+==============
+
+The executable version is named 'ecgsyn' (or, under MS-Windows, 'ecgsyn.exe').
+Once you have this file, move it into any directory in your PATH and run
+it by typing
+	ecgsyn
+in a terminal window.  You may add options (switches) to the 'ecgsyn' command;
+the option '$', as in
+	ecgsyn $
+starts 'ecgsyn' in interactive mode, as shown below:
+
+>> ecgsyn $
+ECGSYN: A program for generating a realistic synthetic ECG
+Copyright (c) 2003 by Patrick McSharry & Gari Clifford. All rights reserved.
+ 
+O Name of output data file                 "ecgsyn.dat"
+n Approximate number of heart beats        256
+s ECG sampling frequency [Hz]              256
+S Internal Sampling frequency [Hz]         256
+a Amplitude of additive uniform noise [mV] 0
+h Heart rate mean [bpm]                    60
+H Heart rate standard deviation [bpm]      1
+f Low frequency [Hz]                       0.1
+F High frequency [Hz]                      0.25
+v Low frequency standard deviation [Hz]    0.01
+V High frequency standard deviation [Hz]   0.01
+q LF/HF ratio                              0.5
+R Seed                                     1
+(Type ? for Help)
+->
+
+At the prompt, you can then type ? for help, or simply specify each parameter
+above that you want to change by typing the corresponding option letter (in the
+first column above) followed by a space and the new value, then <enter>.  To
+review the current settings, enter a blank line.  After you have modified all
+the parameters you want, type = followed by <enter> to run the program. You may
+also specify the parameters in a file called ecgsyn.opt, which is automatically
+read (if it exists) the next time you run the program.
+
+Any of the options can also be entered directly on the command line, by
+prefixing the option letter with '-', as in:
+	ecgsyn -h 80 -n 100
+(which would create output at a mean heart rate of 80 bpm, lasting for about
+100 beats).
+
+The source files opt.c and opt.h provide the option interpreter for ecgsyn;
+they were written by James Theiler.  For additional information, and for the
+most recent version of 'opt', see http://nis-www.lanl.gov/~jt/Software/.
+
+
+Interpreting ECGSYN's output
+============================
+
+Unless you have changed the name of the output file with the 'O' parameter, 
+you will find the synthetic ECG written to a text file called ecgsyn.dat,
+which contains three columns:
+ * the time in seconds
+ * the ECG amplitude in millivolts
+ * markers to indicate the locations of the waveform peaks:
+	0 - (no peak)
+	1 - Top of P-wave
+	2 - Q-point
+	3 - Peak of R-wave
+	4 - S-point
+	5 - Peak of T-wave
+
+To convert the ECG output into PhysioBank (WFDB) format, use a command
+such as
+	wrsamp -F 256 -o synth -x 200 1 <ecgsyn.dat
+(assuming you have not changed the default sampling frequency of 256 Hz).
+This command produces a record named 'synth' (a signal file named 'synth.dat'
+and a header file named 'synth.hea'), which can be read by other PhysioToolkit
+applications.  'wrsamp' is part of the WFDB software package;  see
+http://www.physionet.org/physiotools/wfdb.shtml for details.
+
+
+Further information
+===================
+
+The most recent version of this software can always be obtained from
+	http://www.physionet.org/physiotools/ecgsyn/
+
+See IEEE Transactions on Biomedical Engineering, 50(3),289-294, March 2003.
+
+Authors: P. McSharry (patrick AT mcsharry DOT net)
+	 G. Clifford (gari AT mit DOT edu)   
+

ecgsyn-1.0.0/C/src/Makefile

@@ -0,0 +1,19 @@
+# file: Makefile
+
+# 'make' description file for compiling ecgsyn
+
+CFILES = ecgsyn.c opt.c dfour1.c ran1.c
+CFLAGS = -O
+
+ecgsyn:		$(CFILES) opt.h
+	$(CC) $(CFLAGS) -o ecgsyn $(CFILES) -lm
+
+dfour1.c ran1.c:
+	@echo "To compile ecgsyn, first get copies of dfour1.c and ran1.c"
+	@echo "(from Numerical Recipes in C) and place them in this directory."
+	@echo "Then type:"
+	@echo "    make ecgsyn"
+	@exit 1
+
+clean:
+	rm -f *~ *.o *.obj

