介绍生理学软件门户型综合网站PhysioToolkit

hillside

    以下内容系出自一个综合性的生理学软件门户型网站，其中多为医学类统计软件，不少基本方法与气候统计是类似的，应有明显的参考价值。对于其中的部分内容我已经撰写多帖单独介绍。

                            An Introduction to PhysioToolkit

    PhysioToolkit is a large collection of software for viewing, analyzing, and simulating physiologic time series and signals. All of this software is free (open-source) under the GNU General Public License (GPL), which grants you the right to use, modify, and redistribute it freely. With very few exceptions, PhysioToolkit software runs on all of the popular platforms, including GNU/Linux, Mac OS X, MS-Windows, and Unix.

The PhysioToolkit Software Index is organized by category. If you are looking for software to perform a specific function, looking in the index will help you find it quickly, with links to the home pages, code repositories, and documentation for each software component.

PhysioToolkit's tutorials and reference manuals provide a different perspective than the index, with in-depth information about these software components: what they do, how they work, and how to use them, individually and in combination, to perform complex tasks.

Many visitors use PhysioToolkit programs as tools for exploring PhysioBank and compatible data collections. Begin your exploration by installing the WFDB Software Package. Quick-start installation guides are available for FreeBSD, GNU/Linux, Mac OS X, MS-Windows, and Solaris.

Visitors sometimes ask how to read PhysioBank data with their existing software; our tutorial, How to obtain PhysioBank data in text form, provides easy-to-follow instructions.

Other visitors study the PhysioTookit programs themselves, either as reference implementations of algorithms or as starting points for their own software development. If this is your interest, dig into the code as you read the relevant manuals.

Although we provide precompiled (binary executable) versions of many PhysioToolkit programs as a convenience to visitors, all of the software is available in source form so that the algorithms can be studied, verified, and modified to suit the specific needs of your work.

Software packages that contain many files are usually available here as gzip-compressed tar archives (.tar.gz files). Instructions for unpacking these archives can be found in theFAQ.

If you use software from PhysioNet in a publication, please credit the author(s) of the software when referencing it. You can find authors' names, and in many cases their publications introducing the software, on the home pages for their contributions or in comments in the source code. If you are unsure how to cite a specific piece of software, please ask us!

Please also include the standard citation for PhysioNet:

Goldberger AL, Amaral LAN, Glass L, Hausdorff JM, Ivanov PCh, Mark RG, Mietus JE, Moody GB, Peng C-K, Stanley HE. PhysioBank, PhysioToolkit, and PhysioNet: Components of a New Research Resource for Complex Physiologic Signals. Circulation 101(23):e215-e220 [Circulation Electronic Pages; http://circ.ahajournals.org/cgi/content/full/101/23/e215]; 2000 (June 13).

PhysioToolkit Software Index

• How to use this index
• About software classes
• About other required software
• Other free software
  

If you use software from PhysioNet in a publication, please credit the author(s) of the software when referencing it. You can find authors' names, and in many cases their publications introducing the software, on the home pages for their contributions or in comments in the source code. If you are unsure how to cite a specific piece of software, please ask us!

Please also include the standard citation for PhysioNet:

Goldberger AL, Amaral LAN, Glass L, Hausdorff JM, Ivanov PCh, Mark RG, Mietus JE, Moody GB, Peng C-K, Stanley HE. PhysioBank, PhysioToolkit, and PhysioNet: Components of a New Research Resource for Complex Physiologic Signals. Circulation 101(23):e215-e220 [Circulation Electronic Pages; http://circ.ahajournals.org/cgi/content/full/101/23/e215]; 2000 (June 13).

First-time visitors should read An Introduction to PhysioToolkit before downloading software from this collection.

How to use this index

Look through the list of software categories below and click on any link to view a list of software in that category. Click on the Package link for any of the software to get instructions for downloading and installing it. (Our web service applications don't have package links, because there is nothing that needs to be downloaded; just click on the name of the application to run it in your web browser. The sources for these applications, which might be of interest to those running their own web servers, are available here.)

