simmulate_sounds.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2017-10-08 11:10:17,960 root         INFO     Computer: txori\n"
     ]
    }
   ],
   "source": [
    "# simmulate sounds in a grid of parameter values\n",
    "# split the parameter space in n parallel processes\n",
    "# then merge the files\n",
    "\n",
    "from __future__ import division\n",
    "%matplotlib inline\n",
    "import numpy as np\n",
    "from matplotlib import pyplot as plt\n",
    "from scipy.signal import spectrogram\n",
    "import scipy.signal as sg\n",
    "import socket\n",
    "import os\n",
    "import sys\n",
    "import logging\n",
    "#from mpi4py import MPI\n",
    "import h5py\n",
    "import copy\n",
    "import glob\n",
    "import shutil\n",
    "\n",
    "logger = logging.getLogger()\n",
    "handler = logging.StreamHandler()\n",
    "formatter = logging.Formatter(\n",
    "         '%(asctime)s %(name)-12s %(levelname)-8s %(message)s')\n",
    "handler.setFormatter(formatter)\n",
    "logger.addHandler(handler)\n",
    "logger.setLevel(logging.INFO)\n",
    "\n",
    "# Check wich computer to decide where the things are mounted\n",
    "comp_name=socket.gethostname()\n",
    "logger.info('Computer: ' + comp_name)\n",
    "\n",
    "if 'txori' in comp_name or 'passaro' in comp_name or 'lintu' in comp_name:\n",
    "    repos_folder = os.path.abspath('/mnt/cube/earneodo/repos')\n",
    "    experiment_folder = os.path.join('/mnt/cube/earneodo/bci_zf/')\n",
    "\n",
    "if 'lookfar' in comp_name:\n",
    "    repos_folder = os.path.abspath('/Users/zeke/repos/')\n",
    "    experiment_folder = os.path.join('/Users/zeke/bci_zf/')\n",
    "\n",
    "sys.path.append(os.path.join(repos_folder, 'swissknife'))\n",
    "\n",
    "#setup the data folder\n",
    "from swissknife.h5tools import h5tools\n",
    "from swissknife.h5tools import tables\n",
    "from swissknife.dynamo import finch as zf\n",
    "from swissknife.dynamo import takens as tk\n",
    "from swissknife.bci.core import expstruct as es\n",
    "from swissknife.threadtools import threadedfunction as td\n",
    "\n",
    "def splitlist(a, n):\n",
    "    k, m = len(a) / n, len(a) % n\n",
    "    return (a[i * k + min(i, m):(i + 1) * k + min(i + 1, m)] for i in range(n))\n",
    "\n",
    "def chunkify(lst,n):\n",
    "    return [ lst[i::n] for i in range(n) ]\n",
    "\n",
    "def sim_and_store(sim_pars, h5_file):\n",
    "    sweep_group = h5_file.require_group(sim_pars['sweep_name'])\n",
    "    h5tools.dict_2_group(sweep_group, sim_pars['vocal_pars'], 'vocal_pars')\n",
    "    synth_group = sweep_group.require_group('synth')\n",
    "    # create the group for the gamma\n",
    "    gamma_group = synth_group.require_group('{0:5d}'.format(sim_pars['gamma']))\n",
    "    sweep_table = tables.unlimited_rows_data(gamma_group, 'alpha_beta', \n",
    "                                             np.array([sim_pars['alpha'], \n",
    "                                                       sim_pars['beta']]).reshape([1,2]))\n",
    "                                            \n",
    "    \n",
    "    alpha_values = sim_pars['alpha'] * np.ones(sim_pars['sim_samples'])\n",
    "    beta_values = sim_pars['beta'] * np.ones(sim_pars['sim_samples'])\n",
    "    env_values = np.ones(sim_pars['sim_samples'])\n",
    "    par_stream = np.array([alpha_values, beta_values, env_values]).T\n",
    "    for key in ['alpha', 'beta', 'gamma', 's_f', 'steps_per_sample']:\n",
    "        vocal_pars['sys'][key] = sim_pars[key]\n",
    "    song_synth = zf.finch(vocal_pars, par_stream, x_0=sim_pars['x_0'])\n",
    "    pin_table = tables.unlimited_rows_data(gamma_group, 'pre_in', \n",
    "                                           song_synth[:,1].reshape([1,-1]))\n",
    "    pout_table = tables.unlimited_rows_data(gamma_group, 'pre_out', \n",
    "                                            song_synth[:,0].reshape([1,-1]))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "216\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "[<matplotlib.lines.Line2D at 0x7fb2d34245c0>]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": 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9m/hY5cdomN3gdVm+Zt1/uJ/mg81+DOxzzt1lZncAI51z3+pn+8uA/+qcuzaR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\nAABJRU5ErkJggg==\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7fb3104de0f0>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "sys_pars = {'alpha_1': 0.15,\n",
    "            'beta_1': 0.15,\n",
    "            'alpha_2': 0.15,\n",
    "            'beta_2': 0.15,\n",
