def get_los_geometry(self, insar_obj, print_msg=False):
lat, lon = self.get_stat_lat_lon(print_msg=print_msg)
# get LOS geometry
if isinstance(insar_obj, str):
# geometry file
atr = readfile.read_attribute(insar_obj)
coord = ut.coordinate(atr, lookup_file=insar_obj)
y, x = coord.geo2radar(lat, lon, print_msg=print_msg)[0:2]
box = (x, y, x + 1, y + 1)
inc_angle = readfile.read(insar_obj,
datasetName='incidenceAngle',
box=box,
print_msg=print_msg)[0][0, 0]
az_angle = readfile.read(insar_obj,
datasetName='azimuthAngle',
box=box,
print_msg=print_msg)[0][0, 0]
head_angle = ut.azimuth2heading_angle(az_angle)
elif isinstance(insar_obj, dict):
# use mean inc/head_angle from metadata
inc_angle = ut.incidence_angle(insar_obj,
dimension=0,
print_msg=print_msg)
head_angle = float(insar_obj['HEADING'])
# for old reading of los.rdr band2 data into headingAngle directly
if (head_angle + 180.) > 45.:
head_angle = ut.azimuth2heading_angle(head_angle)
else:
raise ValueError(
'input insar_obj is neight str nor dict: {}'.format(insar_obj))
return inc_angle, head_angle
def read_timeseries_yx(y, x, ts_file, lookup_file=None, ref_y=None, ref_x=None):
""" Read time-series of one pixel with input y/x
Parameters: y/x : int, row/column number of interest
ts_file : string, filename of time-series HDF5 file
lookup_file : string, filename of lookup table file
ref_y/x : int, row/column number of reference pixel
Returns: dates : 1D np.array of datetime.datetime objects, i.e. datetime.datetime(2010, 10, 20, 0, 0)
dis : 1D np.array of float in meter
"""
# read date
obj = timeseries(ts_file)
obj.open(print_msg=False)
dates = ptime.date_list2vector(obj.dateList)[0]
dates = np.array(dates)
# read displacement
box = (x, y, x+1, y+1)
dis = readfile.read(ts_file, box=box)[0]
# reference pixel
if ref_y is not None:
ref_box = (ref_x, ref_y, ref_x+1, ref_y+1)
dis -= readfile.read(ts_file, box=ref_box)[0]
#start at zero
dis -= dis[0]
return dates, dis
def mask_file(fname, mask_file, out_file=None, inps=None):
""" Mask input fname with mask_file
Inputs:
fname/mask_file - string,
inps_dict - dictionary including the following options:
subset_x/y - list of 2 ints, subset in x/y direction
threshold - float, threshold/minValue to generate mask
Output:
out_file - string
"""
if not inps:
inps = cmd_line_parse()
if not out_file:
out_file = '{}_masked{}'.format(
os.path.splitext(fname)[0],
os.path.splitext(fname)[1])
# read mask_file
mask = readfile.read(mask_file)[0]
mask = update_mask_with_inps(mask, inps)
# masking input file
dsNames = readfile.get_dataset_list(fname)
maxDigit = max([len(i) for i in dsNames])
dsDict = {}
for dsName in dsNames:
if dsName not in ['coherence']:
print('masking {d:<{w}} from {f} ...'.format(d=dsName,
w=maxDigit,
f=fname))
data = readfile.read(fname, datasetName=dsName, print_msg=False)[0]
data = mask_matrix(data, mask, fill_value=inps.fill_value)
dsDict[dsName] = data
writefile.write(dsDict, out_file=out_file, ref_file=fname)
def read_timeseries_lalo(lat, lon, ts_file, lookup_file=None, ref_lat=None, ref_lon=None):
""" Read time-series of one pixel with input lat/lon
Parameters: lat/lon : float, latitude/longitude
ts_file : string, filename of time-series HDF5 file
lookup_file : string, filename of lookup table file
ref_lat/lon : float, latitude/longitude of reference pixel
Returns: dates : 1D np.array of datetime.datetime objects, i.e. datetime.datetime(2010, 10, 20, 0, 0)
dis : 1D np.array of float in meter
"""
# read date
obj = timeseries(ts_file)
obj.open(print_msg=False)
dates = ptime.date_list2vector(obj.dateList)[0]
dates = np.array(dates)
# read displacement
coord = coordinate(obj.metadata, lookup_file=lookup_file)
y, x = coord.geo2radar(lat, lon)[0:2]
box = (x, y, x+1, y+1)
dis = readfile.read(ts_file, box=box)[0]
# reference pixel
if ref_lat is not None:
ref_y, ref_x = coord.geo2radar(ref_lat, ref_lon)[0:2]
ref_box = (ref_x, ref_y, ref_x+1, ref_y+1)
dis -= readfile.read(ts_file, box=ref_box)[0]
