def _expand_corrections(ifgs, dm, params, ncoef, offsets):
"""
Convenience func returns model converted to data points.
dm: design matrix (do not filter/remove nan cells)
params: model parameters array from pinv() * dm
ncoef: number of model coefficients (2 planar, 5 quadratic)
offsets: True/False to calculate correction with offsets
"""
# NB: cannot work on singular ifgs due to date ID id/indexing requirement
date_ids = get_date_ids(ifgs)
corrections = []
for ifg in ifgs:
jbm = date_ids[ifg.master] * ncoef # starting row index for master
jbs = date_ids[ifg.slave] * ncoef # row start for slave
par = params[jbs:jbs + ncoef] - params[jbm:jbm + ncoef]
# estimate orbital correction effects
# corresponds to "fullorb = B*parm + offset" in orbfwd.m
cor = dm.dot(par).reshape(ifg.phase_data.shape)
if offsets:
off = np.ravel(ifg.phase_data - cor)
# bring all ifgs to same base level
cor -= nanmedian(off)
corrections.append(cor)
return corrections
def _est_ref_phs_method1(phase_data, comp):
"""
Convenience function for ref phs estimate method 1 parallelisation
"""
ifgv = np.ravel(phase_data, order='F')
ifgv[comp == 1] = np.nan
return nanmedian(ifgv)
def alt_orbital_correction(self, ifg, deg, offset):
data = ifg.phase_data.reshape(ifg.num_cells)
dm = get_design_matrix(ifg, deg, offset)[~isnan(data)]
fd = data[~isnan(data)].reshape((dm.shape[0], 1))
dmt = dm.T
invNbb = inv(dmt.dot(dm))
orbparams = invNbb.dot(dmt.dot(fd))
alt_params = lstsq(dm, fd)[0]
# FIXME: precision
assert_array_almost_equal(orbparams, alt_params, decimal=2)
dm2 = get_design_matrix(ifg, deg, offset)
if offset:
fullorb = np.reshape(np.dot(dm2[:, :-1], orbparams[:-1]),
ifg.phase_data.shape)
else:
fullorb = np.reshape(np.dot(dm2, orbparams), ifg.phase_data.shape)
offset_removal = nanmedian(
np.reshape(ifg.phase_data - fullorb, (1, -1)))
fwd_correction = fullorb - offset_removal
# ifg.phase_data -= (fullorb - offset_removal)
return ifg.phase_data - fwd_correction
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):
"""
remove network orbital error from input interferograms
"""
orb = dm.dot(coefs[ids[ifg.slave]] - coefs[ids[ifg.master]])
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
# set orbfit meta tag and save phase to file
_save_orbital_error_corrected_phase(ifg)
def _est_ref_phs_method2(phase_data, half_chip_size, refpx, refpy, thresh):
"""
Convenience function for ref phs estimate method 2 parallelisation
"""
patch = phase_data[refpy - half_chip_size:refpy + half_chip_size + 1,
refpx - half_chip_size:refpx + half_chip_size + 1]
patch = np.reshape(patch, newshape=(-1, 1), order='F')
nanfrac = np.sum(~np.isnan(patch))
if nanfrac < thresh:
raise ReferencePhaseError('The data window at the reference pixel '
'does not have enough valid observations. '
'Actual = {}, Threshold = {}.'.format(
nanfrac, thresh))
ref_ph = nanmedian(patch)
return ref_ph
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 _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, degree, offset, 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
"""
ifg = shared.Ifg(ifg) if isinstance(ifg, str) else ifg
if not ifg.is_open:
ifg.open()
shared.nan_and_mm_convert(ifg, params)
# 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)
offset_removal = nanmedian(np.ravel(ifg.phase_data - fullorb))
# subtract orbital error from the ifg
ifg.phase_data -= (fullorb - offset_removal)
# set orbfit meta tag and save phase to file
_save_orbital_error_corrected_phase(ifg)
if ifg.open():
ifg.close()
def __orb_correction(fullres_dm,
mlooked_dm,
fullres_phase,
mlooked_phase,
offset=False):
"""
Function to perform the inversion to obtain orbital model parameters
and return the orbital correction as the full resolution forward model.
"""
# perform inversion using pseudoinverse of DM
orbparams = __orb_inversion(mlooked_dm, mlooked_phase)
# compute forward model at full resolution
fullorb = reshape(dot(fullres_dm, orbparams), fullres_phase.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:
offset_removal = nanmedian(np.ravel(fullres_phase - fullorb))
else:
offset_removal = 0
orbital_correction = fullorb - offset_removal
return orbital_correction