ecgsyn-1.0.0/C/src/ecgsyn.c

@@ -0,0 +1,664 @@
+/* 09 Oct 2003 "ecgsyn.c"                                                     */
+/*                                                                            */
+/* Copyright (c)2003 by Patrick McSharry & Gari Clifford, All Rights Reserved */
+/* See IEEE Transactions On Biomedical Engineering, 50(3),289-294, March 2003.*/
+/* Contact P. McSharry (patrick AT mcsharry DOT net) or                       */
+/* G. Clifford (gari AT mit DOT edu)                                          */
+/*                                                                            */      
+/*   This program is free software; you can redistribute it and/or modify     */ 
+/*   it under the terms of the GNU General Public License as published by     */ 
+/*   the Free Software Foundation; either version 2 of the License, or        */ 
+/*   (at your option) any later version.                                      */ 
+/*                                                                            */ 
+/*   This program is distributed in the hope that it will be useful,          */ 
+/*   but WITHOUT ANY WARRANTY; without even the implied warranty of           */ 
+/*   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the            */ 
+/*   GNU General Public License for more details.                             */
+/*                                                                            */      
+/*   You should have received a copy of the GNU General Public License        */
+/*   along with this program; if not, write to the Free Software Foundation   */
+/*   Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA            */ 
+/*                                                                            */ 
+/*  ecgsyn.m and its dependents are freely availble from Physionet -          */ 
+/*  http://www.physionet.org/ - please report any bugs to the authors above.  */
+
+#include <stdio.h>   
+#include <math.h>  
+#include <stdlib.h> 
+#include "opt.h"
+#define PI (2.0*asin(1.0))
+#define SWAP(a,b) tempr=(a);(a)=(b);(b)=tempr
+#define MIN(a,b) (a < b ? a : b)
+#define MAX(a,b) (a > b ? a : b)
+#define PI (2.0*asin(1.0))
+#define OFFSET 1
+#define ARG1 char*
+
+#define IA 16807
+#define IM 2147483647
+#define AM (1.0/IM)
+#define IQ 127773
+#define IR 2836
+#define NTAB 32
+#define NDIV (1+(IM-1)/NTAB)
+#define EPS 1.2e-7
+#define RNMX (1.0-EPS)
+
+/*--------------------------------------------------------------------------*/
+/*    DEFINE PARAMETERS AS GLOBAL VARIABLES                                 */
+/*--------------------------------------------------------------------------*/
+
+char outfile[100]="ecgsyn.dat";/*  Output data file                   */ 
+int N = 256;                   /*  Number of heart beats              */
+int sfecg = 256;               /*  ECG sampling frequency             */
+int sf = 256;                  /*  Internal sampling frequency        */
+double Anoise = 0.0;           /*  Amplitude of additive uniform noise*/
+double hrmean = 60.0;          /*  Heart rate mean                    */
+double hrstd = 1.0;            /*  Heart rate std                     */
+double flo = 0.1;              /*  Low frequency                      */
+double fhi = 0.25;             /*  High frequency                     */
+double flostd = 0.01;          /*  Low frequency std                  */
+double fhistd = 0.01;          /*  High frequency std                 */
+double lfhfratio = 0.5;        /*  LF/HF ratio                        */
+
+int Necg = 0;                  /*  Number of ECG outputs              */
+int mstate = 3;                /*  System state space dimension       */
+double xinitial = 1.0;         /*  Initial x co-ordinate value        */
+double yinitial = 0.0;         /*  Initial y co-ordinate value        */
+double zinitial = 0.04;        /*  Initial z co-ordinate value        */
+int seed = 1;                  /*  Seed                               */
+long rseed; 
+double h; 
+double *rr,*rrpc;
+double *ti,*ai,*bi;
+
+/* prototypes for externally defined functions */
+void dfour1(double data[], unsigned long nn, int isign);
+float ran1(long *idum);
+
+/*---------------------------------------------------------------------------*/
+/*      ALLOCATE MEMORY FOR VECTOR                                           */
+/*---------------------------------------------------------------------------*/
+
+double *mallocVect(long n0, long nx)
+{
+        double *vect;
+ 
+        vect=(double *)malloc((size_t) ((nx-n0+1+OFFSET)*sizeof(double)));
+        if (!vect){
+	  printf("Memory allocation failure in mallocVect");
+	}
+        return vect-n0+OFFSET;
+}
+
+/*---------------------------------------------------------------------------*/
+/*      FREE MEMORY FOR MALLOCVECT                                           */
+/*---------------------------------------------------------------------------*/
+ 
+void freeVect(double *vect, long n0, long nx)
+{
+        free((ARG1) (vect+n0-OFFSET));
+}
+
+/*---------------------------------------------------------------------------*/
+/*      MEAN CALCULATOR                                                      */
+/*---------------------------------------------------------------------------*/
+ 
+double mean(double *x, int n)
+/* n-by-1 vector, calculate mean */
+{
+        int j;
+        double add;
+ 
+        add = 0.0;
+        for(j=1;j<=n;j++)  add += x[j];
+ 
+        return (add/n);
+}
+
+
+/*---------------------------------------------------------------------------*/
+/*      STANDARD DEVIATION CALCULATOR                                        */
+/*---------------------------------------------------------------------------*/
+
+double stdev(double *x, int n)
+/* n-by-1 vector, calculate standard deviation */
+{
+        int j;
+        double add,mean,diff,total;
+
+        add = 0.0;
+        for(j=1;j<=n;j++)  add += x[j];
+        mean = add/n;
+
+        total = 0.0;
+        for(j=1;j<=n;j++)  
+        {
+           diff = x[j] - mean;
+           total += diff*diff;
+        } 
+  
+        return (sqrt(total/(n-1)));
+}
+
+/*--------------------------------------------------------------------------*/
+/*    WRITE VECTOR IN A FILE                                                */
+/*--------------------------------------------------------------------------*/
+
+void vecfile(char filename[], double *x, int n)
+{
+   int i;
+   FILE *fp;
+  
+   fp = fopen(filename,"w");
+   for(i=1;i<=n;i++)  fprintf(fp,"%e\n",x[i]);
+   fclose(fp);
+}
+
+/*--------------------------------------------------------------------------*/
+/*    INTERP                                                                */
+/*--------------------------------------------------------------------------*/
+
+void interp(double *y, double *x, int n, int r)
+{
+   int i,j;
+   double a;
+
+   for(i=1;i<=n-1;i++)
+   {
+      for(j=1;j<=r;j++) 
+      {
+         a = (j-1)*1.0/r;
+         y[(i-1)*r+j] = (1.0-a)*x[i] + a*x[i+1];
+      }
+   }
+}
+
+
+/*--------------------------------------------------------------------------*/
+/*    GENERATE RR PROCESS                                                   */
+/*--------------------------------------------------------------------------*/
+
+void rrprocess(double *rr, double flo, double fhi, 
+double flostd, double fhistd, double lfhfratio,  
+double hrmean, double hrstd, double sf, int n)
+{
+   int i,j;
+   double c1,c2,w1,w2,sig1,sig2,rrmean,rrstd,xstd,ratio;
+   double df,dw1,dw2,*w,*Hw,*Sw,*ph0,*ph,*SwC;
+
+   w = mallocVect(1,n);
+   Hw = mallocVect(1,n);
+   Sw = mallocVect(1,n);
+   ph0 = mallocVect(1,n/2-1);
+   ph = mallocVect(1,n);
+   SwC = mallocVect(1,2*n);
+
+
+   w1 = 2.0*PI*flo;
+   w2 = 2.0*PI*fhi;
+   c1 = 2.0*PI*flostd;
+   c2 = 2.0*PI*fhistd;
+   sig2 = 1.0;
+   sig1 = lfhfratio;
+   rrmean = 60.0/hrmean;
+   rrstd = 60.0*hrstd/(hrmean*hrmean);
+
+   df = sf/n;
+   for(i=1;i<=n;i++) w[i] = (i-1)*2.0*PI*df;
+   for(i=1;i<=n;i++) 
+   {
+      dw1 = w[i]-w1;
+      dw2 = w[i]-w2;
+      Hw[i] = sig1*exp(-dw1*dw1/(2.0*c1*c1))/sqrt(2*PI*c1*c1) 
+            + sig2*exp(-dw2*dw2/(2.0*c2*c2))/sqrt(2*PI*c2*c2); 
+   }
+   for(i=1;i<=n/2;i++) Sw[i] = (sf/2.0)*sqrt(Hw[i]);
+   for(i=n/2+1;i<=n;i++) Sw[i] = (sf/2.0)*sqrt(Hw[n-i+1]);
+
+
+   /* randomise the phases */
+   for(i=1;i<=n/2-1;i++) ph0[i] = 2.0*PI*ran1(&rseed);
+   ph[1] = 0.0;
+   for(i=1;i<=n/2-1;i++) ph[i+1] = ph0[i];
+   ph[n/2+1] = 0.0;
+   for(i=1;i<=n/2-1;i++) ph[n-i+1] = - ph0[i]; 
+
+
+   /* make complex spectrum */
+   for(i=1;i<=n;i++) SwC[2*i-1] = Sw[i]*cos(ph[i]);
+   for(i=1;i<=n;i++) SwC[2*i] = Sw[i]*sin(ph[i]);
+
+   /* calculate inverse fft */
+   dfour1(SwC,n,-1);
+
+   /* extract real part */
+   for(i=1;i<=n;i++) rr[i] = (1.0/n)*SwC[2*i-1];
+
+   xstd = stdev(rr,n);
+   ratio = rrstd/xstd; 
+
+   for(i=1;i<=n;i++) rr[i] *= ratio;
+   for(i=1;i<=n;i++) rr[i] += rrmean;
+
+   freeVect(w,1,n);
+   freeVect(Hw,1,n);
+   freeVect(Sw,1,n);
+   freeVect(ph0,1,n/2-1);
+   freeVect(ph,1,n);
+   freeVect(SwC,1,2*n);
+}
+
+/*--------------------------------------------------------------------------*/
+/*    THE ANGULAR FREQUENCY                                                 */
+/*--------------------------------------------------------------------------*/
+
+double angfreq(double t)
+{
+   int i;
+  
+   i = 1 + (int)floor(t/h);
+  
+   return 2.0*PI/rrpc[i];
+}
+
+/*--------------------------------------------------------------------------*/
+/*    THE EXACT NONLINEAR DERIVATIVES                                       */
+/*--------------------------------------------------------------------------*/
+
+void derivspqrst(double t0,double x[],double dxdt[])
+{
+   int i,k;
+   double a0,w0,r0,x0,y0,z0;
+   double t,dt,dt2,*xi,*yi,zbase;
+ 
+   k = 5; 
+   xi = mallocVect(1,k);
+   yi = mallocVect(1,k); 
+  
+   w0 = angfreq(t0);
+   r0 = 1.0; x0 = 0.0;  y0 = 0.0;  z0 = 0.0;
+   a0 = 1.0 - sqrt((x[1]-x0)*(x[1]-x0) + (x[2]-y0)*(x[2]-y0))/r0;
+
+   for(i=1;i<=k;i++) xi[i] = cos(ti[i]);
+   for(i=1;i<=k;i++) yi[i] = sin(ti[i]);   
+
+   zbase = 0.005*sin(2.0*PI*fhi*t0);
+
+   t = atan2(x[2],x[1]);
+   dxdt[1] = a0*(x[1] - x0) - w0*(x[2] - y0);
+   dxdt[2] = a0*(x[2] - y0) + w0*(x[1] - x0); 
+   dxdt[3] = 0.0;  
+   for(i=1;i<=k;i++)  
+   {
+      dt = fmod(t-ti[i],2.0*PI);
+      dt2 = dt*dt;
+      dxdt[3] += -ai[i]*dt*exp(-0.5*dt2/(bi[i]*bi[i])); 
+   }
+   dxdt[3] += -1.0*(x[3] - zbase);
+  
+   freeVect(xi,1,k);
+   freeVect(yi,1,k);
+}
+
+/*--------------------------------------------------------------------------*/
