#subtract bias file (bias files are also Infragold calibrated)
for index, file in enumerate(sample_filenames):
#data is stored in dictionary
#define key based on file name
key=file.split('tests/',1)[-1]
key=key.rstrip('raw_.txt')
#store wavelength and reflectance data in key
data[key+'_wavelength']=[]
data[key+'_reflectance']=[]
###########################################################
#comment these next 2 lines out if you are not using bias correction
data_bias[key+'_wavelength']=[]
data_bias[key+'_reflectance']=[]
data_corr[key+'_reflectance']=[]
#obtain Infragold calibrated data
data[key+'_wavelength'], data[key+'_reflectance'] = IR_analysis.calibrate_data(file, IG_filenames[index])
###########################################################
#comment these next lines out if you are not using bias correction
#obtain Infragold calibrated bias files
data_bias[key+'_wavelength'], data_bias[key+'_reflectance'] = IR_analysis.calibrate_data(bias_filenames[index], IG_filenames[index])
#bias correction
data_corr[key+'_reflectance'] = IR_analysis.bias_correct(data[key+'_reflectance'], data_bias[key+'_reflectance'])
print 'finished reading file: ', key
print 'plotting...'
#########################################################
#plot IR spectra
#read all data
#divide data by Infragold file
#subtract bias file (bias files are also Infragold calibrated)
#AOTF IR spectrometer benchtop (2012)
for index, file in enumerate(sample_filenames_H2O_corr):
#data stored in dictionary
#define key based on file name
key=file.split('samples/',1)[-1]
key=key.rstrip('.txt')
#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_H2O_corr(file)
print 'finished reading file: ', key
IR_analysis.write_file(key, data[key+'_wavelength'], data[key+'_reflectance'])
#GSFC AOTF, comma seperated txt files (2012 and later)
for index, file in enumerate(sample_filenames_GSFC_comma):
#data stored in dictionary
#define key based on file name
key=file.split('samples/',1)[-1]
key=key.rstrip('.txt')
#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(file, 1)
print 'finished reading file: ', key
