def main(argv):
inps = cmdLineParse()
# Input File Info
atr = readfile.read_attribute(inps.file)
length = int(atr['FILE_LENGTH'])
width = int(atr['WIDTH'])
k = atr['FILE_TYPE']
print 'Input file is '+k+': '+inps.file
# default output filename
if not inps.outfile:
if k == 'temporal_coherence':
inps.outfile = 'maskTempCoh.h5'
else:
inps.outfile = 'mask.h5'
if inps.file.startswith('geo_'):
inps.outfile = 'geo_'+inps.outfile
##### Mask: Non-zero
if inps.nonzero and k == 'interferograms':
print 'generate mask for all pixels with non-zero value'
inps.outfile = ut.nonzero_mask(inps.file, inps.outfile)
return inps.outfile
##### Mask: Threshold
print 'create initial mask with the same size as the input file and all = 1'
mask = np.ones((length, width), dtype=np.float32)
data, atr = readfile.read(inps.file, epoch=inps.epoch)
if inps.nonzero:
print 'all pixels with zero value = 0'
mask[data == 0] = 0
# min threshold
if inps.vmin:
mask[data<inps.vmin] = 0
print 'all pixels with value < %s = 0' % str(inps.vmin)
# max threshold
if inps.vmax:
mask[data>inps.vmax] = 0
print 'all pixels with value > %s = 0' % str(inps.vmax)
# nan value
mask[np.isnan(data)] = 0
print 'all pixels with nan value = 0'
# subset in Y
if inps.subset_y:
y0,y1 = sorted(inps.subset_y)
mask[0:y0,:] = 0
mask[y1:length,:] = 0
print 'all pixels with y OUT of [%d, %d] = 0' % (y0,y1)
# subset in x
if inps.subset_x:
x0,x1 = sorted(inps.subset_x)
mask[:,0:x0] = 0
mask[:,x1:width] = 0
print 'all pixels with x OUT of [%d, %d] = 0' % (x0,x1)
## Write mask file
print 'writing >>> '+inps.outfile
atr['FILE_TYPE'] = 'mask'
writefile.write(mask, atr, inps.outfile)
return inps.outfile
def main(argv):
##### Read Inputs
inps = cmdLineParse()
inps.file = ut.get_file_list(inps.file)
date12_orig = pnet.get_date12_list(inps.file[0])
print 'input file(s) to be modified: ' + str(inps.file)
print 'number of interferograms: ' + str(len(date12_orig))
atr = readfile.read_attribute(inps.file[0])
# Update inps if template is input
if inps.template_file:
inps = read_template2inps(inps.template_file, inps)
if all(not i for i in [inps.reference_file, inps.max_temp_baseline, inps.max_perp_baseline,\
inps.exclude_ifg_index, inps.exclude_date, inps.coherence_based,\
inps.start_date, inps.end_date, inps.reset]):
