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Added some functionalities at reading .sig files #19

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9210ae8
Added functionality for extract latitude and longitude of .sig files
sergiobellido Apr 8, 2022
ba7b583
Added functinality for extract errors of reference and target in each…
sergiobellido Apr 20, 2022
8888dcf
Delete venv directory
sergiobellido Apr 26, 2022
6283b7a
Delete .idea directory
sergiobellido Apr 26, 2022
3101b04
Update README.rst
sergiobellido Apr 26, 2022
81794b5
Update README.rst
sergiobellido Apr 27, 2022
d4cc346
Clean comments code for pull request
sergiobellido Apr 27, 2022
e56cbd3
Merge branch 'master' of github.com:sergiobellido/SpecDAL
sergiobellido Apr 27, 2022
ca3375c
Added changes for extract radiance of every spectral data in the Coll…
sergiobellido May 11, 2022
f0acc38
Added functionality for apply operators(stitch, jump and interpolate)…
sergiobellido May 26, 2022
b374418
Translation of comments
sergiobellido May 26, 2022
1db67ea
Added all metadata available in .sig files.
sergiobellido Oct 4, 2022
cfb0354
Add units for irradiance measurements
jajberni Oct 7, 2022
ff20e96
Prevent FutureWarning: reindexing with a non-unique Index is deprecat…
jajberni Oct 11, 2022
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4 changes: 4 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -6,3 +6,7 @@ __pycache__*
/*.egg-info
*.ipynb_checkpoints*
/_build/
/venv/
.idea
SBJ-specdal_test.py

69 changes: 65 additions & 4 deletions specdal/containers/collection.py
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Original file line number Diff line number Diff line change
Expand Up @@ -107,10 +107,11 @@ class Collection(object):
"""
Represents a dataset consisting of a collection of spectra
"""
def __init__(self, name, directory=None, spectra=None,
def __init__(self, name, directory=None, spectra=None, spectra_radiance=None,
measure_type='pct_reflect', metadata=None, flags=None):
self.name = name
self.spectra = spectra
self.spectra_radiance = spectra_radiance
self.measure_type = measure_type
self.metadata = metadata
self.flags = flags
Expand All @@ -122,6 +123,12 @@ def spectra(self):
A list of Spectrum objects in the collection
"""
return list(self._spectra.values())
@property
def spectra_radiance(self):
"""
A list of Spectrum objects in the collection
"""
return list(self._spectra_radiance.values())


@property
Expand All @@ -136,6 +143,16 @@ def spectra(self, value):
for spectrum in value:
assert spectrum.name not in self._spectra
self._spectra[spectrum.name] = spectrum

@spectra_radiance.setter
def spectra_radiance(self, value):
self._spectra_radiance = OrderedDict()
if value is not None:
# assume value is an iterable such as list
for spectrum in value:
assert spectrum.name not in self._spectra_radiance
self._spectra_radiance[spectrum.name] = spectrum

@property
def flags(self):
"""
Expand Down Expand Up @@ -204,6 +221,26 @@ def data(self):
print("Unexpected exception occurred")
raise e

@property
def radiance(self):
'''
Get measurements as a Pandas.DataFrame
'''
try:
self._check_uniform_wavelengths()
objs = [s.measurement for s in self.spectra_radiance]
keys = [s.name for s in self.spectra_radiance]
return pd.concat(objs=objs, keys=keys, axis=1)
except pd.core.indexes.base.InvalidIndexError as err:
# typically from duplicate index due to overlapping wavelengths
if not all([s.stitched for s in self.spectra_radiance]):
logging.warning('{}: Try after stitching the overlaps'.format(err))
raise err
except Exception as e:
print("Unexpected exception occurred")
raise e


def _unflagged_data(self):
try:
spectra = [s for s in self.spectra if not s.name in self.flags]
Expand All @@ -226,6 +263,15 @@ def append(self, spectrum):
assert spectrum.name not in self._spectra
assert isinstance(spectrum, Spectrum)
self._spectra[spectrum.name] = spectrum


def append_radiance(self, spectrum_radiance):
"""
insert spectrum with radiance to the collection
"""
assert spectrum_radiance.name not in self._spectra_radiance
assert isinstance(spectrum_radiance, Spectrum)
self._spectra_radiance[spectrum_radiance.name] = spectrum_radiance

def data_with_meta(self, data=True, fields=None):
"""
Expand All @@ -247,9 +293,11 @@ def data_with_meta(self, data=True, fields=None):

"""
if fields is None:
fields = ['file', 'instrument_type', 'integration_time',
'measurement_type', 'gps_time_tgt', 'gps_time_ref',
'wavelength_range']
fields = []
for s in self.spectra:
for key in s.metadata.keys():
if key not in fields:
fields.append(key)
meta_dict = {}
for field in fields:
meta_dict[field] = [s.metadata[field] if field in s.metadata
Expand Down Expand Up @@ -317,17 +365,30 @@ def interpolate(self, spacing=1, method='slinear'):
def stitch(self, method='max'):
'''
'''
#Stitch reflectance
for spectrum in self.spectra:
try:
spectrum.stitch(method)
except Exception as e:
logging.error("Error occurred while stitching {}".format(spectrum.name))
raise e
# Stitch radiance
for spectrum_rad in self.spectra_radiance:
try:
spectrum_rad.stitch(method)
except Exception as e:
logging.error("Error occurred while stitching {}".format(spectrum_rad.name))

raise e
def jump_correct(self, splices, reference, method='additive'):
'''
'''
#Jump correct reflectance
for spectrum in self.spectra:
spectrum.jump_correct(splices, reference, method)
# Jump correct radiance
for spectrum_rad in self.spectra_radiance:
spectrum_rad.jump_correct(splices, reference, method)
##################################################
# group operations
def groupby(self, separator, indices, filler=None):
Expand Down
6 changes: 4 additions & 2 deletions specdal/containers/spectrum.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,13 +36,15 @@ class Spectrum(object):
pandas.Series with index named: "wavelength".

"""
def __init__(self, name=None, filepath=None, measurement=None,
measure_type='pct_reflect', metadata=None,
def __init__(self, measure_type=None, name=None, filepath=None, measurement=None,
metadata=None,
interpolated=False, stitched=False, jump_corrected=False,
verbose=False):
if name is None:
assert filepath is not None
name = os.path.splitext(os.path.basename(filepath))[0]
if measure_type is None:
measure_type = 'pct_reflect'
self.name = name
self.measurement = measurement
self.measure_type = measure_type
Expand Down
6 changes: 3 additions & 3 deletions specdal/operators/interpolate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,9 +42,9 @@ def interpolate(series, spacing=1, method='slinear'):
for seq in get_monotonic_series(series):
int_index = np.round(seq.index)
# fill in gaps at 1 nm wavelength
int_index = int_index.reindex(np.arange(int_index.min(),
int_index.max() + 1,
spacing))[0]
int_index = pd.Index(np.arange(int_index.min(),
int_index.max() + 1,
spacing))
tmp_index = seq.index.union(int_index)
seq = seq.reindex(tmp_index)
# interpolate
Expand Down
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