def __init__(self, D, map_file, index_file, datatype):
self.files=[]
self.datatype=datatype
self.map_file=map_file
self.index_file=index_file
print(f"TrackPicker: index_file is {index_file}")
srs_proj4=pc.geoIndex().from_file(index_file).attrs['SRS_proj4']
if datatype == 'ATL06':
for ii, Di in enumerate(D):
Di.get_xy(srs_proj4)
Di.assign({'file_num':np.zeros_like(Di.x)+ii})
self.files += [Di.filename]
self.D_all=pc.data().from_list(D)
elif datatype == 'ATL11':
D_list=[]
for ii, Di in enumerate(D):
self.files += [Di.filename]
Di.get_xy(srs_proj4)
D_list.append(pc.data().from_dict({
'x':Di.x, 'y':Di.y, 'file_num':np.zeros_like(Di.x)+ii,
'h_corr':Di.corrected_h.h_corr[:,-1].ravel()}))
self.D_all=pc.data().from_list(D_list)
else:
self.D_all=pc.data().from_list(D)
self.D=D
XR=[np.nanmin(self.D_all.x), np.nanmax(self.D_all.x)]
YR=[np.nanmin(self.D_all.y), np.nanmax(self.D_all.y)]
self.fig=plt.figure()
if map_file is not None:
get_map(map_file, bounds=[XR, YR])
#for Di in D:
# plt.plot(Di.x, Di.y,'.')
if self.datatype=='ATL06':
plt.scatter(self.D_all.x, self.D_all.y, 6, c=self.D_all.r_eff, linewidth=0, vmax=1, vmin=0)
elif self.datatype=='ATL11':
plt.scatter(self.D_all.x, self.D_all.y, 6, c=self.D_all.h_corr); plt.colorbar()
elif self.datatype=='ATM_waveform_fit':
plt.scatter(self.D_all.x, self.D_all.y, 6, c=np.log10(self.D_all.K0))
elif self.datatype=='CS2':
plt.scatter(self.D_all.x, self.D_all.y, 6, c=self.D_all.h); plt.colorbar()
hax=plt.axes([0.7, 0.05, 0.25, 0.25])
hax.hist((self.D_all.time-730486)/365.25+2000, 100)
self.cid=self.fig.canvas.mpl_connect('button_press_event', self)
plt.show()
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Jan 21 15:56:39 2020
@author: ben
"""
import pointCollection as pc
import numpy as np
import sys
import matplotlib.pyplot as plt
plt.figure()
for index_file in sys.argv[1:]:
xy = pc.geoIndex().from_file(index_file).bins_as_array()
plt.plot(xy[0], xy[1], 'o', label=index_file)
D = pc.geoIndex().from_file(index_file).query_xy(
[[xy[0][0]], [xy[1][0]]],
get_data=True,
fields=['x', 'y', 'h_li', 'pair', 'cycle_number'])
D = pc.data().from_list(D)
plt.plot(D.x, D.y, '.', label='first bin of ' + index_file)
plt.axis('equal')
plt.legend()
plt.show()
'geophysical':['dac'],
'bias_correction':['fpb_n_corr'],
'fit_statistics':['dh_fit_dx','dh_fit_dx_sigma','dh_fit_dy','h_mean', 'h_rms_misfit','h_robust_sprd','n_fit_photons','w_surface_window_final','snr_significance'],
'orbit_info':['rgt','orbit_number'],
'derived': ['BP','spot']}
ATL06_fields=list()
for key in ATL06_field_dict:
ATL06_fields+=ATL06_field_dict[key]
WGS84a=6378137.0
WGS84b=6356752.31424
d2r=np.pi/180.
delta=[10000., 10000.]
