view notebooks/sensitivity_experiment.ipynb @ 15:9847b954c217 branch-tests

added sensitivity experiment

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/mariapanteli/anaconda/lib/python2.7/site-packages/librosa/core/audio.py:33: UserWarning: Could not import scikits.samplerate. Falling back to scipy.signal\n",
      "  warnings.warn('Could not import scikits.samplerate. '\n"
     ]
    }
   ],
   "source": [
    "import numpy as np\n",
    "\n",
    "%matplotlib inline\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "%load_ext autoreload\n",
    "%autoreload 2\n",
    "\n",
    "import sys\n",
    "sys.path.append('../')\n",
    "import scripts.load_dataset as load_dataset\n",
    "import scripts.map_and_average as mapper\n",
    "import scripts.results_classification as results_class\n",
    "import scripts.results as results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "OUTPUT_FILES = ['/import/c4dm-04/mariap/train_data_melodia_'+str(WIN_SIZE)+'.pickle', \n",
    "                '/import/c4dm-04/mariap/val_data_melodia_'+str(WIN_SIZE)+'.pickle', \n",
    "                '/import/c4dm-04/mariap/test_data_melodia_'+str(WIN_SIZE)+'.pickle']\n",
    "n_iters = 10"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "IOError",
     "evalue": "File data/metadata_BLSM_language_all.csv does not exist",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mIOError\u001b[0m                                   Traceback (most recent call last)",
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      "\u001b[0;32m/Users/mariapanteli/Documents/QMUL/Code/MyPythonCode/plosone_underreview/scripts/load_dataset.py\u001b[0m in \u001b[0;36msample_dataset\u001b[0;34m(csv_file)\u001b[0m\n\u001b[1;32m    130\u001b[0m         \u001b[0mThe\u001b[0m \u001b[0mmetadata\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mthe\u001b[0m \u001b[0mselected\u001b[0m \u001b[0msubset\u001b[0m \u001b[0mof\u001b[0m \u001b[0mtracks\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    131\u001b[0m     \"\"\"\n\u001b[0;32m--> 132\u001b[0;31m     \u001b[0mdf\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpd\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread_csv\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcsv_file\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    133\u001b[0m     \u001b[0mdf\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mutil_filter_dataset\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mremove_missing_data\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdf\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    134\u001b[0m     \u001b[0msubset_idx\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msubset_labels\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdf\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'Country'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_values\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[0;32m/Users/mariapanteli/anaconda/lib/python2.7/site-packages/pandas/io/parsers.pyc\u001b[0m in \u001b[0;36mparser_f\u001b[0;34m(filepath_or_buffer, sep, dialect, compression, doublequote, escapechar, quotechar, quoting, skipinitialspace, lineterminator, header, index_col, names, prefix, skiprows, skipfooter, skip_footer, na_values, na_fvalues, true_values, false_values, delimiter, converters, dtype, usecols, engine, delim_whitespace, as_recarray, na_filter, compact_ints, use_unsigned, low_memory, buffer_lines, warn_bad_lines, error_bad_lines, keep_default_na, thousands, comment, decimal, parse_dates, keep_date_col, dayfirst, date_parser, memory_map, float_precision, nrows, iterator, chunksize, verbose, encoding, squeeze, mangle_dupe_cols, tupleize_cols, infer_datetime_format, skip_blank_lines)\u001b[0m\n\u001b[1;32m    463\u001b[0m                     skip_blank_lines=skip_blank_lines)\n\u001b[1;32m    464\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 465\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0m_read\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfilepath_or_buffer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkwds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    466\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    467\u001b[0m     \u001b[0mparser_f\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__name__\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/Users/mariapanteli/anaconda/lib/python2.7/site-packages/pandas/io/parsers.pyc\u001b[0m in \u001b[0;36m_read\u001b[0;34m(filepath_or_buffer, kwds)\u001b[0m\n\u001b[1;32m    239\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    240\u001b[0m     \u001b[0;31m# Create the parser.