# Display network for manually modification when there is no other modification input.
print 'No input option found to remove interferogram'
if inps.template_file:
print 'Keep all interferograms by enable --reset option'
inps.reset = True
else:
print 'To manually modify network, please use --manual option '
return
if inps.reset:
print '----------------------------------------------------------------------------'
for file in inps.file:
reset_pairs(file)
mean_coh_txt_file = os.path.splitext(
inps.coherence_file)[0] + '_spatialAverage.txt'
if os.path.isfile(mean_coh_txt_file):
rmCmd = 'rm ' + mean_coh_txt_file
print rmCmd
os.system(rmCmd)
return
# Convert index : input to continous index list
if inps.exclude_ifg_index:
ifg_index = list(inps.exclude_ifg_index)
inps.exclude_ifg_index = []
for index in ifg_index:
index_temp = [int(i) for i in index.split(':')]
index_temp.sort()
if len(index_temp) == 2:
for j in range(index_temp[0], index_temp[1] + 1):
inps.exclude_ifg_index.append(j)
elif len(index_temp) == 1:
inps.exclude_ifg_index.append(int(index))
else:
print 'Unrecoganized input: ' + index
inps.exclude_ifg_index = sorted(inps.exclude_ifg_index)
if max(inps.exclude_ifg_index) > len(date12_orig):
raise Exception('Input index out of range!\n'+\
'input index:'+str(inps.exclude_ifg_index)+'\n'+\
'index range of file: '+str(len(date12_orig)))
##### Get date12_to_rmv
date12_to_rmv = []
# 1. Update date12_to_rmv from reference file
if inps.reference_file:
date12_to_keep = pnet.get_date12_list(inps.reference_file,
check_drop_ifgram=True)
print '----------------------------------------------------------------------------'
print 'use reference pairs info from file: ' + inps.reference_file
print 'number of interferograms in reference: ' + str(
len(date12_to_keep))
print 'date12 not in reference file:'
date12_to_rmv_temp = []
for date12 in date12_orig:
if date12 not in date12_to_keep:
date12_to_rmv.append(date12)
date12_to_rmv_temp.append(date12)
print date12_to_rmv_temp
# 2.1 Update date12_to_rmv from coherence file
if inps.coherence_based and os.path.isfile(inps.coherence_file):
print '----------------------------------------------------------------------------'
print 'use coherence-based network modification from coherence file: ' + inps.coherence_file
# check mask AOI in lalo
if inps.aoi_geo_box and inps.lookup_file:
print 'input AOI in (lon0, lat1, lon1, lat0): ' + str(
inps.aoi_geo_box)
inps.aoi_pix_box = subset.bbox_geo2radar(inps.aoi_geo_box, atr,
inps.lookup_file)
if inps.aoi_pix_box:
# check mask AOI within the data coverage
inps.aoi_pix_box = subset.check_box_within_data_coverage(
inps.aoi_pix_box, atr)
print 'input AOI in (x0,y0,x1,y1): ' + str(inps.aoi_pix_box)
# Calculate spatial average coherence
coh_list, coh_date12_list = ut.spatial_average(inps.coherence_file, inps.mask_file,\
inps.aoi_pix_box, saveList=True)
# MST network
if inps.keep_mst:
print 'Get minimum spanning tree (MST) of interferograms with inverse of coherence.'
print 'date12 with 1) average coherence < ' + str(
inps.min_coherence) + ' AND 2) not in MST network: '
mst_date12_list = pnet.threshold_coherence_based_mst(
coh_date12_list, coh_list)
else:
print 'date12 with average coherence < ' + str(inps.min_coherence)
mst_date12_list = []
date12_to_rmv_temp = []
for i in range(len(coh_date12_list)):
date12 = coh_date12_list[i]
if coh_list[
i] < inps.min_coherence and date12 not in mst_date12_list:
date12_to_rmv.append(date12)
date12_to_rmv_temp.append(date12)
print date12_to_rmv_temp
# 2.2 Update date12_to_rmv from temp baseline threshold
if inps.max_temp_baseline:
print '----------------------------------------------------------------------------'
print 'Drop pairs with temporal baseline > ' + str(
inps.max_temp_baseline) + ' days'
date8_list = ptime.ifgram_date_list(inps.file[0])
date6_list = ptime.yymmdd(date8_list)
tbase_list = ptime.date_list2tbase(date8_list)[0]
date12_to_rmv_temp = []
for i in range(len(date12_orig)):
date1, date2 = date12_orig[i].split('-')
idx1 = date6_list.index(date1)
idx2 = date6_list.index(date2)
t_diff = tbase_list[idx2] - tbase_list[idx1]
if t_diff > inps.max_temp_baseline:
