SI_quantify_950eV_offset_Cu_Ga_Ge_As_AlK.ipynb

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   "cell_type": "code",
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   "source": [
    "import hyperspy.api as hp\n",
    "%matplotlib qt5"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:hyperspy.signal:<EELSSpectrum, title: EELS Spectrum Image disp1offset950, dimensions: (43, 92|1024)> data is replaced by its optimized copy\n"
     ]
    }
   ],
   "source": [
    "s = hp.load('/Users/veersaysit/Desktop/EELS data/Ge-basedSolarCell_24082015/EELS Spectrum Image disp1offset950time2s.dm3')"
   ]
  },
  {
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   "execution_count": 18,
   "metadata": {
    "collapsed": true
   },
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  },
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   "execution_count": 28,
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   ],
   "source": [
    "s_Cu = s.remove_background(signal_range=(891.,929.)).isig[931.:1031.].integrate1D(axis=\"Energy loss\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [],
   "source": [
    "#roi = hp.roi.SpanROI(left=931, right=10)\n",
    "#s.plot()\n",
    "#roi.add_widget(s, axes=[\"Energy loss\"])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "#s_Cu = s.isig[roi].integrate1D(axis=\"Energy loss\")\n",
    "s_Cu.plot()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:hyperspy.signal:<EELSSpectrum, title: EELS Spectrum Image disp1offset950, dimensions: (43, 92|1024)> data is replaced by its optimized copy\n"
     ]
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   ],
   "source": [
    "s = hp.load('/Users/veersaysit/Desktop/EELS data/Ge-basedSolarCell_24082015/EELS Spectrum Image disp1offset950time2s.dm3')\n",
    "s_Ga = s.remove_background(signal_range=(1023.,1113.)).isig[1115.:1217.].integrate1D(axis=\"Energy loss\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
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   "outputs": [
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     "data": {
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      ]
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     "execution_count": 20,
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   ],
   "source": [
    "#roi_Ga = hp.roi.SpanROI(left=1115, right=1315)\n",
    "#s.plot()\n",
    "#roi_Ga.add_widget(s, axes=[\"Energy loss\"])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:hyperspy.signal:<EELSSpectrum, title: EELS Spectrum Image disp1offset950, dimensions: (43, 92|1024)> data is replaced by its optimized copy\n"
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   ],
   "source": [
    "s = hp.load('/Users/veersaysit/Desktop/EELS data/Ge-basedSolarCell_24082015/EELS Spectrum Image disp1offset950time2s.dm3')\n",
    "s_Ge = s.remove_background(signal_range=(1166.,1215.)).isig[1217.:1323.].integrate1D(axis=\"Energy loss\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
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     "execution_count": 30,
     "metadata": {},
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   ],
   "source": [
    "#roi_As = hp.roi.SpanROI(left=1323, right=1600)\n",
    "#s.plot()\n",
    "#roi_As.add_widget(s, axes=[\"Energy loss\"])"
   ]
  },
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   "cell_type": "code",
   "execution_count": 34,
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   "outputs": [
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     "text": [
      "/Applications/anaconda/lib/python3.6/site-packages/hyperspy/_components/power_law.py:131: RuntimeWarning: invalid value encountered in log\n",
      "  r = 2 * log(I1 / I2) / log(x2 / x1)\n"
     ]
    },
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   ],
   "source": [
    "s_As = s.remove_background(signal_range=(1270.,1321.)).isig[1323.:1560.].integrate1D(axis=\"Energy loss\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Applications/anaconda/lib/python3.6/site-packages/hyperspy/_components/power_law.py:131: RuntimeWarning: invalid value encountered in log\n",
      "  r = 2 * log(I1 / I2) / log(x2 / x1)\n"
     ]
    },
    {
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   ],
   "source": [
    "s_AlK = s.remove_background(signal_range=(1441.,1558.)).isig[1560.:1660.].integrate1D(axis=\"Energy loss\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import scipy.io as sio\n",
    "sio.savemat(\"Cu_hspy\",{\"Cu_hspy\":s_Cu.data})\n",
    "sio.savemat(\"Ga_hspy\",{\"Ga_hspy\":s_Ga.data})\n",
    "sio.savemat(\"Ge_hspy\",{\"Ge_hspy\":s_Ge.data})\n",
    "sio.savemat(\"As_hspy\",{\"As_hspy\":s_As.data})\n",
    "sio.savemat(\"AlK_hspy\",{\"AlK_hspy\":s_AlK.data})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
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