def main(argv):
inps = cmdLineParse()
if not inps.disp_fig:
plt.switch_backend('Agg')
if inps.template_file:
inps = read_template2inps(inps.template_file, inps)
##### 1. Read Info
# Read dateList and bperpList
ext = os.path.splitext(inps.file)[1]
if ext in ['.h5']:
atr = readfile.read_attribute(inps.file)
k = atr['FILE_TYPE']
print 'reading date and perpendicular baseline from ' + k + ' file: ' + os.path.basename(
inps.file)
if not k in multi_group_hdf5_file:
raise ValueError('only the following file type are supported:\n' +
str(multi_group_hdf5_file))
if not inps.coherence_file and k == 'coherence':
inps.coherence_file = inps.file
pbase_list = ut.perp_baseline_ifgram2timeseries(inps.file)[0]
date8_list = ptime.ifgram_date_list(inps.file)
else:
print 'reading date and perpendicular baseline from baseline list file: ' + inps.bl_list_file
date8_list, pbase_list = pnet.read_baseline_file(
inps.bl_list_file)[0:2]
print 'number of acquisitions : ' + str(len(date8_list))
# Read Pairs Info
print 'reading pairs info from file: ' + inps.file
date12_list = pnet.get_date12_list(inps.file)
print 'number of interferograms: ' + str(len(date12_list))
# Read drop_ifgram
date8_list_drop = []
date12_list_drop = []
if ext in ['.h5', '.he5']:
h5 = h5py.File(inps.file, 'r')
ifgram_list_all = sorted(h5[k].keys())
ifgram_list_keep = ut.check_drop_ifgram(h5)
date12_list_keep = ptime.list_ifgram2date12(ifgram_list_keep)
# Get date12_list_drop
date12_list_drop = sorted(
list(set(date12_list) - set(date12_list_keep)))
print 'number of interferograms marked as dropped: ' + str(
len(date12_list_drop))
print 'number of interferograms marked as kept : ' + str(
len(date12_list_keep))
# Get date_list_drop
m_dates = [i.split('-')[0] for i in date12_list_keep]
s_dates = [i.split('-')[1] for i in date12_list_keep]
date8_list_keep = ptime.yyyymmdd(sorted(list(set(m_dates + s_dates))))
date8_list_drop = sorted(list(set(date8_list) - set(date8_list_keep)))
print 'number of acquisitions marked as dropped: ' + str(
len(date8_list_drop))
# Read Coherence List
inps.coherence_list = None
if inps.coherence_file and os.path.isfile(inps.coherence_file):
if inps.mask_file and not os.path.isfile(inps.mask_file):
inps.mask_file = None
inps.coherence_list, inps.coh_date12_list = ut.spatial_average(inps.coherence_file, inps.mask_file, \
saveList=True, checkAoi=False)
if all(np.isnan(inps.coherence_list)):
print 'WARNING: all coherence value are nan! Do not use this and continue.'