+/*    RUNGA-KUTTA FOURTH ORDER INTEGRATION                                  */
+/*--------------------------------------------------------------------------*/
+
+void drk4(double y[], int n, double x, double h, double yout[], 
+          void (*derivs)(double, double [], double []))
+{
+        int i;
+        double xh,hh,h6,*dydx,*dym,*dyt,*yt;
+ 
+        dydx=mallocVect(1,n);
+        dym=mallocVect(1,n);
+        dyt=mallocVect(1,n);
+        yt=mallocVect(1,n);
+
+        hh=h*0.5;
+        h6=h/6.0;
+        xh=x+hh;
+        (*derivs)(x,y,dydx);
+        for (i=1;i<=n;i++) yt[i]=y[i]+hh*dydx[i];
+        (*derivs)(xh,yt,dyt);
+        for (i=1;i<=n;i++) yt[i]=y[i]+hh*dyt[i];
+        (*derivs)(xh,yt,dym);
+        for (i=1;i<=n;i++) {
+                yt[i]=y[i]+h*dym[i];
+                dym[i] += dyt[i];
+        }
+        (*derivs)(x+h,yt,dyt);
+        for (i=1;i<=n;i++)
+                yout[i]=y[i]+h6*(dydx[i]+dyt[i]+2.0*dym[i]);
+
+        freeVect(dydx,1,n);
+        freeVect(dym,1,n);
+        freeVect(dyt,1,n);
+        freeVect(yt,1,n);
+}
+
+/*--------------------------------------------------------------------------*/
+/*    DETECT PEAKS                                                          */
+/*--------------------------------------------------------------------------*/
+
+double detectpeaks(double *ipeak, double *x, double *y, double *z, int n)
+{
+   int i,j,j1,j2,jmin,jmax,d;
+   double thetap1,thetap2,thetap3,thetap4,thetap5;
+   double theta1,theta2,d1,d2,zmin,zmax;
+   
+   /* use globally defined angles for PQRST */
+   thetap1 = ti[1];
+   thetap2 = ti[2];
+   thetap3 = ti[3];
+   thetap4 = ti[4];
+   thetap5 = ti[5];
+
+   for(i=1;i<=n;i++) ipeak[i] = 0.0;
+   theta1 = atan2(y[1],x[1]);
+   for(i=1;i<n;i++)
+   {
+      theta2 = atan2(y[i+1],x[i+1]);
+      if( (theta1 <= thetap1) && (thetap1 <= theta2) )  
+      {
+	d1 = thetap1 - theta1;
+        d2 = theta2 - thetap1;
+        if(d1 < d2)  ipeak[i] = 1.0;
+        else         ipeak[i+1] = 1.0;
+      }
+      else if( (theta1 <= thetap2) && (thetap2 <= theta2) )  
+      {
+	d1 = thetap2 - theta1;
+        d2 = theta2 - thetap2;
+        if(d1 < d2)  ipeak[i] = 2.0;
+        else         ipeak[i+1] = 2.0;
+      }
+      else if( (theta1 <= thetap3) && (thetap3 <= theta2) )  
+      {
+	d1 = thetap3 - theta1;
+        d2 = theta2 - thetap3;
+        if(d1 < d2)  ipeak[i] = 3.0;
+        else         ipeak[i+1] = 3.0;
+      }
+      else if( (theta1 <= thetap4) && (thetap4 <= theta2) )  
+      {
+	d1 = thetap4 - theta1;
+        d2 = theta2 - thetap4;
+        if(d1 < d2)  ipeak[i] = 4.0;
+        else         ipeak[i+1] = 4.0;
+      }
+      else if( (theta1 <= thetap5) && (thetap5 <= theta2) )  
+      {
+	d1 = thetap5 - theta1;
+        d2 = theta2 - thetap5;
+        if(d1 < d2)  ipeak[i] = 5.0;
+        else         ipeak[i+1] = 5.0;
+      }
+      theta1 = theta2; 
+   }
+
+   /* correct the peaks */
+   d = (int)ceil(sfecg/64);
+   for(i=1;i<=n;i++)
+   { 
+     if( ipeak[i]==1 || ipeak[i]==3 || ipeak[i]==5 )
+     {
+        j1 = MAX(1,i-d);
+        j2 = MIN(n,i+d);
+        jmax = j1;
+        zmax = z[j1];
+        for(j=j1+1;j<=j2;j++)
+	{ 
+	   if(z[j] > zmax) 
+           {
+	      jmax = j;
+              zmax = z[j];
+	   }
+	}
+        if(jmax != i)
+	{
+           ipeak[jmax] = ipeak[i];
+           ipeak[i] = 0;
+	}
+     }
+     else if( ipeak[i]==2 || ipeak[i]==4 )
+     {
+        j1 = MAX(1,i-d);
+        j2 = MIN(n,i+d);
+        jmin = j1;
+        zmin = z[j1];
+        for(j=j1+1;j<=j2;j++)
+	{ 
+	   if(z[j] < zmin) 
+           {
+	      jmin = j;
+              zmin = z[j];
+	   }
+	}
+        if(jmin != i)
+	{
+           ipeak[jmin] = ipeak[i];
+           ipeak[i] = 0;
+	}
+     }
+   }
+
+}
+
+/*--------------------------------------------------------------------------*/
+/*      MAIN PROGRAM                                                         */
+/*---------------------------------------------------------------------------*/
+
+main(argc,argv)
+int     argc;
+char    **argv;
+{
+
+    /* First step is to register the options */
+
+    optregister(outfile,CSTRING,'O',"Name of output data file");  
+    optregister(N,INT,'n',"Approximate number of heart beats");    
+    optregister(sfecg,INT,'s',"ECG sampling frequency [Hz]");   
+    optregister(sf,INT,'S',"Internal Sampling frequency [Hz]"); 
+    optregister(Anoise,DOUBLE,'a',"Amplitude of additive uniform noise [mV]");
+    optregister(hrmean,DOUBLE,'h',"Heart rate mean [bpm]");
+    optregister(hrstd,DOUBLE,'H',"Heart rate standard deviation [bpm]");
+    optregister(flo,DOUBLE,'f',"Low frequency [Hz]");
+    optregister(fhi,DOUBLE,'F',"High frequency [Hz]");
+    optregister(flostd,DOUBLE,'v',"Low frequency standard deviation [Hz]");
+    optregister(fhistd,DOUBLE,'V',"High frequency standard deviation [Hz]");
+    optregister(lfhfratio,DOUBLE,'q',"LF/HF ratio");
+    optregister(seed,INT,'R',"Seed");    
+    opt_title_set("ECGSYN: A program for generating a realistic synthetic ECG\n" 
+     "Copyright (c) 2003 by Patrick McSharry & Gari Clifford. All rights reserved.\n");
+
+    getopts(argc,argv);
+
+    dorun();
+}
+
+
+
+/*--------------------------------------------------------------------------*/
+/*    DORUN PART OF PROGRAM                                                 */
+/*--------------------------------------------------------------------------*/
+
+int dorun()
+{
+   int i,j,k,q,Nrr,Nt,Nts;
+   double *x,tstep,tecg,rrmean,qd,hrfact,hrfact2;
+   double *xt,*yt,*zt,*xts,*yts,*zts;
+   double timev,*ipeak,zmin,zmax,zrange;
+   FILE *fp;
+   void (*derivs)(double, double [], double []);
+
+   /* perform some checks on input values */
+   q = (int)rint(sf/sfecg);
+   qd = (double)sf/(double)sfecg;
+   if(q != qd) {
+     printf("Internal sampling frequency must be an integer multiple of the \n"); 
+     printf("ECG sampling frequency!\n"); 
+     printf("Your current choices are:\n");
+     printf("ECG sampling frequency: %d Hertz\n",sfecg);
+     printf("Internal sampling frequency: %d Hertz\n",sf);
+     exit(1);}
+
+
+   /* declare and initialise the state vector */
+   x=mallocVect(1,mstate);
+   x[1] = xinitial; 
+   x[2] = yinitial;
+   x[3] = zinitial;
+
+   /* declare and define the ECG morphology vectors (PQRST extrema parameters) */
+   ti=mallocVect(1,5);
+   ai=mallocVect(1,5);
+   bi=mallocVect(1,5);
+   /* P            Q            R           S           T        */
+   ti[1]=-60.0; ti[2]=-15.0; ti[3]=0.0;  ti[4]=15.0; ti[5]=90.0;
+   ai[1]=1.2;   ai[2]=-5.0;  ai[3]=30.0; ai[4]=-7.5; ai[5]=0.75;
+   bi[1]=0.25;  bi[2]=0.1;   bi[3]=0.1;  bi[4]=0.1;  bi[5]=0.4;
+
+   /* convert angles from degrees to radians */
+   for(i=1;i<=5;i++) ti[i] *= PI/180.0;
+
+   /* adjust extrema parameters for mean heart rate */
+   hrfact = sqrt(hrmean/60.0);
+   hrfact2 = sqrt(hrfact);
+   for(i=1;i<=5;i++) bi[i] *= hrfact;
+   ti[1]*=hrfact2;  ti[2]*=hrfact; ti[3]*=1.0; ti[4]*=hrfact; ti[5]*=1.0;
+
+
+   /* calculate time scales */
+   h = 1.0/sf;
+   tstep = 1.0/sfecg;
+
+   printf("ECGSYN: A program for generating a realistic synthetic ECG\n" 
+    "Copyright (c) 2003 by Patrick McSharry & Gari Clifford. All rights reserved.\n"
+    "See IEEE Transactions On Biomedical Engineering, 50(3), 289-294, March 2003.\n"
+    "Contact P. McSharry (patrick@mcsharry.net) or G. Clifford (gari@mit.edu)\n"); 
+
+   printf("Approximate number of heart beats: %d\n",N);
+   printf("ECG sampling frequency: %d Hertz\n",sfecg);
+   printf("Internal sampling frequency: %d Hertz\n",sf);
+   printf("Amplitude of additive uniformly distributed noise: %g mV\n",Anoise);
+   printf("Heart rate mean: %g beats per minute\n",hrmean);
+   printf("Heart rate std: %g beats per minute\n",hrstd);
+   printf("Low frequency: %g Hertz\n",flo);
+   printf("High frequency std: %g Hertz\n",fhistd);
+   printf("Low frequency std: %g Hertz\n",flostd);
+   printf("High frequency: %g Hertz\n",fhi);
+   printf("LF/HF ratio: %g\n",lfhfratio);
+
+   /* initialise seed */
+   rseed = -seed;  
+
+
+   /* select the derivs to use */
+   derivs = derivspqrst;
+
+   /* calculate length of RR time series */
+   rrmean = (60/hrmean);
+   Nrr = (int)pow(2.0, ceil(log10(N*rrmean*sf)/log10(2.0)));	 
+   printf("Using %d = 2^%d samples for calculating RR intervals\n",
+           Nrr,(int)(log10(1.0*Nrr)/log10(2.0))); 
+
+
+   /* create rrprocess with required spectrum */
+   rr = mallocVect(1,Nrr);
+   rrprocess(rr, flo, fhi, flostd, fhistd, lfhfratio, hrmean, hrstd, sf, Nrr); 
+   vecfile("rr.dat",rr,Nrr);
+
+   /* create piecewise constant rr */
+   rrpc = mallocVect(1,2*Nrr);
+   tecg = 0.0;
+   i = 1;
+   j = 1;
+   while(i <= Nrr)
+   {  
+      tecg += rr[j];
+      j = (int)rint(tecg/h);
+      for(k=i;k<=j;k++) rrpc[k] = rr[i];
+      i = j+1;
+   }
+   Nt = j;
+   vecfile("rrpc.dat",rrpc,Nt);
+
+   printf("Printing ECG signal to file: %s\n",outfile);
+
+   /* integrate dynamical system using fourth order Runge-Kutta*/
+   xt = mallocVect(1,Nt);
+   yt = mallocVect(1,Nt);
+   zt = mallocVect(1,Nt);
+
+   timev = 0.0;
+   for(i=1;i<=Nt;i++)
+   {
+      xt[i] = x[1];
+      yt[i] = x[2];
+      zt[i] = x[3];
+      drk4(x, mstate, timev, h, x, derivs);
+      timev += h;
+   }
+
+
+   /* downsample to ECG sampling frequency */
+   xts = mallocVect(1,Nt);
+   yts = mallocVect(1,Nt);
+   zts = mallocVect(1,Nt);
+
+   j=0;
+   for(i=1;i<=Nt;i+=q)
+   { 
+      j++;
+      xts[j] = xt[i];
+      yts[j] = yt[i];
+      zts[j] = zt[i];
+   }
+   Nts = j;
+
+
+   /* do peak detection using angle */
+   ipeak = mallocVect(1,Nts);
+   detectpeaks(ipeak, xts, yts, zts, Nts);
+ 
+   /* scale signal to lie between -0.4 and 1.2 mV */
+   zmin = zts[1];
+   zmax = zts[1];
+   for(i=2;i<=Nts;i++)
+   {
+     if(zts[i] < zmin)       zmin = zts[i];
+     else if(zts[i] > zmax)  zmax = zts[i];
+   }
+   zrange = zmax-zmin;
+   for(i=1;i<=Nts;i++) zts[i] = (zts[i]-zmin)*(1.6)/zrange - 0.4;
+
+   /* include additive uniformly distributed measurement noise */
+   for(i=1;i<=Nts;i++) zts[i] += Anoise*(2.0*ran1(&rseed) - 1.0);    
+
+   /* output ECG file */
+   fp = fopen(outfile,"w");
+   for(i=1;i<=Nts;i++) fprintf(fp,"%f %f %d\n",(i-1)*tstep,zts[i],(int)ipeak[i]);
+   fclose(fp);
+
+
+   printf("Finished ECG output\n");
+
+freeVect(x,1,mstate);
+freeVect(rr,1,Nrr);
+freeVect(rrpc,1,2*Nrr);
+freeVect(ti,1,5);
+freeVect(ai,1,5);
+freeVect(bi,1,5);
+freeVect(xt,1,Nt);
+freeVect(yt,1,Nt);
+freeVect(zt,1,Nt);
+freeVect(xts,1,Nt);
+freeVect(yts,1,Nt);
+freeVect(zts,1,Nt);
+freeVect(ipeak,1,Nts);
+
+/* END OF DORUN */
+}
+