    "            'gamma': 24000.,\n",
    "            'Ch_inv': 4.5E10,\n",
    "            'Lb_inv': 1.E-4,\n",
    "            'Lg_inv': 1/82.,\n",
    "            'Rb': 5E6,\n",
    "            'Rh': 6E5,\n",
    "            'V_ext': 0.,\n",
    "            'dV_ext': 0.,\n",
    "            'noise': 0.,\n",
    "            'envelope': 0.,\n",
    "            'noise_fraction_beta_1': 0.1,\n",
    "            'noise_fraction_env': 0.1,\n",
    "            's_f': 30000.,\n",
    "            'steps_per_sample': 20\n",
    "            }\n",
    "\n",
    "vocal_pars = {'sys': sys_pars,\n",
    "              'S_1': 0.2,\n",
    "              'S_2': 0.2,\n",
    "              'S_3': 0.2,\n",
    "              'l_1': 1.5,\n",
    "              'l_2': 1.5,\n",
    "              'l_3': 1.0,\n",
    "              'r_out': 0.1,\n",
    "              'r_12': None,\n",
    "              'r_21': None,\n",
    "              'r_23': None,\n",
    "              'r_32': None,\n",
    "              't_12': None,\n",
    "              't_21': None,\n",
    "              't_23': None,\n",
    "              't_32': None,\n",
    "              't_in': 0.5,\n",
    "              'tau_1': None,\n",
    "              'tau_2': None,\n",
    "              'tau_3': None,\n",
    "              'max_tau': None,\n",
    "              'A_1': 0.,\n",
    "              'A_2': None,\n",
    "              'A_3': None}\n",
    "\n",
    "#lines, ab_g= tk.cusp_grid()\n",
    "lines, ab_g = tk.cusp_grid(b_max=0.075, b_min=-1 / 3, a_step=1.5E-3, b_steps=10000, b_log_step_exp=6, f_max=None)\n",
    "plt.plot(lines[:,1], lines[:,0])\n",
    "plt.plot(lines[:,2], lines[:,0])\n",
    "plt.plot(ab_g[:,0], ab_g[:,1], '.')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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I13uoV01AIhJKNYCUiu1H4dUEJCIhVANIqxi+uNub2jUKSERCKQBSKo5OYDUBiUgpagJK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\nKAWAiEhGKQBERDJKASAiklH/H3YtEk/8+mPYAAAAAElFTkSuQmCC\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7fb3104cc320>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# upper line\n",
    "plt.plot(lines[:,1], lines[:,0])\n",
    "# lower line\n",
    "plt.plot(lines[:,2], lines[:,0])\n",
    "#get values that are a<0, b<lowerline\n",
    "\n",
    "def cusp_grid(b_span, b_steps, a_max=-.15, a_min=-0.16, a_step=1e-3, b_log_step_exp=200):\n",
    "    lines = tk.cusp_lines(step=a_step)\n",
    "    b_sweep = np.logspace(0, b_log_step_exp, b_steps)*b_span  / (10 ** (b_log_step_exp))\n",
    "    ab_grid = []\n",
    "    for a in np.linspace(a_max, a_min, int(abs(a_max - a_min)/a_step)):\n",
    "        b_m = lines[np.where(lines[:,2] < a)[0][0], 0]\n",
    "        for b in b_sweep:\n",
    "            ab_grid.append([a, b_m - b])\n",
    "        \n",
    "    return b_sweep, np.array(ab_grid)\n",
    "        \n",
    "l, abg = cusp_grid(3.25, 20000)\n",
    "plt.plot(np.array(abg)[:,0], np.array(abg)[:,1], '*');"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(200000, 2)"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "aba = np.array(abg)\n",
    "aba.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/mnt/cube/earneodo/bci_zf'"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "es.file_names('')['locations']['experiment']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "sweep_id = '004'\n",
    "sweep_name = 'sweep_'+sweep_id\n",
    "file_name_base = 'finch_'+sweep_id \n",
    "sweep_folder = os.path.join(es.file_names('')['locations']['experiment'], 'syn_sweeps')\n",
    "sweep_file_name = '{}.h5'.format(file_name_base)\n",
    "sweep_file_path = os.path.join(sweep_folder, sweep_file_name)\n",
    "\n",
    "sim_pars = {'sweep_name' : sweep_name,\n",
    "            'folder': sweep_folder,\n",
    "            'file_name': sweep_file_name,\n",
    "            'file_path': sweep_file_path,\n",
    "            \n",
    "            'gamma': 24000,\n",
    "            'alpha': 0.,\n",
    "            'beta': 0.,\n",
    "            'vocal_pars': vocal_pars,\n",
    "            'sim_samples': 3000,\n",
    "            's_f': 30000.,\n",
    "            'steps_per_sample': 20,\n",
    "            'x_0': np.array([5.E-12, 1.E-11, 1.E-12, 1.E-11, 1.E-12])\n",
    "           }\n",
    "\n",
    "#s.mkdir_p(os.path.split(h5_path)[0])\n",
    "\n",
    "\n",
    "def merge_sweeps(source_file_path, dest_file_path, sim_pars):\n",
    "    logger.info('Merging sweep in {} into {}'.format(source_file_path, dest_file_path))\n",