inps.coherence_list = None
# Check subset of date12 info between input file and coherence file
if not set(inps.coh_date12_list) >= set(date12_list):
print 'WARNING: not every pair/date12 from input file is in coherence file'
print 'turn off the color plotting of interferograms based on coherence'
inps.coherence_list = None
elif set(inps.coh_date12_list) > set(date12_list):
print 'extract coherence value for all pair/date12 in input file'
inps.coherence_list = [
inps.coherence_list[inps.coh_date12_list.index(i)]
for i in date12_list
]
#inps.coh_thres = 0.7
##### 2. Plot
inps.cbar_label = 'Average spatial coherence'
# Fig 1 - Baseline History
fig = plt.figure()
ax = fig.add_subplot(111)
ax = pnet.plot_perp_baseline_hist(ax, date8_list, pbase_list, vars(inps),
date8_list_drop)
figName = 'BperpHistory' + inps.fig_ext
if inps.save_fig:
fig.savefig(figName, bbox_inches='tight')
print 'save figure to ' + figName
# Fig 2 - Coherence Matrix
if inps.coherence_list:
figName = 'CoherenceMatrix' + inps.fig_ext
if inps.fig_size:
fig = plt.figure(figsize=inps.fig_size)
else:
fig = plt.figure()
ax = fig.add_subplot(111)
ax = pnet.plot_coherence_matrix(ax, date12_list, inps.coherence_list,\
date12_list_drop, plot_dict=vars(inps))
if inps.save_fig:
fig.savefig(figName, bbox_inches='tight', dpi=150)
print 'save figure to ' + figName
# Fig 3 - Min/Max Coherence History
if inps.coherence_list:
figName = 'CoherenceHistory' + inps.fig_ext
fig = plt.figure()
ax = fig.add_subplot(111)
ax = pnet.plot_coherence_history(ax, date12_list, inps.coherence_list)
if inps.save_fig:
fig.savefig(figName, bbox_inches='tight')
print 'save figure to ' + figName
# Fig 4 - Interferogram Network
if inps.fig_size:
fig = plt.figure(figsize=inps.fig_size)
else:
fig = plt.figure()
ax = fig.add_subplot(111)
ax = pnet.plot_network(ax, date12_list, date8_list, pbase_list, vars(inps),
date12_list_drop)
figName = 'Network' + inps.fig_ext
if inps.save_fig:
fig.savefig(figName, bbox_inches='tight')
print 'save figure to ' + figName
if inps.save_list:
txtFile = os.path.splitext(inps.file)[0] + '_date12_list.txt'
np.savetxt(txtFile, date12_list, fmt='%s')
print 'save pairs/date12 info to file: ' + txtFile
if inps.disp_fig:
plt.show()
def main(argv):
# Read inputs
inps = cmdLineParse()
inps = read_template2inps(inps.template_file, inps)
log(os.path.basename(sys.argv[0]) + ' ' + inps.template_file)
project_name = os.path.splitext(os.path.basename(inps.template_file))[0]
print 'project name: ' + project_name
if not inps.sensor:
inps.sensor = project_name2sensor(project_name)
# Auto path setting for Miami user
if not inps.baseline_file and pysar.miami_path and 'SCRATCHDIR' in os.environ:
if pysar.miami_path and 'SCRATCHDIR' in os.environ:
try:
inps.baseline_file = glob.glob(
os.getenv('SCRATCHDIR') + '/' + project_name +
'/SLC/bl_list.txt')[0]
except:
inps.baseline_file = None
# Pair selection from reference
if inps.reference_file:
print 'Use pairs info from reference file: ' + inps.reference_file
date12_list = pnet.get_date12_list(inps.reference_file)
date12_list = [i.replace('_', '-') for i in date12_list]
if inps.baseline_file:
date8_list, pbase_list, dop_list = pnet.read_baseline_file(
inps.baseline_file)[0:3]
date6_list = ptime.yymmdd(date8_list)
tbase_list = ptime.date_list2tbase(date8_list)[0]
# Pair selection from temp/perp/dop baseline info
else:
if not inps.baseline_file:
raise Exception('ERROR: No baseline file found!')
