def plot_init_map(ax, d_v, inps, metadata):
# prepare data
if inps.wrap:
if inps.disp_unit_v == 'radian':
d_v *= inps.range2phase
d_v = ut.wrap(d_v, wrap_range=inps.wrap_range)
# Title and Axis Label
disp_date = inps.dates[inps.init_idx].strftime('%Y-%m-%d')
inps.fig_title = 'N = {}, Time = {}'.format(inps.init_idx, disp_date)
# Initial Pixel
if inps.yx and inps.yx != inps.ref_yx:
inps.pts_yx = np.array(inps.yx).reshape(-1, 2)
if inps.lalo:
inps.pts_lalo = np.array(inps.lalo).reshape(-1, 2)
else:
inps.pts_lalo = None
inps.pts_marker = 'ro'
# call view.py to plot
ax, inps, im, cbar = view.plot_slice(ax, d_v, metadata, inps)
return ax, im
def get_nonzero_phase_closure(ifgram_file,
out_file=None,
thres=0.1,
unwDatasetName='unwrapPhase'):
"""Calculate/Read number of non-zero phase closure
Parameters: ifgram_file : string, path of ifgram stack file
out_file : string, path of num non-zero phase closure file
Returns: num_nonzero_closure : 2D np.array in size of (length, width)
"""
if not out_file:
out_file = 'numNonzeroPhaseClosure_{}.h5'.format(unwDatasetName)
if os.path.isfile(out_file) and readfile.read_attribute(out_file):
print('1. read number of nonzero phase closure from file: {}'.format(
out_file))
num_nonzero_closure = readfile.read(out_file)[0]
else:
obj = ifgramStack(ifgram_file)
obj.open(print_msg=False)
length, width = obj.length, obj.width
ref_phase = obj.get_reference_phase(unwDatasetName=unwDatasetName,
dropIfgram=False)
C = obj.get_design_matrix4triplet(
obj.get_date12_list(dropIfgram=False))
# calculate phase closure line by line to save memory usage
num_nonzero_closure = np.zeros((length, width), np.float32)
print(
'1. calculating phase closure of all pixels from dataset - {} ...'.
format(unwDatasetName))
line_step = 10
num_loop = int(np.ceil(length / line_step))
prog_bar = ptime.progressBar(maxValue=num_loop)
for i in range(num_loop):
# read phase
i0, i1 = i * line_step, min(length, (i + 1) * line_step)
box = (0, i0, width, i1)
pha_data = ifginv.read_unwrap_phase(obj,
box,
ref_phase,
unwDatasetName=unwDatasetName,
dropIfgram=False,
print_msg=False)
# calculate phase closure
pha_closure = np.dot(C, pha_data)
pha_closure = np.abs(pha_closure - ut.wrap(pha_closure))
# get number of non-zero phase closure
num_nonzero = np.sum(pha_closure >= thres, axis=0)
num_nonzero_closure[i0:i1, :] = num_nonzero.reshape(i1 - i0, width)
prog_bar.update(i + 1,
every=1,
suffix='{}/{} lines'.format((i + 1) * line_step,
length))
prog_bar.close()
atr = dict(obj.metadata)
atr['FILE_TYPE'] = 'mask'
atr['UNIT'] = 1
writefile.write(num_nonzero_closure, out_file=out_file, metadata=atr)
return num_nonzero_closure
def update_time_slider(val):
"""Update Displacement Map using Slider"""
idx = np.argmin(np.abs(np.array(inps.yearList) - tslider.val))
disp_date = inps.dates[idx].strftime('%Y-%m-%d')
ax_v.set_title('N = {n}, Time = {t}'.format(n=idx, t=disp_date))
d_v = np.array(ts_data[0][idx, :, :])
if inps.wrap:
if inps.disp_unit_v == 'radian':
d_v *= inps.range2phase
d_v = ut.wrap(d_v, wrap_range=inps.wrap_range)
im.set_data(d_v)
fig_v.canvas.draw()
def correct_unwrap_error(ifgram, C, Dconstraint=True, thres=0.1, alpha=0.25, rcond=1e-5):
"""Estimate unwrapping error from a stack of unwrapped interferometric phase
Parameters: ifgram : 2D np.array in size of (num_ifgram, num_pixel) of unwrap phase
C : 2D np.array in size of (num_triangle, num_ifgram) triangle design matrix
Dconstraint : bool, apply zero phase jump constraint on ifgrams without unwrapping error.
