issueswithspikerecovery.ipynb

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    "% some housekeeping stuff\n",
    "register_graphics_toolkit(\"gnuplot\");\n",
    "available_graphics_toolkits();\n",
    "graphics_toolkit(\"gnuplot\")\n",
    "clear\n",
    "% end of housekeeping"
   ]
  },
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    "%plot -s 600,500 -f 'svg'\n",
    "% start by showing the \"true\" instrument response.\n",
    "\n",
    "slope = 0.02;  conc=0:1:100;\n",
    "\n",
    "response = slope*conc;\n",
    "\n",
    "plot(conc,response,'k','linewidth',2)\n",
    "set(gca,'linewidth',2)\n",
    "xlabel('conc'); ylabel('response')\n"
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   "execution_count": 33,
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   "source": [
    "%plot -s 600,500 -f 'svg'\n",
    "%now prepare 4 calibration samples with -20% error\n",
    "%so response corresponds to solutions with lower concentration then\n",
    "%our targets\n",
    "\n",
    "targetconc=[0 20 60 90];\n",
    "trueconc=0.8*targetconc; % 20% too low\n",
    "\n",
    "calibresponse = slope*trueconc;\n",
    "\n",
    "plot(conc,response,'k','linewidth',2)\n",
    "set(gca,'linewidth',2)\n",
    "xlabel('conc'); ylabel('response')\n",
    "hold on\n",
    "plot(targetconc,calibresponse,'ko','markersize',4,'markerfacecolor','b')\n",
    "\n",
    "% fit that line\n",
    "param=polyfit(targetconc,calibresponse,1); fit=polyval(param,conc);\n",
    "biasslope=param(1);  \n",
    "plot(conc,fit,'k--','linewidth',2)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
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   "source": [
    "%plot -s 600,500 -f 'svg'\n",
    "% now a spike. use 80.  let's see if we get back what we thought\n",
    "\n",
    "spiketarget=80; spiketrue=0.8*spiketarget;  Rspike=slope*spiketrue;\n",
    "\n",
    "plot(conc,response,'k','linewidth',2)\n",
    "set(gca,'linewidth',2)\n",
    "xlabel('conc'); ylabel('response')\n",
    "hold on\n",
    "plot(conc,fit,'k--','linewidth',2)\n",
    "plot(targetconc,calibresponse,'ko','markersize',4,'markerfacecolor','b')\n",
    "plot([spiketarget spiketarget],[0 Rspike],'r--','linewidth',2)\n",
    "plot([0 spiketarget],[Rspike Rspike],'r--','linewidth',2)\n",
    "\n",
    "% recover the known value.  think everythign is fine.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [
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      "text/plain": [
       "<IPython.core.display.SVG object>"
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     },
     "metadata": {},
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   ],
   "source": [
    "%plot -s 600,500 -f 'svg'\n",
    "%now run a known sample that is 40.  what do we recover.\n",
    "\n",
    "SRM=40; RSRM=slope*SRM;\n",
    "biasconcSRM=RSRM/biasslope;\n",
    "\n",
    "plot(conc,response,'k','linewidth',2)\n",
    "set(gca,'linewidth',2)\n",
    "xlabel('conc'); ylabel('response')\n",
    "hold on\n",
    "plot(conc,fit,'k--','linewidth',2)\n",
    "plot(targetconc,calibresponse,'ko','markersize',4,'markerfacecolor','b')\n",
    "plot([spiketarget spiketarget],[0 Rspike],'r--','linewidth',2)\n",
    "plot([0 spiketarget],[Rspike Rspike],'r--','linewidth',2)\n",
    "plot([biasconcSRM biasconcSRM],[0 RSRM],'b--','linewidth',2)\n",
    "plot([0 biasconcSRM],[RSRM RSRM],'b--','linewidth',2)\n",
    "plot([SRM SRM],[0 RSRM],'g--','linewidth',2)\n",
    "axis([0 100 0 2])\n"
   ]
  }
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