def test_reader(self):
for (dirpath, dirnames, filenames) in os.walk(self.filepath):
print(dirpath)
for f in filenames:
filepath = os.path.join(dirpath, f)
print(filepath)
spec = r.read(filepath)
def setUp(self):
self.c = c.Collection()
self.bbpath = os.path.join(os.path.expanduser("~"),
"data/specdal/Big_Bio_2014/20140611/")
for f in os.listdir(self.bbpath):
spec = r.read(os.path.join(self.bbpath, f))
if spec is not None:
self.c.add_spectrum(spec)
def read(self, filepath, measure_type, verbose=False):
'''
Read measurement from a file.
'''
data, meta = read(filepath, verbose=verbose)
self.metadata = meta
if measure_type == 'pct_reflect' and 'pct_reflect' not in data:
self.measurement = self.get_pct_reflect(data)
return
assert measure_type in data # TODO: handle this
self.measurement = data[measure_type]
args = parser.parse_args()
# make output directory
outdir = os.path.abspath(args.outdir)
figdir = os.path.join(outdir, 'figures')
datadir = os.path.join(outdir, 'data')
for d in (outdir, figdir, datadir):
if not os.path.exists(d):
os.makedirs(d)
################################################################################
# read files
coll = c.Collection()
for f in os.listdir(args.indir):
filepath = os.path.join(args.indir, f)
spec = r.read(filepath)
coll.add_spectrum(spec)
# resample
if args.resampler:
for spec in coll.spectra:
spec = res.resample(spec, method=args.resampler)
# stitch
if args.stitcher:
for spec in coll.spectra:
spec = sti.stitch(spec, method=args.stitcher)
# group by
if args.group_by_separator:
groups = coll.group_by_separator(*args.group_by_separator)