This is disabled in fast option
thres : float, threshold of non-zero phase closure beyond which indicates unwrap error
alpha : float, Tikhonov factor, regularization parameter
rcond : float, cut-off value for least square estimation
Returns: ifgram_cor : 2D np.array in size of (num_ifgram, num_pixel) of unwrap phase after correction
U : 2D np.array in size of (num_ifgram, num_pixel) of phase jump integer
Example: ifgram_cor, U = estimate_unwrap_error(ifgram, C)
"""
num_tri, num_ifgram = C.shape
ifgram = ifgram.reshape(num_ifgram, -1)
U = np.zeros(ifgram.shape, np.float32)
I = np.eye(num_ifgram, dtype=np.float32)
A = np.vstack((C, alpha*I))
# Use Tikhonov regularization (alpha*D0) to solve equation in ill-posed scenario:
# e.g.: network is not dense enough AND a lot of unwrapping error exist,
# then A.shape[0] < A.shape[1]: number of unknown > number of observations
if Dconstraint:
# get D
# 1. calculate phase closure for all ifgram triangles --> identy those with unwrap error
# 2. identy ifgrams involved in at least 1 triangle with unwrap error
# 3. get D for ifgram 'without any unwrap error' or 'correctly unwrapped'
pha_closure = np.dot(C, ifgram)
pha_closure = np.abs(pha_closure - ut.wrap(pha_closure))
idx_nonzero_closure = (pha_closure >= thres).flatten()
idx_err_ifgram = np.sum(C[idx_nonzero_closure, :] != 0., axis=0) >= 1.
D = I[~idx_err_ifgram, :]
A = np.vstack((A, D))
# Eq 4.4 (Fattahi, 2015)
try:
A_inv = linalg.pinv2(A, rcond=rcond)
L = np.zeros((A.shape[0], ifgram.shape[1]), np.float32)
L[0:num_tri, :] = np.dot(C, ifgram) / (-2.*np.pi)
U = np.round(np.dot(A_inv, L))
except linalg.LinAlgError:
pass
ifgram_cor = ifgram + 2*np.pi*U
return ifgram_cor, U
def update_time_slider(self, val):
"""Update Displacement Map using Slider"""
idx = np.argmin(np.abs(np.array(self.yearList) - self.tslider.val))
# update title
disp_date = self.dates[idx].strftime('%Y-%m-%d')
self.ax_img.set_title('N = {n}, Time = {t}'.format(n=idx, t=disp_date), fontsize=self.font_size)
# read data
data_img = np.array(self.ts_data[0][idx, :, :])
data_img[self.mask == 0] = np.nan
if self.wrap:
if self.disp_unit_img == 'radian':
data_img *= self.range2phase
data_img = ut.wrap(data_img, wrap_range=self.wrap_range)
# update data
self.img.set_data(data_img)
self.fig_img.canvas.draw()
return
def plot_init_image(self, img_data):
# prepare data
if self.wrap:
if self.disp_unit_img == 'radian':
img_data *= self.range2phase
img_data = ut.wrap(img_data, wrap_range=self.wrap_range)
# Title and Axis Label
disp_date = self.dates[self.init_idx].strftime('%Y-%m-%d')
self.fig_title = 'N = {}, Time = {}'.format(self.init_idx, disp_date)
# Initial Pixel
if self.yx and self.yx != self.ref_yx:
self.pts_yx = np.array(self.yx).reshape(-1, 2)
if self.lalo:
self.pts_lalo = np.array(self.lalo).reshape(-1, 2)
else:
self.pts_lalo = None
# call view.py to plot
self.img, self.cbar_img = view.plot_slice(self.ax_img, img_data, self.atr, self)[2:4]
return self.img, self.cbar_img
def get_common_region_int_ambiguity(ifgram_file,
cc_mask_file,
water_mask_file=None,
num_sample=100,
dsNameIn='unwrapPhase'):
"""Solve the phase unwrapping integer ambiguity for the common regions among all interferograms
Parameters: ifgram_file : str, path of interferogram stack file
cc_mask_file : str, path of common connected components file
water_mask_file : str, path of water mask file
num_sample : int, number of pixel sampled for each region
dsNameIn : str, dataset name of the unwrap phase to be corrected
Returns: common_regions : list of skimage.measure._regionprops._RegionProperties object
