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#!/usr/bin/env python3
#Cunren Liang, 22-MAR-2018
#this command can run multiple times for a stack
#example command
#../../code/s1_select_ion.py -dir . -sn 34/38.5 -nr 5
import os
import sys
import glob
import shutil
import zipfile
import argparse
import datetime
import numpy as np
import xml.etree.ElementTree as ET
class sentinelSLC(object):
"""
A Class representing the SLCs
"""
def __init__(self, safe_file, orbit_file=None):
self.safe_file = safe_file
self.orbit_file = orbit_file
def get_datetime(self):
datefmt = "%Y%m%dT%H%M%S"
safe = os.path.basename(self.safe_file)
fields = safe.split('_')
self.platform = fields[0]
self.start_date_time = datetime.datetime.strptime(fields[5], datefmt)
self.stop_date_time = datetime.datetime.strptime(fields[6], datefmt)
self.date = (datetime.datetime.date(self.start_date_time)).isoformat().replace('-','')
def get_param(self):
#speed of light (m/s)
c = 299792458.0
#1. processing software version
zf = zipfile.ZipFile(self.safe_file, 'r')
manifest = [item for item in zf.namelist() if '.SAFE/manifest.safe' in item][0]
xmlstr = zf.read(manifest)
root = ET.fromstring(xmlstr)
elem = root.find('.//metadataObject[@ID="processing"]')
#setup namespace
nsp = "{http://www.esa.int/safe/sentinel-1.0}"
rdict = elem.find('.//xmlData/' + nsp + 'processing/' + nsp + 'facility').attrib
self.proc_site = rdict['site'] +', '+ rdict['country']
rdict = elem.find('.//xmlData/' + nsp + 'processing/' + nsp + 'facility/' + nsp + 'software').attrib
#ver = rdict['name'] + ' ' + rdict['version']
self.proc_version = rdict['version']
#2. start ranges
anna = sorted([item for item in zf.namelist() if '.SAFE/annotation/s1' in item])
#dual polarization. for the same swath, the slant ranges of two polarizations should be the same.
if len(anna) == 6:
anna = anna[1:6:2]
startingRange = []
for k in range(3):
xmlstr = zf.read(anna[k])
root = ET.fromstring(xmlstr)
startingRange.append(
float(root.find('imageAnnotation/imageInformation/slantRangeTime').text)*c/2.0
)
self.startingRanges = startingRange
#3. snwe
map_overlay = [item for item in zf.namelist() if '.SAFE/preview/map-overlay.kml' in item][0]
xmlstr = zf.read(map_overlay)
xmlstr = xmlstr.decode('utf-8')
start = '<coordinates>'
end = '</coordinates>'
pnts = xmlstr[xmlstr.find(start)+len(start):xmlstr.find(end)].split()
lats=[]
lons=[]
for pnt in pnts:
lons.append(float(pnt.split(',')[0]))
lats.append(float(pnt.split(',')[1]))
self.snwe=[min(lats),max(lats),min(lons),max(lons)]
def get_safe_from_group(group):
safes = []
ngroup = len(group)
for i in range(ngroup):
ngroupi = len(group[i])
for j in range(ngroupi):
safes.append(group[i][j].safe_file)
return safes
def print_group(group):
'''print group parameters
'''
print()
print('slice no ver IW1 (m) IW2 (m) IW3 (m)')
print('+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++')
for i in range(len(group)):
for j in range(len(group[i])):
print_stuff = '%s %3d %s '%(os.path.basename(group[i][j].safe_file), i+1, group[i][j].proc_version)
print_stuff += "{} {} {}".format(group[i][j].startingRanges[0], group[i][j].startingRanges[1], group[i][j].startingRanges[2])
print(print_stuff)
print()
def get_group(dir0):
'''
this routine group the slices, each group is an acquisition
the returned result is a list (acquistions sorted by starting time) containing a number of lists (slices sorted by starting time)
'''
#sort by starting time
zips = sorted(glob.glob(os.path.join(dir0, 'S1*_IW_SLC_*.zip')), key=lambda x: x.split('_')[-5], reverse=False)
nzips = len(zips)
group = []
for i in range(nzips):
safeObj=sentinelSLC(zips[i])
safeObj.get_datetime()
safeObj.get_param()
datefmt = "%Y%m%dT%H%M%S"
fields = zips[i].split('_')
tbef = datetime.datetime.strptime(fields[-5], datefmt)
taft = datetime.datetime.strptime(fields[-4], datefmt)
if i == 0:
#create new group
tbef0 = tbef
group0 = []
#S-1A is capable of operating up to 25 min per orbit [21]
#Yague-Martinez et al., "Interferometric Processing of Sentinel-1 TOPS Data,"
#S1A/B revisit time is 6 days, here we use 1 day to check if from the same orbit
if np.absolute((tbef - tbef0).total_seconds()) < 24 * 3600:
group0.append(safeObj)
else:
group.append(group0)
#create new group
tbef0 = tbef
group0 = []
group0.append(safeObj)
if i == nzips - 1:
group.append(group0)
return group
def check_redundancy(group, threshold=1):
'''
threshold: time difference threshold in seconds between two slices in second.
this routine checks, for a slice, if there are multiple ones.