# Check start/end/exclude date
date8_list = pnet.read_baseline_file(inps.baseline_file)[0]
inps.exclude_date = ptime.yyyymmdd(inps.exclude_date)
if not inps.exclude_date:
inps.exclude_date = []
else:
print 'input exclude dates: ' + str(inps.exclude_date)
if inps.start_date:
print 'input start date: ' + inps.start_date
inps.exclude_date += [
i for i in date8_list
if float(i) < float(ptime.yyyymmdd(inps.start_date))
]
inps.exclude_date = sorted(inps.exclude_date)
if inps.end_date:
print 'input end date: ' + inps.end_date
inps.exclude_date += [
i for i in date8_list
if float(i) > float(ptime.yyyymmdd(inps.end_date))
]
inps.exclude_date = sorted(inps.exclude_date)
if inps.exclude_date:
print 'exclude dates: '
print inps.exclude_date
# Read baseline list file: bl_list.txt
inps.exclude_date = ptime.yymmdd(inps.exclude_date)
date8_list, pbase_list, dop_list = pnet.read_baseline_file(
inps.baseline_file, inps.exclude_date)[0:3]
date6_list = ptime.yymmdd(date8_list)
tbase_list = ptime.date_list2tbase(date8_list)[0]
# Initial network using input methods
inps.method = inps.method.lower().replace('-', '_')
if inps.method in ['star', 'ps']: inps.method = 'star'
elif inps.method.startswith('seq'): inps.method = 'sequential'
elif inps.method.startswith('hierar'): inps.method = 'hierarchical'
elif inps.method in [
'mst', 'min_spanning_tree', 'minimum_spanning_tree'
]:
inps.method = 'mst'
print 'select method: ' + inps.method
if inps.method == 'all':
date12_list = pnet.select_pairs_all(date6_list)
elif inps.method == 'delaunay':
date12_list = pnet.select_pairs_delaunay(date6_list, pbase_list,
inps.norm)
elif inps.method == 'star':
date12_list = pnet.select_pairs_star(date6_list)
elif inps.method == 'sequential':
date12_list = pnet.select_pairs_sequential(date6_list,
inps.increment_num)
elif inps.method == 'hierarchical':
date12_list = pnet.select_pairs_hierarchical(
date6_list, pbase_list, inps.temp_perp_list)
elif inps.method == 'mst':
date12_list = pnet.select_pairs_mst(date6_list, pbase_list)
else:
raise Exception('Unrecoganized select method: ' + inps.method)
print 'initial number of interferograms: ' + str(len(date12_list))
# Filter pairs (optional) using temp/perp/doppler baseline threshold
if inps.method in ['star', 'hierarchical', 'mst']:
inps.threshold = False
if inps.threshold:
# Temporal baseline
date12_list = pnet.threshold_temporal_baseline(date12_list, inps.temp_base_max,\
inps.keep_seasonal, inps.temp_base_min)
print 'number of interferograms after filtering of <%d, %d> days in temporal baseline: %d'\
% (inps.temp_base_min, inps.temp_base_max, len(date12_list))
if inps.keep_seasonal:
print '\tkeep seasonal pairs, i.e. pairs with temporal baseline == N*years +/- one month'
# Perpendicular spatial baseline
date12_list = pnet.threshold_perp_baseline(date12_list, date6_list,
pbase_list,
inps.perp_base_max)
print 'number of interferograms after filtering of max %d meters in perpendicular baseline: %d'\
% (inps.perp_base_max, len(date12_list))
# Doppler Overlap Percentage
if inps.sensor:
bandwidth_az = pnet.azimuth_bandwidth(inps.sensor)
date12_list = pnet.threshold_doppler_overlap(date12_list, date6_list, dop_list,\
bandwidth_az, inps.dop_overlap_min/100.0)
print 'number of interferograms after filtering of min '+str(inps.dop_overlap_min)+'%'+\
' overlap in azimuth Doppler frequency: '+str(len(date12_list))
# Write ifgram_list.txt
if not date12_list:
print 'WARNING: No interferogram selected!'
return None
# date12_list to date_list
m_dates = [
date12.replace('_', '-').split('-')[0] for date12 in date12_list
]
s_dates = [
date12.replace('_', '-').split('-')[1] for date12 in date12_list