Q_GI=pc.geoIndex(SRS_proj4=SRS_proj4).from_file(Qfit_index, read_file=True)
D6_GI=pc.geoIndex(SRS_proj4=SRS_proj4).from_file(ATL06_index, read_file=True)
# the qfit index is at 1 km , the ATL06 index is at 10 km. find the overlap between the two
# Interesect the ATL06 index with the Qfit index
xy_10km_Q=Q_GI.bins_as_array()
xy_10km_Q=np.unique(xy_10km_Q[0]+1j*xy_10km_Q[1])
D6_GI=D6_GI.copy_subset(xyBin=[np.real(xy_10km_Q), np.imag(xy_10km_Q)]);
out_fields=[
'segment_id','x','y','beam', 'BP', 'h_li', 'h_li_sigma', 'atl06_quality_summary',
'dac', 'rgt','orbit_number','spot',
'dh_fit_dx','N_50m','N_seg','h_qfit_seg','dh_qfit_dx','dh_qfit_dy',
'h_robust_sprd', 'snr_significance',
'h_qfit_50m','sigma_qfit_50m', 'sigma_seg','dz_50m','E_seg','RDE_seg',
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--atl06',
'-I',
type=str,
help="ICESat-2 ATL06 directory to run")
parser.add_argument('--atm', '-A', type=str, help='ATM directory to run')
parser.add_argument('--hemisphere',
'-H',
type=int,
default=-1,
help='hemisphere, must be 1 or -1')
parser.add_argument('--query',
'-Q',
type=float,
default=100,
help='KD-Tree query radius')
parser.add_argument('--median',
'-M',
default=False,
action='store_true',
help='Run block median')
parser.add_argument('--verbose',
'-v',
default=False,
action='store_true',
help='verbose output of run')
args = parser.parse_args()
if args.hemisphere == 1:
SRS_proj4 = '+proj=stere +lat_0=90 +lat_ts=70 +lon_0=-45 +k=1 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs '
elif args.hemisphere == -1:
SRS_proj4 = '+proj=stere +lat_0=-90 +lat_ts=-71 +lon_0=0 +k=1 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs'
# tilde expansion of file arguments
ATM_dir = os.path.expanduser(args.atm)
print("working on ATL06 dir {0}, ATM directory {1}".format(
args.atl06, ATM_dir)) if args.verbose else None
# find Qfit files within ATM_dir
Qfit_regex = re.compile(
r"ATM1B.*_(\d{4})(\d{2})(\d{2})_(\d{2})(\d{2})(\d{2}).*.h5")
Qfit_files = [
os.path.join(ATM_dir, f) for f in os.listdir(ATM_dir)
if Qfit_regex.search(f)
]
# output directory
out_dir = os.path.join(ATM_dir, 'xovers')
if not os.path.isdir(out_dir):
os.mkdir(out_dir)
out_file = 'vs_{0}.h5'.format(
os.path.dirname(args.atl06).replace(os.sep, '_'))
if os.path.isfile(os.path.join(out_dir, out_file)):
print("found: {0}".format(os.path.join(
out_dir, out_file))) if args.verbose else None
ATL06_index = os.path.join(os.sep, 'Volumes', 'ice2', 'ben', 'scf',
'AA_06', args.atl06, 'GeoIndex.h5')
SRS_proj4 = '+proj=stere +lat_0=-90 +lat_ts=-71 +lon_0=0 +k=1 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs'
ATL06_field_dict = {
None: [
'delta_time', 'h_li', 'h_li_sigma', 'latitude', 'longitude',
'segment_id', 'sigma_geo_h', 'atl06_quality_summary'
],
'ground_track':
['x_atc', 'y_atc', 'seg_azimuth', 'sigma_geo_at', 'sigma_geo_xt'],
'geophysical': ['dac'],
'bias_correction': ['fpb_n_corr'],
'fit_statistics': [
'dh_fit_dx', 'dh_fit_dx_sigma', 'dh_fit_dy', 'h_mean',
'h_rms_misfit', 'h_robust_sprd', 'n_fit_photons',
'w_surface_window_final', 'snr_significance'
],
'orbit_info': ['rgt', 'orbit_number'],
'derived': ['BP', 'spot']
}
ATL06_fields = list()
for key in ATL06_field_dict:
ATL06_fields += ATL06_field_dict[key]
# read all Qfit files within ATM directory
Qlist = list()
for f in sorted(Qfit_files):
Qlist.append(pc.ATM_Qfit.data().from_h5(f))