'''
print('\nchecking different copies of same slice')
safe_removed_indices = []
ngroup = len(group)
for i in range(ngroup):
ngroupi = len(group[i])
if ngroupi == 1:
continue
else:
for j in range(ngroupi-1):
for k in range(j+1, ngroupi):
if np.absolute((group[i][j].start_date_time - group[i][k].start_date_time).total_seconds()) < threshold and \
np.absolute((group[i][j].stop_date_time - group[i][k].stop_date_time).total_seconds()) < threshold:
#determine which one to be removed
j_version = False
k_version = False
for l in range(ngroupi):
if l != j and l != k:
if group[i][j].proc_version == group[i][l].proc_version:
j_version = True
if group[i][k].proc_version == group[i][l].proc_version:
k_version = True
if j_version == k_version:
safe_removed_index = [i, j]
else:
if j_version == False and k_version == True:
safe_removed_index = [i, j]
else:
safe_removed_index = [i, k]
safe_removed_indices.append(safe_removed_index)
print('in acquistion {}, the following two slices are the same:'.format(i+1))
if safe_removed_index == [i, j]:
print(os.path.basename(group[i][j].safe_file) + ' (not to be used)')
print(os.path.basename(group[i][k].safe_file))
else:
print(os.path.basename(group[i][j].safe_file))
print(os.path.basename(group[i][k].safe_file) + ' (not to be used)')
#remove redundant slices
if safe_removed_indices != []:
group_new = []
for i in range(ngroup):
ngroupi = len(group[i])
group_new.append([group[i][j] for j in range(ngroupi) if [i,j] not in safe_removed_indices])
print('slices removed:')
for index in safe_removed_indices:
print('%s %3d'%(os.path.basename(group[index[0]][index[1]].safe_file), index[0]+1))
else:
group_new = group
print('no slices removed')
return group_new
def check_version(group):
print('\nchecking different slice versions of an acquisition')
acquistion_removed_indices = []
ngroup = len(group)
for i in range(ngroup):
ngroupi = len(group[i])
for j in range(ngroupi):
if group[i][0].proc_version != group[i][j].proc_version:
print('different slice versions found in acquistion {}'.format(i+1))
acquistion_removed_indices.append(i)
break
#remove acquistions
if acquistion_removed_indices != []:
group_new = [group[i] for i in range(ngroup) if i not in acquistion_removed_indices]
print('acquistions removed:')
for i in acquistion_removed_indices:
for j in range(len(group[i])):
print('%s %3d'%(os.path.basename(group[i][j].safe_file), i+1))
else:
group_new = group
print('no acquistions removed')
return group_new
def check_gap(group):
print('\nchecking gaps in an acquistion')
acquistion_removed_indices = []
ngroup = len(group)
for i in range(ngroup):
ngroupi = len(group[i])
if ngroupi == 1:
continue
else:
for j in range(0, ngroupi-1):
if (group[i][j+1].start_date_time - group[i][j].stop_date_time).total_seconds() > 0:
acquistion_removed_indices.append(i)
break
#remove acquistions
if acquistion_removed_indices != []:
group_new = [group[i] for i in range(ngroup) if i not in acquistion_removed_indices]
print('acquistions removed:')
for i in acquistion_removed_indices:
for j in range(len(group[i])):
print('%s %3d'%(os.path.basename(group[i][j].safe_file), i+1))
else:
group_new = group
print('no acquistions removed')
return group_new
def acquistion_snwe(groupi):
'''return snwe of an acquisition consisting a number of slices'''
s = min([x.snwe[0] for x in groupi])
n = max([x.snwe[1] for x in groupi])
w = min([x.snwe[2] for x in groupi])
e = max([x.snwe[3] for x in groupi])
return [s, n, w, e]
def overlap(group):
'''return snwe of the overlap of all acquistions'''
s = max([(acquistion_snwe(x))[0] for x in group])
n = min([(acquistion_snwe(x))[1] for x in group])
w = max([(acquistion_snwe(x))[2] for x in group])
e = min([(acquistion_snwe(x))[3] for x in group])
if s >= n or w >= e:
#raise Exception('no overlap among the acquistions')
print('WARNING: there is no overlap among the acquistions, snwe: {}'.format([s, n, w, e]))
return [s, n, w, e]
def check_aoi(group, s, n):
'''
check each group to see if it fully covers [s, n], if not remove the acquistion
s: south bound
n: north bound
'''
print('\nchecking if each acquistion fully covers user specifed south/north bound [{}, {}]'.format(s, n))
acquistion_removed_indices = []
ngroup = len(group)
for i in range(ngroup):
snwe = acquistion_snwe(group[i])
if not (snwe[0] <= s and snwe[1] >= n):
acquistion_removed_indices.append(i)
#remove acquistions
if acquistion_removed_indices != []:
group_new = [group[i] for i in range(ngroup) if i not in acquistion_removed_indices]
print('acquistions removed:')
for i in acquistion_removed_indices:
for j in range(len(group[i])):
print('%s %3d'%(os.path.basename(group[i][j].safe_file), i+1))
else:
group_new = group
print('no acquistions removed')
return group_new
def check_different_starting_ranges(group):
'''
checking if there are different starting ranges in each acquistion.