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 241\u001b[0;31m     \u001b[0mparser\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mTextFileReader\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfilepath_or_buffer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    242\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    243\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mnrows\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mNone\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mchunksize\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/Users/mariapanteli/anaconda/lib/python2.7/site-packages/pandas/io/parsers.pyc\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, f, engine, **kwds)\u001b[0m\n\u001b[1;32m    555\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moptions\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'has_index_names'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkwds\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'has_index_names'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    556\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 557\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_make_engine\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mengine\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    558\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    559\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m_get_options_with_defaults\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mengine\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/Users/mariapanteli/anaconda/lib/python2.7/site-packages/pandas/io/parsers.pyc\u001b[0m in \u001b[0;36m_make_engine\u001b[0;34m(self, engine)\u001b[0m\n\u001b[1;32m    692\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m_make_engine\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mengine\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'c'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    693\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mengine\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'c'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 694\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_engine\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mCParserWrapper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moptions\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    695\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    696\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mengine\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'python'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/Users/mariapanteli/anaconda/lib/python2.7/site-packages/pandas/io/parsers.pyc\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, src, **kwds)\u001b[0m\n\u001b[1;32m   1059\u001b[0m         \u001b[0mkwds\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'allow_leading_cols'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mindex_col\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1060\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1061\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_reader\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_parser\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mTextReader\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msrc\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1062\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1063\u001b[0m         \u001b[0;31m# XXX\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32mpandas/parser.pyx\u001b[0m in \u001b[0;36mpandas.parser.TextReader.__cinit__ (pandas/parser.c:3163)\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mpandas/parser.pyx\u001b[0m in \u001b[0;36mpandas.parser.TextReader._setup_parser_source (pandas/parser.c:5779)\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;31mIOError\u001b[0m: File data/metadata_BLSM_language_all.csv does not exist"
     ]
    }
   ],
   "source": [
    "for n in range(n_iters):\n",
    "    print \"iteration %d\" % n\n",
    "    df = load_dataset.sample_dataset(csv_file=load_dataset.METADATA_FILE)\n",
    "    load_dataset.OUTPUT_FILES = [output_file.split('.pickle')[0]+'_'+str(n)+'.pickle' for \n",
    "                                 output_file in OUTPUT_FILES]\n",
    "    load_dataset.features_for_train_test_sets(df, write_output=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "for n in range(n_iters):\n",
    "    print \"iteration %d\" % n\n",
    "    \n",
    "    print \"mapping...\"\n",
    "    mapper.INPUT_FILES = [output_file.split('.pickle')[0]+'_'+str(n)+'.pickle' for \n",
    "                                 output_file in OUTPUT_FILES]\n",
    "    _, _, ldadata_list, _, _, Y, Yaudio = mapper.lda_map_and_average_frames(min_variance=0.99)\n",
    "    X = np.concatenate(ldadata_list)\n",
    "    \n",
    "    # classification and confusion\n",
    "    print \"classifying...\"\n",
    "    traininds, testinds = results_class.get_train_test_indices()\n",
    "    X_train, Y_train, X_test, Y_test = results_class.get_train_test_sets(X, Y, traininds, testinds)\n",
    "    accuracy, _ = results_class.confusion_matrix(X_train, Y_train, X_test, Y_test, saveCF=False, plots=False)\n",
    "    print accuracy\n",
    "    \n",
    "    # outliers\n",
    "    print \"detecting outliers...\"\n",
    "    ddf = results.load_metadata(Yaudio, metadata_file=load_dataset.METADATA_FILE)\n",
    "    df_global, threshold, MD = get_outliers_df(X, Y, chi2thr=0.999)\n",
    "    print_most_least_outliers_topN(df_global, N=10)\n",
    "    \n",
    "    # write output\n",
    "    print \"writing file\"\n",
    "    df_global.to_csv('../data/outliers_'+str(n)+'.csv', index=False)"
   ]
  }
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