ecgsyn-1.0.0/C/src/index.html

@@ -0,0 +1,11 @@
+<html>
+<head><title>Index of /static/published-projects/ecgsyn/1.0.0/C/src/</title></head>
+<body>
+<h1>Index of /static/published-projects/ecgsyn/1.0.0/C/src/</h1><hr><pre><a href="../">../</a>
+<a href="00README">00README</a>                                           12-Apr-2019 17:35                4672
+<a href="Makefile">Makefile</a>                                           12-Apr-2019 17:35                 426
+<a href="ecgsyn.c">ecgsyn.c</a>                                           12-Apr-2019 17:35               20586
+<a href="opt.c">opt.c</a>                                              12-Apr-2019 17:35               56582
+<a href="opt.h">opt.h</a>                                              12-Apr-2019 17:35                5237
+</pre><hr></body>
+</html>

ecgsyn-1.0.0/C/src/opt.h

@@ -0,0 +1,159 @@
+/*
+opt.h  version 3.17  -	User Include File for options package.
+
+OPT is a subroutine library which facilitates the convenient 
+input of parameters to a C or C++ program. Parameters are parsed 
+from a command line, with further facilities for reading options 
+from files, from environment strings, or from an interactive 
+environment. The aim of the opt package is to permit programs to 
+be both user- and programmer- friendly. The package attempts to 
+on the one hand provide a direct and relatively full-featured 
+input interface to the ultimate user of the program, and at the 
+same time impose a minimal amount of work on the programmer to 
+"attach" the package to his or her software. A texinfo file is 
+part of the distribution; or you can view the html documentation at:
+http://nis-www.lanl.gov/~jt/Software/opt/opt_toc.html
+
+Download the lastest version of the source code from:
+http://nis-www.lanl.gov/~jt/Software/
+
+opt is available to the public under the GNU General Public License:
+http://www.gnu.org/copyleft/gpl.html
+
+This SOFTWARE has been authored by an employee of the University of
+California, operator of the Los Alamos National Laboratory under
+Contract No. W-7405-ENG-36 with the U.S. Department of Energy. The
+U.S. Government has rights to use, reproduce, and distribute this
+SOFTWARE. The public may copy, distribute, prepare derivative works
+and publicly display this SOFTWARE without charge, provided that this
+Notice and any statement of authorship are reproduced on all
+copies. Neither the Government nor the University makes any warranty,
+express or implied, or assumes any liability or responsibility for the
+use of this SOFTWARE. If SOFTWARE is modified to produce derivative
+works, such modified SOFTWARE should be clearly marked, so as not to
+confuse it with the version available from LANL.
+
+*/
+
+
+#ifndef _OPT_H
+#define	_OPT_H 	/* Signal that this header file has been included */
+
+/* 
+ * These are delimiter characters 
+ */
+#define DELIM		'-'		/* option delimiter character */
+#define	ALTDELIM	'/'		/* alternate delimiter character */
+#define	OPTFROMFILE	'@'		/* denotes options are in a file */
+#define	OPTTOFILE	'%'		/* says to put options in a file */
+#define	DOCUMENT	'-'		/* write document to file */
+#define	INTERACT	'$'		/* Flags interactive menu */
+#define	HELPCH		'?'		/* Help character */
+/*
+ * These are not available on command line 
+ * But may be invoked from a file
+ */
+#define IGNOREEOL       ';'		/* Ignore until the end of line */
+#define	RUN             '='		/* Says to just run to completion */
+#define	QUITCH		    '.'		/* Quit character */
+/*
+ * These are not available on command line or from a file
+ * But may be invoked from the menu
+ */
+#define	BANG		    '!'		/* Shell escape character */
+#define	ADDITIONAL_OPTS	'+'		/* Additional options */
+
+
+typedef enum    {
+                INT,            UNSINT,          LONG,           CHAR,
+                INTLEVEL,       
+                FLOAT,          DOUBLE,
+                FLAG,           NEGFLAG,        ABSFLAG,        ABSNEGFLAG,
+                VSTRING,        CSTRING,        UNDELIMV,       UNDELIMC
+                }
+                opt_TYPE;
+
+
+typedef	int	(*PFI)();
+
+#define	OPT_EXT	".opt"	/* standard options file extension */
+
+#ifndef TRUE
+#define TRUE 1
+#define FALSE 0
+#endif
+
+#ifndef	ARGCHECK
+#ifdef __TURBOC__ 
+#define	ARGCHECK
+#endif /* __TURBOC__ */
+#ifdef __cplusplus 
+#define	ARGCHECK
+#endif /* __cplusplus */
+#endif /* ARGCHECK */
+
+
+#ifdef	ARGCHECK
+	extern  int     opt_register(char *,opt_TYPE,char,char *);
+	extern	void	opt_usage_set(char *);
+	extern	void	opt_title_set(char *);
+	extern	void	opt_verify_set(PFI);
+	extern	void	opt_doc_set(PFI);
+	extern	void	opt_quit_set(PFI);
+	extern	void	opt_run_set(PFI);
+	extern	void	opt_help_setf(PFI);
+	extern	void	opt_help_set(char,char *);
+	extern	void	opt_ufilter_set(PFI);
+	extern	void	opt_dfilter_set(PFI);
+    extern	void	opt_env_set(char *);
+    extern	void	opt_default_set(char *);
+#if DISABLE_VARARGS
+	extern	void	opt_errmess(char *);
+	extern	void	opt_message(char *);
+	extern	void	opt_warning(char *);
+	extern	void	opt_fatal(char *);
+#else
+	extern	void	opt_errmess();
+	extern	void	opt_message();
+	extern	void	opt_warning();
+	extern	void	opt_fatal();
+#endif /* DISABLE_VARARGS */
+	extern	void	opt_abort_run(void);
+	extern	int	    opt_begin_run(PFI);
+	extern	int		getopts(int,char **);
+#else
+	extern  int     opt_register();
+	extern	void	opt_usage_set();
+	extern	void	opt_title_set();
+	extern	void	opt_verify_set();
+	extern	void	opt_doc_set();
+	extern	void	opt_quit_set();
+	extern	void	opt_run_set();
+	extern	void	opt_help_setf();
+	extern	void	opt_help_set();
+	extern	void	opt_help_set();
+	extern	void	opt_ufilter_set();
+	extern	void	opt_dfilter_set();
+    extern	void	opt_env_set();
+    extern	void	opt_default_set();
+
+	extern	void	opt_errmess();
+	extern	void	opt_message();
+	extern	void	opt_warning();
+	extern	void	opt_fatal();
+
+	extern	void	opt_abort_run();
+	extern	int	    opt_begin_run();
+	extern	int		getopts();
+
+#endif /* ARGCHECK */
+
+
+/*********************************
+ * Macro's for registering options
+ */
+
+#define	optregister(val,typ,c,str) opt_register((char *)&val,typ,c,str)
+#define optrunset(r) {int r(); opt_run_set( r );}
+
+#endif /* _OPT_H */