]
try:
print 'number of acquisitions input : ' + str(len(date6_list))
except:
pass
print 'number of acquisitions selected: ' + str(
len(list(set(m_dates + s_dates))))
print 'number of interferograms selected: ' + str(len(date12_list))
# Output directory/filename
if not inps.outfile:
if pysar.miami_path and 'SCRATCHDIR' in os.environ:
inps.out_dir = os.getenv(
'SCRATCHDIR') + '/' + project_name + '/PROCESS'
else:
try:
inps.out_dir = os.path.dirname(
os.path.abspath(inps.reference_file))
except:
inps.out_dir = os.path.dirname(
os.path.abspath(inps.baseline_file))
inps.outfile = inps.out_dir + '/ifgram_list.txt'
inps.outfile = os.path.abspath(inps.outfile)
inps.out_dir = os.path.dirname(inps.outfile)
if not os.path.isdir(inps.out_dir):
os.makedirs(inps.out_dir)
print 'writing >>> ' + inps.outfile
if not inps.baseline_file:
np.savetxt(inps.outfile, date12_list, fmt='%s')
return inps.outfile
## Calculate Bperp, Btemp and predicted coherence
ifgram_num = len(date12_list)
ifgram_pbase_list = []
ifgram_tbase_list = []
for i in range(ifgram_num):
m_date, s_date = date12_list[i].split('-')
m_idx = date6_list.index(m_date)
s_idx = date6_list.index(s_date)
pbase = pbase_list[s_idx] - pbase_list[m_idx]
tbase = tbase_list[s_idx] - tbase_list[m_idx]
ifgram_pbase_list.append(pbase)
ifgram_tbase_list.append(tbase)
try:
inps.coherence_list = pnet.simulate_coherence(
date12_list, inps.baseline_file,
sensor=inps.sensor).flatten().tolist()
inps.cbar_label = 'Simulated coherence'
except:
inps.coherence_list = None
##### Write txt file
fl = open(inps.outfile, 'w')
fl.write('#Interferograms configuration generated by select_network.py\n')
fl.write('# Date12 Btemp(days) Bperp(m) sim_coherence\n')
for i in range(len(date12_list)):
line = '%s %6.0f %6.1f' % (
date12_list[i], ifgram_tbase_list[i], ifgram_pbase_list[i])
if inps.coherence_list:
line += ' %1.4f' % (inps.coherence_list[i])
fl.write(line + '\n')
fl.close()
##### Plot network info
if not inps.disp_fig:
plt.switch_backend('Agg')
out_fig_name = 'BperpHistory.pdf'
print 'plotting baseline history in temp/perp baseline domain to file: ' + out_fig_name
fig2, ax2 = plt.subplots()
ax2 = pnet.plot_perp_baseline_hist(ax2, date8_list, pbase_list)
plt.savefig(inps.out_dir + '/' + out_fig_name, bbox_inches='tight')
out_fig_name = 'Network.pdf'
print 'plotting network / pairs in temp/perp baseline domain to file: ' + out_fig_name
fig1, ax1 = plt.subplots()
ax1 = pnet.plot_network(ax1,
date12_list,
date8_list,
pbase_list,
plot_dict=vars(inps),
print_msg=False)
plt.savefig(inps.out_dir + '/' + out_fig_name, bbox_inches='tight')
out_fig_name = 'CoherenceMatrix.pdf'
if inps.coherence_list:
print 'plotting predicted coherence matrix to file: ' + out_fig_name
fig3, ax3 = plt.subplots()
ax3 = pnet.plot_coherence_matrix(ax3,
date12_list,
inps.coherence_list,
plot_dict=vars(inps))
plt.savefig(inps.out_dir + '/' + out_fig_name, bbox_inches='tight')
if inps.disp_fig:
plt.show()
return inps.outfile
def main(argv):
inps = cmdLineParse()
if not inps.disp_fig:
plt.switch_backend('Agg')
#print '\n******************** Plot Network **********************'
##### 1. Read Info
# Read dateList and bperpList
ext = os.path.splitext(inps.file)[1]
if ext in ['.h5']:
atr = readfile.read_attribute(inps.file)
k = atr['FILE_TYPE']
print 'reading date and perpendicular baseline from '+k+' file: '+os.path.basename(inps.file)
if not k in multi_group_hdf5_file:
raise ValueError('only the following file type are supported:\n'+str(multi_group_hdf5_file))
pbase_list = ut.perp_baseline_ifgram2timeseries(inps.file)[0]
date8_list = ptime.ifgram_date_list(inps.file)
else:
