First commit

.gitignore

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+.so
+.o
+.dat

.ipynb_checkpoints/KSP_notebook-checkpoint.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "import sys\n",
+    "sys.path.insert(0, '../')\n",
+    "\n",
+    "import matplotlib\n",
+    "matplotlib.use(\"nbagg\")\n",
+    "import skimage\n",
+    "import skimage.filters\n",
+    "import skimage.morphology\n",
+    "import math\n",
+    "import numpy.linalg as la\n",
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt\n",
+    "import sklearn\n",
+    "import cv2\n",
+    "import scipy\n",
+    "import scipy.io as sio\n",
+    "import re, os, glob, pickle, shutil\n",
+    "from shutil import *\n",
+    "\n",
+    "import hickle as hkl\n",
+    "\n",
+    "\n",
+    "\n",
+    "import pandas as pd\n",
+    "\n",
+    "from random import randint\n",
+    "\n",
+    "from visualize import *\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "running build_ext\n",
+      "skipping 'kgraph.cpp' Cython extension (up-to-date)\n"
+     ]
+    }
+   ],
+   "source": [
+    "run setup.py build_ext -i"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "from ksp import pyKShorthestPathGraph"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "def get_fake():\n",
+    "    out = np.zeros((37,36)) + 0.00001\n",
+    "    out[15,15] = 0.99\n",
+    "    out[10,20] = 0.99\n",
+    "    \n",
+    "    return out"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "\n",
+    "depth = 10\n",
+    "q_vector = np.zeros(37*36*depth)\n",
+    "\n",
+    "#Prepare flat vector for ksp\n",
+    "for t in range(0,depth):\n",
+    "    #Q_loc = get_Q(t,M_ids[t])\n",
+    "    Q_loc = get_fake()\n",
+    "    flat_q = np.clip(np.ndarray.flatten(Q_loc),1e-6,0.999999)\n",
+    "    q_vector[37*36*t:37*36*(t+1)] = -np.log(flat_q/(1-flat_q))\n",
+    "    \n",
+    "access_points = np.asarray([0])\n",
+    "G = pyKShorthestPathGraph(q_vector,37,36,depth,3,access_points)\n",
+    "v = G.getPath(0,depth)\n",
+    "del G"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[555, 380, 555, 380, 555, 380, 555, 380, 555, 380, 555, 380, 555, 380, 555, 380, 555, 380, 555, 380, 1058, 0]\n"
+     ]
+    }
+   ],
+   "source": [
+    "print v"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "22\n"
+     ]
+    }
+   ],
+   "source": [
+    "555/36\n",
+    "print len(v)"
+   ]
+  },
+  {
+   "cell_type": "raw",
+   "metadata": {},
+   "source": [
+    "print v.shape"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 2",
+   "language": "python",
+   "name": "python2"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.11"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}

pyKSP-Example.py

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+
+import sys
+sys.path.insert(0, 'pyKSP')
+
+import numpy as np
+import matplotlib.pyplot as plt
+
+
+# Define a couple of usefull functions
+def get_fake():
+    # To create fake tracks
+    out = np.zeros((37,36)) + 0.00001
+    out[10,10] = 0.99
+    out[20,20] = 0.99
+
+    return out
+
+def convert_v(v,dims,depth):
+    # To convert the output of KSP into tracks format
+    MAP = np.zeros(dims)
+    n_tracks = len(v)/(depth)
+    out = np.zeros((depth,n_tracks,2))
+    for t in range(depth-1):
+        for i in range(n_tracks):
+            out[t,i,0] = v[t*n_tracks + i]/dims[1]
+            out[t,i,1] = v[t*n_tracks + i]%dims[1]
+
+    return np.int32(out)
+
+
+# Import the wrapper
+from ksp import pyKShorthestPathGraph
+
+'''
+    We will need to create a pyKShorthestPathGraph object. The constructor takes the following inputs, which we are going to build:
+    - A flattened vector containing the costs of going through each grid location at each time step.
+    - The W and H dimensions of your grid here 36 and 37.
+    - The number of frames to be processed, called depth, here 10.
+    - The admissible radius for two consecutive detections of the same track.
+    - The access points of your grid, in flattened format as well. These are the points where tracks can enter and exit the grid.
+'''
+
+depth = 30 #Number of frames
+
+# Prepare flat vector for ksp containing costs at each grid locations at each time step
+q_vector = np.zeros(37*36*depth)
+for t in range(0,depth):
+    Q_loc = get_fake()
+    flat_q = np.clip(np.ndarray.flatten(Q_loc),1e-6,0.999999)
+    q_vector[37*36*t:37*36*(t+1)] = -np.log(flat_q/(1-flat_q)) # Costs in -log() format
+
+access_points = np.asarray([0]) # Define the access points on your grid
+G = pyKShorthestPathGraph(q_vector,36,37,depth,4,access_points) #Be carefull ordering of dimensions inverted
+v = G.getPath(0,depth-1) # From_frame - To_frame (inclusive). Be carrefull if you set To_frame>depth - 1, you get a memory leak
+print v
+del G
+
+
+# Convert output to a "tracks" format
+out = convert_v(v,(37,36),depth)
+print out
+

pyKSP/Makefile

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+########################################################################
+# (c) 2009-2011 Ecole Polytechnique Federale de Lausanne               #
+# All rights reserved.                                                 #
+#                                                                      #
+# EPFL grants a non-exclusive and non-transferable license for non     #
+# commercial use of the Software for education and research purposes   #
+# only. Any other use of the Software is expressly excluded.           #
+#                                                                      #
+# Redistribution of the Software in source and binary forms, with or   #
+# without modification, is not permitted.                              #
+#                                                                      #
+# Written by Engin Turetken and Jerome Berclaz.                        #
+#                                                                      #
+# http://cvlab.epfl.ch/research/body/surv                              #
+# Contact <[email protected]> for comments & bug reports.                    #
+########################################################################
+
+LDFLAGS=
+CXXFLAGS=-O3 -msse2 -mfpmath=sse
+
+all: ksp 
+
+ksp: ksp_graph.o ksp_computer.o main.o
+	$(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS)
+
+clean:
+	$(RM) *.o *~ ksp