date12 = date12_orig[i]
date12_to_rmv.append(date12)
date12_to_rmv_temp.append(date12)
print 'number of pairs to drop: %d' % (len(date12_to_rmv_temp))
print date12_to_rmv_temp
# 2.3 Update date12_to_rmv from perp baseline threshold
if inps.max_perp_baseline:
print '----------------------------------------------------------------------------'
print 'Drop pairs with perpendicular spatial baseline > ' + str(
inps.max_perp_baseline) + ' meters'
ifg_bperp_list = pnet.igram_perp_baseline_list(inps.file[0])
date12_to_rmv_temp = []
for i in range(len(ifg_bperp_list)):
if abs(ifg_bperp_list[i]) > inps.max_perp_baseline:
date12 = date12_orig[i]
date12_to_rmv.append(date12)
date12_to_rmv_temp.append(date12)
print 'number of pairs to drop: %d' % (len(date12_to_rmv_temp))
print date12_to_rmv_temp
# 2.4 Update date12_to_rmv from exclude_ifg_index
if inps.exclude_ifg_index:
print '----------------------------------------------------------------------------'
print 'drop date12/pair with the following index number:'
for index in inps.exclude_ifg_index:
date12 = date12_orig[index - 1]
date12_to_rmv.append(date12)
print str(index) + ' ' + date12
# 2.5 Update date12_to_rmv from exclude_date
if inps.exclude_date:
inps.exclude_date = ptime.yymmdd(inps.exclude_date)
print '----------------------------------------------------------------------------'
print 'Drop pairs including the following dates: \n' + str(
inps.exclude_date)
date12_to_rmv_temp = []
for i in range(len(date12_orig)):
date1, date2 = date12_orig[i].split('-')
if (date1 in inps.exclude_date) or (date2 in inps.exclude_date):
date12 = date12_orig[i]
date12_to_rmv.append(date12)
date12_to_rmv_temp.append(date12)
print date12_to_rmv_temp
# 2.6 Update date12_to_rmv from start_date
if inps.start_date:
inps.start_date = ptime.yymmdd(inps.start_date)
print '----------------------------------------------------------------------------'
print 'Drop pairs with date earlier than start-date: ' + inps.start_date
min_date = int(ptime.yyyymmdd(inps.start_date))
date12_to_rmv_temp = []
for i in range(len(date12_orig)):
date12 = date12_orig[i]
if any(
int(j) < min_date
for j in ptime.yyyymmdd(date12.split('-'))):
date12_to_rmv.append(date12)
date12_to_rmv_temp.append(date12)
print date12_to_rmv_temp
# 2.7 Update date12_to_rmv from end_date
if inps.end_date:
inps.end_date = ptime.yymmdd(inps.end_date)
print '----------------------------------------------------------------------------'
print 'Drop pairs with date earlier than end-date: ' + inps.end_date
max_date = int(ptime.yyyymmdd(inps.end_date))
date12_to_rmv_temp = []
for i in range(len(date12_orig)):
date12 = date12_orig[i]
if any(
int(j) > max_date
for j in ptime.yyyymmdd(date12.split('-'))):
date12_to_rmv.append(date12)
date12_to_rmv_temp.append(date12)
print date12_to_rmv_temp
# 3. Manually drop pairs
if inps.disp_network:
date12_click = manual_select_pairs_to_remove(inps.file[0])
for date12 in list(date12_click):
if date12 not in date12_orig:
date12_click.remove(date12)
print 'date12 selected to remove:'
print date12_click
date12_to_rmv += date12_click
# 4. drop duplicate date12 and sort in order
date12_to_rmv = sorted(list(set(date12_to_rmv)))
date12_keep = sorted(list(set(date12_orig) - set(date12_to_rmv)))
print '----------------------------------------------------------------------------'
print 'number of interferograms to remove: ' + str(len(date12_to_rmv))
print 'number of interferograms kept : ' + str(len(date12_keep))
##### Calculated date12_to_drop v.s. existing date12_to_drop
# Get list of date12 of interferograms already been marked to drop
k = readfile.read_attribute(inps.file[0])['FILE_TYPE']
h5 = h5py.File(inps.file[0], 'r')
ifgram_list_all = sorted(h5[k].keys())
ifgram_list_keep = ut.check_drop_ifgram(h5, print_msg=False)
ifgram_list_dropped = sorted(
list(set(ifgram_list_all) - set(ifgram_list_keep)))
date12_list_dropped = ptime.list_ifgram2date12(ifgram_list_dropped)
h5.close()
if date12_to_rmv == date12_list_dropped and inps.mark_attribute:
print 'Calculated date12 to drop is the same as exsiting marked input file, skip update file attributes.'
