def extract_features(fname,
file_type,
path_out,
baseline,
substance,
sample=None):
"""
Process the s06av95a_envi file and extract the <substance> and/or <sample>
features according to the <baseline> value.
"""
print('Running extract_features')
if file_type == 'ENVI': rd = spectro.EnviReader(fname)
if file_type == 'JSON': rd = spectro.JSONReader(fname)
lib = spectro.USGS06SpecLib(rd)
wvl = lib.get_wvl()
for spectrum, sample_id, descrip, idx in lib.get_substance(
substance, sample):
fea = spectro.FeaturesConvexHullQuotient(spectrum,
wvl,
baseline=baseline)
plot_name = '{0}_{1}'.format(substance, sample_id)
fea.plot_convex_hull_quotient(path_out, plot_name)
fea.plot(path_out, plot_name, feature='all')
#fea.plot(path_out, plot_name, feature=10)
fea.print_stats('all')
def search_biotite(lib_name, file_type, biotite, dist):
"""
"""
if file_type == 'ENVI': rd = spectro.EnviReader(lib_name)
if file_type == 'JSON': rd = spectro.JSONReader(lib_name)
lib = spectro.USGS06SpecLib(rd)
match_spectrum, where = lib.distance_match(biotite, distfn=dist)
return where
def get_biotite_WS660(lib_name, file_type):
"""
"""
if file_type == 'ENVI': rd = spectro.EnviReader(lib_name)
if file_type == 'JSON': rd = spectro.JSONReader(lib_name)
lib = spectro.USGS06SpecLib(rd)
for spectrum, sample_id, descrip, idx in lib.get_substance('Biotite', 'WS660'):
return spectrum, idx
def get_random_n_endmembers(fname, file_type, n):
import random
if file_type == 'ENVI': rd = spectro.EnviReader(fname)
if file_type == 'JSON': rd = spectro.JSONReader(fname)
lib = spectro.USGS06SpecLib(rd)
dim = lib.get_dim()
idx = random.sample(list(range(dim)), n)
# 224 is the number of bands
U = np.zeros((224, n), dtype=np.float)
for i, j in enumerate(idx):
U[:,i] = lib.get(j)
# the USGS library sometimes have very small numbers that create numeric
# instability, normalize get rid of them
return util.normalize(U)
def batch_usgs_spec_plot(fname, file_type, path_out):
"""
Process the s06av95a_envi file and plot for each spectrum the spectrum,
the convex hull and the convex hull quotient.
"""
print('Running batch_usgs_spec_plot')
if file_type == 'ENVI': rd = spectro.EnviReader(fname)
if file_type == 'JSON': rd = spectro.JSONReader(fname)
lib = spectro.USGS06SpecLib(rd)
wvl = lib.get_wvl()
for spectrum, mineral, sample_id, descrip, idx in lib.get_next():
schq = spectro.SpectrumConvexHullQuotient(spectrum, wvl)
plot_name = '{0}_{1}_{2}'.format(idx, mineral, sample_id)
schq.plot(path_out, plot_name)
def __init__(self, lib_name):
rd = spectro.EnviReader(lib_name)
self.lib = spectro.USGS06SpecLib(rd)