ecgsyn-1.0.0/C/windows/HEADER.shtml

@@ -0,0 +1,14 @@
+<!--#set var="TITLE" value="ECGSYN for Windows"-->
+<!--#include virtual="/head.shtml"-->
+
+<p>
+  There are two versions of the <code>ecgsyn.exe</code> executable in this directory. Using the
+  <a href="../src/">ECGSYN source files</a>, the first version was compiled with <code>Cygwin64 2.6.0 gcc 5.4.0</code>,
+  and the second version with <code>MinGW-w64 gcc 4.9.2</code>, both under Windows 10.</p>
+
+<p>
+To run the Cygwin executable, you will need to have the Cygwin DLLs installed in your PATH in
+order to run this program successfully. The simplest and most reliable
+way to do this is to install the <a href="http://www.cygwin.com/" target="other">Cygwin development toolkit</a>.
+To run the MinGW executable, you should install <a href="https://sourceforge.net/projects/mingw-w64/" target="other">MinGW-w64</a>.
+</p>

ecgsyn-1.0.0/C/windows/index.html

@@ -0,0 +1,10 @@
+<html>
+<head><title>Index of /static/published-projects/ecgsyn/1.0.0/C/windows/</title></head>
+<body>
+<h1>Index of /static/published-projects/ecgsyn/1.0.0/C/windows/</h1><hr><pre><a href="../">../</a>
+<a href="HEADER.shtml">HEADER.shtml</a>                                       12-Apr-2019 17:35                 821
+<a href="HEADER.shtml~">HEADER.shtml~</a>                                      12-Apr-2019 17:35                 647
+<a href="cygwin_ecgsyn.zip">cygwin_ecgsyn.zip</a>                                  12-Apr-2019 17:35               35146
+<a href="mingw_ecgsyn.zip">mingw_ecgsyn.zip</a>                                   12-Apr-2019 17:35               34966
+</pre><hr></body>
+</html>

ecgsyn-1.0.0/Java/HEADER.shtml

@@ -0,0 +1,21 @@
+<!--#set var="TITLE" value="ECGSYN implemented in Java"-->
+<!--#include virtual="/head.shtml"-->
+
+
+<p>
+This directory contains Mauricio Villarroel's implementation of
+<a href="../">ECGSYN</a> as a Java applet.
+
+<p>
+To run the applet in your web browser, click
+<a href="ecgsyn-java.html">here</a>.
+
+<p>
+The individual Java files can be downloaded by following the links
+below, or you may download all of them, together with the C and Matlab
+implementations of ECGSYN, as a single gzip-compressed tar archive, <a
+href="../ecgsyn.tar.gz"><tt>ecgsyn.tar.gz</tt></a>.  (See <a
+href="/faq.shtml#tar-gz">How can I unpack a .tar.gz archive?</a> if
+you need help doing this.)
+
+<hr>

ecgsyn-1.0.0/Java/ecgApplet.html

@@ -0,0 +1,64 @@
+<HTML>
+<HEAD>
+   <TITLE>ECGSYN Java Application</TITLE>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"></HEAD>
+<BODY bgcolor="#003366" text="#FFFFCC" link="#FFFF33" vlink="#FFCC00" leftmargin="0" topmargin="0" marginwidth="0" marginheight="0">
+<table width="925" border="0" align="center" cellpadding="0" cellspacing="5">
+  <tr> 
+    <td height="50" colspan="2">&nbsp;
+<H3> 
+  <HR WIDTH="100%">
+</H3>
+<H3 align="center"><font color="#FF9900">JAVA Application for <br>
+	ECGSYN: A Dynamical Model for Generating 
+  Synthetic Electrocardiogram Signals
+  </font></H3>
+<H3>
+  <HR WIDTH="100%">
+</H3>	
+	</td>
+  </tr>
+  <tr> 
+    <td width="300" align="left" valign="top"><p><strong>ECGSYN</strong>:</p>
+      <p><strong>&copy;</strong> ECGSYN Copyright by Patrick E. McSharry and Gari 
+        D. Clifford. <br>
+        &copy; Java code copyright by Mauricio Villarroel.<br>
+        <br>
+        For the Mathematical Model, see:</p>
+      <table width="100%" border="1" cellspacing="0" cellpadding="5">
+        <tr> 
+          <td align="left" valign="top">IEEE Transactions On Biomedical Engineering, 
+            50(3), 289-294, March 2003</td>
+        </tr>
+      </table>
+      <p> Contact: </p>
+      <ul>
+        <li><a href="mailto:patrick@mcsharry.net">Patrck McSharry</a></li>
+        <li><a href="mailto:gari@mit.edu">Gari Clifford</a></li>
+        <li><a href="mailto:mauricio.villarroel@estudiantes.ucb.edu.bo">Mauricio Villarroel</a></li>
+      </ul>
+      <p>Please read the <a href="ecgLicense.txt">Software License</a>. 
+</p></td>
+    <td align="center" valign="middle">ECG Ouput Sample image:<br><p><img src="ecgplot.PNG" alt="ECGSYN-Java Output Sample image" width="580" height="330" border="1"></p>
+      <p>Source code: <a href="ecgApplet.tar.gz">ecgApplet.tar.gz</a></p></td>
+  </tr>
+  <tr> 
+    <td height="50">&nbsp;</td>
+    <td height="50" align="center" valign="middle">&nbsp;</td>
+  </tr>
+  <tr> 
+    <td colspan="2" align="center" valign="top"><strong><font size="4">You can 
+      test the ECGSYN Java Application:</font></strong></td>
+  </tr>
+  <tr> 
+    <td colspan="2" align="center" valign="top"><applet name= "ecgApplet" code="ecgApplet.class" width=915 height=570>
+      </applet></td>
+  </tr>
+</table>
+<H3>&nbsp; </H3>
+<P>&nbsp; </P>
+<HR WIDTH="100%"><FONT SIZE=-1><I>ECGSYN Java Application<br>
+Last updated on October 27, 2003</I></FONT>
+<p align="justify">Return to ECGSYN <a href="http://www.maths.ox.ac.uk/~mcsharry/ecgsyn">Home page</a>.</p>
+</BODY>
+</HTML>