print 'reading date and perpendicular baseline from baseline list file: '+inps.bl_list_file
date8_list, pbase_list = pnet.read_baseline_file(inps.bl_list_file)[0:2]
print 'number of acquisitions : '+str(len(date8_list))
# Read Pairs Info
print 'reading pairs info from file: '+inps.file
date12_list = pnet.get_date12_list(inps.file)
print 'number of interferograms: '+str(len(date12_list))
# Read drop_ifgram
date8_list_drop = []
date12_list_drop = []
if ext in ['.h5','.he5']:
h5 = h5py.File(inps.file, 'r')
ifgram_list_all = sorted(h5[k].keys())
ifgram_list_keep = ut.check_drop_ifgram(h5, atr, ifgram_list_all)
date12_list_keep = ptime.list_ifgram2date12(ifgram_list_keep)
# Get date12_list_drop
date12_list_drop = sorted(list(set(date12_list) - set(date12_list_keep)))
print 'number of interferograms marked as dropped: '+str(len(date12_list_drop))
# Get date_list_drop
m_dates = [i.split('-')[0] for i in date12_list_keep]
s_dates = [i.split('-')[1] for i in date12_list_keep]
date8_list_keep = ptime.yyyymmdd(sorted(list(set(m_dates + s_dates))))
date8_list_drop = sorted(list(set(date8_list) - set(date8_list_keep)))
print 'number of acquisitions marked as dropped: '+str(len(date8_list_drop))
# Read Coherence List
inps.coherence_list = None
if inps.coherence_file and os.path.isfile(inps.coherence_file):
ext = os.path.splitext(inps.coherence_file)[1]
if ext in ['.h5']:
listFile = os.path.splitext(inps.coherence_file)[0]+'_spatialAverage.txt'
if os.path.isfile(listFile):
print 'reading coherence value from existed '+listFile
fcoh = np.loadtxt(listFile, dtype=str)
inps.coherence_list = [float(i) for i in fcoh[:,1]]
inps.coh_date12_list = [i for i in fcoh[:,0]]
else:
print 'calculating average coherence value from '+inps.coherence_file
if inps.mask_file:
mask = readfile.read(inps.mask_file)[0]
else:
mask = None
inps.coherence_list = ut.spatial_average(inps.coherence_file, mask, saveList=True)
inps.coh_date12_list = pnet.get_date12_list(inps.coherence_file)
else:
print 'reading coherence value from '+inps.coherence_file
fcoh = np.loadtxt(inps.coherence_file, dtype=str)
inps.coherence_list = [float(i) for i in fcoh[:,1]]
inps.coh_date12_list = [i for i in fcoh[:,0]]
# Check length of coherence file and input file
if not set(inps.coh_date12_list) == set(date12_list):
print 'WARNING: input coherence list has different pairs/date12 from input file'
print 'turn off the color plotting of interferograms based on coherence'
inps.coherence_list = None
#inps.coh_thres = 0.7
##### 2. Plot
# Fig 1 - Baseline History
fig = plt.figure()
ax = fig.add_subplot(111)
ax = pnet.plot_perp_baseline_hist(ax, date8_list, pbase_list, vars(inps), date8_list_drop)
figName = 'BperpHistory'+inps.fig_ext
if inps.save_fig:
fig.savefig(figName,bbox_inches='tight')
print 'save figure to '+figName
# Fig 2 - Coherence Matrix
if inps.coherence_list:
figName = 'CoherenceMatrix'+inps.fig_ext
if inps.fig_size:
fig = plt.figure(figsize=inps.fig_size)
else:
fig = plt.figure()
ax = fig.add_subplot(111)
ax = pnet.plot_coherence_matrix(ax, date12_list, inps.coherence_list)
if inps.save_fig:
fig.savefig(figName, bbox_inches='tight')
print 'save figure to '+figName
# Fig 3 - Min/Max Coherence History
if inps.coherence_list:
figName = 'CoherenceHistory'+inps.fig_ext
fig = plt.figure()
ax = fig.add_subplot(111)
ax = pnet.plot_coherence_history(ax, date12_list, inps.coherence_list)
if inps.save_fig:
fig.savefig(figName, bbox_inches='tight')
print 'save figure to '+figName
# Fig 4 - Interferogram Network
if inps.fig_size:
fig = plt.figure(figsize=inps.fig_size)
else:
fig = plt.figure()
ax = fig.add_subplot(111)
