notebooks/InstallationTest.ipynb

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    "# 1-2-3 INSTALLATION TEST\n",
    "\n",
    "Questions or Comments? Find the answer on our github Issues page or Raise an New Issue: [https://github.com/EarthBigData/openSAR/issues](https://github.com/EarthBigData/openSAR/issues)\n",
    "\n",
    "### 1. Provide the path where your unzipped **data/test** folder resides\n",
    "\n",
    "    **IMPORTANT: In WINDOWS all '\\' need to be replaced with '/' in your path!!!**\n",
    "    e.g. C:/PATH/TO/MY/TESTDATA"
   ]
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   "source": [
    "datapath=\"/mnt/s/github/public/openSAR/data/testdata\"          "
   ]
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    "### 2. Start the Jupyter Notebook server as per instructions and open this notebook\n",
    "\n",
    "### 3. Run this Notebook\n",
    "\n",
    "See if you have a correct installation by selecting\n",
    "\n",
    "    > Kernel > Change Kernel > Python[conda env:ebd]\n",
    "    (other Kernels might be ok too)\n",
    "    \n",
    "    > Cell > Run All\n",
    "    \n",
    "### If you don't see any errors and see an image at the bottom, everything is successfully installed. \n",
    "### Your result should look similar to this [output](http://nbviewer.jupyter.org/github/EarthBigData/openSAR/blob/master/notebooks/notebookviews/html/InstallationTest.html)"
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    "\n",
    "# TEST SECTION\n",
    "\n",
    "## Python package import"
   ]
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    "# Generic\n",
    "import os\n",
    "\n",
    "# Data Analysis packages\n",
    "import pandas as pd\n",
    "from osgeo import gdal\n",
    "import numpy as np\n",
    "import skimage\n",
    "\n",
    "# Plotting packages\n",
    "# MATPLOTLIB\n",
    "%matplotlib inline\n",
    "import matplotlib.pylab as plt\n",
    "\n",
    "# BOKEH\n",
    "import bokeh.plotting as bplt\n",
    "import bokeh.resources\n",
    "bplt.output_notebook(resources=bokeh.resources.INLINE)"
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   "source": [
    "## Test Data Import"
   ]
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   "source": [
    "**Set the data path and filename**"
   ]
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   "source": [
    "datefile ='S32631X402380Y1491460sS1_A_vh_mtfil.dates'\n",
    "imagefile='S32631X402380Y1491460sS1_A_vh_mtfil.vrt'\n",
    "os.chdir(datapath)"
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   "source": [
    "### Time series indices"
   ]
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   "source": [
    "# Get the date indices via pandas\n",
    "dates=open(datefile,\"r\").readlines()\n",
    "tindex=pd.DatetimeIndex(dates)\n",
    "tindex"
   ]
  },
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   "source": [
    "### Image data"
   ]
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    "img=gdal.Open(imagefile)\n",
    "rasterDN=img.ReadAsArray()\n",
    "rasterdB=20.*np.log10(rasterDN)-83\n",
    "ts=pd.Series(rasterdB[:,20,5],index=tindex)\n",
    "ts.index.name='Date'"
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   "source": [
    "## Matplotlib Time Series Plot"
   ]
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    "ax=ts.plot(figsize=(16,4))\n",
    "ax.set_title('Time Series Sentinel-1 C-VH backscatter, Niamay Example')\n",
    "_=ax.set_ylabel('$\\gamma^o$ [dB]')   # Matplotlib accepts Latex Style typesetting\n"
   ]
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    "## Bokeh Time Series Plot - Interactive"
   ]
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    "source=pd.DataFrame(ts)\n",
    "source.columns=['gamma0']\n",
    "p = bplt.figure(x_axis_type=\"datetime\", plot_width=800, plot_height=350,title='Time Series Sentinel-1 C-VH backscatter, Niamay Example')\n",
    "p.line('Date','gamma0',source=source)\n",
    "p.xaxis.axis_label='Date'\n",
    "p.yaxis.axis_label='γᵒ [dB]'   # To get the symbols in text for bokeh use Unicode directly with \\gamma<TAB>\\^o<TAB> (python3)\n",
    "\n",
    "bplt.show(p)"
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   "source": [
    "## Matplotlib Image Plot"
   ]
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    "fig,ax = plt.subplots(figsize=(8,8))\n",
    "ax.axis('off')\n",
    "ax.imshow(rasterdB[0],cmap='gray')\n",
    "_=ax.set_title('Niamey Example, Sentinel-1 C-vh '+ str(tindex[0].date()))"
   ]
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