Data visualizationPhysioBank data visualizationView signals and annotations from PhysioBank and compatible data filesGeneral-purpose data visualizationPlot text or binary data, functions, and imagesData miningPhysioBank data miningCollect, index, and search for essential characteristics of PhysioBank and compatible data filesImporting and exporting dataFormat convertersImport and export physiologic data in text and a variety of binary formatsCreating PhysioBank-compatible recordingsPrepare and annotate your own dataDeidentification (Anonymization)Deidentification (Anonymization)Remove protected health information (PHI) from data to be sharedSignal and time series analysisPhysiologic signal processingQRS and BP pulse detectors, ECG-derived respiration, apnea detectionGeneral signal processingLinear and nonlinear filters, signal averaging, etc.Frequency-domain analysis of time seriesFourier and other algorithms for power spectral density estimationNonlinear analysis of time seriesDetrended fluctuation analysis, multiscale entropy, and other methodsRR intervals, heart rate, and HRV analysisCalculate RR intervals, NN intervals, instantaneous heart rate, heart rate variability, ectopic beat dynamicsModelsPhysiologic models and simulationsSynthesize cardiovascular system variables and ECGsSoftware developmentLibraries and software development toolsUse these subroutines in your own software, when you need to read or write PhysioBank-compatible signal and annotation filesDevelopment and evaluation of ECG analyzersTest arrhythmia and ST change detection algorithms using PhysioBank and compatible data and standard software for measuring analysis algorithm performanceOtherMiscellaneous softwareBuild shell scripts (batch files) using these mini-applications
  

PhysioBank data visualization
Software	Package	Class	Description	Documentation	Requires
WAVE	WFDB	1	Analyze, view, and edit PhysioBank (and compatible) data	man page WAVE User's Guide	XView
pschart	WFDB	1	Produce annotated `chart recordings'	man page	PostScript printer or interpreter
psfd	WFDB	1	Produce annotated `full-disclosure' (compact) plots	man page	PostScript printer or interpreter
PhysioBank ATM		1	Show PhysioBank data in a web browser	PhysioBank ATM	a graphical web browser
SEMIA	SEMIA	2	View time series of diagnostic and morphologic parameters of the Long-Term ST Database, together with the corresponding ECG waveforms and their annotations	SEMIA home page; Long-Term ST Database	WFDB[url=],[/url]XView
rddata.m	rddata.m	3	View PhysioBank signals and annotations in a Matlab figure	rddata.m	Matlab

General-purpose data visualization
Software	Package	Class	Description	Documentation	Requires
plt	plt	1	Make 2-D plots from text or binary data	plt home page; man page
pltf	plt	1	Make function plots using GNU bc and plt	man page	GNU bc
imageplt	plt	1	plot a greyscale image using plt	man page
lwcat	plt	1	Postprocess plt output to make PostScript, EPS, PDF, or PNG	man page
plot2d, plot3d	WFDB	1	Make 2-D or 3-D plots from text data, using gnuplot	man page	gnuplot

PhysioBank data mining
Software	Package	Class	Description	Documentation	Requires
pbindex	pbindex	1	Collect and index essential data from PhysioBank-compatible records	pbindex home page PhysioBank Index	WFDB
pbsqsd, pbsqs	pbsearch	1	PhysioBank Simple Query Server (and stand-alone command-line search tool)	pbsearch home page	WFDB
pbsqsc	pbsearch	1	Command-line client for searching the PhysioBank Index	pbsearch home page	Perl 5
pbsearch	pbsearch	1	Web client for searching the PhysioBank Index	pbsearch home page PhysioBank Record Search	a web browser

Format converters
Software	Package	Class	Description	Documentation	Requires
xform	WFDB	1	Convert one PhysioBank-compatible format to another, optionally changing signal amplitudes and sampling frequencies	man page
a2m, ad2m, ahaconvert, m2a, md2a	WFDB	1	Convert between PhysioBank-compatible formats and AHA Database formats	man page
ann2rr, rr2ann	WFDB	1	Convert between PhysioBank-compatible annotation files and annotation interval lists	man page RR Intervals, Heart Rate, and HRV Howto
edf2mit, mit2edf	WFDB	1	Convert between PhysioBank-compatible formats and European Data Format (EDF)	man page
wav2mit, mit2wav	WFDB	1	Convert between PhysioBank-compatible formats and .wav audio file format	man page
rdann, rdsamp, wrann, wrsamp	WFDB	1	Convert between PhysioBank-compatible formats and text	man pages for rdann, rdsamp,wrann, and wrsamp
PhysioBank ATM		1	Convert PhysioBank data to text, CSV, EDF, .mat, .tar.gz, or .zip formats	PhysioBank ATM	a web browser