#start at zero
dis -= dis[0]
return dates, dis
def set_initial_map():
global d_v, h5, k, dateList, inps, data_lim
d_v = h5['timeseries'][inps.epoch_num][:] * inps.unit_fac
# Initial Map
print(str(dateList))
d_v = readfile.read(inps.timeseries_file, datasetName=dateList[inps.epoch_num])[0] * inps.unit_fac
#d_v = h5[k].get(dateList[inps.epoch_num])[:]*inps.unit_fac
if inps.ref_date:
inps.ref_d_v = readfile.read(inps.timeseries_file, datasetName=inps.ref_date)[0]*inps.unit_fac
d_v -= inps.ref_d_v
if mask is not None:
d_v = mask_matrix(d_v, mask)
if inps.ref_yx:
d_v -= d_v[inps.ref_yx[0], inps.ref_yx[1]]
data_lim = [np.nanmin(d_v), np.nanmax(d_v)]
if not inps.ylim_mat:
inps.ylim_mat = data_lim
print(('Initial data range: '+str(data_lim)))
print(('Display data range: '+str(inps.ylim_mat)))
print(('Initial data range: ' + str(data_lim)))
print(('Display data range: ' + str(inps.ylim)))
def add_file(fnames, out_file=None):
"""Generate sum of all input files
Parameters: fnames : list of str, path/name of input files to be added
out_file : str, optional, path/name of output file
Returns: out_file : str, path/name of output file
Example: 'mask_all.h5' = add_file(['mask_1.h5','mask_2.h5','mask_3.h5'], 'mask_all.h5')
"""
# Default output file name
ext = os.path.splitext(fnames[0])[1]
if not out_file:
out_file = os.path.splitext(fnames[0])[0]
for i in range(1, len(fnames)):
out_file += '_plus_' + os.path.splitext(os.path.basename(
fnames[i]))[0]
out_file += ext
atr = readfile.read_attribute(fnames[0])
dsNames = readfile.get_dataset_list(fnames[0])
dsDict = {}
for dsName in dsNames:
print('adding {} ...'.format(dsName))
data = readfile.read(fnames[0], datasetName=dsName)[0]
for i in range(1, len(fnames)):
d = readfile.read(fnames[i], datasetName=dsName)[0]
data = add_matrix(data, d)
dsDict[dsName] = data
writefile.write(dsDict,
out_file=out_file,
metadata=atr,
ref_file=fnames[0])
return out_file
def prepare_regular_grid_interpolator(self):
"""Prepare aux data for RGI module"""
# source points in regular grid
src_length = int(self.src_metadata['LENGTH'])
src_width = int(self.src_metadata['WIDTH'])
self.src_pts = (np.arange(src_length), np.arange(src_width))
# destination points
dest_y = readfile.read(self.file, datasetName='azimuthCoord')[0]
dest_x = readfile.read(self.file, datasetName='rangeCoord')[0]
if 'SUBSET_XMIN' in self.src_metadata.keys():
print('input data file was cropped before.')
dest_y[dest_y != 0.] -= float(self.src_metadata['SUBSET_YMIN'])
dest_x[dest_x != 0.] -= float(self.src_metadata['SUBSET_XMIN'])
self.interp_mask = np.multiply(np.multiply(dest_y > 0, dest_y < src_length),
np.multiply(dest_x > 0, dest_x < src_width))
self.dest_pts = np.hstack((dest_y[self.interp_mask].reshape(-1, 1),
dest_x[self.interp_mask].reshape(-1, 1)))
# destimation data size
self.length = int(self.lut_metadata['LENGTH'])
self.width = int(self.lut_metadata['WIDTH'])
lat0 = float(self.lut_metadata['Y_FIRST'])
lon0 = float(self.lut_metadata['X_FIRST'])
lat_step = float(self.lut_metadata['Y_STEP'])
lon_step = float(self.lut_metadata['X_STEP'])
self.laloStep = (lat_step, lon_step)
self.SNWE = (lat0 + lat_step * (self.length - 1),
lat0,
lon0,
lon0 + lon_step * (self.width - 1))
def read_timeseries_yx(y, x, ts_file, ref_y=None, ref_x=None, win_size=1):
""" Read time-series of one pixel with input y/x
Parameters: y/x : int, row/column number of interest
ts_file : string, filename of time-series HDF5 file
ref_y/x : int, row/column number of reference pixel
Returns: dates : 1D np.array of datetime.datetime objects, i.e. datetime.datetime(2010, 10, 20, 0, 0)
dis : 1D np.array of float in meter
"""
# read date
obj = timeseries(ts_file)
obj.open(print_msg=False)
dates = ptime.date_list2vector(obj.dateList)[0]
dates = np.array(dates)
# read displacement
print('input y / x: {} / {}'.format(y, x))
box = (x, y, x + 1, y + 1)
dis = readfile.read(ts_file, box=box)[0]
if win_size != 1:
buf = int(win_size / 2)