ecgsyn-1.0.0/Java/ecgLicense.txt

@@ -0,0 +1,39 @@
+/************************************************************************/
+/*                                                                      */
+/* ECGSYN Java Application                                              */
+/*                                                                      */
+/* Copyright (C) 2003 Mauricio Villarroel                               */
+/* (mauricio DOT villarroel AT estudiantes DOT ucb DOT edu DOT bo)      */
+/*                                                                      */
+/* ecgApplet.java and all its components are free software; you can     */
+/* redistribute them and/or modify it under the terms of the            */
+/* GNU General Public License as published by the Free Software         */
+/* Foundation; either version 2 of the License, or (at your option)     */
+/* any later version.                                                   */
+/*                                                                      */
+/* This file is distributed in the hope that it will be useful, but     */
+/* WITHOUT ANY WARRANTY; without even the implied warranty of           */
+/* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.                 */
+/* See the GNU General Public License for more details.                 */
+/*                                                                      */
+/************************************************************************/
+/*                                                                      */
+/* This file was created for the ECGSYN Application.                    */
+/*                                                                      */
+/* ECGSYN: A program for generating a realistic synthetic               */
+/* Electrocardiogram Signals.                                           */
+/* Copyright (c) 2003 by Patrick McSharry & Gari Clifford.              */
+/* All rights reserved.                                                 */
+/*                                                                      */
+/* See IEEE Transactions On Biomedical Engineering,                     */
+/* 50(3), 289-294, March 2003.                                          */
+/* Contact:                                                             */
+/* P. McSharry (patrick AT mcsharry DOT net)                            */
+/* G. Clifford (gari AT mit DOT edu)                                    */
+/*                                                                      */
+/************************************************************************/
+/*                                                                      */
+/* Further updates to this software will be published on:               */
+/* http://www.physionet.org/                                            */
+/*                                                                      */
+/************************************************************************/

ecgsyn-1.0.0/Java/ecgsyn-java.html

@@ -0,0 +1,64 @@
+<HTML>
+<HEAD>
+   <TITLE>ECGSYN Java Application</TITLE>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"></HEAD>
+<BODY bgcolor="#003366" text="#FFFFCC" link="#FFFF33" vlink="#FFCC00" leftmargin="0" topmargin="0" marginwidth="0" marginheight="0">
+<table width="925" border="0" align="center" cellpadding="0" cellspacing="5">
+  <tr> 
+    <td height="50" colspan="2">&nbsp;
+<H3> 
+  <HR WIDTH="100%">
+</H3>
+<H3 align="center"><font color="#FF9900">JAVA Application for <br>
+	ECGSYN: A Dynamical Model for Generating 
+  Synthetic Electrocardiogram Signals
+  </font></H3>
+<H3>
+  <HR WIDTH="100%">
+</H3>	
+	</td>
+  </tr>
+  <tr> 
+    <td width="300" align="left" valign="top"><p><strong>ECGSYN</strong>:</p>
+      <p><strong>&copy;</strong> ECGSYN Copyright by Patrick E. McSharry and Gari 
+        D. Clifford. <br>
+        &copy; Java code copyright by Mauricio Villarroel.<br>
+        <br>
+        For the Mathematical Model, see:</p>
+      <table width="100%" border="1" cellspacing="0" cellpadding="5">
+        <tr> 
+          <td align="left" valign="top">IEEE Transactions On Biomedical Engineering, 
+            50(3), 289-294, March 2003</td>
+        </tr>
+      </table>
+      <p> Contact: </p>
+      <ul>
+        <li><a href="mailto:patrick@mcsharry.net">Patrck McSharry</a></li>
+        <li><a href="mailto:gari@mit.edu">Gari Clifford</a></li>
+        <li><a href="mailto:mauricio.villarroel@estudiantes.ucb.edu.bo">Mauricio Villarroel</a></li>
+      </ul>
+      <p>Please read the <a href="ecgLicense.txt">Software License</a>. 
+</p></td>
+    <td align="center" valign="middle">ECG Ouput Sample image:<br><p><img src="ecgplot.PNG" alt="ECGSYN-Java Output Sample image" width="580" height="330" border="1"></p>
+      <p>Source code: <a href="../ecgsyn.tar.gz">ecgsyn.tar.gz</a></p></td>
+  </tr>
+  <tr> 
+    <td height="50">&nbsp;</td>
+    <td height="50" align="center" valign="middle">&nbsp;</td>
+  </tr>
+  <tr> 
+    <td colspan="2" align="center" valign="top"><strong><font size="4">You can 
+      test the ECGSYN Java Application:</font></strong></td>
+  </tr>
+  <tr> 
+    <td colspan="2" align="center" valign="top"><applet name= "ecgApplet" code="ecgApplet.class" width=915 height=570>
+      </applet></td>
+  </tr>
+</table>
+<H3>&nbsp; </H3>
+<P>&nbsp; </P>
+<HR WIDTH="100%"><FONT SIZE=-1><I>ECGSYN Java Application<br>
+Last updated on October 27, 2003</I></FONT>
+<p align="justify">Return to ECGSYN <a href="../">Home page</a>.</p>
+</BODY>
+</HTML>

ecgsyn-1.0.0/Java/index.html

@@ -0,0 +1,40 @@
+<html>
+<head><title>Index of /static/published-projects/ecgsyn/1.0.0/Java/</title></head>
+<body>
+<h1>Index of /static/published-projects/ecgsyn/1.0.0/Java/</h1><hr><pre><a href="../">../</a>
+<a href="FormatNumber.class">FormatNumber.class</a>                                 12-Apr-2019 17:35                1020
+<a href="HEADER.shtml">HEADER.shtml</a>                                       12-Apr-2019 17:35                 673
+<a href="ecgApplet%241.class">ecgApplet$1.class</a>                                  12-Apr-2019 17:35                 989
+<a href="ecgApplet%2410.class">ecgApplet$10.class</a>                                 12-Apr-2019 17:35                 671
+<a href="ecgApplet%2411.class">ecgApplet$11.class</a>                                 12-Apr-2019 17:35                 671
+<a href="ecgApplet%2412.class">ecgApplet$12.class</a>                                 12-Apr-2019 17:35                 671
+<a href="ecgApplet%2413.class">ecgApplet$13.class</a>                                 12-Apr-2019 17:35                 671
+<a href="ecgApplet%2414.class">ecgApplet$14.class</a>                                 12-Apr-2019 17:35                 671
+<a href="ecgApplet%2415.class">ecgApplet$15.class</a>                                 12-Apr-2019 17:35                 671
+<a href="ecgApplet%2416.class">ecgApplet$16.class</a>                                 12-Apr-2019 17:35                 672
+<a href="ecgApplet%2417.class">ecgApplet$17.class</a>                                 12-Apr-2019 17:35                 672
+<a href="ecgApplet%2418.class">ecgApplet$18.class</a>                                 12-Apr-2019 17:35                 672
+<a href="ecgApplet%242.class">ecgApplet$2.class</a>                                  12-Apr-2019 17:35                 669
+<a href="ecgApplet%243.class">ecgApplet$3.class</a>                                  12-Apr-2019 17:35                 669
+<a href="ecgApplet%244.class">ecgApplet$4.class</a>                                  12-Apr-2019 17:35                 669
+<a href="ecgApplet%245.class">ecgApplet$5.class</a>                                  12-Apr-2019 17:35                 941
+<a href="ecgApplet%246.class">ecgApplet$6.class</a>                                  12-Apr-2019 17:35                 941
+<a href="ecgApplet%247.class">ecgApplet$7.class</a>                                  12-Apr-2019 17:35                 941
+<a href="ecgApplet%248.class">ecgApplet$8.class</a>                                  12-Apr-2019 17:35                1108
+<a href="ecgApplet%249.class">ecgApplet$9.class</a>                                  12-Apr-2019 17:35                 669
+<a href="ecgApplet%24ECGAnimate.class">ecgApplet$ECGAnimate.class</a>                         12-Apr-2019 17:35                2716
+<a href="ecgApplet%24doubleVerifier.class">ecgApplet$doubleVerifier.class</a>                     12-Apr-2019 17:35                1485
+<a href="ecgApplet%24ecgCalc.class">ecgApplet$ecgCalc.class</a>                            12-Apr-2019 17:35               13305
+<a href="ecgApplet%24ecgPanel.class">ecgApplet$ecgPanel.class</a>                           12-Apr-2019 17:35                2618
+<a href="ecgApplet%24integerVerifier.class">ecgApplet$integerVerifier.class</a>                    12-Apr-2019 17:35                1489
+<a href="ecgApplet%24sfVerifier.class">ecgApplet$sfVerifier.class</a>                         12-Apr-2019 17:35                1825
+<a href="ecgApplet%24sfecgVerifier.class">ecgApplet$sfecgVerifier.class</a>                      12-Apr-2019 17:35                1615
+<a href="ecgApplet.class">ecgApplet.class</a>                                    12-Apr-2019 17:35               40664
+<a href="ecgApplet.form">ecgApplet.form</a>                                     12-Apr-2019 17:35               79509
+<a href="ecgApplet.html">ecgApplet.html</a>                                     12-Apr-2019 17:35                2583
+<a href="ecgApplet.java">ecgApplet.java</a>                                     12-Apr-2019 17:35              109386
+<a href="ecgLicense.txt">ecgLicense.txt</a>                                     12-Apr-2019 17:35                2964
+<a href="ecgplot.PNG">ecgplot.PNG</a>                                        12-Apr-2019 17:35               10273
+<a href="ecgsyn-java.html">ecgsyn-java.html</a>                                   12-Apr-2019 17:35                2541
+</pre><hr></body>
+</html>