# merge the list of ATM data and build the search tree
Q_full = pc.data().from_list(Qlist).get_xy(SRS_proj4)
# run block median for qsub
if args.median:
Q_full = blockmedian_for_qsub(Q_full, 5)
# construct search tree from ATM Qfit coords
Qtree = KDTree(np.c_[Q_full.x, Q_full.y])
# could pickle Qtree here to save computational time for future runs
# read 10 km ATL06 index
D6_GI = pc.geoIndex(SRS_proj4=SRS_proj4).from_file(ATL06_index,
read_file=True)
# Query the Qfit search tree to find intersecting ATL06 bins
# search within radius equal to diagonal of bin with 1km buffer (12/sqrt(2))
x_10km, y_10km = D6_GI.bins_as_array()
D6ind, = np.nonzero(
Qtree.query_radius(np.c_[x_10km, y_10km], 8485, count_only=True))
# reduce ATL06 bins to valid
D6_GI = D6_GI.copy_subset(xyBin=[x_10km[D6ind], y_10km[D6ind]])
out_fields = [
'segment_id', 'x', 'y', 'beam', 'BP', 'h_li', 'h_li_sigma',
'atl06_quality_summary', 'dac', 'rgt', 'orbit_number', 'spot',
'dh_fit_dx', 'N_50m', 'N_seg', 'h_qfit_seg', 'dh_qfit_dx',
'dh_qfit_dy', 'h_robust_sprd', 'snr_significance', 'h_qfit_50m',
'sigma_qfit_50m', 'sigma_seg', 'dz_50m', 'E_seg', 'RDE_seg',
'hbar_20m', 'RDE_50m', 't_seg', 't_qfit', 'y_atc', 'x_seg_mean',
'y_seg_mean'
]
out_template = {f: np.NaN for f in out_fields}
out = list()
for bin_name in sorted(D6_GI.keys()):
print(bin_name) if args.verbose else None
bin_xy = [int(coord) for coord in bin_name.split('_')]
# query ATL06 for the current bin, and index it
D6list = D6_GI.query_xy([[bin_xy[0]], [bin_xy[1]]],
get_data=True,
fields=ATL06_field_dict)
if not isinstance(D6list, list):
D6list = [D6list]
D6sub = pc.ATL06.data().from_list(D6list).get_xy(SRS_proj4)
# query the search tree to find points within query radius
D6xy = np.concatenate((D6sub.x[:, None], D6sub.y[:, None]), axis=1)
Qquery = Qtree.query_radius(D6xy, args.query)
# indices of ATL06 points within bin
D6ind, = np.nonzero([np.any(i) for i in Qquery])
# loop over queries in the ATL06 data
for i_AT in D6ind:
D6i = D6sub.copy_subset(np.array([i_AT]))
# grab the Qfit bins around the ATL06 bin
Qdata = Q_full.copy_subset(Qquery[i_AT], by_row=True)
Qdata.index(
np.isfinite(Qdata.elevation) & np.isfinite(Qdata.latitude)
& np.isfinite(Qdata.longitude))
# create output dictionary of ATL06 and plane-fit ATM comparison
this_out = compare_seg_with_qfit(D6i, Qdata, 0, out_template)
if this_out is not None:
out.append(this_out)
D = dict()
with h5py.File(os.path.join(out_dir, out_file), 'w') as h5f:
for field in out[0].keys():
D[field] = np.array([ii[field] for ii in out])
print(field, D[field].dtype) if args.verbose else None
h5f.create_dataset(field, data=D[field])
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed May 6 14:10:10 2020
@author: ben
"""
import pointCollection as pc
SRS_proj4 = '+proj=stere +lat_0=90 +lat_ts=70 +lon_0=-45 +k=1 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs'
gI = pc.geoIndex(SRS_proj4=SRS_proj4).for_file(
'/Volumes/ice2/ben/scf/AA_11/U07/ATL11_000110_0306_02_vU07.h5',
file_type='ATL11')
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sat Apr 4 08:32:55 2020
@author: ben
"""
import pointCollection as pc
import numpy as np
xy0 = (np.array(-360000.), np.array(-1140000.))
gi = pc.geoIndex().from_file(
'/Volumes/ice2/ben/CS2_data/GL/retrack_BC/2019/index_POCA.h5')
D = gi.query_xy(xy0, fields=['x', 'y', 'h'])
gi = None
def get_xover_data(x0, y0, rgt, GI_files, xover_cache, index_bin_size,
params_11):
"""
Read the data from other tracks.
