Add NDVI contrib module

Former-commit-id: 9c1970574c

contrib/ndvi/README.md

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+# NDVI 
+
+This script produces a NDVI raster from a CIR orthophoto (odm_orthophoto.tif in your project)
+
+## Requirements
+* python_gdal package from apt
+* numpy python package (included in ODM build)
+
+## Usage
+```
+ndvi.py [-h] [--overwrite] <orthophoto.tif> N N <outfile.tif>
+
+positional arguments:
+  <orthophoto.tif>  The CIR orthophoto. Must be a GeoTiff.
+  N                 NIR band number
+  N                 Vis band number
+  <outfile.tif>     The output file. Also must be in GeoTiff format
+
+optional arguments:
+  -h, --help        show this help message and exit
+  --overwrite, -o   Will overwrite output file if it exists.
+```
+
+**Argument order matters! NIR first, then VIS**
+
+## Examples:
+Use the [Seneca](https://github.com/OpenDroneMap/odm_data_seneca) dataset for a good working CIR. The band order for that set is NIR-G-B, so you will want to use bands 1 and 2 for this script. After running ODM, the command goes as follows:
+
+`python ndvi.py /path/to/odm_orthophoto.tif 1 2 /path/to/ndvi.tif`
+
+The output in QGIS (with a spectral pseudocolor): ![](http://i.imgur.com/TdLECII.png)

contrib/ndvi/ndvi.py

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+# A script to calculate the NDVI from a color-infrared orthophoto.
+# requires python-gdal
+
+import numpy
+import argparse
+import os.path
+try:
+    from osgeo import gdal
+    from osgeo import osr
+except ImportError:
+    raise ImportError("You need to install python-gdal. run `apt-get install python-gdal`")
+    exit()
+
+
+def parse_args():
+    p = argparse.ArgumentParser("A script that calculates the NDVI of a CIR orthophoto")
+
+    p.add_argument("orthophoto", metavar="<orthophoto.tif>",
+                   type=argparse.FileType('r'),
+                   help="The CIR orthophoto. Must be a GeoTiff.")
+    p.add_argument("nir", metavar="N", type=int,
+                   help="NIR band number")
+    p.add_argument("vis", metavar="N", type=int,
+                   help="Vis band number")
+    p.add_argument("out", metavar="<outfile.tif>",
+                   type=argparse.FileType('w'),
+                   help="The output file. Also must be in GeoTiff format")
+    p.add_argument("--overwrite", "-o",
+                   action='store_true',
+                   default=False,
+                   help="Will overwrite output file if it exists. ")
+    return p.parse_args()
+
+
+def calc_ndvi(nir, vis):
+    """
+    Calculates the NDVI of an orthophoto using nir and vis bands.
+    :param nir: An array containing the nir band
+    :param vis: An array containing the vis band
+    :return: An array that will be exported as a tif
+    """
+
+    # Take the orthophoto and do nir - vis / nir + vis
+    # for each cell, calculate ndvi (masking out where divide by 0)
+    ndvi = numpy.empty(nir.shape, dtype=float)
+    mask = numpy.not_equal((nirb + visb), 0.0)
+    return numpy.choose(mask, (-1.0, numpy.true_divide(numpy.subtract(nirb, visb), numpy.add(nirb, visb))))
+
+
+if __name__ == "__main__":
+
+    rootdir = os.path.dirname(os.path.abspath(__file__))
+
+    # Parse args
+    args = parse_args()
+
+    if not args.overwrite and os.path.isfile(os.path.join(rootdir, args.out.name)):
+        print("File exists, rename or use -o to overwrite.")
+        exit()
+
+    # import raster
+    raster = gdal.Open(args.orthophoto.name)
+    orthophoto = raster.ReadAsArray()
+    # parse out bands
+    nirb = orthophoto[args.nir - 1].astype(float)
+    visb = orthophoto[args.vis - 1].astype(float)
+
+    outfile = args.out
+
+    # Do ndvi calc
+    ndvi = calc_ndvi(nirb, visb)
+
+    # export raster
+    out_driver = gdal.GetDriverByName('GTiff')\
+        .Create(outfile.name, int(ndvi.shape[1]), int(ndvi.shape[0]), 1, gdal.GDT_Float32)
+    outband = out_driver.GetRasterBand(1)
+    outband.WriteArray(ndvi)
+    outcrs = osr.SpatialReference()
+    outcrs.ImportFromWkt(raster.GetProjectionRef())
+    out_driver.SetProjection(outcrs.ExportToWkt())
+    out_driver.SetGeoTransform(raster.GetGeoTransform())
+    outband.FlushCache()