#obtain Infragold calibrated data
data[key+'_wavelength'], data[key+'_reflectance'] = IR_analysis.calibrate_data_PASA_lite(file, IG_filenames_PASA_lite[index])
print 'finished reading file: ', key
IR_analysis.write_file(key, data[key+'_wavelength'], data[key+'_reflectance'])
#asc files downloaded from USGS spectral library
for index, file in enumerate(sample_filenames_USGS):
#data stored in dictionary
#define key based on file name
key=file.split('samples/',1)[-1]
key=key.rstrip('.asc')
#store wavelength and reflectance data in key
data[key+'_wavelength']=[]
data[key+'_reflectance']=[]
#obtain Infragold calibrated data
data[key+'_wavelength'], data[key+'_reflectance'] = IR_analysis.calibrate_data_USGS(file)
print 'finished reading file: ', key
IR_analysis.write_file(key, data[key+'_wavelength'], data[key+'_reflectance'])
print 'plotting...'
#example of a single spectrum plot
#(wavelength, reflectance, xrange, title, save file, smoothing integer)
#Goethite
IR_plot.plot_IR_spectrum(np.array(data['Geothite_avg_Corrected_Results_wavelength']), np.array(data['Geothite_avg_Corrected_Results_reflectance']), [1.6,3.6], '', 'output/Goethite.png', 2)
#example of multiple spectra (2) plot
#([wavelength1, wavelength2, ...], [reflectance1, reflectance2, ...], xrange, title, save file, legend, smoothing integer)
IR_plot.plot_IR_spectra([np.array(data['gypsum_vacuum_1_day_wavelength']), np.array(data['gypsum_vacuum_5days_wavelength'])], [np.array(data['gypsum_vacuum_1_day_reflectance']), np.array(data['gypsum_vacuum_5days_reflectance'])], [1.6,3.6], ' ', 'output/gypsum_vacuum_comparison.png', ['1 day in vacuum', '5 days in vacuum'], 2)
#epsomite