date12_to_rmv = []
##### Update date12 to drop
if date12_to_rmv:
##### Update Input Files with date12_to_rmv
Modified_CoherenceFile = 'Modified_coherence.h5'
for File in inps.file:
Modified_File = modify_file_date12_list(File, date12_to_rmv,
inps.mark_attribute)
k = readfile.read_attribute(File)['FILE_TYPE']
# Update Mask File
if k == 'interferograms' and inps.update_aux:
print 'update mask file for input ' + k + ' file based on ' + Modified_File
inps.mask_file = 'mask.h5'
print 'writing >>> ' + inps.mask_file
ut.nonzero_mask(Modified_File, inps.mask_file)
elif k == 'coherence' and inps.update_aux:
inps.coherence_file = Modified_File
print 'update average spatial coherence for input ' + k + ' file based on: ' + Modified_File
outFile = 'averageSpatialCoherence.h5'
print 'writing >>> ' + outFile
ut.temporal_average(Modified_File, outFile)
# Touch spatial average txt file of coherence if it's existed
coh_spatialAverage_file = os.path.splitext(
Modified_File)[0] + '_spatialAverage.txt'
if os.path.isfile(coh_spatialAverage_file):
touchCmd = 'touch ' + coh_spatialAverage_file
print touchCmd
os.system(touchCmd)
# Plot result
if inps.plot:
print '\nplot modified network and save to file.'
plotCmd = 'plot_network.py ' + inps.coherence_file + ' --coherence ' + inps.coherence_file + ' --nodisplay'
if inps.template_file:
plotCmd += ' --template ' + inps.template_file
print plotCmd
os.system(plotCmd)
print 'Done.'
return
def main(argv):
start = time.time()
inps = cmdLineParse()
#########################################
# Initiation
#########################################
print LOGO
# Read template
inps.project_name = os.path.splitext(os.path.basename(
inps.template_file))[0]
print 'Project name: ' + inps.project_name
inps.template_file = os.path.abspath(inps.template_file)
template = readfile.read_template(inps.template_file)
for key in template.keys():
if template[key].lower() == 'default': template[key] = 'auto'
if template[key].lower() in ['off', 'false']: template[key] = 'no'
if template[key].lower() in ['on', 'true']: template[key] = 'yes'
if 'pysar.deramp' in template.keys():
template['pysar.deramp'] = template['pysar.deramp'].lower().replace(
'-', '_')
if 'pysar.troposphericDelay.method' in template.keys():
template['pysar.troposphericDelay.method'] = template[
'pysar.troposphericDelay.method'].lower().replace('-', '_')
# work directory
if not inps.work_dir:
if pysar.miami_path and 'SCRATCHDIR' in os.environ:
inps.work_dir = os.getenv(
'SCRATCHDIR') + '/' + inps.project_name + "/PYSAR"
print 'Use file/dir structure in University of Miami.'+\
'(To turn it off, change miami_path value to False in pysar/__init__.py)'
else:
inps.work_dir = os.getcwd()
else:
inps.work_dir = os.path.abspath(inps.work_dir)
if not os.path.isdir(inps.work_dir): os.mkdir(inps.work_dir)
os.chdir(inps.work_dir)
print "Go to work directory: " + inps.work_dir
#########################################
# Loading Data
#########################################
print '\n*************** Load Data ****************'
loadCmd = 'load_data.py ' + inps.template_file + ' --dir ' + inps.work_dir
print loadCmd
os.system(loadCmd)
print '--------------------------------------------'
## Find initial files name/path - required files
# 1. Unwrapped interferograms
inps.ifgram_file = 'unwrapIfgram.h5'
try:
inps.ifgram_file = glob.glob(inps.work_dir + '/' + inps.ifgram_file)[0]
except:
inps.ifgram_file = None
if inps.ifgram_file: print 'Unwrapped interferograms: ' + inps.ifgram_file
else: sys.exit('\nERROR: No interferograms file found!\n')
# 2. Mask
inps.mask_file = 'Mask.h5'
try:
inps.mask_file = glob.glob(inps.work_dir + '/' + inps.mask_file)[0]
except:
inps.mask_file = None
if not inps.mask_file:
print 'No mask file found. Creating one using non-zero pixels in file: ' + inps.ifgram_file
inps.mask_file = ut.nonzero_mask(inps.ifgram_file, inps.mask_file)
print 'Mask: ' + inps.mask_file
## Find initial files name/path - recommended files (None if not found)
# 3. Spatial coherence for each interferograms
inps.coherence_file = 'coherence.h5'
try:
inps.coherence_file = glob.glob(inps.work_dir + '/' +
inps.coherence_file)[0]
except:
inps.coherence_file = None
if inps.coherence_file: print 'Coherences: ' + inps.coherence_file
else:
def main(argv):
##### Read Inputs
inps = cmdLineParse()
inps.file = ut.get_file_list(inps.file)
date12_orig = pnet.get_date12_list(inps.file[0])
#print '\n****************** Network Modification ********************'
if (not inps.reference_file and not inps.template_file and\
not inps.max_temp_baseline and not inps.max_perp_baseline and\
not inps.drop_ifg_index and not inps.drop_date and \
not inps.coherence_file):