    "    for table_name in ['alpha_beta', 'pre_in', 'pre_out']:\n",
    "        table_path = '/{0}/synth/{1}/{2}'.format(sim_pars['sweep_name'], sim_pars['gamma'], table_name)\n",
    "        tables.merge_tables(source_file_path, dest_file_path, table_path)\n",
    "    logger.info('Table merged')\n",
    "\n",
    "def merge_all_sweeps(pars, mode='x'):\n",
    "    logger.info('Merging all sweeps for {}'.format(pars['sweep_name']))\n",
    "    \n",
    "    files_list=glob.glob(os.path.join(pars['folder'], pars['file_name'] + '.*'))\n",
    "    files_list.sort()\n",
    "    logger.info('Found {} sweep files'.format(len(files_list)))\n",
    "    if mode=='x' or (not os.path.isfile(pars['file_path'])):\n",
    "        logger.info('Copying first file to {}'.format(pars['file_path']))\n",
    "        shutil.copy2(files_list.pop(0), pars['file_path'])\n",
    "    else: \n",
    "        logger.info('Appending sweeps to existing file {}'.format(pars['file_path']))\n",
    "    \n",
    "    for source_file in files_list:\n",
    "        merge_sweeps(source_file, pars['file_path'], pars)\n",
    "\n",
    "@h5tools.h5_decorator(leave_open=False)\n",
    "def sweep_to_file(h5_path, ab_list, sim_pars, mode='x'):\n",
    "    logger.info('Sweeping {0} values of alpha, beta with g={1} to file {2}'.format(\n",
    "            ab_list.shape[0], sim_pars['gamma'], h5_path))\n",
    "    try:\n",
    "        total_sim = ab_list.shape[0]\n",
    "        count = 0\n",
    "        round_count = 0\n",
    "        \n",
    "        for sim_pars['alpha'], sim_pars['beta'] in np.nditer([ab_list[:,0], ab_list[:,1]]):\n",
    "            if round_count==0:\n",
    "                logger.info('Simulating {0}/{1} with {2}, {3}'.format(count,\n",
    "                                                                  total_sim, \n",
    "                                                                  sim_pars['alpha'],\n",
    "                                                                  sim_pars['beta']))\n",
    "                round_count = 100\n",
    "                count+= 100\n",
    "            sim_and_store(sim_pars, h5_path)\n",
    "            round_count-=1\n",
    "        logger.info('Sweep done successfully')\n",
    "    except UnboundLocalError as err:\n",
    "        logger.error(err)\n",
    "\n",
    "\n",
    "def parallel_sweep(h5_path, ab_list, sim_pars, mode='x', threads=1):\n",
    "    es.mkdir_p(os.path.split(h5_path)[0])\n",
    "    logger.info('Sweeping {0} values of alpha, beta with g={1} to file {2} in {3} threads'.format(\n",
    "            ab_list.shape[0], sim_pars['gamma'], h5_path, threads))\n",
    "    try:\n",
    "        sweep_threads = []\n",
    "        f = h5py.File(h5_path, mode, driver='mpio', comm=MPI.COMM_WORLD)\n",
    "        for chunk in chunkify(range(ab_list.shape[0]), threads):\n",
    "            a_sweep = td.threadedFunction(args=(sweep_to_file,\n",
    "                                                f,\n",
    "                                                ab_list[chunk, :],\n",
    "                                                sim_pars))\n",
    "            a_sweep.start()\n",
    "            sweep_threads.append(a_sweep)\n",
    "        logger.info('Parallel sweep done successfully')\n",
    "    except UnboundLocalError as err:\n",
    "        f.close()\n",
    "        logger.error(err)\n",
    "        \n",
    "def parallel_files_sweep(h5_path, ab_list, sim_pars, mode='x', threads=1):\n",
    "    file_path = os.path.split(h5_path)[0]\n",
    "    file_name = os.path.split(h5_path)[-1]\n",
    "    \n",
    "    es.mkdir_p(file_path)\n",
    "    logger.info('Sweeping {0} values of alpha, beta with g={1} to file {2} in {3} threads'.format(\n",
    "            ab_list.shape[0], sim_pars['gamma'], h5_path, threads))\n",
    "    try:\n",
    "        sweep_threads = []\n",
    "        sim_pars_base = []\n",
    "        f_chunk_paths = []\n",
    "        for i_chunk, chunk in enumerate(chunkify(range(ab_list.shape[0]), threads)):\n",
    "            f_chunk_path = os.path.join(file_path, file_name + '.{}'.format(i_chunk))\n",
    "            f_chunk_paths.append(f_chunk_path)\n",
    "            sim_pars_base.append(copy.deepcopy(sim_pars))\n",
    "            a_sweep = td.threadedFunction(args=(sweep_to_file,\n",
    "                                                f_chunk_path,\n",
    "                                                ab_list[chunk, :],\n",
    "                                                sim_pars_base[i_chunk]),\n",