box_win = (x - buf, y - buf, x + buf + 1, y + buf + 1)
dis_win = readfile.read(ts_file, box=box_win)[0]
dis = np.nanmean(dis_win.reshape((obj.numDate, -1)), axis=1)
# reference pixel
if ref_y is not None:
ref_box = (ref_x, ref_y, ref_x + 1, ref_y + 1)
dis -= readfile.read(ts_file, box=ref_box)[0]
#start at zero
dis -= dis[0]
return dates, dis
def correct_local_oscilator_drift(fname, rg_dist_file=None, out_file=None):
print('-'*50)
print('correct Local Oscilator Drift for Envisat using an empirical model (Marinkovic and Larsen, 2013)')
print('-'*50)
atr = readfile.read_attribute(fname)
# Check Sensor Type
platform = atr['PLATFORM']
print('platform: '+platform)
if not platform.lower() in ['env', 'envisat']:
print('No need to correct LOD for '+platform)
return
# output file name
if not out_file:
out_file = '{}_LODcor{}'.format(os.path.splitext(fname)[0], os.path.splitext(fname)[1])
# Get LOD ramp rate from empirical model
if not rg_dist_file:
print('calculate range distance from file metadata')
rg_dist = get_relative_range_distance(atr)
else:
print('read range distance from file: %s' % (rg_dist_file))
rg_dist = readfile.read(rg_dist_file, datasetName='slantRangeDistance', print_msg=False)[0]
rg_dist -= rg_dist[int(atr['REF_Y']), int(atr['REF_X'])]
ramp_rate = np.array(rg_dist * 3.87e-7, np.float32)
# Correct LOD Ramp for Input fname
range2phase = -4*np.pi / float(atr['WAVELENGTH'])
k = atr['FILE_TYPE']
if k == 'timeseries':
# read
obj = timeseries(fname)
obj.open()
data = obj.read()
# correct LOD
diff_year = np.array(obj.yearList)
diff_year -= diff_year[obj.refIndex]
for i in range(data.shape[0]):
data[i, :, :] -= ramp_rate * diff_year[i]
# write
obj_out = timeseries(out_file)
obj_out.write2hdf5(data, refFile=fname)
elif k in ['.unw']:
data, atr = readfile.read(fname)
dates = ptime.yyyymmdd2years(ptime.yyyymmdd(atr['DATE12'].split('-')))
dt = dates[1] - dates[0]
data -= ramp_rate * range2phase * dt
writefile.write(data, out_file=out_file, metadata=atr)
else:
print('No need to correct for LOD for %s file' % (k))
return out_file
def extract_geometry_metadata(geom_dir, metadata=dict()):
"""extract metadata from geometry files"""
def get_nonzero_row_number(data, buffer=2):
"""Find the first and last row number of rows without zero value
for multiple swaths data
"""
if np.all(data):
r0, r1 = 0 + buffer, -1 - buffer
else:
row_flag = np.sum(data != 0., axis=1) == data.shape[1]
row_idx = np.where(row_flag)[0]
r0, r1 = row_idx[0] + buffer, row_idx[-1] - buffer
return r0, r1
# grab existing files
geom_files = [os.path.join(os.path.abspath(geom_dir), '{}.rdr'.format(i))
for i in ['hgt','lat','lon','los']]
geom_files = [i for i in geom_files if os.path.isfile(i)]
print('extract metadata from geometry files: {}'.format(
[os.path.basename(i) for i in geom_files]))
# get A/RLOOKS
metadata = extract_multilook_number(geom_dir, metadata)
# update pixel_size for multilooked data
metadata['rangePixelSize'] *= metadata['RLOOKS']
metadata['azimuthPixelSize'] *= metadata['ALOOKS']
# get LAT/LON_REF1/2/3/4 and HEADING into metadata
for geom_file in geom_files:
if 'lat' in os.path.basename(geom_file):
data = readfile.read(geom_file)[0]
r0, r1 = get_nonzero_row_number(data)
metadata['LAT_REF1'] = str(data[r0, 0])
metadata['LAT_REF2'] = str(data[r0, -1])
metadata['LAT_REF3'] = str(data[r1, 0])
metadata['LAT_REF4'] = str(data[r1, -1])
if 'lon' in os.path.basename(geom_file):
data = readfile.read(geom_file)[0]
r0, r1 = get_nonzero_row_number(data)
metadata['LON_REF1'] = str(data[r0, 0])
metadata['LON_REF2'] = str(data[r0, -1])
metadata['LON_REF3'] = str(data[r1, 0])
metadata['LON_REF4'] = str(data[r1, -1])
if 'los' in os.path.basename(geom_file):
data = readfile.read(geom_file, datasetName='az')[0]
data[data == 0.] = np.nan
az_angle = np.nanmean(data)
# convert isce azimuth angle to roipac orbit heading angle
head_angle = -1 * (270 + az_angle)
head_angle -= np.round(head_angle / 360.) * 360.