ecgsyn-1.0.0/Matlab/HEADER.shtml

@@ -0,0 +1,9 @@
+<!--#set var="TITLE" value="ECGSYN for Matlab/Octave"-->
+<!--#include virtual="/head.shtml"-->
+
+
+<p>
+This directory contains <a href="../">ECGSYN</a> implemented in Matlab
+m-code.
+
+<hr>

ecgsyn-1.0.0/Matlab/derivsecgsyn.m

@@ -0,0 +1,52 @@
+function dxdt = derivsecgsyn(t,x,flag,rr,sfint,ti,ai,bi)
+% dxdt = derivsecgsyn(t,x,flag,rr,sampfreq,ti,ai,bi)
+% ODE file for generating the synthetic ECG
+% This file provides dxdt = F(t,x) taking input paramters: 
+% rr: rr process 
+% sfint: Internal sampling frequency [Hertz]
+% Order of extrema: [P Q R S T]
+% ti = angles of extrema [radians] 
+% ai = z-position of extrema 
+% bi = Gaussian width of peaks 
+% Copyright (c) 2003 by Patrick McSharry & Gari Clifford, All Rights Reserved  
+% See IEEE Transactions On Biomedical Engineering, 50(3), 289-294, March 2003.
+% Contact P. McSharry (patrick AT mcsharry DOT net) or 
+% G.D. Clifford (gari AT mit DOT edu)
+
+%    This program is free software; you can redistribute it and/or modify
+%    it under the terms of the GNU General Public License as published by
+%    the Free Software Foundation; either version 2 of the License, or
+%    (at your option) any later version.
+%
+%    This program is distributed in the hope that it will be useful,
+%    but WITHOUT ANY WARRANTY; without even the implied warranty of
+%    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%    GNU General Public License for more details.
+%
+%    You should have received a copy of the GNU General Public License
+%    along with this program; if not, write to the Free Software
+%    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+% 
+% ecgsyn.m and its dependents are freely availble from Physionet - 
+% http://www.physionet.org/ - please report any bugs to the authors above.
+
+
+xi = cos(ti);
+yi = sin(ti);
+ta = atan2(x(2),x(1));
+r0 = 1;
+a0 = 1.0 - sqrt(x(1)^2 + x(2)^2)/r0;
+ip = 1+floor(t*sfint); 
+w0 = 2*pi/rr(ip);
+
+
+fresp = 0.25;
+zbase = 0.005*sin(2*pi*fresp*t);
+
+dx1dt = a0*x(1) - w0*x(2);
+dx2dt = a0*x(2) + w0*x(1);
+
+dti = rem(ta - ti, 2*pi);
+dx3dt = - sum(ai.*dti.*exp(-0.5*(dti./bi).^2)) - 1.0*(x(3) - zbase);
+
+dxdt = [dx1dt; dx2dt; dx3dt];

ecgsyn-1.0.0/Matlab/ecgsyn.m

@@ -0,0 +1,240 @@
+function [s, ipeaks] = ecgsyn(sfecg,N,Anoise,hrmean,hrstd,lfhfratio,sfint,ti,ai,bi)
+% [s, ipeaks] = ecgsyn(sfecg,N,Anoise,hrmean,hrstd,lfhfratio,sfint,ti,ai,bi)
+% Produces synthetic ECG with the following outputs:
+% s: ECG (mV)
+% ipeaks: labels for PQRST peaks: P(1), Q(2), R(3), S(4), T(5)
+% A zero lablel is output otherwise ... use R=find(ipeaks==3); 
+% to find the R peaks s(R), etc. 
+% 
+% Operation uses the following parameters (default values in []s):
+% sfecg: ECG sampling frequency [256 Hertz]
+% N: approximate number of heart beats [256]
+% Anoise: Additive uniformly distributed measurement noise [0 mV]
+% hrmean: Mean heart rate [60 beats per minute]
+% hrstd: Standard deviation of heart rate [1 beat per minute]
+% lfhfratio: LF/HF ratio [0.5]
+% sfint: Internal sampling frequency [256 Hertz]
+% Order of extrema: [P Q R S T]
+% ti = angles of extrema [-70 -15 0 15 100] degrees
+% ai = z-position of extrema [1.2 -5 30 -7.5 0.75]
+% bi = Gaussian width of peaks [0.25 0.1 0.1 0.1 0.4]
+% Copyright (c) 2003 by Patrick McSharry & Gari Clifford, All Rights Reserved  
+% See IEEE Transactions On Biomedical Engineering, 50(3), 289-294, March 2003.
+% Contact P. McSharry (patrick@mcsharry.net) or G. Clifford (gari@mit.edu)
+
+%    This program is free software; you can redistribute it and/or modify
+%    it under the terms of the GNU General Public License as published by
+%    the Free Software Foundation; either version 2 of the License, or
+%    (at your option) any later version.
+%
+%    This program is distributed in the hope that it will be useful,
+%    but WITHOUT ANY WARRANTY; without even the implied warranty of
+%    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%    GNU General Public License for more details.
+%
+%    You should have received a copy of the GNU General Public License
+%    along with this program; if not, write to the Free Software
+%    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+% 
+% ecgsyn.m and its dependents are freely availble from Physionet - 
+% http://www.physionet.org/ - please report any bugs to the authors above.
+
+% set parameter default values
+if nargin < 1
+   sfecg = 256;
+end
+if nargin < 2
+   N = 256;
+end
+if nargin < 3
+   Anoise = 0;
+end
+if nargin < 4
+   hrmean = 60;
+end
+if nargin < 5
+   hrstd = 1;
+end
+if nargin < 6
+   lfhfratio = 0.5;
+end
+if nargin < 7
+   sfint = 512;
+end
+if nargin <8
+    %     P  Q  R  S  T  
+   ti = [-70 -15 0 15 100];
+end
+% convert to radians
+ti = ti*pi/180;
+if nargin <9 % z position of attractor
+      %  P   Q   R   S   T   
+   ai = [1.2 -5 30 -7.5 0.75];
+end
+if nargin <10 % Gaussian width of each attractor
+    %    P    Q   R   S   T   
+   bi = [0.25 0.1 0.1 0.1 0.4];
+end
+
+% adjust extrema parameters for mean heart rate 
+hrfact =  sqrt(hrmean/60);
+hrfact2 = sqrt(hrfact);
+bi = hrfact*bi;
+ti = [hrfact2 hrfact 1 hrfact hrfact2].*ti;
+
+% check that sfint is an integer multiple of sfecg 
+q = round(sfint/sfecg);
+qd = sfint/sfecg;
+if q ~= qd
+   error(['Internal sampling frequency (sfint) must be an integer multiple ' ... 
+'of the ECG sampling frequency (sfecg). Your current choices are: ' ... 
+'sfecg = ' int2str(sfecg) ' and sfint = ' int2str(sfint) '.']);
+end
+
+% define frequency parameters for rr process 
+% flo and fhi correspond to the Mayer waves and respiratory rate respectively
+flo = 0.1;
+fhi = 0.25;
+flostd = 0.01;
+fhistd = 0.01;
+
+fid = 1;
+fprintf(fid,'ECG sampled at %d Hz\n',sfecg);
+fprintf(fid,'Approximate number of heart beats: %d\n',N);
+fprintf(fid,'Measurement noise amplitude: %d \n',Anoise);
+fprintf(fid,'Heart rate mean: %d bpm\n',hrmean);
+fprintf(fid,'Heart rate std: %d bpm\n',hrstd);
+fprintf(fid,'LF/HF ratio: %g\n',lfhfratio);
+fprintf(fid,'Internal sampling frequency: %g\n',sfint);
+fprintf(fid,'      P  Q  R  S  T\n'); 
+fprintf(fid,'ti = [%g %g %g %g %g] radians\n',ti(1),ti(2),ti(3),ti(4),ti(5));
+fprintf(fid,'ai = [%g %g %g %g %g]\n',ai(1),ai(2),ai(3),ai(4),ai(5));
+fprintf(fid,'bi = [%g %g %g %g %g]\n',bi(1),bi(2),bi(3),bi(4),bi(5));
+
+
+% calculate time scales for rr and total output
+sampfreqrr = 1;
+trr = 1/sampfreqrr; 
+tstep = 1/sfecg;
+rrmean = (60/hrmean);	 
+Nrr = 2^(ceil(log2(N*rrmean/trr)));
+
+% compute rr process
+rr0 = rrprocess(flo,fhi,flostd,fhistd,lfhfratio,hrmean,hrstd,sampfreqrr,Nrr);
+
+% upsample rr time series from 1 Hz to sfint Hz
+rr = interp(rr0,sfint);
+
+% make the rrn time series
+dt = 1/sfint;
+rrn = zeros(length(rr),1);
+tecg=0;
+i = 1;
+while i <= length(rr)
+   tecg = tecg+rr(i);
+   ip = round(tecg/dt);
+   rrn(i:ip) = rr(i);
+   i = ip+1;
+end 
+Nt = ip;
+
+% integrate system using fourth order Runge-Kutta
+fprintf(fid,'Integrating dynamical system\n');
+x0 = [1,0,0.04];
+Tspan = [0:dt:(Nt-1)*dt];
+[T,X0] = ode45('derivsecgsyn',Tspan,x0,[],rrn,sfint,ti,ai,bi);
+
+% downsample to required sfecg
+X = X0(1:q:end,:);
+
+% extract R-peaks times
+ipeaks = detectpeaks(X, ti, sfecg);
+
+% Scale signal to lie between -0.4 and 1.2 mV
+z = X(:,3);
+zmin = min(z);
+zmax = max(z);
+zrange = zmax - zmin;
+z = (z - zmin)*(1.6)/zrange -0.4;
+
+% include additive uniformly distributed measurement noise 
+eta = 2*rand(length(z),1)-1;
+s = z + Anoise*eta;
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function rr = rrprocess(flo, fhi, flostd, fhistd, lfhfratio, hrmean, hrstd, sfrr, n)
+w1 = 2*pi*flo;
+w2 = 2*pi*fhi;
+c1 = 2*pi*flostd;
+c2 = 2*pi*fhistd;
+sig2 = 1;
+sig1 = lfhfratio;
+rrmean = 60/hrmean;
+rrstd = 60*hrstd/(hrmean*hrmean);
+
+df = sfrr/n;
+w = [0:n-1]'*2*pi*df;
+dw1 = w-w1;
+dw2 = w-w2;
+
+Hw1 = sig1*exp(-0.5*(dw1/c1).^2)/sqrt(2*pi*c1^2);
+Hw2 = sig2*exp(-0.5*(dw2/c2).^2)/sqrt(2*pi*c2^2);
+Hw = Hw1 + Hw2;
+Hw0 = [Hw(1:n/2); Hw(n/2:-1:1)];
+Sw = (sfrr/2)*sqrt(Hw0);
+
+ph0 = 2*pi*rand(n/2-1,1);
+ph = [ 0; ph0; 0; -flipud(ph0) ]; 
+SwC = Sw .* exp(j*ph);
+x = (1/n)*real(ifft(SwC));
+
+xstd = std(x);
+ratio = rrstd/xstd;
+rr = rrmean + x*ratio;
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function ind = detectpeaks(X, thetap, sfecg)
+N = length(X);
+irpeaks = zeros(N,1);
+
+theta = atan2(X(:,2),X(:,1));
+ind0 = zeros(N,1);
+for i=1:N-1
+   a = ( (theta(i) <= thetap) & (thetap <= theta(i+1)) );
+   j = find(a==1);
+   if ~isempty(j)
+      d1 = thetap(j) - theta(i);
+      d2 = theta(i+1) - thetap(j);
+      if d1 < d2
+         ind0(i) = j;
+      else 
+         ind0(i+1) = j;
+      end  
+   end
+end
+
+d = ceil(sfecg/64);
+d = max([2 d])
+ind = zeros(N,1);
+z = X(:,3);
+zmin = min(z);
+zmax = max(z);
+zext = [zmin zmax zmin zmax zmin];
+sext = [1 -1 1 -1 1];
+for i=1:5
+   clear ind1 Z k vmax imax iext;
+   ind1 = find(ind0==i);
+   n = length(ind1);
+   Z = ones(n,2*d+1)*zext(i)*sext(i);
+   for j=-d:d
+      k = find( (1 <= ind1+j) & (ind1+j <= N) );
+      Z(k,d+j+1) = z(ind1(k)+j)*sext(i);
+   end
+   [vmax, ivmax] = max(Z,[],2);
+   iext = ind1 + ivmax-d-1;
+   ind(iext) = i;
+end
+
+