    "                                         kwargs = {'mode':mode})\n",
    "            a_sweep.start()\n",
    "            sweep_threads.append(a_sweep)\n",
    "            \n",
    "        logger.info('Will wait for {} sweeps to end before merging'.format(len(sweep_threads)))\n",
    "        sweeps_merge = td.threadedFunction(name='merge_{}'.format(sim_pars['sweep_name']),\n",
    "                                           args=(merge_all_sweeps,\n",
    "                                                 sim_pars),\n",
    "                                           kwargs={'mode':mode})\n",
    "        for i_sweep, sweep_thread in enumerate(sweep_threads):\n",
    "            sweep_thread.join()\n",
    "            logger.info('Thread {} done'.format(sweep_thread.name))\n",
    "        logger.info('Done with all sweeps')\n",
    "        sweeps_merge.start()\n",
    "        \n",
    "    except UnboundLocalError as err:\n",
    "        f.close()\n",
    "        logger.error(err)\n",
    "    \n",
    "    return sweep_threads + [sweeps_merge], sim_pars_base\n",
    "    \n",
    "\n",
    "par_list = np.array([np.linspace(-.15, -.3, 2), np.linspace(0, -.5, 2)]).T\n",
    "#sweep_to_file(sweep_file_path, ab_g, sim_pars, mode='a')\n",
    "#parallel_sweep(sweep_file_path, ab_g, sim_pars, mode='a')\n",
    "#merge_all_sweeps(sim_pars)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "log_path = os.path.split(sweep_file_path)[0]\n",
    "log_file = os.path.split(sweep_file_path)[1].split('.')[0] + '.log'\n",
    "log_file_path = os.path.join(log_path, log_file)\n",
    "\n",
    "\n",
    "#handler = logging.StreamHandler()\n",
    "handler = logging.FileHandler(log_file_path)\n",
    "formatter = logging.Formatter(\n",
    "        '%(asctime)s %(name)-12s %(levelname)-8s (%(threadName)-10s) %(message)s')\n",
    "handler.setFormatter(formatter)\n",
    "logger.addHandler(handler)\n",
    "logger.setLevel(logging.INFO)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2017-10-08 11:10:25,092 threadtools.threadedfunction INFO     Starting function  in thread threadedFunction-1\n",
      "2017-10-08 11:10:25,096 root         INFO     Sweeping 200000 values of alpha, beta with g=24000 to file /mnt/cube/earneodo/bci_zf/syn_sweeps/finch_004.h5 in 6 threads\n",
      "2017-10-08 11:10:25,111 threadtools.threadedfunction INFO     Starting function  in thread threadedFunction-1:1\n",
      "2017-10-08 11:10:25,115 root         INFO     Sweeping 33334 values of alpha, beta with g=24000 to file <HDF5 file \"finch_004.h5.0\" (mode r+)>\n",
      "2017-10-08 11:10:25,116 root         INFO     Simulating 0/33334 with -0.15, 0.0037037037037037646\n",
      "2017-10-08 11:10:25,123 threadtools.threadedfunction INFO     Starting function  in thread threadedFunction-1:2\n",
      "2017-10-08 11:10:25,127 root         INFO     Sweeping 33334 values of alpha, beta with g=24000 to file <HDF5 file \"finch_004.h5.1\" (mode r+)>\n",
      "2017-10-08 11:10:25,128 root         INFO     Simulating 0/33334 with -0.15, 0.0037037037037037646\n",
      "2017-10-08 11:10:25,134 threadtools.threadedfunction INFO     Starting function  in thread threadedFunction-1:3\n",
      "2017-10-08 11:10:25,137 root         INFO     Sweeping 33333 values of alpha, beta with g=24000 to file <HDF5 file \"finch_004.h5.2\" (mode r+)>\n",
      "2017-10-08 11:10:25,138 root         INFO     Simulating 0/33333 with -0.15, 0.0037037037037037646\n",
      "2017-10-08 11:10:25,145 threadtools.threadedfunction INFO     Starting function  in thread threadedFunction-1:4\n",
      "2017-10-08 11:10:25,149 root         INFO     Sweeping 33333 values of alpha, beta with g=24000 to file <HDF5 file \"finch_004.h5.3\" (mode r+)>\n",
      "2017-10-08 11:10:25,150 root         INFO     Simulating 0/33333 with -0.15, 0.0037037037037037646\n",
      "2017-10-08 11:10:25,157 threadtools.threadedfunction INFO     Starting function  in thread threadedFunction-1:5\n",
      "2017-10-08 11:10:25,162 root         INFO     Sweeping 33333 values of alpha, beta with g=24000 to file <HDF5 file \"finch_004.h5.4\" (mode r+)>\n",
      "2017-10-08 11:10:25,164 root         INFO     Simulating 0/33333 with -0.15, 0.0037037037037037646\n",
      "2017-10-08 11:10:25,166 root         INFO     Will wait for 6 sweeps to end before merging\n",
      "2017-10-08 11:10:25,167 threadtools.threadedfunction INFO     Starting function  in thread threadedFunction-1:6\n",
      "2017-10-08 11:10:25,170 root         INFO     Sweeping 33333 values of alpha, beta with g=24000 to file <HDF5 file \"finch_004.h5.5\" (mode r+)>\n",