metadata['HEADING'] = str(head_angle)
return metadata
def read_aux_subset2inps(inps):
# Convert All Inputs into subset_y/x/lat/lon
# Input Priority: subset_y/x/lat/lon > reference > template > tight
if all(not i for i in
[inps.subset_x, inps.subset_y, inps.subset_lat, inps.subset_lon]):
# 1. Read subset info from Reference File
if inps.reference:
ref_atr = readfile.read_attribute(inps.reference)
pix_box, geo_box = get_coverage_box(ref_atr)
print('using subset info from ' + inps.reference)
# 2. Read subset info from template options
elif inps.template_file:
pix_box, geo_box = read_subset_template2box(inps.template_file)
print('using subset info from ' + inps.template_file)
# 3. Use subset from tight info
elif inps.tight:
inps.lookup_file = ut.get_lookup_file(inps.lookup_file)
if not inps.lookup_file:
raise Exception(
'No lookup file found! Can not use --tight option without it.'
)
atr_lut = readfile.read_attribute(inps.lookup_file)
coord = ut.coordinate(atr_lut)
if 'Y_FIRST' in atr_lut.keys():
rg_lut = readfile.read(inps.lookup_file,
datasetName='range')[0]
rg_unique, rg_pos = np.unique(rg_lut, return_inverse=True)
idx_row, idx_col = np.where(
rg_lut != rg_unique[np.bincount(rg_pos).argmax()])
pix_box = (np.min(idx_col) - 10, np.min(idx_row) - 10,
np.max(idx_col) + 10, np.max(idx_row) + 10)
geo_box = coord.box_pixel2geo(pix_box)
del rg_lut
else:
lat = readfile.read(inps.lookup_file,
datasetName='latitude')[0]
lon = readfile.read(inps.lookup_file,
datasetName='longitude')[0]
geo_box = (np.nanmin(lon), np.nanmax(lat), np.nanmax(lon),
np.nanmin(lat))
pix_box = None
del lat, lon
else:
raise Exception('No subset inputs found!')
# Update subset_y/x/lat/lon
inps = subset_box2inps(inps, pix_box, geo_box)
return inps
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 generate_temporal_coherence_mask(self):
"""Generate reliable pixel mask from temporal coherence"""
geom_file = ut.check_loaded_dataset(self.workDir, print_msg=False)[2]
tcoh_file = 'temporalCoherence.h5'
mask_file = 'maskTempCoh.h5'
tcoh_min = self.template['pysar.networkInversion.minTempCoh']
scp_args = '{} -m {} -o {} --shadow {}'.format(tcoh_file, tcoh_min,
mask_file, geom_file)
print('generate_mask.py', scp_args)
# update mode: run only if:
# 1) output file exists and newer than input file, AND
# 2) all config keys are the same
config_keys = ['pysar.networkInversion.minTempCoh']
print('update mode: ON')
flag = 'skip'
if ut.run_or_skip(out_file=mask_file,
in_file=tcoh_file,
print_msg=False) == 'run':
flag = 'run'
else:
print(
'1) output file: {} already exists and newer than input file: {}'
.format(mask_file, tcoh_file))
atr = readfile.read_attribute(mask_file)
if any(
str(self.template[i]) != atr.get(i, 'False')
for i in config_keys):
flag = 'run'
print(
'2) NOT all key configration parameters are the same: {}'.
format(config_keys))
else:
print('2) all key configuration parameters are the same: {}'.
format(config_keys))
print('run or skip: {}'.format(flag))
if flag == 'run':
pysar.generate_mask.main(scp_args.split())
# update configKeys
atr = {}
for key in config_keys:
atr[key] = self.template[key]
ut.add_attribute(mask_file, atr)
# check number of pixels selected in mask file for following analysis
num_pixel = np.sum(readfile.read(mask_file)[0] != 0.)