modified by adding two more variables:
sample_coords : 2D np.ndarray in size of (num_sample, 2) in int64 format
int_ambiguity : 1D np.ndarray in size of (num_ifgram,) in int format
"""
print('-' * 50)
print(
'calculating the integer ambiguity for the common regions defined in',
cc_mask_file)
# stack info
stack_obj = ifgramStack(ifgram_file)
stack_obj.open()
date12_list = stack_obj.get_date12_list(dropIfgram=True)
num_ifgram = len(date12_list)
C = matrix(
ifgramStack.get_design_matrix4triplet(date12_list).astype(float))
ref_phase = stack_obj.get_reference_phase(unwDatasetName=dsNameIn,
dropIfgram=True).reshape(
num_ifgram, -1)
# prepare common label
print('read common mask from', cc_mask_file)
cc_mask = readfile.read(cc_mask_file)[0]
if water_mask_file is not None and os.path.isfile(water_mask_file):
water_mask = readfile.read(water_mask_file)[0]
print('refine common mask based on water mask file', water_mask_file)
cc_mask[water_mask == 0] = 0
label_img, num_label = connectComponent.get_large_label(cc_mask,
min_area=2.5e3,
print_msg=True)
common_regions = measure.regionprops(label_img)
print('number of common regions:', num_label)
# add sample_coords / int_ambiguity
print('number of samples per region:', num_sample)
print('solving the phase-unwrapping integer ambiguity for {}'.format(
dsNameIn))
print(
'\tbased on the closure phase of interferograms triplets (Yunjun et al., 2019)'
)
print(
'\tusing the L1-norm regularzed least squares approximation (LASSO) ...'
)
for i in range(num_label):
common_reg = common_regions[i]
# sample_coords
idx = sorted(
np.random.choice(common_reg.area, num_sample, replace=False))
common_reg.sample_coords = common_reg.coords[idx, :].astype(int)
# solve for int_ambiguity
U = np.zeros((num_ifgram, num_sample))
if common_reg.label == label_img[stack_obj.refY, stack_obj.refX]:
print('{}/{} skip calculation for the reference region'.format(
i + 1, num_label))
else:
prog_bar = ptime.progressBar(maxValue=num_sample,
prefix='{}/{}'.format(
i + 1, num_label))
for j in range(num_sample):
# read unwrap phase
y, x = common_reg.sample_coords[j, :]
unw = ifginv.read_unwrap_phase(stack_obj,
box=(x, y, x + 1, y + 1),
ref_phase=ref_phase,
unwDatasetName=dsNameIn,
dropIfgram=True,
print_msg=False).reshape(
num_ifgram, -1)
# calculate closure_int
closure_pha = np.dot(C, unw)
closure_int = matrix(
np.round(
(closure_pha - ut.wrap(closure_pha)) / (2. * np.pi)))
# solve for U
U[:, j] = np.round(
l1regls(-C, closure_int, alpha=1e-2,
show_progress=0)).flatten()
prog_bar.update(j + 1, every=5)
prog_bar.close()
# add int_ambiguity
common_reg.int_ambiguity = np.median(U, axis=1)
common_reg.date12_list = date12_list
#sort regions by size to facilitate the region matching later
common_regions.sort(key=lambda x: x.area, reverse=True)
# plot sample result
fig_size = pp.auto_figure_size(label_img.shape, disp_cbar=False)
fig, ax = plt.subplots(figsize=fig_size)
ax.imshow(label_img, cmap='jet')
for common_reg in common_regions:
ax.plot(common_reg.sample_coords[:, 1],
common_reg.sample_coords[:, 0],
'k.',
ms=2)
pp.auto_flip_direction(stack_obj.metadata, ax, print_msg=False)
out_img = 'common_region_sample.png'
fig.savefig(out_img, bbox_inches='tight', transparent=True, dpi=300)
print('saved common regions and sample pixels to file', out_img)
return common_regions
def run_unwrap_error_patch(ifgram_file, box=None, mask_file=None, ref_phase=None, fast_mode=False,
thres=0.1, dsNameIn='unwrapPhase'):
"""Estimate/Correct unwrapping error in ifgram stack on area defined by box.