Creating PhysioBank-compatible recordings
Software	Package	Class	Description	Documentation	Requires
WAVE	WFDB	1	Analyze, view, and edit PhysioBank (and compatible) data	man page WAVE User's Guide	XView
calsig	WFDB	1	Calibrate signals of a PhysioBank-compatible record	man page	WAVE (recommended) or another signal viewer
mrgann	WFDB	1	Merge PhysioBank-compatible annotation files	man page
skewedit	WFDB	1	Modify inter-signal skews in a PhysioBank-compatible record	man page
snip	WFDB	1	Copy an excerpt of a PhysioBank-compatible record	man page
sortann	WFDB	1	Rearrange annotations in canonical order	man page
wfdbcollate	WFDB	1	Collate PhysioBank-compatible records into a multi-segment record	man page
record	record	3	Captures data from a Philips CMS monitor	record home page	MS-DOS

Deidentification (Anonymization)
Software	Package	Class	Description	Documentation	Requires
deid	deid	3	Deidentify free text in medical records	home page user manual	Perl 5
edf-anonymize	edf-anonymize	1	Deidentify EDF and EDF+ files	man page	-

Physiologic signal processing
Software	Package	Class	Description	Documentation	Requires
sqrs, sqrs125	WFDB	1	Single-channel QRS detector based on ECG slope	man page
wqrs	WFDB	1	Single-channel QRS detector based on length transform	man page
wabp	WFDB	1	Arterial blood pressure (ABP) pulse detector	man page
apdet	apdet	2	Hilbert transform based sleep apnea detection using a single ECG signal	apdet home page	WFDB
ecgpuwave	ecgpuwave	2	QRS detector and ECG waveform limit locator	man page	WFDB; ANSI Fortran 77 compiler (recommended:g77)
pr-comp	pr-comp	1	Principal component analysis of waveforms	Morphology Representation Using Principal Components	WFDB
CO estimators	COABP	2	Algorithms for estimating cardiac output from arterial blood pressure waveforms	COABP home page	Matlab
EDR	edr	2	Derive a respiration signal from one or more ECG signals	EDR home page; man page	WFDB
puka	puka	2	Detect phases of respiration in strain gauge recordings	puka home page, puka manual	WFDB, ecgpuwave, Matlab, Java, JMatLink,MySQL [optional], Cygwin [MS-Windows only]
TWAnalyser	TWAnalyser	2	Detect and quantify T-wave alternans in the ECG	TWAnalyser home page	Matlab

General signal processing
Software	Package	Class	Description	Documentation	Requires
fir	WFDB	1	General-purpose FIR filter for PhysioBank-compatible records	man page
mfilt	WFDB	1	General-purpose median filter for PhysioBank-compatible records	man page
sigamp	WFDB	1	Measure signal amplitudes of a PhysioBank-compatible record	man page
sigavg	WFDB	1	Calculate averages of annotated waveforms	man page

Frequency domain analysis of time series
Software	Package	Class	Description	Documentation	Requires
coherence	WFDB	1	Estimate the coherence and cross-spectrum of two time series of arbitrary length	man page
fft	WFDB	1	Estimate the power spectrum of an evenly sampled time series of arbitrary length, using a fast Fourier transform	man page
lomb	WFDB	1	Estimate the power spectrum of an evenly or unevenly sampled time series of arbitrary length, using the Lomb periodogram method	man page
memse	WFDB	1	Estimate the power spectrum of an evenly sampled time series of arbitrary length, using the maximum entropy (all-poles) method	man page