print('number of reliable pixels: {}'.format(num_pixel))
min_num_pixel = float(
self.template['pysar.networkInversion.minNumPixel'])
if num_pixel < min_num_pixel:
msg = "Not enough reliable pixels (minimum of {}). ".format(
int(min_num_pixel))
msg += "Try the following:\n"
msg += "1) Check the reference pixel and make sure it's not in areas with unwrapping errors\n"
msg += "2) Check the network and make sure it's fully connected without subsets"
raise RuntimeError(msg)
return
def plot_bridge(ax, mask_cc_file, bridges):
"""Plot mask of connected components with bridges info
Parameters: mask_cc_file : string, path of mask cc file
bridges : list of dict
"""
mask_cc, metadata = readfile.read(mask_cc_file)
num_bridge = len(bridges)
# plot 1. mask_cc data
im = ax.imshow(mask_cc)
# plot 2. bridge data
for i in range(num_bridge):
bridge = bridges[i]
ax.imshow(np.ma.masked_where(~bridge['mask0'],
np.zeros(mask_cc.shape)),
cmap='gray',
alpha=0.3,
vmin=0,
vmax=1)
ax.imshow(np.ma.masked_where(~bridge['mask1'],
np.zeros(mask_cc.shape)),
cmap='gray',
alpha=0.3,
vmin=0,
vmax=1)
ax.plot([bridge['x0'], bridge['x1']], [bridge['y0'], bridge['y1']],
'-',
ms=5,
mfc='none')
ax = pp.auto_flip_direction(metadata, ax=ax, print_msg=False)
return ax, im
def main(iargs=None):
inps = cmd_line_parse(iargs)
plt.switch_backend('Agg') # Backend setting
# Read data
data, atr = readfile.read(inps.file, datasetName=inps.dset)
# Data Operation - Display Unit & Rewrapping
(data, inps.disp_unit, inps.disp_scale,
inps.wrap) = pp.scale_data4disp_unit_and_rewrap(
data,
metadata=atr,
disp_unit=inps.disp_unit,
wrap=inps.wrap,
wrap_range=inps.wrap_range)
if inps.wrap:
inps.vlim = inps.wrap_range
# Output filename
inps.fig_title = pp.auto_figure_title(inps.file,
datasetNames=inps.dset,
inps_dict=vars(inps))
if not inps.outfile:
inps.outfile = '{}.kmz'.format(inps.fig_title)
# 2. Generate Google Earth KMZ
kmz_file = write_kmz_file(data,
metadata=atr,
out_file=inps.outfile,
inps=inps)
print('Done.')
return
def main(iargs=None):
inps = cmd_line_parse(iargs)
#plt.switch_backend('Agg')
# Read data
data, atr = readfile.read(inps.file, datasetName=inps.dset)
# Data Operation - Display Unit & Rewrapping
data, inps.disp_unit, inps.disp_scale, inps.wrap = pp.scale_data4disp_unit_and_rewrap(
data=data, metadata=atr, disp_unit=inps.disp_unit, wrap=inps.wrap)
if inps.wrap:
inps.ylim = [-np.pi, np.pi]
# Output filename
if not inps.outfile:
inps.outfile = pp.auto_figure_title(inps.file,
datasetNames=inps.dset,
inps_dict=vars(inps))
# 2. Generate Google Earth KMZ
kmz_file = write_kmz_file(data,
metadata=atr,
out_name_base=inps.outfile,
inps=inps)
print('Done.')
return
def main(iargs=None):
inps = cmd_line_parse(iargs)
plt.switch_backend('Agg') # Backend setting
#print("The Python version is %s.%s.%s" % sys.version_info[:3])
# Read data
data, atr = readfile.read(inps.file, datasetName=inps.dset)
# Data Operation - Display Unit & Rewrapping
(data, inps.disp_unit, inps.disp_scale,
inps.wrap) = pp.scale_data4disp_unit_and_rewrap(data=data,
metadata=atr,
disp_unit=inps.disp_unit,
wrap=inps.wrap)
if inps.wrap:
inps.ylim = [-np.pi, np.pi]
# Output filename
if not inps.outfile:
inps.outfile = '{}.kmz'.format(
pp.auto_figure_title(inps.file,
datasetNames=inps.dset,
inps_dict=vars(inps)))
# 2. Generate Google Earth KMZ
kmz_file = write_kmz_file(data,
metadata=atr,
out_file=inps.outfile,
inps=inps)
print('Done.')
return
def manual_select_start_end_point(File):
"""Manual Select Start/End Point in display figure."""
print('reading ' + File + ' ...')
data, atr = readfile.read(File)
print('displaying ' + File + ' ...')
