def test_orb_error(self, orbfit_method, orbfit_degrees):
self.params[cf.ORBITAL_FIT_METHOD] = orbfit_method
self.params[cf.ORBITAL_FIT_DEGREE] = orbfit_degrees
multi_paths = self.params[cf.INTERFEROGRAM_FILES]
self.ifg_paths = [p.tmp_sampled_path for p in multi_paths]
remove_orbital_error(self.ifg_paths, self.params)
# test_orb_errors_written
orb_error_files = [MultiplePaths.orb_error_path(i, self.params) for i in self.ifg_paths]
assert all(p.exists() for p in orb_error_files)
last_mod_times = np.array([os.stat(o).st_mtime for o in orb_error_files])
# run orbit removal again
remove_orbital_error(self.ifg_paths, self.params)
orb_error_files2 = [MultiplePaths.orb_error_path(i, self.params) for i in self.ifg_paths]
# if files are written again - times will change
last_mod_times_2 = np.array([os.stat(o).st_mtime for o in orb_error_files2])
# test_orb_error_reused_if_params_unchanged
assert all(a == b for a, b in zip(last_mod_times, last_mod_times_2))
# change one of the params
_degrees = set(cf.ORB_DEGREE_NAMES.keys())
_degrees.discard(orbfit_degrees)
# test_orb_errors_recalculated_if_params_change
self.params[cf.ORBITAL_FIT_DEGREE] = _degrees.pop()
remove_orbital_error(self.ifg_paths, self.params)
orb_error_files3 = [MultiplePaths.orb_error_path(i, self.params) for i in self.ifg_paths]
last_mod_times_3 = np.array([os.stat(o).st_mtime for o in orb_error_files3])
assert all(a != b for a, b in zip(last_mod_times, last_mod_times_3))
def independent_orbital_correction(ifg, params):
"""
Calculates and removes an orbital error surface from a single independent
interferogram.
Warning: This will write orbital error corrected phase_data to the ifg.
:param Ifg class instance ifg: the interferogram to be corrected
:param str degree: model to fit (PLANAR / QUADRATIC / PART_CUBIC)
:param bool offset: True to calculate the model using an offset
:param dict params: dictionary of configuration parameters
:return: None - interferogram phase data is updated and saved to disk
"""
degree = params[cf.ORBITAL_FIT_DEGREE]
offset = params[cf.ORBFIT_OFFSET]
orbfit_correction_on_disc = MultiplePaths.orb_error_path(
ifg.data_path, params)
if not ifg.is_open:
ifg.open()
shared.nan_and_mm_convert(ifg, params)
if orbfit_correction_on_disc.exists():
log.info(
f'Reusing already computed orbital fit correction for {ifg.data_path}'
)
orbital_correction = np.load(file=orbfit_correction_on_disc)
else:
# vectorise, keeping NODATA
vphase = reshape(ifg.phase_data, ifg.num_cells)
dm = get_design_matrix(ifg, degree, offset)
# filter NaNs out before getting model
clean_dm = dm[~isnan(vphase)]
data = vphase[~isnan(vphase)]
model = lstsq(clean_dm, data)[0] # first arg is the model params
# calculate forward model & morph back to 2D
if offset:
fullorb = np.reshape(np.dot(dm[:, :-1], model[:-1]),
ifg.phase_data.shape)
else:
fullorb = np.reshape(np.dot(dm, model), ifg.phase_data.shape)
if not orbfit_correction_on_disc.parent.exists():
shared.mkdir_p(orbfit_correction_on_disc.parent)
offset_removal = nanmedian(np.ravel(ifg.phase_data - fullorb))
orbital_correction = fullorb - offset_removal
# dump to disc
np.save(file=orbfit_correction_on_disc, arr=orbital_correction)
# subtract orbital error from the ifg
ifg.phase_data -= orbital_correction
# set orbfit meta tag and save phase to file
_save_orbital_error_corrected_phase(ifg)
ifg.close()
def _remove_network_orb_error(coefs, dm, ifg, ids, offset, params):
"""
remove network orbital error from input interferograms
"""
saved_orb_err_path = MultiplePaths.orb_error_path(ifg.data_path, params)
orb = dm.dot(coefs[ids[ifg.second]] - coefs[ids[ifg.first]])
orb = orb.reshape(ifg.shape)
# offset estimation
if offset:
# bring all ifgs to same base level
orb -= nanmedian(np.ravel(ifg.phase_data - orb))
# subtract orbital error from the ifg
ifg.phase_data -= orb
