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heartbeats [2010/05/29 01:45] jochen Missing paranthesis |
heartbeats [2010/06/29 19:17] jochen updated help |
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The [[xff]] IO reading class now supports reading the following formats: | The [[xff]] IO reading class now supports reading the following formats: | ||
* ACQ (up until version <= 3.9.7) | * ACQ (up until version <= 3.9.7) | ||
- | * TXT (use ''<nowiki>object = xff('*.ntt');</nowiki>'' to read!) | + | * TXT (use ''<nowiki>object = xff('*.ntt');</nowiki>'' or ''<nowiki>object = xff(filename, 'ntt');</nowiki>'' to read!) |
and further formats might be added based on request and urgency. | and further formats might be added based on request and urgency. | ||
+ | |||
+ | In case the data is in a different format, you must ensure to first convert into one of the formats above or into a MAT file, which then can be read used like this: | ||
+ | |||
+ | <code matlab heartbeats_readmat.m>% load a mat file (e.g. an ACQ->MAT converted file) | ||
+ | load HPS1344_session1_ECG.mat; | ||
+ | |||
+ | % create new NTT (used for methods on data!) | ||
+ | ntt = xff('new:ntt'); | ||
+ | |||
+ | % store data from mat file in ntt | ||
+ | ntt.Data = data;</code> | ||
===== Reference (help) ===== | ===== Reference (help) ===== | ||
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<file> heartbeats - detect heart beats and frequency in physio data | <file> heartbeats - detect heart beats and frequency in physio data | ||
- | FORMAT: [bp, bs, bf, bv, cp, wgd, wd] = heartbeats(sig [, opts]) | + | FORMAT: [bp, bs, bf, bv, cp, wgd, wd, hrv] = heartbeats(sig [, opts]) |
Input fields: | Input fields: | ||
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.badt t-threshold for detecing irregularity (default: 25) | .badt t-threshold for detecing irregularity (default: 25) | ||
.bppre pre-defined positions (no detection, only inspection) | .bppre pre-defined positions (no detection, only inspection) | ||
+ | .calc preprocessing calculcation, one of | ||
+ | {'none'} - don't to anything (default) | ||
+ | {'absdiff'} - use abs(diff(data)) | ||
+ | if .detlength is not given, will be set to 0.02 | ||
+ | if .skewdt is not given, will be set to 0.1 | ||
+ | {'diffsq'} - square the diff of the data | ||
+ | if .detlength is not given, will be set to 0.01 | ||
+ | if .skewdt is not given, will be set to 0.05 | ||
+ | {'fourthz'} - fourth power of the z-transformed data | ||
+ | if .detlength is not given, will be set to 0.02 | ||
+ | if .skewdt is not given, will be set to 0.04 | ||
+ | {'squarez'} - square the z-transformed data | ||
+ | if .detlength is not given, will be set to 0.03 | ||
+ | if .skewdt is not given, will be set to 0.1 | ||
+ | {'thirdz'} - third power of the abs z-transformed data | ||
+ | if .detlength is not given, will be set to 0.02 | ||
+ | if .skewdt is not given, will be set to 0.06 | ||
.cleanup interactive cleanup (default: false) | .cleanup interactive cleanup (default: false) | ||
.detlength detection length threshold in seconds (default: 0.05) | .detlength detection length threshold in seconds (default: 0.05) | ||
+ | .freq data frequency in Hz (default: 1000) | ||
.pflength pre-filter length in seconds (default: 0.025) | .pflength pre-filter length in seconds (default: 0.025) | ||
.pfreps pre-filter repetitions (default: 2) | .pfreps pre-filter repetitions (default: 2) | ||
- | .freq data frequency in Hz (default: 1000) | ||
.plot plot mean +/- std estimate of signal (default: false) | .plot plot mean +/- std estimate of signal (default: false) | ||
+ | .plotfreq samples per second to plot (default: 50) | ||
.plotwin plot window size in seconds (default: 6) | .plotwin plot window size in seconds (default: 6) | ||
+ | .resfreq resample data prior to detection (default: []) | ||
.segsize segmentation size in seconds (default: 5) | .segsize segmentation size in seconds (default: 5) | ||
.segstep stepping (window shift) in seconds (default: 1) | .segstep stepping (window shift) in seconds (default: 1) | ||
- | .windsor windsorizing threshold in std's (default: 3) | + | .skewdt skewness detection threshold multiplier (default: 0.5) |
+ | .winsor winsorizing threshold in std's (default: 3) | ||
Output fields: | Output fields: | ||
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wgd guess whether window is good or not | wgd guess whether window is good or not | ||
wd windowed data (in 100Hz resolution, interpolated) | wd windowed data (in 100Hz resolution, interpolated) | ||
+ | hrv output of computehrv(bp) | ||
- | Note: this function is still preliminary</file> | + | Note: this function is still preliminary, other options passed on to |
+ | computehrv (if 8th output is requested), with .hrvrfreq being | ||
+ | set to .resfreq</file> | ||
===== Usage overview ===== | ===== Usage overview ===== | ||
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Naturally, it is possible to script this function, save the pre-detected heartbeats (without manual interaction/plotting) and then, at a later time, revisit the inspection (for instance, if several subjects' datasets are to be examined, it usually is preferable to perform the extraction and detection of all datasets prior to engaging in the fine tuning). | Naturally, it is possible to script this function, save the pre-detected heartbeats (without manual interaction/plotting) and then, at a later time, revisit the inspection (for instance, if several subjects' datasets are to be examined, it usually is preferable to perform the extraction and detection of all datasets prior to engaging in the fine tuning). | ||
+ | For instance, if the raw signal looks like this | ||
+ | |||
+ | {{:heartbeats_crisp_example.png|crisp raw signal with very short spikes}} | ||
+ | |||
+ | A two-pass detection scheme can be employed: | ||
+ | |||
+ | <code matlab heartbeats_crisp_detection.m>% first, load the data | ||
+ | data = xff('*.ntt'); | ||
+ | |||
+ | % then z-transform the third column (in our case) and take the 4th power | ||
+ | pdata = ztrans(data.Data(:, 3)) .^ 4; | ||
+ | |||
+ | % pre-detect beats | ||
+ | % since we used the 4th power, the skew detection threshold must be lowered | ||
+ | % and our signal has short spikes, so the detection length threshold also! | ||
+ | bp = heartbeats(pdata, struct( ... | ||
+ | 'skewdt', 0.05, ... | ||
+ | 'detlength', 0.01, ... | ||
+ | 'freq', 500)); | ||
+ | |||
+ | % then pass this along with the actual signal back in | ||
+ | [bp, bs, bf, bv, cp, wgd, wd] = heartbeats(data.Data(:, 3), struct( ... | ||
+ | 'bppre', bp, ... | ||
+ | 'cleanup', true, ... | ||
+ | 'freq', 500, ... | ||
+ | 'plot', true));</code> |