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fix tests
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4 files changed

+224
-29
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‎devtests.ipynb

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@@ -285,6 +285,224 @@
285285
"wfdb.dldatabasefiles(pbdb = 'tmpdb', dlbasedir = '/home/chen/Downloads/dbfolder', files = ['test01_00s.hea', 'test01_00s.dat', 'a/A/test02_45s.hea', 'a/A/test01_00s.hea'], keepsubdirs = True, overwrite = False)"
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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": 1,
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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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"data": {
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"text/plain": [
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"array([[-6., 0.],\n",
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" [-7., 0.],\n",
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" [-6., 0.],\n",
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" [-7., 0.],\n",
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" [-7., 0.],\n",
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" [-7., 0.],\n",
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" [-7., 0.],\n",
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" [-7., 0.],\n",
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" [-6., 0.],\n",
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" [-7., 0.]])"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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},
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{
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"data": {
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"text/plain": [
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"array([[-8., 6.],\n",
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" [-8., 6.],\n",
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" [-8., 7.],\n",
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" [-8., 7.],\n",
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" [-8., 7.],\n",
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" [-8., 7.],\n",
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" [-8., 7.],\n",
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" [-7., 6.],\n",
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" [-8., 7.],\n",
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" [-7., 6.]])"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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},
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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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"\n",
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"Target:\n"
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]
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},
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{
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"data": {
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"text/plain": [
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"array([[-6., 0.],\n",
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" [-7., 0.],\n",
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" [-6., 0.],\n",
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" [-7., 0.],\n",
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" [-7., 0.],\n",
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" [-7., 0.],\n",
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" [-7., 0.],\n",
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" [-7., 0.],\n",
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" [-6., 0.],\n",
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" [-7., 0.]])"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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},
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{
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"data": {
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"text/plain": [
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"array([[-8., 6.],\n",
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" [-8., 6.],\n",
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" [-8., 7.],\n",
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" [-8., 7.],\n",
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" [-8., 7.],\n",
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" [-8., 7.],\n",
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" [-8., 7.],\n",
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" [-7., 6.],\n",
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" [-8., 7.],\n",
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" [-7., 6.]])"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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},
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{
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"data": {
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"text/plain": [
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"True"
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]
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},
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"execution_count": 1,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"import wfdb\n",
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"from IPython.display import display\n",
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"import numpy as np\n",
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"\n",
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"record = wfdb.rdsamp('sampledata/310derive', sampfrom=2, physical=False)\n",
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"sig = record.d_signals\n",
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"targetsig = np.genfromtxt('tests/targetoutputdata/target13')\n",
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"\n",
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"\n",
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"display(sig[0:10,:])\n",
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"display(sig[-10:,:])\n",
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"\n",
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"print('\\nTarget:')\n",
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"display(targetsig[0:10,:])\n",
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"display(targetsig[-10:,:])\n",
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"\n",
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"np.array_equal(sig, targetsig)\n"
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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": 4,
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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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"ename": "SystemExit",
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"evalue": "The plotted signal 'record.p_signals' must be a 2d numpy array",
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"output_type": "error",
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"traceback": [
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"An exception has occurred, use %tb to see the full traceback.\n",
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"\u001b[0;31mSystemExit\u001b[0m\u001b[0;31m:\u001b[0m The plotted signal 'record.p_signals' must be a 2d numpy array\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/home/chen/Software/pythonenvs/python3.5/lib/python3.5/site-packages/IPython/core/interactiveshell.py:2889: UserWarning: To exit: use 'exit', 'quit', or Ctrl-D.\n",
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" warn(\"To exit: use 'exit', 'quit', or Ctrl-D.\", stacklevel=1)\n"
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]
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}
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],
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"source": [
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"wfdb.plotrec(record)"
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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": 1,
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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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"sigbytes: [246 223 0 ..., 48 242 7]\n",
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"2736\n",
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"uint64\n",
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"float64\n"
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]
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},
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{
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"ename": "NameError",
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"evalue": "name 'display' is not defined",
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"output_type": "error",
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"traceback": [
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"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
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"\u001b[0;32m<ipython-input-1-8237e8d15253>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mwfdb\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0ms\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mwfdb\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrdsamp\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'sampledata/310derive'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mphysical\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0md_signals\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mdisplay\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ms\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 4\u001b[0m \u001b[0mdisplay\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ms\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
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"\u001b[0;31mNameError\u001b[0m: name 'display' is not defined"
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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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"s = wfdb.rdsamp('sampledata/310derive', physical=False).d_signals\n",
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"display(s[0:10,:])\n",
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"display(s[-10:,:])"
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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": 3,
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"metadata": {
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"collapsed": false
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},
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"outputs": [],
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"source": [
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"import numpy as np\n",
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"x = np.array([[1,2], [3,4]], dtype = 'uint')"
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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": 4,
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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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"data": {
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"text/plain": [
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"array([[1, 2],\n",
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" [3, 4]], dtype=uint64)"
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]
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},
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"execution_count": 4,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"x"
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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,