Nonlinear analysis of time series
Software	Package	Class	Description	Documentation	Requires
dfa	DFA	1	Detrended fluctuation analysis of a time series of arbitrary length	DFA home page; man page
ibs	IBS	2	Information-based similarity for comparison and classification of time series	IBS home page
L1D2	L1D2	2	Estimate the largest Lyapunov exponent and the correlation dimension of a time series	L1D2 home page
mse	MSE	2	Multiscale entropy analysis	MSE tutorial; man page
multifractal	multifractal	3	Multifractal analysis of time series	multifractal home page; A Brief Overview of Multifractal Time Series
sampen	SampEn	1	Measure the sample entropy of a time series (both C and Matlab implementations are available)	man page

RR intervals, heart rate, and HRV analysis
Software	Package	Class	Description	Documentation	Requires
ann2rr, rr2ann	WFDB	1	Convert between WFDB-compatible annotation files and annotation interval lists	man page; RR Intervals, Heart Rate, and HRV Howto
hrfft, hrlomb, hrmem, hrplot	WFDB	1	Calculate and plot heart rate time series and power spectra	man page; RR Intervals, Heart Rate, and HRV Howto	plt
HRV toolkit	HRV	1	Visualize and filter inter-beat interval time series, and calculate time- and frequency-domain HRV statistics from them	Heart Rate Variability Analysis with the HRV Toolkit	plt,WFDB
ihr	WFDB	1	Calculate instantaneous heart rate series from an annotation file	man page; RR Intervals, Heart Rate, and HRV Howto
nguess	WFDB	1	Guess the times of missing normal beats in a PhysioBank-compatible annotation file	man page
pnnlist, pNNx	pNNx	1	Derive pNNx statistics from an annotation interval list or an annotation file	pNNx home page; man page	WFDB
tach	WFDB	1	Heart rate tachometer	man page
activity	activity	2	Estimate activity from instantaneous heart rate	home page; ECG-based indices of physical activity
heartprints	heartprints	1	Visualize dynamics of ventricular ectopic activity	heartprints home page

Physiologic models and simulations
Software	Package	Class	Description	Documentation	Requires
CVSim	CVSim	3	Cardiovascular simulator for education and research; an elaboration of the model used in RCVSIM, with a comprehensive graphical user interface	CVSim home page	Java (JRE including Java Web Start required; JDK needed only to rebuild); GNU/Linux, Mac OS X (PPC or x86), or MS-Windows (not supported on other platforms)
RCVSIM	RCVSIM	1	Lumped parameter model of the heart and circulation, incorporating a short-term regulatory system model and a model of resting physiologic perturbations	RCVSIM home page; A Cardiovascular Simulator for Research: User's Manual and Software Guide	Matlab (recommended; standalone GNU/Linux binaries are also available); WFDB
RR generators	RR generators	2	Realistic RR interval time series generators from the PhysioNet / Computers in Cardiology Challenge 2002	Challenge 2002 home page
AFVP	AFVP	2	Realistic generator for AA and RR intervals during atrial fibrillation	AFVP home page
ECGSYN	ECGSYN	2	A realistic ECG waveform generator; includes C, Java applet, and Matlab implementations	ECGSYN home page; A dynamical model for generating synthetic electrocardiogram signals
ECGwaveGen	ECGwaveGen	3	ECG waveform generator for Matlab or Octave	ECGwaveGen home page	Matlab or Octave

Libraries and software development tools
Software	Package	Class	Description	Documentation	Requires
wfdb	WFDB	1	Waveform Database library for C and C++	WFDB home page; WFDB Programmer's Guide; man page	ANSI/ISO C compiler (recommended: gcc); optional: either libcurl(preferred) or libwww
wfdbf	WFDB	1	WFDB library wrappers for Fortran	man page	ANSI Fortran 77 compiler (recommended: g77)
wfdb-swig	wfdb-swig	3	WFDB library wrappers for Java, Perl, Python, and other languages	home page	WFDB, SWIG; and at least one of: Sun's Java development kit,Perl 5, Python, or another language supported by SWIG
WFDB Toolkit for Matlab	wfdb-swig-matlab	1	WFDB applications implemented as Matlab functions	home page	Matlab 7 (R14, 2004) or later, Sun Java Runtime Environment 1.5 or later