'''
print('\nchecking if there are different starting ranges in each acquistion')
acquistion_removed_indices = []
ngroup = len(group)
for i in range(ngroup):
ngroupi = len(group[i])
for j in range(1, ngroupi):
if group[i][0].startingRanges != group[i][j].startingRanges:
acquistion_removed_indices.append(i)
#print('++++++++++++++{} {}'.format(group[i][0].safe_file, group[i][j].safe_file))
break
#remove acquistions
if acquistion_removed_indices != []:
group_new = [group[i] for i in range(ngroup) if i not in acquistion_removed_indices]
print('acquistions removed:')
for i in acquistion_removed_indices:
for j in range(len(group[i])):
print('%s %3d'%(os.path.basename(group[i][j].safe_file), i+1))
else:
group_new = group
print('no acquistions removed')
return group_new
def check_small_number_of_acquisitions_with_same_starting_ranges(group, threshold=1):
'''
for the same subswath starting ranges,
if the number of acquistions < threshold, remove these acquistions
'''
print('\nchecking small-number of acquistions with same starting ranges')
ngroup = len(group)
starting_ranges = [x[0].startingRanges for x in group]
#get unique starting_ranges
starting_ranges_unique = []
for i in range(ngroup):
if starting_ranges[i] not in starting_ranges_unique:
starting_ranges_unique.append(starting_ranges[i])
#get number of acquistions for each unique starting ranges
ngroup_unique = len(starting_ranges_unique)
starting_ranges_unique_number = [0 for i in range(ngroup_unique)]
for k in range(ngroup_unique):
for i in range(ngroup):
if starting_ranges_unique[k] == starting_ranges[i]:
starting_ranges_unique_number[k] += 1
#get starting ranges to be removed (number of acquistions < threshold)
starting_ranges_removed = []
for k in range(ngroup_unique):
if starting_ranges_unique_number[k] < threshold:
starting_ranges_removed.append(starting_ranges_unique[k])
#remove acquistions
if starting_ranges_removed != []:
group_new = [group[i] for i in range(ngroup) if group[i][0].startingRanges not in starting_ranges_removed]
print('acquistions removed:')
for i in range(ngroup):
if group[i][0].startingRanges in starting_ranges_removed:
for j in range(len(group[i])):
print('%s %3d'%(os.path.basename(group[i][j].safe_file), i+1))
else:
group_new = group
print('no acquistions removed')
return group_new
def cmdLineParse():
'''
Command line parser.
'''
parser = argparse.ArgumentParser( description='select Sentinel-1A/B acquistions good for ionosphere correction. not used slices are moved to folder: not_used')
parser.add_argument('-dir', dest='dir', type=str, required=True,
help = 'directory containing the "S1*_IW_SLC_*.zip" files')
parser.add_argument('-sn', dest='sn', type=str, required=True,
help='south/north bound of area of interest, format: south/north')
parser.add_argument('-nr', dest='nr', type=int, default=10,
help = 'minimum number of acquisitions for same starting ranges. default: 10')
if len(sys.argv) <= 1:
print('')
parser.print_help()
sys.exit(1)
else:
return parser.parse_args()
if __name__ == '__main__':
inps = cmdLineParse()
s,n=[float(x) for x in inps.sn.split('/')]
#group the slices
group = get_group(inps.dir)
safes_all = get_safe_from_group(group)
#print overlap of group
#print('overlap among acquisitions: {}'.format(overlap(group)))
#print group before removing slices/acquistions
print_group(group)
#do checks and remove the slices/acquisitions
group = check_redundancy(group, threshold=1)
group = check_version(group)
group = check_gap(group)
group = check_aoi(group, s, n)
group = check_different_starting_ranges(group)
group = check_small_number_of_acquisitions_with_same_starting_ranges(group, threshold=inps.nr)
#print group after removing slices/acquistions
print_group(group)
#move slices that are not used to 'not_used'
safes_used = get_safe_from_group(group)
not_used_dir = os.path.join(inps.dir, 'not_used')
os.makedirs(not_used_dir, exist_ok=True)
for safe in safes_all:
if safe not in safes_used:
shutil.move(safe, not_used_dir)