Maintain a cache of data so that subsequent reads don't have to reload data from disk
Inputs:
x0, y0: bin centers
rgt: current rgt
GI_files: lsti of geograpic index file
xover_cache: data cache (dict)
index_bin_size: size of the bins in the index
params_11: default parameter values for the ATL11 fit
"""
# identify the crossover centers
x0_ctrs = buffered_bins(x0, y0, 2 * params_11.L_search_XT, index_bin_size)
D_xover = []
this_field_dict = params_11.ATL06_field_dict.copy()
this_field_dict.pop('dem')
for x0_ctr in x0_ctrs:
this_key = (np.real(x0_ctr), np.imag(x0_ctr))
# check if we have already read in the data for this bin
if this_key not in xover_cache:
# if we haven't already read in the data, read it in. These data will be in xover_cache[this_key]
temp = []
for GI_file in GI_files:
new_data = pc.geoIndex().from_file(GI_file).query_xy(
this_key, fields=this_field_dict)
if new_data is not None:
temp += new_data
if len(temp) == 0:
xover_cache[this_key] = None
continue
xover_cache[this_key] = {
'D':
pc.data(
fields=params_11.ATL06_xover_field_list).from_list(temp)
}
# remove the current rgt from data in the cache
xover_cache[this_key]['D'].index(
~np.in1d(xover_cache[this_key]['D'].rgt, [rgt]))
if xover_cache[this_key]['D'].size == 0:
continue
xover_cache[this_key]['D'].get_xy(EPSG=params_11.EPSG)
# index the cache at 100-m resolution
xover_cache[this_key]['index'] = pc.geoIndex(
delta=[100, 100], data=xover_cache[this_key]['D'])
# now read the data from the crossover cache
if (xover_cache[this_key] is not None) and (xover_cache[this_key]['D']
is not None):
try:
Q = xover_cache[this_key]['index'].query_xy([x0, y0],
pad=1,
get_data=False)
except KeyError:
Q = None
if Q is None:
continue
# if we have read in any data for the current bin, subset it to the bins around the reference point
for key in Q:
for i0, i1 in zip(Q[key]['offset_start'],
Q[key]['offset_end']):
D_xover.append(xover_cache[this_key]['D'][np.arange(
i0, i1 + 1, dtype=int)])
if len(D_xover) > 0:
D_xover = pc.data().from_list(D_xover)
# cleanup the cache if it is too large
if len(xover_cache.keys()) > 50:
cleanup_xover_cache(xover_cache, x0, y0, 2e4)
return D_xover
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--gps', '-G', type=str, help="GPS file to run")
parser.add_argument('--atl06',
'-I',
type=str,
help='ICESat-2 ATL06 directory to run')
parser.add_argument('--hemisphere',
'-H',
type=int,
default=-1,
help='hemisphere, must be 1 or -1')
parser.add_argument('--query',
'-Q',
type=float,
default=100,
help='KD-Tree query radius')
parser.add_argument('--median',
'-M',
default=False,
action='store_true',
help='Run block median')
parser.add_argument('--verbose',
'-v',
default=False,
action='store_true',
help='verbose output of run')
args = parser.parse_args()
if args.hemisphere == 1:
SRS_proj4 = '+proj=stere +lat_0=90 +lat_ts=70 +lon_0=-45 +k=1 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs '
elif args.hemisphere == -1:
SRS_proj4 = '+proj=stere +lat_0=-90 +lat_ts=-71 +lon_0=0 +k=1 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs'
# tilde expansion of file arguments
GPS_file = os.path.expanduser(args.gps)
GPS_dir = os.path.dirname(GPS_file)
print("working on ATL06 dir {0}, GPS file {1}".format(
args.atl06, GPS_file)) if args.verbose else None
# output directory
out_dir = os.path.join(GPS_dir, 'xovers')
if not os.path.isdir(out_dir):
os.mkdir(out_dir)
out_file = 'vs_{0}.h5'.format(
os.path.dirname(args.atl06).replace(os.sep, '_'))
if os.path.isfile(os.path.join(out_dir, out_file)):
print("found: {0}".format(os.path.join(
out_dir, out_file))) if args.verbose else None
ATL06_index = os.path.join(os.sep, 'Volumes', 'ice2', 'ben', 'scf',
'AA_06', args.atl06, 'GeoIndex.h5')
SRS_proj4 = '+proj=stere +lat_0=-90 +lat_ts=-71 +lon_0=0 +k=1 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs'
ATL06_field_dict = {
None: [
'delta_time', 'h_li', 'h_li_sigma', 'latitude', 'longitude',
'segment_id', 'sigma_geo_h', 'atl06_quality_summary'
],
'ground_track':
['x_atc', 'y_atc', 'seg_azimuth', 'sigma_geo_at', 'sigma_geo_xt'],
'geophysical': ['dac'],
'bias_correction': ['fpb_n_corr'],
'fit_statistics': [
'dh_fit_dx', 'dh_fit_dx_sigma', 'dh_fit_dy', 'h_mean',
'h_rms_misfit', 'h_robust_sprd', 'n_fit_photons',
'w_surface_window_final', 'snr_significance'
],
'orbit_info': ['rgt', 'orbit_number'],