ecgsyn-1.0.0/Matlab/index.html

@@ -0,0 +1,9 @@
+<html>
+<head><title>Index of /static/published-projects/ecgsyn/1.0.0/Matlab/</title></head>
+<body>
+<h1>Index of /static/published-projects/ecgsyn/1.0.0/Matlab/</h1><hr><pre><a href="../">../</a>
+<a href="HEADER.shtml">HEADER.shtml</a>                                       12-Apr-2019 17:35                 186
+<a href="derivsecgsyn.m">derivsecgsyn.m</a>                                     12-Apr-2019 17:35                1911
+<a href="ecgsyn.m">ecgsyn.m</a>                                           12-Apr-2019 17:35                6795
+</pre><hr></body>
+</html>

ecgsyn-1.0.0/index.html

@@ -0,0 +1,12 @@
+<html>
+<head><title>Index of /static/published-projects/ecgsyn/1.0.0/</title></head>
+<body>
+<h1>Index of /static/published-projects/ecgsyn/1.0.0/</h1><hr><pre><a href="../">../</a>
+<a href="C/">C/</a>                                                 12-Apr-2019 17:35                   -
+<a href="Java/">Java/</a>                                              12-Apr-2019 17:35                   -
+<a href="Matlab/">Matlab/</a>                                            12-Apr-2019 17:35                   -
+<a href="paper/">paper/</a>                                             12-Apr-2019 17:35                   -
+<a href="sample-output/">sample-output/</a>                                     12-Apr-2019 17:35                   -
+<a href="ecgsyn.tar.gz">ecgsyn.tar.gz</a>                                      12-Apr-2019 17:35              165286
+</pre><hr></body>
+</html>

ecgsyn-1.0.0/paper/ecgpqrst.css

@@ -0,0 +1,30 @@
+/* Century Schoolbook font is very similar to Computer Modern Math: cmmi */
+.MATH    { font-family: "Century Schoolbook", serif; }
+.MATH I  { font-family: "Century Schoolbook", serif; font-style: italic }
+.BOLDMATH { font-family: "Century Schoolbook", serif; font-weight: bold }
+
+/* implement both fixed-size and relative sizes */
+SMALL.XTINY		{ font-size : xx-small }
+SMALL.TINY		{ font-size : x-small  }
+SMALL.SCRIPTSIZE	{ font-size : smaller  }
+SMALL.FOOTNOTESIZE	{ font-size : small    }
+SMALL.SMALL		{  }
+BIG.LARGE		{  }
+BIG.XLARGE		{ font-size : large    }
+BIG.XXLARGE		{ font-size : x-large  }
+BIG.HUGE		{ font-size : larger   }
+BIG.XHUGE		{ font-size : xx-large }
+
+/* heading styles */
+H1		{  }
+H2		{  }
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+H5		{  }
+
+/* mathematics styles */
+DIV.displaymath		{ }	/* math displays */
+TD.eqno			{ }	/* equation-number cells */
+
+
+/* document-specific styles come next */

ecgsyn-1.0.0/paper/footnode.html

@@ -0,0 +1,79 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by:  Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Footnotes</TITLE>
+<META NAME="description" CONTENT="Footnotes">
+<META NAME="keywords" CONTENT="ecgpqrst">
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+<LINK REL="up" HREF="index.shtml">
+</HEAD>
+
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+
+<DL>
+<DT><A NAME="foot31">...<IMG
+ WIDTH="21" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img6.png"
+ ALT="$^{2,3}$"></A><A
+ HREF="index.shtml#tex2html1"><SUP><IMG  ALIGN="BOTTOM" BORDER="1" ALT="[*]"
+ SRC="file:/usr/share/latex2html/icons/footnote.png"></SUP></A></DT>
+<DD><IMG
+ WIDTH="11" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img5.png"
+ ALT="$^1$">Department of Engineering Science, 
+University of Oxford, Oxford OX1 3PJ.
+
+<PRE>.
+</PRE>
+</DD>
+<DT><A NAME="foot32">...</A><A
+ HREF="index.shtml#tex2html2"><SUP><IMG  ALIGN="BOTTOM" BORDER="1" ALT="[*]"
+ SRC="file:/usr/share/latex2html/icons/footnote.png"></SUP></A></DT>
+<DD><IMG
+ WIDTH="11" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img7.png"
+ ALT="$^2$">Mathematical Institute, University of Oxford, Oxford OX1 3LB.
+
+<PRE>.
+</PRE>
+</DD>
+<DT><A NAME="foot33">...</A><A
+ HREF="index.shtml#tex2html3"><SUP><IMG  ALIGN="BOTTOM" BORDER="1" ALT="[*]"
+ SRC="file:/usr/share/latex2html/icons/footnote.png"></SUP></A></DT>
+<DD><IMG
+ WIDTH="11" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img8.png"
+ ALT="$^3$">Centre for the Analysis of Time Series, London School
+of Economics, London WC2A 2AE.
+
+<PRE>.
+</PRE>
+</DD>
+<DT><A NAME="foot34">...</A><A
+ HREF="index.shtml#tex2html4"><SUP><IMG  ALIGN="BOTTOM" BORDER="1" ALT="[*]"
+ SRC="file:/usr/share/latex2html/icons/footnote.png"></SUP></A></DT>
+<DD>E-mail: mcsharry@robots.ox.ac.uk
+
+<PRE>.
+</PRE>
+</DD>
+</DL>
+</BODY>
+</HTML>