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‎README.md

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</p>
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## Introduction
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<p>Native python scripts for reading and writing WFDB signals and annotations. Currently in development. Library files are in the <strong>wfdb</strong> directory.</p>
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<ul>
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<li>15 July 2016 - <code>rdsamp</code> (for reading WFDB signals) is ready for beta usage.</li>
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<li>27 July 2016 - <code>rdann</code> (for reading WFDB annotations) is ready for beta usage.</li>
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<li>27 July 2016 - <code>plotwfdb</code> is able to plot signals and annotations output by <em>rdsamp</em> and <em>rdann</em></li>
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</ul>
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<p>Native python scripts for reading and writing WFDB signals and annotations.
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## Usage
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@@ -25,9 +17,14 @@ See the <strong>wfdbdemo.ipynb</strong> file for example scripts on how to call
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<strong>rdsamp</strong> - Read a WFDB file and return the signal as a numpy array and the metadata as a dictionary.
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```
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sig, fields = rdsamp(recordname, sampfrom=0, sampto=[], channels=[], physical=1, stacksegments=1, pbdl=0, dldir=os.cwd(), keepfiles=0)
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```
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Example Usage:
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```
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import wfdb
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sig, fields = wfdb.rdsamp(recordname, sampfrom, sampto, channels, physical, stacksegments)
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sig, fields = wfdb.rdsamp('mitdb/100', sampto=2000, pbdl=1)
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```
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Input Arguments:
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<li><code>channels</code> (default=all channels) - Indices specifying the channel to be returned.</li>
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<li><code>physical</code> (default=1) - Flag that specifies whether to return signals in physical (1) or digital (0) units.</li>
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<li><code>stacksegments</code> (default=1) - Flag used only for multi-segment files. Specifies whether to return the signal as a single stacked/concatenated numpy array (1) or as a list of one numpy array for each segment (0). </li>
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<li>pbdl (default=0): If this argument is set, the function will assume that the user is trying to download a physiobank file. Therefore the 'recordname' argument will be interpreted as a physiobank record name including the database subdirectory, rather than a local directory.</li>
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<li>dldir (default=os.getcwd()): The directory to download physiobank files to.</li>
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<li>keepfiles (default=0): Flag specifying whether to keep physiobank files newly downloaded through the function call.</li>
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</ul>
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Output Arguments:
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<strong>rdann</strong> - Read a WFDB annotation file <code>recordname.annot</code> and return the fields as lists or arrays.
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```
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annsamp, anntype, subtype, chan, num, aux, annfs = wfdb.rdann(recordname, annot, sampfrom=0, sampto=[], anndisp=1)
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```
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Example Usage:
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```
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import wfdb
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annsamp, anntype, subtype, chan, num, aux, annfs) = wfdb.rdann(recordname, annot, sampfrom, sampto, anndisp)
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annsamp, anntype, subtype, chan, num, aux, annfs = wfdb.rdann('100', 'atr')
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```
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Input Arguments:
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<strong>plotwfdb</strong> - Subplot and label each channel of an nxm signal on a graph. Also subplot annotation locations on selected channels if present.
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```
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plotwfdb(sig, fields, annsamp=[], annch=[0], title=[], plottime=1)
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```
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Example Usage:
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```
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import wfdb
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sig, fields = wfdb.rdsamp(recordname)
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annsamp=wfdb.rdann('recordname', 'annot')[0]
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wfdb.plotwfdb(sig, fields, annsamp, annch, title, plottime):
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sig, fields = wfdb.rdsamp('100')
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annsamp=wfdb.rdann('100', 'atr')[0]
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wfdb.plotwfdb(sig, fields, annsamp, 'mitdb record 100'):
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```
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‎devtests.ipynb

