use for loops for dates/pairs processing
CunrenLiang
parent
b341c669b0
commit
78a5ddead6
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@ -89,10 +89,25 @@ ${PATH_ALOSSTACK}/create_cmds.py -stack_par alosStack.xml
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4. Do most of the single date processing. Run
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./cmd_1.sh
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In all command files including cmd_1.sh, note that same commands for processing different dates either
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listed repeatedly or in a loop can run parallelly. The 'resample to a common grid' step in cmd_1.sh is
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a very time consuming step. These commands can of course run parallelly, but note that each command may
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use up to 7G memory.
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In cmd_1.sh and other command files, note that you can split the 'for loop' in each step into a number
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of parallel runs. See command file for details.
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Higly recommended parallel processing steps in each command file.
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cmd_1.sh:
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estimate SLC offsets
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resample to a common grid (WD1 SLC size may be up to 7.2 G, so each run requires this much memory!)
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cmd_2.sh
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form interferograms (does not requires a lot of computation, more parallel runs recommended)
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mosaic interferograms (does not requires a lot of computation, more parallel runs recommended)
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cmd_3.sh
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subband interferograms (does not requires a lot of computation, more parallel runs recommended)
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cmd_4.sh
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all steps
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5. InSAR processing before ionosphere correction. Run
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./cmd_2.sh
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@ -279,6 +279,45 @@ def createCmds(stack, datesProcess, pairsProcess, pairsProcessIon, mode):
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stackScriptPath = os.environ['PATH_ALOSSTACK']
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def parallelSettings(array):
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settings = '''
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# For parallelly processing the dates/pairs.
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# Uncomment and set the following variables, put these settings and the following
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# one or multiple for loops for a group (with an individual group_i) in a seperate
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# bash script. Then you can run the different groups parallelly. E.g. if you have
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# 38 pairs and if you want to process them in 4 parallel runs, then you may set
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# group_n=10, and group_i=1 for the first bash script (and 2, 3, 4 for the other
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# three bash scripts).
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# Number of threads for this run
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# export OMP_NUM_THREADS=1
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# CUDA device you want to use for this run. Only need to set if you have CUDA GPU
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# installed on your computer. To find GPU IDs, run nvidia-smi
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# export CUDA_VISIBLE_DEVICES=7
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# Parallel processing mode. 0: no, 1 yes.
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# Must set 'parallel=1' for parallel processing!
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# parallel=1
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# Group number for this run (group_i starts from 1)
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# group_i=1
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# Number of dates or pairs in a group
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# group_n=10
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# set the array variable used in this for loop here. The array can be found at the
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# beginning of this command file.
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# {}=()
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'''.format(array)
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return settings
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parallelCommands = ''' if [[ ${parallel} -eq 1 ]]; then
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if !(((0+(${group_i}-1)*${group_n} <= ${i})) && ((${i} <= ${group_n}-1+(${group_i}-1)*${group_n}))); then
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continue
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fi
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fi'''
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print(' * * *')
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if stack.dateReferenceStack in datesProcess:
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@ -316,6 +355,13 @@ def createCmds(stack, datesProcess, pairsProcess, pairsProcessIon, mode):
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#start new commands: processing each date
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#################################################################################
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cmd = '#!/bin/bash\n\n'
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cmd += '#########################################################################\n'
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cmd += '#set the environment variable before running the following steps\n'
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cmd += 'dates=({})\n'.format(' '.join(datesProcess))
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cmd += 'dates2=({})\n'.format(' '.join(datesProcessSecondary))
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cmd += '#########################################################################\n'