# Display network for manually modification when there is no other modification input.
print 'No input found to remove interferogram, continue by display the network to select it manually ...'
inps.disp_network = True
# Update inps if template is input
if inps.template_file:
inps = update_inps_with_template(inps, inps.template_file)
# Convert index : input to continous index list
if inps.drop_ifg_index:
ifg_index = list(inps.drop_ifg_index)
inps.drop_ifg_index = []
for index in ifg_index:
index_temp = [int(i) for i in index.split(':')]
index_temp.sort()
if len(index_temp) == 2:
for j in range(index_temp[0], index_temp[1] + 1):
inps.drop_ifg_index.append(j)
elif len(index_temp) == 1:
inps.drop_ifg_index.append(int(index))
else:
print 'Unrecoganized input: ' + index
inps.drop_ifg_index = sorted(inps.drop_ifg_index)
if max(inps.drop_ifg_index) > len(date12_orig):
raise Exception('Input index out of range!\n'+\
'input index:'+str(inps.drop_ifg_index)+'\n'+\
'index range of file: '+str(len(date12_orig)))
##### Get date12_to_rmv
date12_to_rmv = []
# 1. Update date12_to_rmv from reference file
if inps.reference_file:
date12_to_keep = pnet.get_date12_list(inps.reference_file)
print '----------------------------------------------------------------------------'
print 'use reference pairs info from file: ' + inps.reference_file
print 'number of interferograms in reference: ' + str(
len(date12_to_keep))
print 'date12 not in reference file:'
for date12 in date12_orig:
if date12 not in date12_to_keep:
date12_to_rmv.append(date12)
print date12
# 2.1 Update date12_to_rmv from coherence file
if inps.coherence_file:
print '----------------------------------------------------------------------------'
print 'use coherence-based network modification from coherence file: ' + inps.coherence_file
# Calculate spatial average coherence
if not inps.mask_file:
mask = readfile.read(inps.mask_file)[0]
print 'mask coherence with file: ' + inps.mask_file
else:
mask = None
cohTextFile = os.path.splitext(
inps.coherence_file)[0] + '_spatialAverage.list'
if os.path.isfile(cohTextFile):
print 'average coherence in space has been calculated before and store in file: ' + cohTextFile
print 'read it directly, or delete it and re-run the script to re-calculate the list'
cohTxt = np.loadtxt(cohTextFile, dtype=str)
mean_coherence_list = [float(i) for i in cohTxt[:, 1]]
coh_date12_list = [i for i in cohTxt[:, 0]]
else:
print 'calculating average coherence of each interferogram ...'