'derived': ['BP', 'spot']
}
ATL06_fields = list()
for key in ATL06_field_dict:
ATL06_fields += ATL06_field_dict[key]
# read GPS HDF5 file
GPS_field_dict = {None: ['latitude', 'longitude', 'z']}
GPS_full = pc.data().from_h5(GPS_file,
field_dict=GPS_field_dict).get_xy(SRS_proj4)
# run block median over GPS data
if args.median:
GPS_full = blockmedian_for_gps(GPS_full, 5)
# construct search tree from GPS coordinates
# pickle tree to save computational time for future runs
if os.path.isfile(os.path.join(GPS_dir, 'tree.p')):
tree = pickle.load(open(os.path.join(GPS_dir, 'tree.p'), 'rb'))
else:
tree = KDTree(np.c_[GPS_full.x, GPS_full.y])
pickle.dump(tree, open(os.path.join(GPS_dir, 'tree.p'), 'wb'))
# read 10 km ATL06 index
D6_GI = pc.geoIndex(SRS_proj4=SRS_proj4).from_file(ATL06_index,
read_file=True)
# Query the gps search tree to find intersecting ATL06 bins
# search within radius equal to diagonal of bin with 1km buffer (12/sqrt(2))
x_10km, y_10km = D6_GI.bins_as_array()
D6ind, = np.nonzero(
tree.query_radius(np.c_[x_10km, y_10km], 8485, count_only=True))
# reduce ATL06 bins to valid
D6_GI = D6_GI.copy_subset(xyBin=[x_10km[D6ind], y_10km[D6ind]])
out_fields = [
'segment_id', 'x', 'y', 'BP', 'h_li', 'h_li_sigma',
'atl06_quality_summary', 'dac', 'rgt', 'orbit_number', 'spot',
'dh_fit_dx', 'N_50m', 'N_seg', 'h_gps_seg', 'dh_gps_dx', 'dh_gps_dy',
'h_robust_sprd', 'snr_significance', 'h_gps_50m', 'sigma_gps_50m',
'sigma_seg', 'dz_50m', 'E_seg', 'RDE_seg', 'hbar_20m', 'RDE_50m',
't_seg', 'y_atc', 'x_seg_mean', 'y_seg_mean'
]
out_template = {f: np.NaN for f in out_fields}
out = list()
for bin_name in sorted(D6_GI.keys()):
print(bin_name) if args.verbose else None
bin_xy = [int(coord) for coord in bin_name.split('_')]
# query ATL06 for the current bin, and index it
D6list = D6_GI.query_xy([[bin_xy[0]], [bin_xy[1]]],
get_data=True,
fields=ATL06_field_dict)
if not isinstance(D6list, list):
D6list = [D6list]
D6sub = pc.ATL06.data().from_list(D6list).get_xy(SRS_proj4)
D6sub.ravel_fields()
# query the search tree to find points within query radius
#D6xy = np.c_[(np.nanmean(D6sub.x, axis=1),np.nanmean(D6sub.y, axis=1))]
D6sub.index(np.isfinite(D6sub.x) & np.isfinite(D6sub.h_li))
D6xy = np.c_[D6sub.x, D6sub.y]
query = tree.query_radius(D6xy, args.query)
# indices of ATL06 points within bin
D6ind, = np.nonzero([np.any(i) for i in query])
# loop over queries in the ATL06 data
for i_AT in D6ind:
D6i = D6sub.copy_subset(np.array([i_AT]))
# grab the gps bins around the ATL06 bin
GPS = GPS_full.copy_subset(query[i_AT], by_row=True)
GPS.index(
np.isfinite(GPS.z) & np.isfinite(GPS.latitude)
& np.isfinite(GPS.longitude))
# create output dictionary of ATL06 and GPS comparison
this_out = compare_seg_with_gps(D6i, GPS, out_template)
if this_out is not None:
out.append(this_out)
D = dict()
with h5py.File(os.path.join(out_dir, out_file), 'w') as h5f:
for field in out[0].keys():
D[field] = np.array([ii[field] for ii in out])
print(field, D[field].dtype) if args.verbose else None
h5f.create_dataset(field, data=D[field])
def read_ATL11(xy0, Wxy, index_file, SRS_proj4, sigma_geo=6.5):
'''
read ATL11 data from an index file
inputs:
xy0 : 2-element iterable specifying the domain center
Wxy : Width of the domain
index_file : file made by pointCollection.geoindex pointing at ATL11 data
SRS_proj4: projection information for the data
output:
D: data structure
file_list: list of ATL11 files read
'''
field_dict_11={None:['latitude','longitude','delta_time',\
'h_corr','h_corr_sigma','h_corr_sigma_systematic', 'ref_pt'],\
'__calc_internal__' : ['rgt'],
'cycle_stats' : {'tide_ocean','dac'},
'ref_surf':['e_slope','n_slope', 'x_atc', 'fit_quality']}
try:
# catch empty data
D11_list=pc.geoIndex().from_file(index_file).query_xy_box(
xy0[0]+np.array([-Wxy/2, Wxy/2]), \
xy0[1]+np.array([-Wxy/2, Wxy/2]), fields=field_dict_11)
except ValueError:
return None, []
if D11_list is None:
return None, []
D_list=[]
XO_list=[]
file_list= [ Di.filename for Di in D11_list ]
for D11 in D11_list:
D11.get_xy(proj4_string=SRS_proj4)
# select the subset of the data within the domain
D11.index((np.abs(D11.x[:,0]-xy0[0]) <= Wxy/2) &\
(np.abs(D11.y[:,0]-xy0[1]) <= Wxy/2))
if D11.size==0:
continue
sigma_corr=np.sqrt((sigma_geo*np.abs(np.median(D11.n_slope)))**2+\
(sigma_geo*np.abs(np.median(D11.e_slope)))**2+0.03**2)
