H5file = h5py.File(
filePath, 'r') # 'r' means that hdf5 file is open in read-only mode
#Select the reflectance dataset within the flightline
reflectance = H5file['/Reflectance']
#get plot name
if file.endswith('.h5'):
plot = file[:-3]
#default NDVI bands redBand=53,NIRband=95, redEnd=57, NIRend=99
ndviOut = processNDVI(reflectance)
#write the NDVI out as a geotif
filenameNDVI = ('data/NDVItiff/' + plot + 'NDVI.tif')
writeGeotiff(filenameNDVI, ndviOut, plotBound[plot][0][0],
plotBound[plot][0][2])
#create dictionary of NDVI values for kicks
#NOTE: this is problematic now because of low NDVI values in some plots (senescent grass)
#- might need to look at the lidar as well for this
NDVIdict[plot] = ndviOut
brightestBool = ndviOut > .6
#check to see how many bright pixels are in the tiff
print plot, 'brightpixels: ', (np.count_nonzero(brightestBool))
#delete testing1=reflectance
#to save code, simply apply all non bright pixels (boolean= false) to -999
#not sure how to do the above gracefully
#delete testing=reflectance[:,:,brightestBool] = -999
#open the h5 file
H5file = h5py.File(filePath, 'r') # 'r' means that hdf5 file is open in read-only mode
#Select the reflectance dataset within the flightline
reflectance=H5file['/Reflectance']
#get plot name
if file.endswith('.h5'):
plot = file[:-3]
#default NDVI bands redBand=53,NIRband=95, redEnd=57, NIRend=99
ndviOut=processNDVI(reflectance)
#write the NDVI out as a geotif
filenameNDVI=('data/NDVItiff/' + plot + 'NDVI.tif' )
writeGeotiff(filenameNDVI,ndviOut,plotBound[plot][0][0],plotBound[plot][0][2])
#create dictionary of NDVI values for kicks
#NOTE: this is problematic now because of low NDVI values in some plots (senescent grass)
#- might need to look at the lidar as well for this
NDVIdict[plot]=ndviOut
brightestBool=ndviOut>.6
#check to see how many bright pixels are in the tiff
print plot, 'brightpixels: ', (np.count_nonzero(brightestBool))
#delete testing1=reflectance
#to save code, simply apply all non bright pixels (boolean= false) to -999
#not sure how to do the above gracefully
#delete testing=reflectance[:,:,brightestBool] = -999