      "2017-10-08 11:10:25,172 root         INFO     Simulating 0/33333 with -0.15, 0.0037037037037037646\n"
     ]
    }
   ],
   "source": [
    "par_process = td.threadedFunction(args=(parallel_files_sweep, \n",
    "                                        sweep_file_path, \n",
    "                                        abg[:,:], \n",
    "                                        sim_pars),\n",
    "                                  kwargs={'mode':'a',\n",
    "                                          'threads':6})\n",
    "par_process.start()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'alpha': 0.0,\n",
       " 'beta': 0.0,\n",
       " 'file_name': 'finch_004.h5',\n",
       " 'file_path': '/mnt/cube/earneodo/bci_zf/syn_sweeps/finch_004.h5',\n",
       " 'folder': '/mnt/cube/earneodo/bci_zf/syn_sweeps',\n",
       " 'gamma': 24000,\n",
       " 's_f': 30000.0,\n",
       " 'sim_samples': 3000,\n",
       " 'steps_per_sample': 20,\n",
       " 'sweep_name': 'sweep_004',\n",
       " 'vocal_pars': {'A_1': 0.0,\n",
       "  'A_2': None,\n",
       "  'A_3': None,\n",
       "  'S_1': 0.2,\n",
       "  'S_2': 0.2,\n",
       "  'S_3': 0.2,\n",
       "  'l_1': 1.5,\n",
       "  'l_2': 1.5,\n",
       "  'l_3': 1.0,\n",
       "  'max_tau': None,\n",
       "  'r_12': None,\n",
       "  'r_21': None,\n",
       "  'r_23': None,\n",
       "  'r_32': None,\n",
       "  'r_out': 0.1,\n",
       "  'sys': {'Ch_inv': 45000000000.0,\n",
       "   'Lb_inv': 0.0001,\n",
       "   'Lg_inv': 0.012195121951219513,\n",
       "   'Rb': 5000000.0,\n",
       "   'Rh': 600000.0,\n",
       "   'V_ext': 0.0,\n",
       "   'alpha_1': 0.15,\n",
       "   'alpha_2': 0.15,\n",
       "   'beta_1': 0.15,\n",
       "   'beta_2': 0.15,\n",
       "   'dV_ext': 0.0,\n",
       "   'envelope': 0.0,\n",
       "   'gamma': 24000.0,\n",
       "   'noise': 0.0,\n",
       "   'noise_fraction_beta_1': 0.1,\n",
       "   'noise_fraction_env': 0.1,\n",
       "   's_f': 30000.0,\n",
       "   'steps_per_sample': 20},\n",
       "  't_12': None,\n",
       "  't_21': None,\n",
       "  't_23': None,\n",
       "  't_32': None,\n",
       "  't_in': 0.5,\n",
       "  'tau_1': None,\n",
       "  'tau_2': None,\n",
       "  'tau_3': None},\n",
       " 'x_0': array([  5.00000000e-12,   1.00000000e-11,   1.00000000e-12,\n",
       "          1.00000000e-11,   1.00000000e-12])}"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sim_pars"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 91,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2016-10-26 16:51:32,158 root         INFO     Merging all sweeps for sweep_000\n",
      "2016-10-26 16:51:32,160 root         INFO     Found 6 sweep files\n",
      "2016-10-26 16:51:32,161 root         INFO     Copying first file to /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:51:38,112 root         INFO     Merging sweep in /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.1 into /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:51:38,114 root         DEBUG    Appending table /sweep_000/synth/23500/alpha_beta from file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.1 into file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:51:38,116 root         DEBUG    Appending /sweep_000/synth/23500/alpha_beta onto /sweep_000/synth/23500/alpha_beta\n",
      "2016-10-26 16:51:38,117 root         DEBUG    Counting channels\n",
      "2016-10-26 16:51:38,118 root         INFO     Channel count: 2\n",
      "2016-10-26 16:51:38,119 root         DEBUG    About to append 0 entire chunks plus change\n",
      "2016-10-26 16:51:38,120 root         DEBUG    Chunk start: 0\n",
      "2016-10-26 16:51:38,400 tables       DEBUG    Appending 26584 rows to dataset /sweep_000/synth/23500/alpha_beta\n",
      "2016-10-26 16:51:38,598 root         DEBUG    106336 elements written\n",
      "2016-10-26 16:51:38,642 root         DEBUG    Appending table /sweep_000/synth/23500/pre_in from file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.1 into file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:51:38,643 root         DEBUG    Appending /sweep_000/synth/23500/pre_in onto /sweep_000/synth/23500/pre_in\n",
      "2016-10-26 16:51:38,644 root         DEBUG    Counting channels\n",
      "2016-10-26 16:51:38,645 root         INFO     Channel count: 4410\n",
      "2016-10-26 16:51:38,646 root         DEBUG    About to append 0 entire chunks plus change\n",
      "2016-10-26 16:51:38,647 root         DEBUG    Chunk start: 0\n",