Evaluation of ECG analyzers
Software	Package	Class	Description	Documentation	Requires
bxb, ecgeval, epicmp, mxm, plotstm, rxr, sumstats	WFDB	1	ANSI/AAMI EC-38 and EC-57 standard performance measuring software	Evaluating ECG Analyzers; man pages for bxb, ecgeval,epicmp, mxm, plotstm, rxr, and sumstats
nst	WFDB	1	Noise stress test for ECG analysis programs	man page; Evaluating ECG Analyzers; MIT-BIH Noise Stress Test Database
EVAL_ST	EVAL_ST	2	Evaluate ST episode analyzers	README	lesstif orMotif

Miscellaneous software
Software	Package	Class	Description	Documentation	Requires
log10	WFDB	1	Log-transform two-column data	man page
sampfreq	WFDB	1	Show sampling frequency for a record	man page
setwfdb, cshsetwfdb	WFDB	1	Set WFDB environment variables	man page
sumann	WFDB	1	Summarize the contents of an annotation file	man page
time2sec	WFDB	1	Convert HH:MM:SS time to seconds	man page
wfdb-config	WFDB	1	Print WFDB library version and configuration information	man page
wfdbcat	WFDB	1	Copy WFDB files to standard output	man page
wfdbdesc	WFDB	1	Summarize the contents of a PhysioBank-compatible record	man page
wfdbwhich	WFDB	1	Find a WFDB file and print its pathname or URL	man page

About software classes

As for PhysioBank data, we describe the software available here in terms of three classes:

• Class 1 (fully supported, extensively and rigorously tested software)
• Class 2 (archival copies of software that supports published research, contributed by authors, together with corrections and improvements submitted by authors and users)
• Class 3 (code not supported by PhysioNet; includes contributed code that may be supported by its authors, as well as beta-quality code that may require further development, testing, and documentation)
  

We make class 2 and class 3 software available via PhysioNet as a service to the research community. Contributed code is placed in classes 2 and 3 on acceptance, and may be admitted to class 1 after review and a public comment period.

About other required software

The column headed "Requires" in the software listing indicates prerequisites for each package. In a very few cases, these may indicate specific platforms, but almost all of the software available here is portable across all popular platforms, including GNU/Linux, Mac OS X, MS-Windows, and all versions of Unix.

All software is provided in source form, and since most of it is written in the C programming language, you will need a C compiler for your platform in order to compile the sources. We use and recommend gcc (a free, high quality C compiler that runs on a vast number of platforms, including all of the popular ones). Under MS-Windows, we recommend the free Cygwin development environment, which includes gcc as well as a comprehensive set of Unix-compatible development tools.

PhysioNet web service applications, such as the PhysioBank ATM, are compatible with any modern browser. We use and recommend Firefox and Chrome, and test withLynx, Safari, and recent versions of Internet Explorer.

The WFDB software package includes many HTTP client applications that read signals and annotations directly from PhysioNet web servers without the use of a web browser. You can add this capability to your own C, C++, Fortran, and Matlab applications by linking them with the WFDB library (which provides HTTP client support via the World Wide Web Consortium's libwww library, available here).

Some of our graphical software requires the XView or LessTif toolkits. These are freely available libraries of GUI components for X Window System (X11) clients. You will also need to have an X11 server in order run X11 clients. X11 servers, XView, and LessTif are all freely available for all of the popular platforms, including GNU/Linux, Mac OS X, MS-Windows, and Unix. (For MS-Windows users, XView is available here, and LessTif and an excellent free X11 server are available as optional Cygwin packages.)

Some software requires Matlab, a popular commercial program that provides an interactive environment for numeric computation and graphics using an interpreted programming language that optionally can be compiled. Most software that requires Matlab can also be used with Octave, a freely available open-source program that is compatible with Matlab. Both Octave and Matlab can run under most popular operating systems, including GNU/Linux, Mac OS X, many versions of Unix, and MS-Windows. Sources for Octave are available here and from the official Octave web site.

Other free software

Open-source software useful for the study of physiologic signals and time series is available from other sources. Information about several such software packages is availablehere.

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请问你能用一点自己的话概括下吗