# fix for early ATL11 versions that had some zero error estimates.
bad=np.any(D11.h_corr_sigma==0, axis=1)
D11.h_corr_sigma[bad,:]=np.NaN
n_cycles=np.sum(np.isfinite(D11.h_corr), axis=1)
n_cycles=np.reshape(n_cycles, (D11.shape[0],1))
n_cycles=np.tile(n_cycles, [1, D11.shape[1]])
D_list += [pc.data().from_dict({'z':D11.h_corr,
'sigma_corr':sigma_corr+np.zeros_like(D11.h_corr),
'sigma':D11.h_corr_sigma,
'x':D11.x,
'y':D11.y,
'x_atc': D11.x_atc,
'latitude':D11.latitude,
'longitude':D11.longitude,
'rgt':D11.rgt,
'pair':np.zeros_like(D11.x)+D11.pair,
'ref_pt':D11.ref_pt,
'cycle':D11.cycle_number,
'n_cycles': n_cycles,
'fit_quality': D11.fit_quality,
'tide_ocean': D11.tide_ocean,
'dac': D11.dac,
'delta_time': D11.delta_time,
'time':D11.delta_time/24/3600/365.25+2018,
'n_slope':D11.n_slope,
'e_slope':D11.e_slope,
'time':D11.delta_time/24/3600/365.25+2018,
'along_track':np.ones_like(D11.x, dtype=bool)})]
if len(D11.ref_pt) == 0:
continue
# N.B. D11 is getting indexed in this step, and it's leading to the warning in
# line 76. Can fix by making crossover_data.from_h5 copy D11 on input
D_x = pc.ATL11.crossover_data().from_h5(D11.filename, pair=D11.pair, D_at=D11)
if D_x is None:
continue
# fit_quality D11 applies to all cycles, but is mapped only to some specific
# cycle.
temp=np.nanmax(D_x.fit_quality[:,:,0], axis=1)
for cycle in range(D_x.shape[1]):
D_x.fit_quality[:,cycle,1]=temp
D_x.get_xy(proj4_string=SRS_proj4)
good=np.isfinite(D_x.h_corr)[:,0:2,1].ravel()
for field in D_x.fields:
# Pull out only cycles 1 and 2
temp=getattr(D_x, field)[:,0:2,1]
setattr(D_x, field, temp.ravel()[good])
# select the subset of the data within the domain
D_x.index((np.abs(D_x.x-xy0[0]) <= Wxy/2) &\
(np.abs(D_x.y-xy0[1]) <= Wxy/2))
if D_x.size==0:
continue
#N.B. Check whether n_slope and e_slope are set correctly.