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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 5,
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"metadata": {
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"collapsed": false
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},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Created local directory: /home/cx1111/Downloads/wfdbrecords/macecgdb\n",
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"Downloading missing file(s) into directory: /home/cx1111/Downloads/wfdbrecords/macecgdb\n",
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"Downloaded all missing files for record.\n",
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"[[ 1.00000000e-01 -3.05110000e+02 -2.87190000e+02 -2.66720000e+02]\n",
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" [ -2.87190000e+02 -2.71830000e+02 -2.87190000e+02 1.10000000e-01]\n",
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" [ -2.99990000e+02 -2.87190000e+02 -2.64160000e+02 -2.87190000e+02]\n",
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" ..., \n",
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" [ -2.79520000e+02 -2.87190000e+02 -2.66710000e+02 -2.87190000e+02]\n",
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" [ 1.20000000e-01 -2.00160000e+02 -2.87190000e+02 -2.79520000e+02]\n",
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" [ -2.87190000e+02 -2.84640000e+02 -2.87190000e+02 1.20000000e-01]]\n"
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]
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}
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],
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"source": [
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"import wfdb\n",
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"sig, fields=wfdb.rdsamp('macecgdb/test01_00s', pbdl=1, dldir='/home/cx1111/Downloads/wfdbrecords/macecgdb', keepfiles=1)\n",
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"sig, fields=wfdb.rdsamp('macecgdb/test01_00s', pbdl=1, dldir='/home/cx1111/Downloads/wfdbrecords/macecgdb')\n",
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"\n",
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"print(sig)"
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]
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"print(sig)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {
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"collapsed": false
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},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Help on built-in function array in module numpy.core.multiarray:\n",
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"\n",
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"array(...)\n",
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" array(object, dtype=None, copy=True, order=None, subok=False, ndmin=0)\n",
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" \n",
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" Create an array.\n",
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" \n",
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" Parameters\n",
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" ----------\n",
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" object : array_like\n",
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" An array, any object exposing the array interface, an\n",
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" object whose __array__ method returns an array, or any\n",
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" (nested) sequence.\n",
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" dtype : data-type, optional\n",
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" The desired data-type for the array. If not given, then\n",
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" the type will be determined as the minimum type required\n",
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" to hold the objects in the sequence. This argument can only\n",
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" be used to 'upcast' the array. For downcasting, use the\n",
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" .astype(t) method.\n",
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" copy : bool, optional\n",
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" If true (default), then the object is copied. Otherwise, a copy\n",
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" will only be made if __array__ returns a copy, if obj is a\n",
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" nested sequence, or if a copy is needed to satisfy any of the other\n",
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" requirements (`dtype`, `order`, etc.).\n",
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" order : {'C', 'F', 'A'}, optional\n",
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" Specify the order of the array. If order is 'C', then the array\n",
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" will be in C-contiguous order (last-index varies the fastest).\n",
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" If order is 'F', then the returned array will be in\n",
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" Fortran-contiguous order (first-index varies the fastest).\n",
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" If order is 'A' (default), then the returned array may be\n",
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" in any order (either C-, Fortran-contiguous, or even discontiguous),\n",
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" unless a copy is required, in which case it will be C-contiguous.\n",
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" subok : bool, optional\n",
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" If True, then sub-classes will be passed-through, otherwise\n",
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" the returned array will be forced to be a base-class array (default).\n",
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" ndmin : int, optional\n",
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" Specifies the minimum number of dimensions that the resulting\n",
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" array should have. Ones will be pre-pended to the shape as\n",
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" needed to meet this requirement.\n",
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" \n",
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" Returns\n",
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" -------\n",
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" out : ndarray\n",
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" An array object satisfying the specified requirements.\n",
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" \n",
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" See Also\n",
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" --------\n",
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" empty, empty_like, zeros, zeros_like, ones, ones_like, fill\n",
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" \n",
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" Examples\n",
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" --------\n",
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" >>> np.array([1, 2, 3])\n",
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" array([1, 2, 3])\n",
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" \n",
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" Upcasting:\n",
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" \n",
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" >>> np.array([1, 2, 3.0])\n",
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" array([ 1., 2., 3.])\n",
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" \n",
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" More than one dimension:\n",
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" \n",
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" >>> np.array([[1, 2], [3, 4]])\n",
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" array([[1, 2],\n",
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" [3, 4]])\n",
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" \n",
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" Minimum dimensions 2:\n",
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" \n",
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" >>> np.array([1, 2, 3], ndmin=2)\n",
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" array([[1, 2, 3]])\n",
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" \n",
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" Type provided:\n",
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" \n",
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" >>> np.array([1, 2, 3], dtype=complex)\n",
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" array([ 1.+0.j, 2.+0.j, 3.+0.j])\n",
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" \n",
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" Data-type consisting of more than one element:\n",
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" \n",
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" >>> x = np.array([(1,2),(3,4)],dtype=[('a','<i4'),('b','<i4')])\n",
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" >>> x['a']\n",
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" array([1, 3])\n",
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" \n",
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" Creating an array from sub-classes:\n",
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" \n",
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" >>> np.array(np.mat('1 2; 3 4'))\n",
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" array([[1, 2],\n",
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" [3, 4]])\n",
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" \n",
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" >>> np.array(np.mat('1 2; 3 4'), subok=True)\n",
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" matrix([[1, 2],\n",
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" [3, 4]])\n",
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"\n"
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]
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}
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],
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"source": [
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"import numpy as np\n",
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"\n",
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"help(np.array)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"metadata": {
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"collapsed": false
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},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Help on function rdann in module wfdb._rdann:\n",
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"\n",
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"rdann(recordname, annot, sampfrom=0, sampto=[], anndisp=1)\n",
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" Read a WFDB annotation file recordname.annot and return the fields as lists or arrays\n",
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" \n",
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" Usage: annsamp, anntype, num, subtype, chan, aux, annfs = rdann(recordname, annot, \n",
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" sampfrom=0, sampto=[], \n",
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" anndisp=1)\n",
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" \n",
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" Input arguments:\n",
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" - recordname (required): The record name of the WFDB annotation file. ie. for \n",
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" file '100.atr', recordname='100'\n",
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" - annot (required): The annotator extension of the annotation file. ie. for \n",
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" file '100.atr', annot='atr'\n",
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" - sampfrom (default=0): The minimum sample number for annotations to be returned.\n",
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" - sampto (default=the final annotation sample): The maximum sample number for \n",
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" annotations to be returned.\n",
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" - anndisp (default = 1): The annotation display flag that controls the data type \n",
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" of the 'anntype' output parameter. 'anntype' will either be an integer key(0), \n",
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" a shorthand display symbol(1), or a longer annotation code.\n",
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" \n",
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" Output arguments:\n",
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" - annsamp: The annotation location in samples relative to the beginning of the record.\n",
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" - anntype: The annotation type according the the standard WFDB keys.\n",
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" - subtype: The marked class/category of the annotation.\n",
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" - chan: The signal channel associated with the annotations.\n",
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" - num: The marked annotation number. This is not equal to the index of the current annotation.\n",
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" - aux: The auxiliary information string for the annotation.\n",
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" - annfs: The sampling frequency written in the beginning of the annotation file if present.\n",
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" \n",
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" *NOTE: Every annotation contains the 'annsamp' and 'anntype' field. All \n",
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" other fields default to 0 or empty if not present.\n",
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"\n"
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]
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}
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],
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"source": [
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"help(wfdb.rdann)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,

