Merge pull request #83 from mbeyeler/mb/cython

[MRG] Cython implementation of Nanduri et al. (2012)

.travis.yml

@@ -40,7 +40,8 @@ before_install:
 
 install:
   - travis_wait
-  - python setup.py install --record installed_files.txt
+  - pip install -r requirements.txt
+  - pip install -e .
 
 script:
   - flake8 --ignore E501 `find . -name \*.py | grep -v setup.py | grep -v version.py | grep -v __init__.py | grep -v /doc/ | grep -v /scripts/`
@@ -56,4 +57,4 @@ after_success:
 after failure:
   - ls -alh
   - ulimit -a
-  - free -m
+  - free -m

examples/notebooks/compare-nanduri-naive-cython.ipynb

@@ -0,0 +1,167 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/mbeyeler/anaconda3/lib/python3.5/site-packages/skvideo/__init__.py:356: UserWarning: avconv/avprobe not found in path: \n",
+      "  warnings.warn(\"avconv/avprobe not found in path: \" + str(path), UserWarning)\n",
+      "2017-10-31 22:03:23,168 [pulse2percept] [INFO] Welcome to pulse2percept\n"
+     ]
+    }
+   ],
+   "source": [
+    "import numpy as np\n",
+    "import pulse2percept as p2p"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "tsample = 0.005 / 1000\n",
+    "stim = p2p.stimuli.PulseTrain(tsample, freq=20, amp=50, pulse_dur=0.45 / 1000, dur=0.5)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "old_model = p2p.retina.Nanduri2012(tsample=tsample)\n",
+    "new_model = p2p.retina.NanduriCython(tsample=tsample)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "layers = ['OFL']\n",
+    "use_jit = True\n",
+    "in_arr = np.array([1, 1], dtype=np.float).reshape((2, 1))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "old_out = old_model.model_cascade(in_arr, [stim.data], layers, use_jit)\n",
+    "new_out = new_model.model_cascade(in_arr, [stim.data], layers, use_jit)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "False"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "np.allclose(old_out.data, new_out.data)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "%load_ext line_profiler"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/mbeyeler/anaconda3/lib/python3.5/site-packages/line_profiler.py:294: UserWarning: Could not extract a code object for the object <class 'pulse2percept.retina.Nanduri2012'>\n",
+      "  profile = LineProfiler(*funcs)\n"
+     ]
+    }
+   ],
+   "source": [
+    "%lprun -f p2p.retina.Nanduri2012 old_model.model_cascade(in_arr, [stim.data], layers, use_jit)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "585 ms ± 7.93 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+     ]
+    }
+   ],
+   "source": [
+    "%timeit new_model.model_cascade(in_arr, [stim.data], layers, use_jit)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python [default]",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.5.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}