fig = plt.figure()
ax = fig.add_subplot(111)
ax.imshow(data)
xc = []
yc = []
print('please click on start and end point of the desired profile')
print('then close the figure to continue')
def onclick(event):
if event.button == 1:
xcc, ycc = int(event.xdata), int(event.ydata)
xc.append(xcc)
yc.append(ycc)
print('x = ' + str(xcc) + '\ny = ' + str(ycc))
ax.plot(xcc, ycc, 'ro')
cid = fig.canvas.mpl_connect('button_release_event', onclick)
plt.show()
start_yx = [yc[0], xc[0]]
end_yx = [yc[1], xc[1]]
return start_yx, end_yx
def timeseries2ifgram(ts_file, ifgram_file, out_file='reconUnwrapIfgram.h5'):
# read time-series
atr = readfile.read_attribute(ts_file)
range2phase = -4. * np.pi / float(atr['WAVELENGTH'])
print('reading timeseries data from file {} ...'.format(ts_file))
ts_data = readfile.read(ts_file)[0] * range2phase
num_date, length, width = ts_data.shape
ts_data = ts_data.reshape(num_date, -1)
# reconstruct unwrapPhase
print('reconstructing the interferograms from timeseries')
stack_obj = ifgramStack(ifgram_file)
stack_obj.open(print_msg=False)
A1 = stack_obj.get_design_matrix4timeseries_estimation(dropIfgram=False)[0]
num_ifgram = A1.shape[0]
A0 = -1. * np.ones((num_ifgram, 1))
A = np.hstack((A0, A1))
ifgram_est = np.dot(A, ts_data).reshape(num_ifgram, length, width)
ifgram_est = np.array(ifgram_est, dtype=ts_data.dtype)
del ts_data
# write to ifgram file
dsDict = {}
dsDict['unwrapPhase'] = ifgram_est
writefile.write(dsDict, out_file=out_file, ref_file=ifgram_file)
return ifgram_file
def transect_list(fileList, inps):
"""Get transection along input line from file list
Inputs:
fileList : list of str, path of files to get transect
inps : Namespace including the following items:
start/end_lalo
start/end_yx
interpolation
Outputs:
transectList : list of N*2 matrix containing distance and its value
atrList : list of attribute dictionary, for each input file
"""
transectList = []
atrList = []
for File in fileList:
print('reading ' + File)
data, atr = readfile.read(File)
if inps.start_lalo and inps.end_lalo:
transect = transect_lalo(data, atr, inps.start_lalo, inps.end_lalo,
inps.interpolation)
else:
transect = transect_yx(data, atr, inps.start_yx, inps.end_yx,
inps.interpolation)
transectList.append(transect)
atrList.append(atr)
return transectList, atrList
def multilook_file(infile, lks_y, lks_x, outfile=None):
lks_y = int(lks_y)
lks_x = int(lks_x)
# input file info
atr = readfile.read_attribute(infile)
k = atr['FILE_TYPE']
print('multilooking {} {} file: {}'.format(atr['PROCESSOR'], k, infile))
print('number of looks in y / azimuth direction: %d' % lks_y)
print('number of looks in x / range direction: %d' % lks_x)
# output file name
if not outfile:
if os.getcwd() == os.path.dirname(os.path.abspath(infile)):
ext = os.path.splitext(infile)[1]
outfile = os.path.splitext(infile)[0] + '_' + str(
lks_y) + 'alks_' + str(lks_x) + 'rlks' + ext
else:
outfile = os.path.basename(infile)
#print('writing >>> '+outfile)
# read source data and multilooking
dsNames = readfile.get_dataset_list(infile)
maxDigit = max([len(i) for i in dsNames])
dsDict = dict()
for dsName in dsNames:
print('multilooking {d:<{w}} from {f} ...'.format(
d=dsName, w=maxDigit, f=os.path.basename(infile)))
data = readfile.read(infile, datasetName=dsName, print_msg=False)[0]
data = multilook_data(data, lks_y, lks_x)
dsDict[dsName] = data
atr = multilook_attribute(atr, lks_y, lks_x)
writefile.write(dsDict, out_file=outfile, metadata=atr, ref_file=infile)
return outfile
def main(iargs=None):
inps = cmd_line_parse(iargs)
if not inps.outfile:
inps.outfile = os.path.splitext(inps.file)[0]+'.h5'
if inps.data_type:
if inps.data_type in ['float', 'float32', 'np.float32']:
inps.data_type = np.float32
elif inps.data_type in ['float64', 'np.float64']:
inps.data_type = np.float64
elif inps.data_type in ['int', 'int16', 'np.int16']:
inps.data_type = np.int16
elif inps.data_type in ['bool', 'np.bool_']:
inps.data_type = np.bool_
elif inps.data_type in ['complex', 'np.complex64']:
inps.data_type = np.complex64
elif inps.data_type in ['complex128', 'np.complex128']:
inps.data_type = np.complex128
else:
raise ValueError('un-recognized input data type: {}'.format(inps.data_type))
atr = readfile.read_attribute(inps.file)
dsNames = readfile.get_dataset_list(inps.file)
dsDict = {}
for dsName in dsNames:
data = readfile.read(inps.file, datasetName=dsName)[0]
if inps.data_type:
data = np.array(data, inps.data_type)
dsDict[dsName] = data
writefile.write(dsDict, out_file=inps.outfile, metadata=atr)
return inps.outfile
def plot_coherence_matrix4pixel(self, yx):
"""Plot coherence matrix for one pixel
Parameters: yx : list of 2 int
"""
# read coherence
box = (yx[1], yx[0], yx[1]+1, yx[0]+1)
coh = readfile.read(self.ifgram_file, datasetName='coherence', box=box)[0]
# prep metadata
plotDict = {}
plotDict['fig_title'] = 'Y = {}, X = {}'.format(yx[0], yx[1])
plotDict['colormap'] = self.colormap
plotDict['disp_legend'] = False
# plot
coh_mat = pp.plot_coherence_matrix(self.ax_mat,
date12List=self.date12_list,
cohList=coh.tolist(),
date12List_drop=self.ex_date12_list,
plot_dict=plotDict)[1]
self.fig.canvas.draw()
# status bar
def format_coord(x, y):
row, col = int(y+0.5), int(x+0.5)
date12 = sorted([self.date_list[row], self.date_list[col]])
date12 = ['{}-{}-{}'.format(i[0:4], i[4:6], i[6:8]) for i in date12]
return 'x={}, y={}, v={:.3f}'.format(date12[0], date12[1], coh_mat[row, col])
self.ax_mat.format_coord = format_coord
# info
vprint('-'*30)
vprint('pixel: yx = {}'.format(yx))
vprint('min/max coherence: {:.2f} / {:.2f}'.format(np.min(coh), np.max(coh)))
return
def file_operation(fname, operator, operand, out_file=None):
"""Mathmathic operation of file"""
# Basic Info
atr = readfile.read_attribute(fname)
k = atr['FILE_TYPE']
print('input is ' + k + ' file: ' + fname)
print('operation: file %s %f' % (operator, operand))
# default output filename
if not out_file:
if operator in ['+', 'plus', 'add', 'addition']:
suffix = 'plus'
elif operator in ['-', 'minus', 'substract', 'substraction']:
suffix = 'minus'
elif operator in ['*', 'times', 'multiply', 'multiplication']:
suffix = 'multiply'
elif operator in ['/', 'obelus', 'divide', 'division']:
suffix = 'divide'
elif operator in ['^', 'pow', 'power']:
suffix = 'pow'
out_file = '{}_{}{}{}'.format(
os.path.splitext(fname)[0], suffix, str(operand),
os.path.splitext(fname)[1])
atr = readfile.read_attribute(fname)
dsNames = readfile.get_dataset_list(fname)
dsDict = {}
for dsName in dsNames:
data = readfile.read(fname, datasetName=dsName)[0]
data = data_operation(data, operator, operand)
dsDict[dsName] = data
writefile.write(dsDict, out_file=out_file, metadata=atr, ref_file=fname)
return out_file
def read_lookup_table(self, print_msg=True):
if 'Y_FIRST' in self.lut_metadata.keys():
self.lut_y = readfile.read(self.lookup_file[0],
datasetName='azimuthCoord',
print_msg=print_msg)[0]
self.lut_x = readfile.read(self.lookup_file[1],
datasetName='rangeCoord',
print_msg=print_msg)[0]
else:
self.lut_y = readfile.read(self.lookup_file[0],
datasetName='latitude',
print_msg=print_msg)[0]
self.lut_x = readfile.read(self.lookup_file[1],
datasetName='longitude',
print_msg=print_msg)[0]
return self.lut_y, self.lut_x
def main(iargs=None):
inps = cmd_line_parse(iargs)
# Calculate look angle
atr = readfile.read_attribute(inps.file)
dem = None
if inps.dem_file:
dem = readfile.read(inps.dem_file, datasetName='height')[0]
angle = ut.incidence_angle(atr, dem=dem, dimension=2)
# Geo coord
if 'Y_FIRST' in atr.keys():
print(
'Input file is geocoded, only center incident angle is calculated: '
)
print(angle)
length = int(atr['LENGTH'])
width = int(atr['WIDTH'])
angle_mat = np.zeros((length, width), np.float32)
angle_mat[:] = angle
angle = angle_mat
atr['FILE_TYPE'] = 'mask'
atr['UNIT'] = 'degree'
if 'REF_DATE' in atr.keys():
atr.pop('REF_DATE')
if not inps.outfile:
inps.outfile = 'incidenceAngle.h5'
writefile.write(angle, out_file=inps.outfile, metadata=atr)
return inps.outfile
def run_geocode(inps):
"""geocode all input files"""
start_time = time.time()
# Prepare geometry for geocoding
res_obj = resample(lookupFile=inps.lookupFile,
dataFile=inps.file[0],
SNWE=inps.SNWE,
laloStep=inps.laloStep,
processor=inps.processor)
res_obj.open()
if not inps.nprocs:
inps.nprocs = multiprocessing.cpu_count()
# resample input files one by one
for infile in inps.file:
print('-' * 50+'\nresampling file: {}'.format(infile))
atr = readfile.read_attribute(infile, datasetName=inps.dset)
outfile = auto_output_filename(infile, inps)
if inps.updateMode and ut.run_or_skip(outfile, in_file=[infile, inps.lookupFile]) == 'skip':
print('update mode is ON, skip geocoding.')
