def process_directory(params):
#parameters for processing
input_dir = params["input_directory"]
ws = params["subset_wavelength_range"][0]
we = params["subset_wavelength_range"][1]
#read the spectrums
extension = {'asd': 1, 'ASD': 1}
spec_files = [os.path.join(input_dir, f) for f in os.listdir(input_dir)
if get_extension(f) in extension]
raw_specs = [SdalReader().read_spectrum(f) for f in spec_files]
if len(raw_specs) == 0: return
print("Data directory: {}".format(input_dir))
print(" Read {} {} files".format(len(raw_specs), extension))
#perform jump correction
jumpcorrector = JumpCorrector(params["jumpcorrection_wavelengths"],
params["jumpcorrection_stablezone"])
jc_specs = [jumpcorrector.correct(s) for s in raw_specs]
print(" Jump corrected {} spectrums(s)".format(len(jc_specs)))
#separate into green vegetation and non-green vegetation spectra
gvd = GreenVegDetector()
raw_white_specs, raw_target_specs = [], []
jc_white_specs, jc_target_specs = [], []
ndvis, reflectance_ranges = [], []
for (raw, jc) in zip(raw_specs, jc_specs):
(status, ndvi, reflectance_range) = gvd.is_green_vegetation(jc)
ndvis.append(ndvi)
reflectance_ranges.append(reflectance_range)
if status:
raw_target_specs.append(raw)
jc_target_specs.append(jc)
else:
raw_white_specs.append(raw)
jc_white_specs.append(jc)
print(" # white spectra: {}".format(len(jc_white_specs)))
print(" # target spectra: {}".format(len(jc_target_specs)))
#subset to desired wavelength range
#do this for the jc_target_specs only
proc_target_specs = [s.wavelength_subset(ws, we) for s in jc_target_specs]
print(" Subsetted spectra to range: {}, {}".format(ws, we))
#create SpectrumGroup object for raw_target_specs
raw_target_sg = SpectrumGroup()
raw_target_sg.group(raw_target_specs, "raw_target")
raw_target_sg.save_dataframe(input_dir)
raw_target_sg.save_plots(input_dir)
#create SpectrumGroup object for raw_white_specs
raw_white_sg = SpectrumGroup()
raw_white_sg.group(raw_white_specs, "raw_white")
raw_white_sg.save_dataframe(input_dir)
raw_white_sg.save_plots(input_dir)
#create SpectrumGroup object for proc_target_specs
proc_target_sg = SpectrumGroup()
proc_target_sg.group(proc_target_specs, "proc_target")
proc_target_sg.save_dataframe(input_dir)
proc_target_sg.save_plots(input_dir)
def process_directory(params):
#parameters for processing
input_dir = params["input_directory"]
ws = params["subset_wavelength_range"][0]
we = params["subset_wavelength_range"][1]
#read the spectrums
extension = {'asd': 1, 'ASD': 1}
spec_files = [
os.path.join(input_dir, f) for f in os.listdir(input_dir)
if get_extension(f) in extension
]
raw_specs = [SdalReader().read_spectrum(f) for f in spec_files]
if len(raw_specs) == 0: return
print("Data directory: {}".format(input_dir))
print(" Read {} {} files".format(len(raw_specs), extension))
#perform jump correction
jumpcorrector = JumpCorrector(params["jumpcorrection_wavelengths"],
params["jumpcorrection_stablezone"])
jc_specs = [jumpcorrector.correct(s) for s in raw_specs]
print(" Jump corrected {} spectrums(s)".format(len(jc_specs)))
#separate into green vegetation and non-green vegetation spectra
gvd = GreenVegDetector()
raw_white_specs, raw_target_specs = [], []
jc_white_specs, jc_target_specs = [], []
ndvis, reflectance_ranges = [], []
for (raw, jc) in zip(raw_specs, jc_specs):
(status, ndvi, reflectance_range) = gvd.is_green_vegetation(jc)
ndvis.append(ndvi)
reflectance_ranges.append(reflectance_range)
if status:
raw_target_specs.append(raw)
jc_target_specs.append(jc)
else:
raw_white_specs.append(raw)
jc_white_specs.append(jc)
print(" # white spectra: {}".format(len(jc_white_specs)))
print(" # target spectra: {}".format(len(jc_target_specs)))
#subset to desired wavelength range
#do this for the jc_target_specs only
proc_target_specs = [s.wavelength_subset(ws, we) for s in jc_target_specs]
print(" Subsetted spectra to range: {}, {}".format(ws, we))
#create SpectrumGroup object for raw_target_specs
raw_target_sg = SpectrumGroup()
raw_target_sg.group(raw_target_specs, "raw_target")
raw_target_sg.save_dataframe(input_dir)
raw_target_sg.save_plots(input_dir)
#create SpectrumGroup object for raw_white_specs
raw_white_sg = SpectrumGroup()
raw_white_sg.group(raw_white_specs, "raw_white")
raw_white_sg.save_dataframe(input_dir)
raw_white_sg.save_plots(input_dir)
#create SpectrumGroup object for proc_target_specs
proc_target_sg = SpectrumGroup()
proc_target_sg.group(proc_target_specs, "proc_target")
proc_target_sg.save_dataframe(input_dir)
proc_target_sg.save_plots(input_dir)