ax = pnet.plot_network(ax, date12_list, date8_list, pbase_list, vars(inps), date12_list_drop)
figName = 'Network'+inps.fig_ext
if inps.save_fig:
fig.savefig(figName,bbox_inches='tight')
print 'save figure to '+figName
if inps.save_list:
txtFile = os.path.splitext(inps.file)[0]+'_date12_list.txt'
np.savetxt(txtFile, date12_list, fmt='%s')
print 'save pairs/date12 info to file: '+txtFile
if inps.disp_fig:
plt.show()
def main(argv):
inps = cmdLineParse()
if not inps.disp_fig:
plt.switch_backend('Agg')
print '\n******************** Plot Network **********************'
# Output figure name
figName1 = 'BperpHist' + inps.fig_ext
figName2 = 'Network' + inps.fig_ext
if 'Modified' in inps.file:
figName1 = 'BperpHist_Modified' + inps.fig_ext
figName2 = 'Network_Modified' + inps.fig_ext
##### 1. Read Info
# Read dateList and bperpList
ext = os.path.splitext(inps.file)[1]
if ext in ['.h5']:
k = readfile.read_attribute(inps.file)['FILE_TYPE']
print 'reading date and perpendicular baseline from ' + k + ' file: ' + os.path.basename(
inps.file)
if not k in multi_group_hdf5_file:
print 'ERROR: only the following file type are supported:\n' + str(
multi_group_hdf5_file)
sys.exit(1)
Bp = ut.Baseline_timeseries(inps.file)
date8List = ptime.igram_date_list(inps.file)
date6List = ptime.yymmdd(date8List)
else:
print 'reading date and perpendicular baseline from baseline list file: ' + inps.bl_list_file
date8List, Bp = pnet.read_baseline_file(inps.bl_list_file)[0:2]
date6List = ptime.yymmdd(date8List)
print 'number of acquisitions: ' + str(len(date8List))
# Read Pairs Info
print 'reading pairs info from file: ' + inps.file
date12_list = pnet.get_date12_list(inps.file)
pairs_idx = pnet.date12_list2index(date12_list, date6List)
print 'number of pairs : ' + str(len(pairs_idx))
# Read Coherence List
inps.coherence_list = None
if inps.coherence_file and os.path.isfile(inps.coherence_file):
ext = os.path.splitext(inps.coherence_file)[1]
if ext in ['.h5']:
listFile = os.path.splitext(
inps.coherence_file)[0] + '_spatialAverage.list'
if os.path.isfile(listFile):
print 'reading coherence value from existed ' + listFile
fcoh = np.loadtxt(listFile, dtype=str)
inps.coherence_list = [float(i) for i in fcoh[:, 1]]
coh_date12_list = [i for i in fcoh[:, 0]]
else:
print 'calculating average coherence value from ' + inps.coherence_file
inps.coherence_list = ut.spatial_average(inps.coherence_file,
saveList=True)
coh_date12_list = pnet.get_date12_list(inps.coherence_file)
else:
print 'reading coherence value from ' + inps.coherence_file
fcoh = np.loadtxt(inps.coherence_file, dtype=str)
inps.coherence_list = [float(i) for i in fcoh[:, 1]]
coh_date12_list = [i for i in fcoh[:, 0]]
# Check length of coherence file and input file
if not set(coh_date12_list) == set(date12_list):
print 'WARNING: input coherence list has different pairs/date12 from input file'
print 'turn off the color plotting of interferograms based on coherence'
inps.coherence_list = None
##### 2. Plot
# Fig 1 - Baseline History
fig1 = plt.figure(1)
ax1 = fig1.add_subplot(111)
ax1 = pnet.plot_perp_baseline_hist(ax1, date8List, Bp, vars(inps))
if inps.save_fig:
fig1.savefig(figName1, bbox_inches='tight')
print 'save figure to ' + figName1
# Fig 2 - Interferogram Network
fig2 = plt.figure(2)
ax2 = fig2.add_subplot(111)
ax2 = pnet.plot_network(ax2, pairs_idx, date8List, Bp, vars(inps))
if inps.save_fig:
fig2.savefig(figName2, bbox_inches='tight')
print 'save figure to ' + figName2
if inps.save_list:
txtFile = os.path.splitext(inps.file)[0] + '_date12.list'
np.savetxt(txtFile, date12_list, fmt='%s')
print 'save pairs/date12 info to file: ' + txtFile
if inps.disp_fig:
plt.show()