mean_coherence_list = ut.spatial_average(inps.coherence_file,
mask,
saveList=True)
coh_date12_list = pnet.get_date12_list(inps.coherence_file)
print 'date12 with average coherence < ' + str(
inps.min_coherence) + ': '
for i in range(len(coh_date12_list)):
if mean_coherence_list[i] < inps.min_coherence:
date12 = coh_date12_list[i]
date12_to_rmv.append(date12)
print date12
# 2.2 Update date12_to_rmv from perp baseline threshold
if inps.max_perp_baseline:
print '----------------------------------------------------------------------------'
print 'Drop pairs with perpendicular spatial baseline > ' + str(
inps.max_perp_baseline) + ' meters'
ifg_bperp_list = pnet.igram_perp_baseline_list(inps.file[0])
for i in range(len(ifg_bperp_list)):
if ifg_bperp_list[i] > inps.max_perp_baseline:
date12 = date12_orig[i]
date12_to_rmv.append(date12)
print date12
# 2.3 Update date12_to_rmv from temp baseline threshold
if inps.max_temp_baseline:
print '----------------------------------------------------------------------------'
print 'Drop pairs with temporal baseline > ' + str(
inps.max_temp_baseline) + ' days'
date8_list = ptime.igram_date_list(inps.file[0])
date6_list = ptime.yymmdd(date8_list)
tbase_list = ptime.date_list2tbase(date8_list)[0]
for i in range(len(date12_orig)):
date1, date2 = date12_orig[i].split('-')
idx1 = date6_list.index(date1)
idx2 = date6_list.index(date2)
t_diff = tbase_list[idx2] - tbase_list[idx1]
if t_diff > inps.max_temp_baseline:
date12 = date12_orig[i]
date12_to_rmv.append(date12)
print date12
# 2.4 Update date12_to_rmv from drop_ifg_index
if inps.drop_ifg_index:
print '----------------------------------------------------------------------------'
print 'drop date12/pair with the following index number:'
for index in inps.drop_ifg_index:
date12 = date12_orig[index - 1]
date12_to_rmv.append(date12)
print str(index) + ' ' + date12
# 2.5 Update date12_to_rmv from drop_date
if inps.drop_date:
inps.drop_date = ptime.yymmdd(inps.drop_date)
print '----------------------------------------------------------------------------'
print 'Drop pairs including the following dates: \n' + str(
inps.drop_date)
for i in range(len(date12_orig)):
date1, date2 = date12_orig[i].split('-')
if (date1 in inps.drop_date) or (date2 in inps.drop_date):
date12 = date12_orig[i]
date12_to_rmv.append(date12)
print date12
# 3. Manually drop pairs
if inps.disp_network:
date12_click = manual_select_pairs_to_remove(inps.file[0])
for date12 in list(date12_click):
if date12 not in date12_orig:
date12_click.remove(date12)
print 'date12 selected to remove:'
print date12_click
date12_to_rmv += date12_click
# 4. drop duplicate date12 and sort in order
date12_to_rmv = list(set(date12_to_rmv))
date12_to_rmv = sorted(date12_to_rmv)
print '----------------------------------------------------------------------------'
print 'number of interferograms to remove: ' + str(len(date12_to_rmv))
print 'list of interferograms to remove:'
print date12_to_rmv
if date12_to_rmv:
##### Update Input Files with date12_to_rmv
Modified_CoherenceFile = 'Modified_coherence.h5'
for File in inps.file:
Modified_File = modify_file_date12_list(File, date12_to_rmv)
k = readfile.read_attribute(File)['FILE_TYPE']
# Update Mask File
if k == 'interferograms':
print 'update mask file for input ' + k + ' file based on ' + Modified_File
outFile = 'Modified_Mask.h5'
print 'writing >>> ' + outFile
ut.nonzero_mask(Modified_File, outFile)
elif k == 'coherence':
print 'update average spatial coherence for input ' + k + ' file based on: ' + Modified_File
outFile = 'Modified_average_spatial_coherence.h5'
print 'writing >>> ' + outFile
ut.temporal_average(Modified_File, outFile)
Modified_CoherenceFile = Modified_File
# Plot result
if inps.plot:
print '\nplot modified network and save to file.'
plotCmd = 'plot_network.py ' + Modified_File + ' --coherence ' + Modified_CoherenceFile + ' --nodisplay'
print plotCmd
os.system(plotCmd)
print 'Done.'
return
else:
print 'No interferogram dropped, skip update.'
return