zero = np.zeros_like(D_x.h_corr)
blank = zero+np.NaN
XO_list += [pc.data().from_dict({'z':D_x.h_corr,
'sigma':D_x.h_corr_sigma,
'sigma_corr': sigma_corr+np.zeros_like(D_x.h_corr),
'x':D_x.x,
'y':D_x.y,
'latitude':D_x.latitude,
'longitude':D_x.longitude,
'rgt':D_x.rgt,
'pair':np.zeros_like(D_x.x)+D_x.pair,
'ref_pt':blank,
'cycle':D_x.cycle_number,
'n_cycles':blank,
'fit_quality':D_x.fit_quality,
'tide_ocean':D_x.tide_ocean,
'dac':D_x.dac,
'delta_time':D_x.delta_time,
'n_slope':D_x.n_slope,
'e_slope':D_x.e_slope,
'time':D_x.delta_time/24/3600/365.25+2018,
'along_track':np.zeros_like(D_x.x, dtype=bool)})]
try:
D=pc.data().from_list(D_list+XO_list).ravel_fields()
D.index(np.isfinite(D.z))
except ValueError:
# catch empty data
return None, file_list
D.index(( D.fit_quality ==0 ) | ( D.fit_quality == 2 ))
return D, file_list
def read_ICESat2(xy0, W, gI_file, sensor=2, SRS_proj4=None, tiled=True, seg_diff_tol=2, blockmedian_scale=None, cplx_accept_threshold=0.):
field_dict={None:['delta_time','h_li','h_li_sigma','latitude','longitude','atl06_quality_summary','segment_id','sigma_geo_h'],
'fit_statistics':['dh_fit_dx', 'dh_fit_dy', 'n_fit_photons','w_surface_window_final','snr_significance'],
'geophysical':['tide_ocean'],
'ground_track':['x_atc'],
'orbit_info':['rgt','cycle_number'],
'derived':['valid', 'BP','LR']}
if tiled:
fields=[]
for key in field_dict:
fields += field_dict[key]
fields += ['x','y']
else:
fields=field_dict
px, py=np.meshgrid(np.arange(xy0[0]-W['x']/2, xy0[0]+W['x']/2+1.e4, 1.e4),np.arange(xy0[1]-W['y']/2, xy0[1]+W['y']/2+1.e4, 1.e4) )
D0=pc.geoIndex().from_file(gI_file).query_xy((px.ravel(), py.ravel()), fields=fields)
if D0 is None or len(D0)==0:
return [None]
# check the D6 filenames against the blacklist of bad files
if tiled:
D0=pc.reconstruct_ATL06_tracks(pc.data(fields=fields).from_list(D0))
hold_list = read_hold_files()
hold_list = {(item[0], item[1]) for item in hold_list}
D1=list()
for ind, D in enumerate(D0):
if D.size<2:
continue
delete_file = (D.cycle_number[0], D.rgt[0]) in hold_list
if delete_file==0:
D1.append(D)
# D1 is now a filtered version of D0
D_pt=pc.data().from_list(D1)
bin_xy=1.e4*np.round((D_pt.x+1j*D_pt.y)/1.e4)
cplx_bins=[]
for xy0 in np.unique(bin_xy):
ii=np.flatnonzero(bin_xy==xy0)
if np.mean(D_pt.atl06_quality_summary[ii]==0) < cplx_accept_threshold:
cplx_bins+=[xy0]
cplx_bins=np.array(cplx_bins)
sigma_corr=np.zeros(len(D1))
for ind, D in enumerate(D1):
valid=segDifferenceFilter(D, setValid=False, toNaN=False, tol=seg_diff_tol)
D.assign({'quality':D.atl06_quality_summary})
cplx_data=np.in1d(1.e4*np.round((D.x+1j*D.y)/1.e4), cplx_bins)
if np.any(cplx_data):
D.quality[cplx_data] = (D.snr_significance[cplx_data] > 0.02) | \
(D.n_fit_photons[cplx_data]/D.w_surface_window_final[cplx_data] < 5)
valid[cplx_data] |= segDifferenceFilter(D, setValid=False, toNaN=False, tol=2*seg_diff_tol)[cplx_data]
D.h_li[valid==0] = np.NaN
D.h_li[D.quality==1] = np.NaN
if blockmedian_scale is not None:
D.blockmedian(blockmedian_scale, field='h_li')
# rename the h_li field to 'z', and set time to the year
# note that the extra half day is needed because 2018 is in between two leap years
D.assign({'z': D.h_li, 'time':D.delta_time/24/3600/365.25+2018+0.5/365.25,
'sigma':D.h_li_sigma,'cycle':D.cycle_number})
# thin to 40 m
D.index(np.mod(D.segment_id, 2)==0)