continue
# read source data and resample
dsNames = readfile.get_dataset_list(infile, datasetName=inps.dset)
maxDigit = max([len(i) for i in dsNames])
dsResDict = dict()
for dsName in dsNames:
print('reading {d:<{w}} from {f} ...'.format(d=dsName,
w=maxDigit,
f=os.path.basename(infile)))
data = readfile.read(infile,
datasetName=dsName,
print_msg=False)[0]
if atr['FILE_TYPE'] == 'timeseries' and len(data.shape) == 2:
data = np.reshape(data, (1, data.shape[0], data.shape[1]))
res_data = res_obj.run_resample(src_data=data,
interp_method=inps.interpMethod,
fill_value=inps.fillValue,
nprocs=inps.nprocs,
print_msg=True)
dsResDict[dsName] = res_data
# update metadata
if inps.radar2geo:
atr = metadata_radar2geo(atr, res_obj)
else:
atr = metadata_geo2radar(atr, res_obj)
#if len(dsNames) == 1 and dsName not in ['timeseries']:
# atr['FILE_TYPE'] = dsNames[0]
# infile = None
writefile.write(dsResDict, out_file=outfile, metadata=atr, ref_file=infile)
m, s = divmod(time.time()-start_time, 60)
print('time used: {:02.0f} mins {:02.1f} secs.\n'.format(m, s))
return outfile
def get_temporal_coherence_mask(inps, template):
"""Generate mask from temporal coherence"""
configKeys = ['pysar.networkInversion.minTempCoh']
inps.maskFile = 'maskTempCoh.h5'
inps.minTempCoh = template['pysar.networkInversion.minTempCoh']
maskCmd = 'generate_mask.py {} -m {} -o {} --shadow {}'.format(
inps.tempCohFile, inps.minTempCoh, inps.maskFile, inps.geomFile)
print(maskCmd)
# update mode checking
# run if 1) output file exists; 2) newer than input file and 3) all config keys are the same
run = False
if ut.run_or_skip(out_file=inps.maskFile,
in_file=inps.tempCohFile,
print_msg=False) == 'run':
run = True
else:
print(
' 1) output file: {} already exists and newer than input file: {}'
.format(inps.maskFile, inps.tempCohFile))
meta_dict = readfile.read_attribute(inps.maskFile)
if any(
str(template[i]) != meta_dict.get(i, 'False')
for i in configKeys):
run = True
print(
' 2) NOT all key configration parameters are the same --> run.\n\t{}'
.format(configKeys))
else:
print(' 2) all key configuration parameters are the same:\n\t{}'.
format(configKeys))
# result
print('run this step:', run)
if run:
status = subprocess.Popen(maskCmd, shell=True).wait()
if status is not 0:
raise Exception(
'Error while generating mask file from temporal coherence.')
# update configKeys
meta_dict = {}
for key in configKeys:
meta_dict[key] = template[key]
ut.add_attribute(inps.maskFile, meta_dict)
# check number of pixels selected in mask file for following analysis
min_num_pixel = float(template['pysar.networkInversion.minNumPixel'])
msk = readfile.read(inps.maskFile)[0]
num_pixel = np.sum(msk != 0.)
print('number of pixels selected: {}'.format(num_pixel))
if num_pixel < min_num_pixel:
msg = "Not enought coherent pixels selected (minimum of {}). ".format(
int(min_num_pixel))
msg += "Try the following:\n"
msg += "1) Check the reference pixel and make sure it's not in areas with unwrapping errors\n"
msg += "2) Check the network and make sure it's fully connected without subsets"
raise RuntimeError(msg)
del msk
return
def read_topographic_data(geom_file, metadata):
print('read DEM from file: ' + geom_file)
dem = readfile.read(geom_file, datasetName='height', print_msg=False)[0]
print('considering the incidence angle of each pixel ...')
inc_angle = readfile.read(geom_file,
datasetName='incidenceAngle',
print_msg=False)[0]
dem *= 1.0 / np.cos(inc_angle * np.pi / 180.0)
ref_y = int(metadata['REF_Y'])
ref_x = int(metadata['REF_X'])
dem -= dem[ref_y, ref_x]
# Design matrix for elevation v.s. phase
# dem = dem.flatten()
return dem
def set_dem_file():
global ax_v, inps, img
if inps.dem_file:
dem = readfile.read(inps.dem_file, datasetName='height')[0]
ax_v = pp.plot_dem_yx(ax_v, dem)
img = ax_v.imshow(d_v, cmap=inps.colormap, clim=inps.ylim_mat, interpolation='nearest')