      "2016-10-26 16:51:50,069 tables       DEBUG    Appending 26584 rows to dataset /sweep_000/synth/23500/pre_in\n",
      "2016-10-26 16:51:51,490 root         DEBUG    234470880 elements written\n",
      "2016-10-26 16:51:51,623 root         DEBUG    Appending table /sweep_000/synth/23500/pre_out from file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.1 into file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:51:51,625 root         DEBUG    Appending /sweep_000/synth/23500/pre_out onto /sweep_000/synth/23500/pre_out\n",
      "2016-10-26 16:51:51,626 root         DEBUG    Counting channels\n",
      "2016-10-26 16:51:51,627 root         INFO     Channel count: 4410\n",
      "2016-10-26 16:51:51,628 root         DEBUG    About to append 0 entire chunks plus change\n",
      "2016-10-26 16:51:51,629 root         DEBUG    Chunk start: 0\n",
      "2016-10-26 16:51:58,741 tables       DEBUG    Appending 26584 rows to dataset /sweep_000/synth/23500/pre_out\n",
      "2016-10-26 16:52:00,370 root         DEBUG    234470880 elements written\n",
      "2016-10-26 16:52:00,521 root         INFO     Table merged\n",
      "2016-10-26 16:52:00,522 root         INFO     Merging sweep in /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.2 into /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:52:00,523 root         DEBUG    Appending table /sweep_000/synth/23500/alpha_beta from file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.2 into file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:52:00,526 root         DEBUG    Appending /sweep_000/synth/23500/alpha_beta onto /sweep_000/synth/23500/alpha_beta\n",
      "2016-10-26 16:52:00,527 root         DEBUG    Counting channels\n",
      "2016-10-26 16:52:00,528 root         INFO     Channel count: 2\n",
      "2016-10-26 16:52:00,529 root         DEBUG    About to append 0 entire chunks plus change\n",
      "2016-10-26 16:52:00,530 root         DEBUG    Chunk start: 0\n",
      "2016-10-26 16:52:00,821 tables       DEBUG    Appending 26583 rows to dataset /sweep_000/synth/23500/alpha_beta\n",
      "2016-10-26 16:52:01,018 root         DEBUG    106332 elements written\n",
      "2016-10-26 16:52:01,061 root         DEBUG    Appending table /sweep_000/synth/23500/pre_in from file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.2 into file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:52:01,063 root         DEBUG    Appending /sweep_000/synth/23500/pre_in onto /sweep_000/synth/23500/pre_in\n",
      "2016-10-26 16:52:01,065 root         DEBUG    Counting channels\n",
      "2016-10-26 16:52:01,066 root         INFO     Channel count: 4410\n",
      "2016-10-26 16:52:01,067 root         DEBUG    About to append 0 entire chunks plus change\n",
      "2016-10-26 16:52:01,068 root         DEBUG    Chunk start: 0\n",
      "2016-10-26 16:52:16,847 tables       DEBUG    Appending 26583 rows to dataset /sweep_000/synth/23500/pre_in\n",
      "2016-10-26 16:52:18,340 root         DEBUG    234462060 elements written\n",
      "2016-10-26 16:52:18,519 root         DEBUG    Appending table /sweep_000/synth/23500/pre_out from file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.2 into file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:52:18,520 root         DEBUG    Appending /sweep_000/synth/23500/pre_out onto /sweep_000/synth/23500/pre_out\n",
      "2016-10-26 16:52:18,521 root         DEBUG    Counting channels\n",
      "2016-10-26 16:52:18,522 root         INFO     Channel count: 4410\n",
      "2016-10-26 16:52:18,522 root         DEBUG    About to append 0 entire chunks plus change\n",
      "2016-10-26 16:52:18,523 root         DEBUG    Chunk start: 0\n",
      "2016-10-26 16:52:25,610 tables       DEBUG    Appending 26583 rows to dataset /sweep_000/synth/23500/pre_out\n",
      "2016-10-26 16:52:27,138 root         DEBUG    234462060 elements written\n",
      "2016-10-26 16:52:27,286 root         INFO     Table merged\n",
      "2016-10-26 16:52:27,286 root         INFO     Merging sweep in /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.3 into /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:52:27,287 root         DEBUG    Appending table /sweep_000/synth/23500/alpha_beta from file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.3 into file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:52:27,290 root         DEBUG    Appending /sweep_000/synth/23500/alpha_beta onto /sweep_000/synth/23500/alpha_beta\n",
      "2016-10-26 16:52:27,290 root         DEBUG    Counting channels\n",
      "2016-10-26 16:52:27,291 root         INFO     Channel count: 2\n",