if 'x' not in D.fields:
D.get_xy(SRS_proj4)
#D.index(np.isfinite(D.h_li), list_of_fields=['x','y','z','time','year','sigma','sigma_corr','rgt','cycle'])
D.assign({'sensor':np.zeros_like(D.x)+sensor})
if np.any(np.isfinite(D.dh_fit_dy)):
dhdy_med=np.nanmedian(D.dh_fit_dy)
dhdx_med=np.nanmedian(D.dh_fit_dx)
else:
dhdy_med=np.NaN
dhdx_med=np.NaN
sigma_geo_x=8
sigma_corr[ind]=np.sqrt(0.03**2+sigma_geo_x**2*(dhdx_med**2+dhdy_med**2))
if ~np.isfinite(sigma_corr[ind]):
sigma_corr[ind]=0.1
D.assign({'sigma_corr':np.zeros_like(D.h_li)+sigma_corr[ind]})
D1[ind]=D.copy_subset(np.isfinite(D.h_li), datasets=['x','y','z','time',\
'delta_time','sigma','sigma_corr','rgt','cycle',\
'sensor', 'BP','LR'])
return D1
def read_ATL11(xy0, Wxy, index_file, SRS_proj4):
field_dict_11={None:['latitude','longitude','delta_time',\
'h_corr','h_corr_sigma','h_corr_sigma_systematic', 'ref_pt'],\
'__calc_internal__' : ['rgt'],
'cycle_stats' : {'tide_ocean','dac'},
'ref_surf':['e_slope','n_slope', 'x_atc', 'fit_quality']}
D11_list=pc.geoIndex().from_file(index_file).query_xy_box(xy0[0]+\
np.array([-Wxy/2, Wxy/2]), xy0[1]+np.array([-Wxy/2, Wxy/2]), fields=field_dict_11)
D_list = []
XO_list = []
for D11 in D11_list:
D11.get_xy(proj4_string=SRS_proj4)
sigma_corr=np.sqrt((7.5*np.abs(np.median(D11.n_slope)))**2+\
(7.5*np.abs(np.median(D11.e_slope)))**2+0.03**2)
# fix for early ATL11 versions that had some zero error estimates.
bad = np.any(D11.h_corr_sigma == 0, axis=1)
D11.h_corr_sigma[bad, :] = np.NaN
n_cycles = np.sum(np.isfinite(D11.h_corr), axis=1)
n_cycles = np.reshape(n_cycles, (D11.shape[0], 1))
n_cycles = np.tile(n_cycles, [1, D11.shape[1]])
D_list += [
pc.data().from_dict({
'z':
D11.h_corr,
'sigma_corr':
sigma_corr + np.zeros_like(D11.h_corr),
'sigma':
D11.h_corr_sigma,
'x':
D11.x,
'y':
D11.y,
'x_atc':
D11.x_atc,
'latitude':
D11.latitude,
'longitude':
D11.longitude,
'rgt':
D11.rgt,
'ref_pt':
D11.ref_pt,
'cycle':
D11.cycle_number,
'n_cycles':
n_cycles,
'fit_quality':
D11.fit_quality,
'tide_ocean':
D11.tide_ocean,
'dac':
D11.dac,
'delta_time':
D11.delta_time,
'time':
D11.delta_time / 24 / 3600 / 365.25 + 2018
})
]
D_x = pc.ATL11.crossover_data().from_h5(D11.filename,
pair=D11.pair,
D_at=D11)
# fit_quality D11 applies to all cycles, but is mapped only to some specific
# cycle.
temp = np.nanmax(D_x.fit_quality[:, :, 0], axis=1)
for cycle in range(D_x.shape[1]):
D_x.fit_quality[:, cycle, 1] = temp
D_x.get_xy(proj4_string=SRS_proj4)
good = np.isfinite(D_x.h_corr)[:, 0:2, 1].ravel()
for field in D_x.fields:
# Pull out only cycles 1 and 2
temp = getattr(D_x, field)[:, 0:2, 1]
setattr(D_x, field, temp.ravel()[good])
zero = np.zeros_like(D_x.h_corr)
blank = zero + np.NaN
XO_list += [
pc.data().from_dict({
'z':
D_x.h_corr,
'sigma':
D_x.h_corr_sigma,
'sigma_corr':
sigma_corr + np.zeros_like(D_x.h_corr),
'x':
D_x.x,
'y':
D_x.y,
'latitude':
D_x.latitude,
'longitude':
D_x.longitude,
'rgt':
D_x.rgt,
'ref_pt':
blank,
'cycle':
D_x.cycle_number,
'n_cycles':
blank,
'fit_quality':
D_x.fit_quality,
'tide_ocean':
D_x.tide_ocean,
'dac':
D_x.dac,
'delta_time':
D_x.delta_time,
'time':
D_x.delta_time / 24 / 3600 / 365.25 + 2018
})
]
D = pc.data().from_list(D_list + XO_list).ravel_fields()
print({field: getattr(D, field).shape for field in D.fields})
D.index((D.fit_quality == 0) | (D.fit_quality == 2))
return D