def create_subset_dataset(inps, pix_box=None, geo_box=None):
'''Create/prepare subset of datasets in different folder for time series analysis.
For dataset (unwrapped interferograms) in radar coord, only support subset in row/col or y/x
For dataset (unwrapped interferograms) in geo coord, lalo has higher priority than yx, if both are specified.
'''
# Subset directory
subset_dir = inps.work_dir + '/subset'
if not os.path.isdir(subset_dir): os.mkdir(subset_dir)
os.chdir(subset_dir)
print '\n--------------------------------------------'
print 'Creating subset datasets ...'
print "Go to directory: " + subset_dir
atr = readfile.read_attribute(inps.ifgram_file)
if not 'X_FIRST' in atr.keys():
print 'Loaded dataset is in radar coordinate.'
geomap_file_orig = inps.geomap_file
# subset.lalo has higher priority than subset.yx, except when no geomap*.trans exists.
# don't subset if only subset.lalo without geomap*.trans exsits, because glob2radar won't be accurate.
if geo_box:
if inps.geomap_file:
pix_box = None
else:
geo_box = None
print 'turn off subset.lalo because no geomap*.trans file exsits.'
if not geo_box and not pix_box:
sys.exit('ERROR: no valid subset input!')
# Calculate subset range in lat/lon for geo files and y/x for radar files
if geo_box:
print 'use subset input in lat/lon'
print 'calculate corresponding bounding box in radar coordinate.'
pix_box = subset.bbox_geo2radar(geo_box, atr, geomap_file_orig)
else:
print 'use subset input in y/x'
print 'calculate corresponding bounding box in geo coordinate.'
geo_box = subset.bbox_radar2geo(pix_box, atr, geomap_file_orig)
# subset
inps = subset_dataset(inps, geo_box, pix_box)
else:
print 'Loaded dataset is in geo coordinate.'
return inps
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 read_subset_box(inpsDict):
# Read subset info from template
inpsDict['box'] = None
inpsDict['box4geo_lut'] = None
pix_box, geo_box = subset.read_subset_template2box(
inpsDict['template_file'])
# Grab required info to read input geo_box into pix_box
try:
lookupFile = [
glob.glob(str(inpsDict['pysar.load.lookupYFile']))[0],
glob.glob(str(inpsDict['pysar.load.lookupXFile']))[0]
]
except:
lookupFile = None
try:
pathKey = [
i for i in datasetName2templateKey.values()
if i in inpsDict.keys()
][0]
file = glob.glob(str(inpsDict[pathKey]))[0]
atr = readfile.read_attribute(file)
except:
atr = dict()
geocoded = None
if 'Y_FIRST' in atr.keys():
geocoded = True
else:
geocoded = False
# Check conflict
if geo_box and not geocoded and lookupFile is None:
geo_box = None
print(('WARNING: pysar.subset.lalo is not supported'
' if 1) no lookup file AND'
' 2) radar/unkonwn coded dataset'))
print('\tignore it and continue.')
if not geo_box and not pix_box:
return inpsDict
# geo_box --> pix_box
if geo_box is not None:
if geocoded:
pix_box = (0, 0, 0, 0)
pix_box[0:3:2] = ut.coord_geo2radar(geo_box[0:3:2], atr, 'lon')
pix_box[1:4:2] = ut.coord_geo2radar(geo_box[1:4:2], atr, 'lat')
else:
pix_box = subset.bbox_geo2radar(geo_box, atr, lookupFile)
print('input bounding box of interest in lalo: {}'.format(geo_box))
print('box to read for datasets in y/x: {}'.format(pix_box))
# Get box for geocoded lookup table (for gamma/roipac)
box4geo_lut = None
if lookupFile is not None:
atrLut = readfile.read_attribute(lookupFile[0])
if not geocoded and 'Y_FIRST' in atrLut.keys():
geo_box = subset.bbox_radar2geo(pix_box, atr, lookupFile)
box4geo_lut = subset.bbox_geo2radar(geo_box, atrLut)
print('box to read for geocoded lookup file in y/x: {}'.format(
box4geo_lut))
inpsDict['box'] = pix_box
inpsDict['box4geo_lut'] = box4geo_lut
return inpsDict
def get_date12_to_drop(inps):
"""Get date12 list to dropped
Return [] if no ifgram to drop, thus KEEP ALL ifgrams;
None if nothing to change, exit without doing anything.
