bug in metrics calc

bug.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Using temp dir:/disk/scratch/mhennig/tmp\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/disk/scratch/mhennig/miniconda3/envs/spikesorting/lib/python3.7/site-packages/networkx/classes/reportviews.py:95: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working\n",
      "  from collections import Mapping, Set, Iterable\n"
     ]
    }
   ],
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2\n",
    "\n",
    "import matplotlib.pyplot as plt\n",
    "import numpy as np\n",
    "import time\n",
    "import sys, os\n",
    "import pickle\n",
    "from pathlib import Path\n",
    "import pandas as pd\n",
    "\n",
    "sys.path.insert(0, '../../spikeinterface/spikeextractors/')\n",
    "sys.path.insert(0, '../../spikeinterface/spiketoolkit/')\n",
    "sys.path.insert(0, '../../spikeinterface/spikesorters/')\n",
    "sys.path.insert(0, '../../spikeinterface/spikewidgets/')\n",
    "sys.path.insert(0, '../../spikeinterface/spikemetrics/')\n",
    "sys.path.insert(0, '../../spikeinterface/spikecomparison/')\n",
    "\n",
    "os.environ[\"TMPDIR\"] = \"/disk/scratch/mhennig/tmp\"\n",
    "\n",
    "import spikeextractors as se\n",
    "import spiketoolkit as st\n",
    "import spikesorters as ss\n",
    "import spikecomparison as sc\n",
    "import spikewidgets as sw\n",
    "\n",
    "import tempfile\n",
    "print('Using temp dir:'+tempfile.gettempdir())\n",
    "\n",
    "\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Could not load plane information. Assuming probe is in yz plane\n"
     ]
    }
   ],
   "source": [
    "p = Path('/disk/scratch/mhennig/spikeinterface/paper/MEArec/')\n",
    "study_folder = p / 'study_mearec_SqMEA1015um/'\n",
    "\n",
    "mearec_filename = p / 'recordings_50cells_SqMEA-10-15um_60.0_10.0uV_27-03-2019_13-31-005.h5'\n",
    "\n",
    "# SX_gt = se.MEArecSortingExtractor(mearec_filename)\n",
    "RX = se.MEArecRecordingExtractor(mearec_filename)\n",
    "SX = se.KiloSortSortingExtractor(study_folder/'sorter_folders/rec0/kilosort2/')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "mc = st.validation.MetricCalculator(SX, recording=RX, apply_filter=False, verbose=True,\n",
    "                                    sampling_frequency=RX.get_sampling_frequency())\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "spike_times.shape (26103, 1)\n",
      "spike_times_amps.shape (26103, 1)\n",
      "spike_clusters.shape (26103, 1)\n",
      "spike_clusters_amps.shape (17839,)\n",
      "spike_clusters_pca.shape (17839,)\n"
     ]
    },
    {
     "ename": "IndexError",
     "evalue": "index 19850 is out of bounds for axis 0 with size 17839",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mIndexError\u001b[0m                                Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-5-09372d0116f2>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;31m# fails:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mmc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcompute_all_metric_data\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[0m\u001b[1;32m      3\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0;31m# works:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0;31m#mc.compute_all_metric_data(max_spikes_for_pca=10000, max_spikes_per_unit=10000)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/disk/scratch/mhennig/spikeinterface/spiketoolkit/spiketoolkit/validation/metric_calculator.py\u001b[0m in \u001b[0;36mcompute_all_metric_data\u001b[0;34m(self, recording, n_comp, ms_before, ms_after, dtype, max_spikes_per_unit, amp_method, amp_peak, amp_frames_before, amp_frames_after, recompute_info, max_spikes_for_pca, apply_filter, freq_min, freq_max, save_features_props, seed)\u001b[0m\n\u001b[1;32m    410\u001b[0m             \u001b[0mrecompute_info\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mrecompute_info\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    411\u001b[0m             \u001b[0msave_features_props\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0msave_features_props\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 412\u001b[0;31m             \u001b[0mseed\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mseed\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    413\u001b[0m         )\n\u001b[1;32m    414\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/disk/scratch/mhennig/spikeinterface/spiketoolkit/spiketoolkit/validation/validation_tools.py\u001b[0m in \u001b[0;36mget_all_metric_data\u001b[0;34m(recording, sorting, n_comp, ms_before, ms_after, dtype, amp_method, amp_peak, amp_frames_before, amp_frames_after, max_spikes_per_unit, max_spikes_for_pca, recompute_info, save_features_props, verbose, seed)\u001b[0m\n\u001b[1;32m    245\u001b[0m         \u001b[0mrecompute_info\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mrecompute_info\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    246\u001b[0m         \u001b[0msave_features_props\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0msave_features_props\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 247\u001b[0;31m         verbose=verbose, seed=seed)\n\u001b[0m\u001b[1;32m    248\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    249\u001b[0m     \u001b[0;32mreturn\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msqueeze\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrecording\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mframe_to_time\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mspike_times\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msqueeze\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrecording\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mframe_to_time\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mspike_times_amps\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;31m \u001b[0m\u001b[0;31m\\\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/disk/scratch/mhennig/spikeinterface/spiketoolkit/spiketoolkit/postprocessing/postprocessing_tools.py\u001b[0m in \u001b[0;36m_get_quality_metric_data\u001b[0;34m(recording, sorting, n_comp, ms_before, ms_after, dtype, amp_method, amp_peak, amp_frames_before, amp_frames_after, max_spikes_per_unit, max_spikes_for_pca, recompute_info, save_features_props, verbose, seed)\u001b[0m\n\u001b[1;32m   1073\u001b[0m     \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'spike_clusters_amps.shape'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mspike_clusters_amps\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshape\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1074\u001b[0m     \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'spike_clusters_pca.shape'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mspike_clusters_pca\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshape\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1075\u001b[0;31m     \u001b[0mspike_clusters_amps\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mspike_clusters_amps\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0msorting_idxs_amps\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnewaxis\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mastype\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mint\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1076\u001b[0m     \u001b[0mspike_clusters_pca\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mspike_clusters_pca\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0msorting_idxs_pca\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnewaxis\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mastype\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mint\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1077\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mIndexError\u001b[0m: index 19850 is out of bounds for axis 0 with size 17839"
     ]
    }
   ],
   "source": [
    "# fails:\n",
    "mc.compute_all_metric_data()\n",
    "\n",
    "# works:\n",
    "#mc.compute_all_metric_data(max_spikes_for_pca=10000, max_spikes_per_unit=10000)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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