def test(testsdir, verbose = False):
idir = os.path.join(testsdir, "input")
statuses = []
testcount = 0
testcount = testcount + 1
fs = sorted(os.listdir(idir))
fps = [os.path.join(idir, f) for f in fs]
ins = [SdalReader().read_spectrum(f) for f in fps]
reqdet = [False]*len(ins)
reqdet[0] = True
reqdet[12:15] = [True, True, True]
refdet = ReferenceDetector(context = "gveg")
det = [refdet.is_reference(s) for s in ins]
statuses.append(reqdet == det)
if not all(statuses):
print("Failed TEST {}".format(testcount))
#status message
if all(statuses):
print("{}: PASSED".format(__file__))
else:
print("{}: FAILED".format(__file__))
def test(testsdir, verbose=False):
idir = os.path.join(testsdir, "input")
statuses = []
testcount = 0
testcount = testcount + 1
fs = sorted(os.listdir(idir))
fps = [os.path.join(idir, f) for f in fs]
ins = [SdalReader().read_spectrum(f) for f in fps]
reqdet = [False] * len(ins)
reqdet[0] = True
reqdet[12:15] = [True, True, True]
refdet = ReferenceDetector(context="gveg")
det = [refdet.is_reference(s) for s in ins]
statuses.append(reqdet == det)
if not all(statuses):
print("Failed TEST {}".format(testcount))
#status message
if all(statuses):
print("{}: PASSED".format(__file__))
else:
print("{}: FAILED".format(__file__))
def process(params):
# params.print_params()
#get the project params and verify
project = params.get_params("project")
if project:
verify_project(project)
else:
print("--project is required")
sys.exit(0)
#get the resampling params
resampling = params.get_params("resampling")
#get the jumpcorrection params and verify
jumpcorrection = params.get_params("jumpcorrection")
if jumpcorrection:
verify_jumpcorrection(jumpcorrection)
#get the groupings and verify them
groupings = {grp:params.get_params(grp) for grp in params.get_groups()}
verify_groupings(params.default_group, params.get_groups(), groupings)
tags = ["raw", params.default_group]
specs = defaultdict(list)
#specs["raw"] created
#get the filenames
allfiles = os.listdir(project["indir"])
extfiles = []
for f in allfiles:
ext = get_directory_filename_extension(f)[2]
if ext == project["fileext"]:
extfiles.append(os.path.join(project["indir"], f))
#read the raw spectrums
uniquifier = WaveUniquifier()
rawspecs = [SdalReader().read_spectrum(f) for f in extfiles]
uniqspecs = [uniquifier.uniquify(s) for s in rawspecs]
specs["raw"] = uniqspecs
#specs["preproc"] created
#do the pre-processing
prepspecs = specs["raw"]
if resampling:
resampler = WaveResampler(rstype = resampling["type"],
wavestart = resampling["range"][0],
wavestop = resampling["range"][1],
spacing = resampling["spacing"])
rsspecs = [resampler.resample(s) for s in prepspecs]
prepspecs = rsspecs
if jumpcorrection:
corrector = JumpCorrector(jumpcorrection["wavelengths"],
jumpcorrection["stablezone"])
jcspecs = [corrector.correct(s) for s in prepspecs]
prepspecs = jcspecs
#detect the references
refdet = ReferenceDetector(context = "gveg")
nonrefs = []
refs = []
for s in prepspecs:
if refdet.is_reference(s):
refs.append(s)
else:
nonrefs.append(s)
specs[params.default_group] = nonrefs
#specs[group_tag] created
#do the grouping
for t in groupings:
tags.append(t)
itag = groupings[t]["intag"]
patt = groupings[t]["pattern"]
regex = SpectrumRegex()
tgrps = regex.make_groups(specs[itag], patt)
for tg in tgrps:
sg = SpectrumGroup(spectrums = tgrps[tg])
ms = sg.mean_spectrum()
ms.idstr = tg
specs[t].append(ms)
# subsets = {grp:params.get_params(grp) for grp in params.get_subsets()}
# print(subsets)
# for t in subsets:
# itag = subsets[t]["intag"]
# otag = subsets[t]["outtag"]
# wavestart = subsets[t]["range"][0]
# wavestop = subsets[t]["range"][1]
# for s in specs[itag]:
# subspec = s.wavelength_subset(wavestart, wavestop)
# subspec.idstr = subspec.idstr + otag
# print("idstr = {}".format(subspec.idstr))
# specs[otag].append(subspec)
#create outputs
prjdir = os.path.join(project["outdir"], project["name"])
os.mkdir(prjdir)
for t in specs:
tdir = os.path.join(prjdir, t)
os.mkdir(tdir)
tgrpfn = "___{}___.csv".format(t)
for s in specs[t]:
s.write_csv(odir = tdir)
sg = SpectrumGroup(spectrums = specs[t])
sg.write_csv(tdir, tgrpfn)