"""
obj = ifgramStack(inps.file)
obj.open()
date12ListAll = obj.date12List
print('number of interferograms: {}'.format(len(date12ListAll)))
# Get date12_to_drop
date12_to_drop = []
# 1. Update date12_to_drop from reference file
if inps.referenceFile:
date12_to_keep = ifgramStack(
inps.referenceFile).get_date12_list(dropIfgram=True)
print('--------------------------------------------------')
print('use reference pairs info from file: {}'.format(
inps.referenceFile))
print('number of interferograms in reference: {}'.format(
len(date12_to_keep)))
tempList = sorted(list(set(date12ListAll) - set(date12_to_keep)))
date12_to_drop += tempList
print('date12 not in reference file: ({})\n{}'.format(
len(tempList), tempList))
# 2.1 Update date12_to_drop from coherence file
if inps.coherenceBased:
print('--------------------------------------------------')
print('use coherence-based network modification')
if inps.aoi_geo_box and inps.lookupFile:
print('input AOI in (lon0, lat1, lon1, lat0): {}'.format(
inps.aoi_geo_box))
inps.aoi_pix_box = subset.bbox_geo2radar(inps.aoi_geo_box,
obj.metadata,
inps.lookupFile)
if inps.aoi_pix_box:
inps.aoi_pix_box = subset.check_box_within_data_coverage(
inps.aoi_pix_box, obj.metadata)
print('input AOI in (x0,y0,x1,y1): {}'.format(inps.aoi_pix_box))
# Calculate spatial average coherence
cohList = ut.spatial_average(inps.file,
datasetName='coherence',
maskFile=inps.maskFile,
box=inps.aoi_pix_box,
saveList=True)[0]
coh_date12_list = list(
np.array(date12ListAll)[np.array(cohList) >= inps.minCoherence])
# MST network
if inps.keepMinSpanTree:
print(
'Get minimum spanning tree (MST) of interferograms with inverse of coherence.'
)
msg = 'Drop ifgrams with 1) average coherence < {} AND 2) not in MST network: '.format(
inps.minCoherence)
mst_date12_list = pnet.threshold_coherence_based_mst(
date12ListAll, cohList)
else:
msg = 'Drop ifgrams with average coherence < {}: '.format(
inps.minCoherence)
mst_date12_list = []
tempList = [
i for i in date12ListAll
if (i in coh_date12_list and i not in mst_date12_list)
]
#tempList = sorted(list(set(date12ListAll) - set(coh_date12_list) - set(mst_date12_list)))
date12_to_drop += tempList
print(msg + '({})\n{}'.format(len(tempList), tempList))
# 2.2 Update date12_to_drop from temp baseline threshold
if inps.tempBaseMax:
tempIndex = np.abs(obj.tbaseIfgram) > inps.tempBaseMax
tempList = list(np.array(date12ListAll)[tempIndex])
date12_to_drop += tempList
print('--------------------------------------------------')
print('Drop ifgrams with temporal baseline > {} days: ({})\n{}'.format(
inps.tempBaseMax, len(tempList), tempList))
# 2.3 Update date12_to_drop from perp baseline threshold
if inps.perpBaseMax:
tempIndex = np.abs(obj.pbaseIfgram) > inps.perpBaseMax
tempList = list(np.array(date12ListAll)[tempIndex])
date12_to_drop += tempList
print('--------------------------------------------------')
print('Drop ifgrams with perp baseline > {} meters: ({})\n{}'.format(
inps.perpBaseMax, len(tempList), tempList))
# 2.4 Update date12_to_drop from excludeIfgIndex
if inps.excludeIfgIndex:
tempList = [date12ListAll[i] for i in inps.excludeIfgIndex]
date12_to_drop += tempList
print('--------------------------------------------------')
print('Drop ifgrams with the following index number: {}\n{}'.format(
len(tempList), zip(inps.excludeIfgIndex, tempList)))
# 2.5 Update date12_to_drop from excludeDate
if inps.excludeDate:
tempList = [
i for i in date12ListAll
if any(j in inps.excludeDate for j in i.split('_'))
]
date12_to_drop += tempList
print('-' * 50 +
'\nDrop ifgrams including the following dates:\n{}'.format(
inps.excludeDate))
print('-' * 20 +
'Ifgrams dropped: ({})\n{}'.format(len(templist), tempList))
# 2.6 Update date12_to_drop from startDate
if inps.startDate:
minDate = int(inps.startDate)
tempList = [
i for i in date12ListAll if any(
int(j) < minDate for j in i.split('_'))
]
date12_to_drop += tempList
print('--------------------------------------------------')
print('Drop ifgrams with date earlier than: {} ({})\n{}'.format(
inps.startDate, len(tempList), tempList))
# 2.7 Update date12_to_drop from endDate
if inps.endDate:
maxDate = int(inps.endDate)
tempList = [
i for i in date12ListAll if any(
int(j) > maxDate for j in i.split('_'))
]
date12_to_drop += tempList
print('--------------------------------------------------')
print('Drop ifgrams with date later than: {} ({})\n{}'.format(
inps.endDate, len(tempList), tempList))
# 3. Manually drop pairs
if inps.manual:
tempList = manual_select_pairs_to_remove(inps.file)
if tempList is None:
return None
tempList = [i for i in tempList if i in date12ListAll]
print('date12 selected to remove: ({})\n{}'.format(
len(tempList), tempList))
date12_to_drop += tempList
# 4. drop duplicate date12 and sort in order
date12_to_drop = sorted(list(set(date12_to_drop)))
date12_to_keep = sorted(list(set(date12ListAll) - set(date12_to_drop)))
print('--------------------------------------------------')
print('number of interferograms to remove: {}'.format(len(date12_to_drop)))
print('number of interferograms to keep : {}'.format(len(date12_to_keep)))
date12ListKept = obj.get_date12_list(dropIfgram=True)
date12ListDropped = sorted(list(set(date12ListAll) - set(date12ListKept)))
if date12_to_drop == date12ListDropped:
print(
'Calculated date12 to drop is the same as exsiting marked input file, skip updating file.'
)
date12_to_drop = None
return date12_to_drop