‎setup.py

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,7 @@
2020
# Versions should comply with PEP440. For a discussion on single-sourcing
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# the version across setup.py and the project code, see
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# https://packaging.python.org/en/latest/single_source_version.html
23-
version='0.1.2',
23+
version='0.2.0',
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2525
description='The WFDB Python Toolbox',
2626
long_description=long_description,
@@ -56,8 +56,8 @@
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'numpy>=1.11.0',
5757
'matplotlib>=1.5.1',
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'requests>=2.10.0',
59-
'pandas>=0.19.1',
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'ipython>=5.1.0'
59+
'pandas>=0.19.1',
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'ipython>=5.1.0',
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],
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6363
# List additional groups of dependencies here (e.g. development

‎wfdb/_signals.py

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -414,6 +414,7 @@ def processwfdbbytes(filename, dirname, pbdir, fmt, startbyte, readlen, nsig, sa
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if tsampsperframe == nsig: # No extra samples/frame
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# Turn the bytes into actual samples.
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# 1d array of actual samples. Fill the individual triplets.
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sig = np.zeros(nsamp)
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sig[0::3] = (sigbytes[0::4] >> 1)[0:len(sig[0::3])] + 128 * \
@@ -601,7 +602,7 @@ def getdatbytes(filename, dirname, pbdir, fmt, nsamp, startbyte):
601602

602603
# For special formats that were read as unsigned 1 byte blocks to be further processed,
603604
# convert dtype from uint8 to uint64
604-
if fmt == ['212', '310', '311']:
605+
if fmt in ['212', '310', '311']:
605606
sigbytes = sigbytes.astype('uint')
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607608
fp.close()

‎wfdb/downloads.py

Lines changed: 1 addition & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -63,7 +63,7 @@ def streamdat(filename, pbdir, fmt, bytecount, startbyte, datatypes):
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# For special formats that were read as unsigned 1 byte blocks to be further processed,
6565
# convert dtype from uint8 to uint64
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if fmt == ['212', '310', '311']:
66+
if fmt in ['212', '310', '311']:
6767
sigbytes = sigbytes.astype('uint')
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return sigbytes
@@ -103,30 +103,6 @@ def getdblist():
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105105

106-
# Download specific files from a physiobank database
107-
def dldatabasefiles(pbdb, dlbasedir, files, keepsubdirs = True, overwrite = False):
108-
# Full url physiobank database
109-
dburl = os.path.join(dbindexurl, pbdb)
110-
# Check if the database is valid
111-
r = requests.get(dburl)
112-
r.raise_for_status()
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114-
# Construct the urls to download
115-
dlinputs = [(os.path.split(file)[1], os.path.split(file)[0], pbdb, dlbasedir, keepsubdirs, overwrite) for file in files]
116-
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# Make any required local directories
118-
makelocaldirs(dlbasedir, dlinputs, keepsubdirs)
119-
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print('Downloading files...')
121-
# Create multiple processes to download files.
122-
# Limit to 2 connections to avoid overloading the server
123-
pool = multiprocessing.Pool(processes=2)
124-
pool.map(dlpbfile, dlinputs)
125-
print('Finished downloading files')
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return
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130106
# ---- Helper functions for downloading physiobank files ------- #
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132108
def getrecordlist(dburl, records):

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