      "2016-10-26 16:52:27,291 root         DEBUG    About to append 0 entire chunks plus change\n",
      "2016-10-26 16:52:27,292 root         DEBUG    Chunk start: 0\n",
      "2016-10-26 16:52:27,541 tables       DEBUG    Appending 26583 rows to dataset /sweep_000/synth/23500/alpha_beta\n",
      "2016-10-26 16:52:27,716 root         DEBUG    106332 elements written\n",
      "2016-10-26 16:52:27,750 root         DEBUG    Appending table /sweep_000/synth/23500/pre_in from file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.3 into file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:52:27,751 root         DEBUG    Appending /sweep_000/synth/23500/pre_in onto /sweep_000/synth/23500/pre_in\n",
      "2016-10-26 16:52:27,752 root         DEBUG    Counting channels\n",
      "2016-10-26 16:52:27,753 root         INFO     Channel count: 4410\n",
      "2016-10-26 16:52:27,754 root         DEBUG    About to append 0 entire chunks plus change\n",
      "2016-10-26 16:52:27,754 root         DEBUG    Chunk start: 0\n",
      "2016-10-26 16:52:39,007 tables       DEBUG    Appending 26583 rows to dataset /sweep_000/synth/23500/pre_in\n",
      "2016-10-26 16:52:40,914 root         DEBUG    234462060 elements written\n",
      "2016-10-26 16:52:41,049 root         DEBUG    Appending table /sweep_000/synth/23500/pre_out from file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.3 into file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:52:41,051 root         DEBUG    Appending /sweep_000/synth/23500/pre_out onto /sweep_000/synth/23500/pre_out\n",
      "2016-10-26 16:52:41,051 root         DEBUG    Counting channels\n",
      "2016-10-26 16:52:41,052 root         INFO     Channel count: 4410\n",
      "2016-10-26 16:52:41,052 root         DEBUG    About to append 0 entire chunks plus change\n",
      "2016-10-26 16:52:41,053 root         DEBUG    Chunk start: 0\n",
      "2016-10-26 16:52:48,428 tables       DEBUG    Appending 26583 rows to dataset /sweep_000/synth/23500/pre_out\n",
      "2016-10-26 16:52:50,554 root         DEBUG    234462060 elements written\n",
      "2016-10-26 16:52:50,711 root         INFO     Table merged\n",
      "2016-10-26 16:52:50,712 root         INFO     Merging sweep in /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.4 into /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:52:50,713 root         DEBUG    Appending table /sweep_000/synth/23500/alpha_beta from file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.4 into file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:52:50,722 root         DEBUG    Appending /sweep_000/synth/23500/alpha_beta onto /sweep_000/synth/23500/alpha_beta\n",
      "2016-10-26 16:52:50,723 root         DEBUG    Counting channels\n",
      "2016-10-26 16:52:50,724 root         INFO     Channel count: 2\n",
      "2016-10-26 16:52:50,725 root         DEBUG    About to append 0 entire chunks plus change\n",
      "2016-10-26 16:52:50,726 root         DEBUG    Chunk start: 0\n",
      "2016-10-26 16:52:52,618 tables       DEBUG    Appending 26583 rows to dataset /sweep_000/synth/23500/alpha_beta\n",
      "2016-10-26 16:52:52,828 root         DEBUG    106332 elements written\n",
      "2016-10-26 16:52:52,867 root         DEBUG    Appending table /sweep_000/synth/23500/pre_in from file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.4 into file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:52:52,869 root         DEBUG    Appending /sweep_000/synth/23500/pre_in onto /sweep_000/synth/23500/pre_in\n",
      "2016-10-26 16:52:52,870 root         DEBUG    Counting channels\n",
      "2016-10-26 16:52:52,871 root         INFO     Channel count: 4410\n",
      "2016-10-26 16:52:52,872 root         DEBUG    About to append 0 entire chunks plus change\n",
      "2016-10-26 16:52:52,872 root         DEBUG    Chunk start: 0\n",
      "2016-10-26 16:53:04,118 tables       DEBUG    Appending 26583 rows to dataset /sweep_000/synth/23500/pre_in\n",
      "2016-10-26 16:53:05,609 root         DEBUG    234462060 elements written\n",
      "2016-10-26 16:53:05,744 root         DEBUG    Appending table /sweep_000/synth/23500/pre_out from file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.4 into file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:53:05,745 root         DEBUG    Appending /sweep_000/synth/23500/pre_out onto /sweep_000/synth/23500/pre_out\n",
      "2016-10-26 16:53:05,745 root         DEBUG    Counting channels\n",
      "2016-10-26 16:53:05,746 root         INFO     Channel count: 4410\n",