Parameters: ifgram_file : string, ifgramStack file
box : tuple of 4 int, indicating areas to be read and analyzed
mask_file : string, file name of mask file for pixels to be analyzed
ref_pahse : 1D np.array in size of (num_ifgram,) phase value on reference pixel, because:
1) phase value stored in pysar is not reference yet
2) reference point may be out of box definition
fast_mode : bool, apply zero jump constraint on ifgrams without unwrapping error.
thres : float, threshold of non-zero phase closure to be identified as unwrapping error.
Returns: pha_data : 3D np.array in size of (num_ifgram_all, box[3]-box[2], box[2]-box[0]),
unwrapped phase value after error correction
"""
# Basic info
stack_obj = ifgramStack(ifgram_file)
stack_obj.open(print_msg=False)
num_ifgram = stack_obj.numIfgram
# Size Info - Patch
if box:
num_row = box[3] - box[1]
num_col = box[2] - box[0]
else:
num_row = stack_obj.length
num_col = stack_obj.width
num_pixel = num_row * num_col
C = stack_obj.get_design_matrix4ifgram_triangle(dropIfgram=True)
print('number of interferograms: {}'.format(C.shape[1]))
print('number of triangles: {}'.format(C.shape[0]))
# read unwrapPhase
pha_data_all = ifginv.read_unwrap_phase(stack_obj, box, ref_phase,
unwDatasetName=dsNameIn,
dropIfgram=False)
pha_data = np.array(pha_data_all[stack_obj.dropIfgram, :])
# mask of pixels to analyze
mask = np.ones((num_pixel), np.bool_)
print('number of pixels read: {}'.format(num_pixel))
# mask 1. mask of water or area of interest
if mask_file:
dsNames = readfile.get_dataset_list(mask_file)
dsName = [i for i in dsNames if i in ['waterMask', 'mask']][0]
waterMask = readfile.read(mask_file, datasetName=dsName, box=box)[0].flatten()
mask *= np.array(waterMask, np.bool_)
del waterMask
print('number of pixels left after mask: {}'.format(np.sum(mask)))
# mask 2. mask of pixels without unwrap error: : zero phase closure on all triangles
print('calculating phase closure of all possible triangles ...')
pha_closure = np.dot(C, pha_data)
pha_closure = np.abs(pha_closure - ut.wrap(pha_closure)) # Eq 4.2 (Fattahi, 2015)
num_nonzero_closure = np.sum(pha_closure >= thres, axis=0)
mask *= (num_nonzero_closure != 0.)
del pha_closure
print('number of pixels left after checking phase closure: {}'.format(np.sum(mask)))
# mask summary
num_pixel2proc = int(np.sum(mask))
if num_pixel2proc > 0:
ifgram = pha_data[:, mask]
ifgram_cor = np.array(ifgram, np.float32)
print('number of pixels to process: {} out of {} ({:.2f}%)'.format(num_pixel2proc, num_pixel,
num_pixel2proc/num_pixel*100))
# correcting unwrap error based on phase closure
print('correcting unwrapping error ...')
if fast_mode:
ifgram_cor = correct_unwrap_error(ifgram, C, Dconstraint=False)[0]
else:
prog_bar = ptime.progressBar(maxValue=num_pixel2proc)
for i in range(num_pixel2proc):
ifgram_cor[:, i] = correct_unwrap_error(ifgram[:, i], C, Dconstraint=True)[0].flatten()
prog_bar.update(i+1, every=10, suffix='{}/{}'.format(i+1, num_pixel2proc))
prog_bar.close()
pha_data[:, mask] = ifgram_cor
pha_data_all[stack_obj.dropIfgram, :] = pha_data
pha_data_all = pha_data_all.reshape(num_ifgram, num_row, num_col)
num_nonzero_closure = num_nonzero_closure.reshape(num_row, num_col)
return pha_data_all, num_nonzero_closure