# save orb error on disc
np.save(file=saved_orb_err_path, arr=orb)
# set orbfit meta tag and save phase to file
_save_orbital_error_corrected_phase(ifg)
def __check_and_apply_orberrors_found_on_disc(ifg_paths, params):
saved_orb_err_paths = [
MultiplePaths.orb_error_path(ifg_path, params)
for ifg_path in ifg_paths
]
for p, i in zip(saved_orb_err_paths, ifg_paths):
if p.exists():
orb = np.load(p)
if isinstance(i, str):
# are paths
ifg = Ifg(i)
ifg.open(readonly=False)
shared.nan_and_mm_convert(ifg, params)
else:
ifg = i
ifg.phase_data -= orb
# set orbfit meta tag and save phase to file
_save_orbital_error_corrected_phase(ifg)
return all(p.exists() for p in saved_orb_err_paths)
def _remove_network_orb_error(coefs, dm, ifg, ids, offset, params):
"""
remove network orbital error from input interferograms
"""
saved_orb_err_path = MultiplePaths.orb_error_path(ifg.data_path, params)
orb = dm.dot(coefs[ids[ifg.second]] - coefs[ids[ifg.first]])
orb = orb.reshape(ifg.shape)
# Estimate the offset of the interferogram as the median of ifg minus model
# Only needed if reference phase correction has already been applied?
if offset:
# brings all ifgs to same reference level
orb -= nanmedian(np.ravel(ifg.phase_data - orb))
# subtract orbital error from the ifg
ifg.phase_data -= orb
# save orb error on disc
np.save(file=saved_orb_err_path, arr=orb)
# set orbfit meta tag and save phase to file
_save_orbital_error_corrected_phase(ifg, params)
def independent_orbital_correction(ifg_path, params):
"""
Calculates and removes an orbital error surface from a single independent
interferogram.
Warning: This will write orbital error corrected phase_data to the ifg.
:param Ifg class instance ifg: the interferogram to be corrected
:param dict params: dictionary of configuration parameters
:return: None - interferogram phase data is updated and saved to disk
"""
log.debug(f"Orbital correction of {ifg_path}")
degree = params[C.ORBITAL_FIT_DEGREE]
offset = params[C.ORBFIT_OFFSET]
intercept = params[C.ORBFIT_INTERCEPT]
xlooks = params[C.ORBITAL_FIT_LOOKS_X]
ylooks = params[C.ORBITAL_FIT_LOOKS_Y]
ifg0 = shared.Ifg(ifg_path) if isinstance(ifg_path, str) else ifg_path
# get full-resolution design matrix
fullres_dm = get_design_matrix(ifg0, degree, intercept=intercept)
ifg = shared.dem_or_ifg(ifg_path) if isinstance(ifg_path,
str) else ifg_path
multi_path = MultiplePaths(ifg.data_path, params)
orb_on_disc = MultiplePaths.orb_error_path(ifg.data_path, params)
if not ifg.is_open:
ifg.open()
shared.nan_and_mm_convert(ifg, params)
fullres_ifg = ifg # keep a backup
fullres_phase = fullres_ifg.phase_data
if orb_on_disc.exists():
log.info(
f'Reusing already computed orbital fit correction: {orb_on_disc}')
orbital_correction = np.load(file=orb_on_disc)
else:
# Multi-look the ifg data if either X or Y is greater than 1
if (xlooks > 1) or (ylooks > 1):
exts, _, _ = __extents_from_params(params)
mlooked = _create_mlooked_dataset(multi_path, ifg.data_path, exts,
params)
ifg = Ifg(mlooked) # multi-looked Ifg object
ifg.initialize()
shared.nan_and_mm_convert(ifg, params)
# vectorise phase data, keeping NODATA
vphase = reshape(ifg.phase_data, ifg.num_cells)
# compute design matrix for multi-looked data
mlooked_dm = get_design_matrix(ifg, degree, intercept=intercept)
# invert to obtain the correction image (forward model) at full-res
orbital_correction = __orb_correction(fullres_dm,
mlooked_dm,
fullres_phase,
vphase,
offset=offset)
# save correction to disc
if not orb_on_disc.parent.exists():
shared.mkdir_p(orb_on_disc.parent)
np.save(file=orb_on_disc, arr=orbital_correction)
# subtract orbital correction from the full-res ifg
fullres_ifg.phase_data -= orbital_correction
# set orbfit meta tag and save phase to file
_save_orbital_error_corrected_phase(fullres_ifg, params)