‎wfdb/_rdann.py

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annotations to be returned.
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- anndisp (default = 1): The annotation display flag that controls the data type
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of the 'anntype' output parameter. 'anntype' will either be an integer key(0),
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a shorthand display symbol(1), or a longer annotation code.
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a shorthand display symbol(1), or a longer annotation code(2).
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Output arguments:
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- annsamp: The annotation location in samples relative to the beginning of the record.

‎wfdb/_rdsamp.py

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"""Read a WFDB record and return the signal as a numpy array and the metadata as a dictionary.
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Usage:
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sig, fields = rdsamp(recordname, sampfrom, sampto, channels, physical, stacksegments)
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sig, fields = rdsamp(recordname, sampfrom=0, sampto=[], channels=[], physical=1, stacksegments=1, pbdl=0, dldir=os.cwd(), keepfiles=0)
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Input arguments:
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- recordname (required): The name of the WFDB record to be read (without any file extensions). If the argument contains any path delimiter characters, the argument will be interpreted as PATH/baserecord and the data files will be searched for in the local path. If the pbdownload flag is set to 1, recordname will be interpreted as a physiobank record name including the database subdirectory.
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of metadata about the layout specification header.
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: The last list element will be a list of dictionaries of metadata for each segment.
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For empty segments, the dictionary will be replaced by a single string: 'Empty Segment'
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Example: sig, fields = wfdb.rdsamp('macecgdb/test01_00s', sampfrom=800, pbdl=1, dldir='/home/username/Downloads/wfdb')
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"""
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if sampfrom < 0:

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