doc/source/notebooks/Statistics.ipynb

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   "source": [
    "# Statistics\n",
    "\n",
    "This notebook shows show the do some basic statistics on Neuropixels `ChannelMap` and its blueprint."
   ]
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   "source": [
    "## Number of selected electrodes\n",
    "\n",
    "For a channelmap"
   ]
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   "source": [
    "from neurocarto.probe_npx import ChannelMap\n",
    "\n",
    "chmap = ChannelMap(24)\n",
    "len(chmap) # empty map"
   ]
  },
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   "source": [
    "chmap.add_electrode((0,0,0))\n",
    "len(chmap)"
   ]
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    "For a blueprint"
   ]
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   "source": [
    "from neurocarto.probe_npx import NpxProbeDesp\n",
    "\n",
    "D = NpxProbeDesp()\n",
    "\n",
    "# all electrodes, chmap here used as a probe type reference, we do not use its content inside.\n",
    "blueprint = D.all_electrodes(chmap)\n",
    "len([e for e in blueprint if e.state == D.STATE_USED])"
   ]
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   "source": [
    "# Get selected electrodes\n",
    "# This function will read the content of chmap\n",
    "len(D.all_channels(chmap))"
   ]
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   "source": [
    "## Number of electrode set with full-density category"
   ]
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   "source": [
    "blueprint = D.load_blueprint('Fig3_example.blueprint.npy', chmap)\n",
    "\n",
    "len([e for e in blueprint if e.category == D.CATE_FULL])"
   ]
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   "source": [
    "## Area Efficiency\n",
    "\n",
    "we define the area efficiency $Aeff$ of a given blueprint $Q$ and its outcomes channel map $S$ as\n",
    "\n",
    "$Aeff(S|Q) = \\cfrac{selected(S|Q)}{request(Q)}$, $0$ if $request(Q)=0$ \n",
    "\n",
    "Where $selected$ and $request$ are defined below:"
   ]
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    "def selected(S, Q):\n",
    "    \"\"\"How many electrodes are selected in density-category.\"\"\"\n",
    "    # we do not use S here, because Q contains the selecting information.\n",
    "    v1 = len([e for e in Q if e.state == D.STATE_USED and e.category == D.CATE_SET])\n",
    "    v2 = len([e for e in Q if e.state == D.STATE_USED and e.category == D.CATE_FULL])\n",
    "    v3 = len([e for e in Q if e.state == D.STATE_USED and e.category == D.CATE_HALF])\n",
    "    v4 = len([e for e in Q if e.state == D.STATE_USED and e.category == D.CATE_QUARTER])\n",
    "    return v1 + v2 + v3 + v4\n",
    "\n",
    "def request(Q):\n",
    "    \"\"\"How many electrodes are requested in density-category.\"\"\"\n",
    "    v1 = len([e for e in Q if e.category == D.CATE_SET])\n",
    "    v2 = len([e for e in Q if e.category == D.CATE_FULL])\n",
    "    v3 = len([e for e in Q if e.category == D.CATE_HALF])\n",
    "    v4 = len([e for e in Q if e.category == D.CATE_QUARTER])\n",
    "    return v1 + v2 + v3/2 + v4/4"
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   "source": [
    "When $Aeff < 1$ , it means area are not well used on average. When $Aeff > 1$ , it means area are over-used on average."
   ]
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   "source": [
    "## Channel Efficiency\n",
    "\n",
    "We define the channel efficiency $Ceff$ of a given blueprint $Q$ and its outcomes channel map $S$ as\n",
    "\n",
    "$Ceff(S|Q) = min \\{ Aeff(S|Q), \\cfrac{1}{Aeff(S|Q)} \\}$, $0$ if $Aeff(S|Q) = 0$"
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   "source": [
    "We define the channel efficiency $Ceff$ of a blueprint $Q$ as\n",
    "\n",
    "$Ceff(Q) = max \\{ Ceff(S|Q) | S \\in \\mathcal{S} \\}$\n",
    "\n",
    "where $\\mathcal{S}$ is all possible outcomes from the given blueprint $Q$."
   ]
  }
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