      "2016-10-26 16:53:05,746 root         DEBUG    About to append 0 entire chunks plus change\n",
      "2016-10-26 16:53:05,747 root         DEBUG    Chunk start: 0\n",
      "2016-10-26 16:53:13,070 tables       DEBUG    Appending 26583 rows to dataset /sweep_000/synth/23500/pre_out\n",
      "2016-10-26 16:53:14,626 root         DEBUG    234462060 elements written\n",
      "2016-10-26 16:53:14,761 root         INFO     Table merged\n",
      "2016-10-26 16:53:14,762 root         INFO     Merging sweep in /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.5 into /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:53:14,763 root         DEBUG    Appending table /sweep_000/synth/23500/alpha_beta from file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.5 into file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:53:14,766 root         DEBUG    Appending /sweep_000/synth/23500/alpha_beta onto /sweep_000/synth/23500/alpha_beta\n",
      "2016-10-26 16:53:14,767 root         DEBUG    Counting channels\n",
      "2016-10-26 16:53:14,767 root         INFO     Channel count: 2\n",
      "2016-10-26 16:53:14,768 root         DEBUG    About to append 0 entire chunks plus change\n",
      "2016-10-26 16:53:14,769 root         DEBUG    Chunk start: 0\n",
      "2016-10-26 16:53:15,061 tables       DEBUG    Appending 26583 rows to dataset /sweep_000/synth/23500/alpha_beta\n",
      "2016-10-26 16:53:15,262 root         DEBUG    106332 elements written\n",
      "2016-10-26 16:53:15,302 root         DEBUG    Appending table /sweep_000/synth/23500/pre_in from file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.5 into file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:53:15,303 root         DEBUG    Appending /sweep_000/synth/23500/pre_in onto /sweep_000/synth/23500/pre_in\n",
      "2016-10-26 16:53:15,304 root         DEBUG    Counting channels\n",
      "2016-10-26 16:53:15,304 root         INFO     Channel count: 4410\n",
      "2016-10-26 16:53:15,305 root         DEBUG    About to append 0 entire chunks plus change\n",
      "2016-10-26 16:53:15,305 root         DEBUG    Chunk start: 0\n",
      "2016-10-26 16:53:26,966 tables       DEBUG    Appending 26583 rows to dataset /sweep_000/synth/23500/pre_in\n",
      "2016-10-26 16:53:29,063 root         DEBUG    234462060 elements written\n",
      "2016-10-26 16:53:29,241 root         DEBUG    Appending table /sweep_000/synth/23500/pre_out from file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5.5 into file /usr/local/experiment/tmp_data/syn_sweeps/finch_000.h5\n",
      "2016-10-26 16:53:29,242 root         DEBUG    Appending /sweep_000/synth/23500/pre_out onto /sweep_000/synth/23500/pre_out\n",
      "2016-10-26 16:53:29,243 root         DEBUG    Counting channels\n",
      "2016-10-26 16:53:29,243 root         INFO     Channel count: 4410\n",
      "2016-10-26 16:53:29,244 root         DEBUG    About to append 0 entire chunks plus change\n",
      "2016-10-26 16:53:29,244 root         DEBUG    Chunk start: 0\n",
      "2016-10-26 16:53:40,188 tables       DEBUG    Appending 26583 rows to dataset /sweep_000/synth/23500/pre_out\n",
      "2016-10-26 16:53:41,755 root         DEBUG    234462060 elements written\n",
      "2016-10-26 16:53:41,897 root         INFO     Table merged\n"
     ]
    }
   ],
   "source": [
    "def merge_sweeps(source_file_path, dest_file_path, sim_pars):\n",
    "    logger.info('Merging sweep in {} into {}'.format(source_file_path, dest_file_path))\n",
    "    for table_name in ['alpha_beta', 'pre_in', 'pre_out']:\n",
    "        table_path = '/{0}/synth/{1}/{2}'.format(sim_pars['sweep_name'], sim_pars['gamma'], table_name)\n",
    "        tables.merge_tables(source_file_path, dest_file_path, table_path)\n",
    "    logger.info('Table merged')\n",
    "\n",
    "def merge_all_sweeps(pars):\n",
    "    logger.info('Merging all sweeps for {}'.format(pars['sweep_name']))\n",
    "    \n",
    "    files_list=glob.glob(os.path.join(pars['folder'], pars['file_name'] + '.*'))\n",
    "    files_list.sort()\n",
    "    logger.info('Found {} sweep files'.format(len(files_list)))\n",
    "    logger.info('Copying first file to {}'.format(pars['file_path']))\n",
    "    shutil.copy2(files_list.pop(0), pars['file_path'])\n",
    "    \n",
    "    for source_file in files_list:\n",
    "        merge_sweeps(source_file, pars['file_path'], pars)\n",
    "\n",
    "#merge_sweeps(parallel_files_list[0], sweep_file_path, sim_pars)\n",
    "\n",
    "merge_all_sweeps(sim_pars)"
   ]
  }
 ],
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