source: framspy/dissimilarity/.ipynb_checkpoints/fdc-checkpoint.ipynb @ 1208

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     "text": [
      "Using Framsticks version: 5.0rc25\n",
      "Home (writable) dir     : /home/oriona/framsticks/framspy/Framsticks50rc25/data\n",
      "Resources dir           : /home/oriona/framsticks/framspy/Framsticks50rc25/data\n",
      "\n"
     ]
    }
   ],
   "source": [
    "import sys\n",
    "sys.path.append('..')\n",
    "import frams\n",
    "import numpy as np\n",
    "import importlib\n",
    "density = importlib.import_module(\"density-distribution\")\n",
    "from scipy import stats\n",
    "import gc\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "\n",
    "DIR = 'genos/'\n",
    "files = [[\"swim.gen\", \"velocity\"], [\"walk.gen\", \"velocity\"], [\"vposa.gen\", \"velocity\"], [\"vposp.gen\", \"velocity\"]]\n",
    "\n",
    "def parse_fit(fname, goal):\n",
    "    values = []\n",
    "    with open(DIR+fname) as f:\n",
    "        for line in f:\n",
    "            if goal in line:\n",
    "                splt = line.split(\":\")\n",
    "                values.append(float(splt[1]))\n",
    "    return values\n",
    "\n",
    "def get_dist(matrix, fits):\n",
    "    n = len(matrix[0])\n",
    "    dists = []\n",
    "    for geno in range(n):\n",
    "        better = []\n",
    "        for other in range(n):\n",
    "            if fits[other] >= fits[geno]:\n",
    "                better.append(matrix[geno][other])\n",
    "        sum_ = sum(better)\n",
    "        if sum_ > 0:\n",
    "            dists.append(sum_/len(better))\n",
    "        else:\n",
    "            dists.append(0)\n",
    "    return dists\n",
    "\n",
    "path = '/home/oriona/framsticks/framspy/Framsticks50rc25'\n",
    "frams.init(path)\n",
    "\n",
    "measures = [[\"distribution\", False], [\"frequency\", True]]\n",
    "metrics = [\"l1\", \"l2\", \"emd\"]\n",
    "\n",
    "def plot_fdc(file):\n",
    "    frams.Simulator.ximport(file[0])\n",
    "    fits = parse_fit(file[0], file[1])\n",
    "\n",
    "    fig, ax = plt.subplots(nrows=2, ncols=3, figsize=(15, 10))\n",
    "    for i, measure in enumerate(measures):\n",
    "        labels = []\n",
    "        for j, metric in enumerate(metrics):\n",
    "            print(measure[0], metric)\n",
    "            dissim = density.DensityDistribution(path, frequency=measure[1], metric=metric)\n",
    "            matrix = dissim.getDissimilarityMatrix([g.genotype for g in frams.GenePools[0]])\n",
    "            dists = get_dist(matrix, fits)\n",
    "            cor = stats.spearmanr(fits, dists)\n",
    "            print(\"r=\", round(cor.correlation,2))\n",
    "            ax[i, j].scatter(dists, fits)\n",
    "            ax[i, j].set_xlabel(\"distance\")\n",
    "            ax[i, j].set_ylabel(\"fitness\")\n",
    "            ax[i,j].set_title(measure[0]+\" \"+metric+\" \"+str(round(cor.correlation, 2)))\n",
    "    plt.show()\n",
    "    plt.savefig(file[0][:-4]+\".pdf\")\n",
    "    plt.cla()\n",
    "    plt.clf()\n",
    "    plt.close(fig)\n",
    "    gc.collect()\n",
    "\n",
    "    frams.GenePools[0].clear()    \n",
    "\n",
    "#for file in [files[0]]:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f8e0932c-11e4-4884-8d14-86b3590d93d6",
   "metadata": {
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   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "distribution l1\n",
      "Using Framsticks version: 5.0rc25\n",
      "Home (writable) dir     : /home/oriona/framsticks/framspy/Framsticks50rc25/data\n",
      "Resources dir           : /home/oriona/framsticks/framspy/Framsticks50rc25/data\n",
      "\n",
      "r= -0.52\n",
      "distribution l2\n",
      "Using Framsticks version: 5.0rc25\n",
      "Home (writable) dir     : /home/oriona/framsticks/framspy/Framsticks50rc25/data\n",
      "Resources dir           : /home/oriona/framsticks/framspy/Framsticks50rc25/data\n",
      "\n",
      "r= -0.54\n",
      "distribution emd\n",
      "Using Framsticks version: 5.0rc25\n",
      "Home (writable) dir     : /home/oriona/framsticks/framspy/Framsticks50rc25/data\n",
      "Resources dir           : /home/oriona/framsticks/framspy/Framsticks50rc25/data\n",
      "\n",
      "r= -0.65\n",
      "frequency l1\n",
      "Using Framsticks version: 5.0rc25\n",
      "Home (writable) dir     : /home/oriona/framsticks/framspy/Framsticks50rc25/data\n",
      "Resources dir           : /home/oriona/framsticks/framspy/Framsticks50rc25/data\n",
      "\n",
      "r= -0.54\n",
      "frequency l2\n",
      "Using Framsticks version: 5.0rc25\n",
      "Home (writable) dir     : /home/oriona/framsticks/framspy/Framsticks50rc25/data\n",
      "Resources dir           : /home/oriona/framsticks/framspy/Framsticks50rc25/data\n",
      "\n",
      "r= -0.53\n",
      "frequency emd\n",
      "Using Framsticks version: 5.0rc25\n",
      "Home (writable) dir     : /home/oriona/framsticks/framspy/Framsticks50rc25/data\n",
      "Resources dir           : /home/oriona/framsticks/framspy/Framsticks50rc25/data\n",
      "\n"
     ]
    }
   ],
   "source": [
    "plot_fdc(files[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "bba87fc1-454e-4aad-b71e-bc52096d864e",
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   "source": []
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