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cmd += '\n\n'
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#read data
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if datesProcess != []:
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@ -331,6 +377,7 @@ def createCmds(stack, datesProcess, pairsProcess, pairsProcessIon, mode):
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cmd += ' -virtual'
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cmd += '\n'
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cmd += '\n'
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cmd += '\n'
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#frame and swath names use those from frame and swath dirs from now on
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@ -340,6 +387,7 @@ def createCmds(stack, datesProcess, pairsProcess, pairsProcessIon, mode):
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cmd += os.path.join(stackScriptPath, 'compute_baseline.py') + ' -idir {} -odir {} -ref_date {} -sec_date {} -baseline_center baseline_center.txt -baseline_grid -baseline_grid_width 10 -baseline_grid_length 10'.format(stack.datesProcessingDir, stack.baselineDir, stack.dateReferenceStack, ' '.join(datesProcessSecondary))
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cmd += '\n'
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cmd += '\n'
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cmd += '\n'
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#compute burst synchronization
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@ -349,21 +397,37 @@ def createCmds(stack, datesProcess, pairsProcess, pairsProcessIon, mode):
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cmd += os.path.join(stackScriptPath, 'compute_burst_sync.py') + ' -idir {} -burst_sync_file burst_synchronization.txt -ref_date {}'.format(stack.datesProcessingDir, stack.dateReferenceStack)
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cmd += '\n'
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cmd += '\n'
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cmd += '\n'
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#estimate SLC offsets
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if datesProcessSecondary != []:
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cmd += header('estimate SLC offsets')
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for i in range(len(datesProcessSecondary)):
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cmd += os.path.join(stackScriptPath, 'estimate_slc_offset.py') + ' -idir {} -ref_date {} -sec_date {} -wbd {} -dem {}'.format(stack.datesProcessingDir, stack.dateReferenceStack, datesProcessSecondary[i], insar.wbd, stack.dem)
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extraArguments = ''
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if insar.useWbdForNumberOffsets is not None:
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cmd += ' -use_wbd_offset'
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extraArguments += ' -use_wbd_offset'
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if insar.numberRangeOffsets is not None:
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for x in insar.numberRangeOffsets:
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cmd += ' -num_rg_offset {}'.format(' '.join(x))
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extraArguments += ' -num_rg_offset {}'.format(' '.join(x))
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if insar.numberAzimuthOffsets is not None:
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for x in insar.numberAzimuthOffsets:
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cmd += ' -num_az_offset {}'.format(' '.join(x))
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extraArguments += ' -num_az_offset {}'.format(' '.join(x))
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cmd += header('estimate SLC offsets')
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cmd += parallelSettings('dates2')
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cmd += '''for ((i=0;i<${{#dates2[@]}};i++)); do
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{extraCommands}
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{script} -idir {datesProcessingDir} -ref_date {dateReferenceStack} -sec_date ${{dates2[i]}} -wbd {wbd} -dem {dem}{extraArguments}
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done'''.format(extraCommands = parallelCommands,
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script = os.path.join(stackScriptPath, 'estimate_slc_offset.py'),
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datesProcessingDir = stack.datesProcessingDir,
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dateReferenceStack = stack.dateReferenceStack,
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wbd = insar.wbd,
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dem = stack.dem,
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extraArguments = extraArguments)
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cmd += '\n'
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cmd += '\n'
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cmd += '\n'
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@ -376,6 +440,7 @@ def createCmds(stack, datesProcess, pairsProcess, pairsProcessIon, mode):
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cmd += ' -match'
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cmd += '\n'
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cmd += '\n'
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cmd += '\n'
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#estimate frame offsets
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@ -386,19 +451,36 @@ def createCmds(stack, datesProcess, pairsProcess, pairsProcessIon, mode):
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cmd += ' -match'
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cmd += '\n'
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cmd += '\n'
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cmd += '\n'
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#resample to a common grid
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if datesProcess != []:
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cmd += header('resample to a common grid')
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for x in datesProcess:
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cmd += os.path.join(stackScriptPath, 'resample_common_grid.py') + ' -idir {} -odir {} -ref_date {} -sec_date {} -nrlks1 {} -nalks1 {}'.format(stack.datesProcessingDir, stack.datesResampledDir, stack.dateReferenceStack, x, insar.numberRangeLooks1, insar.numberAzimuthLooks1)
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extraArguments = ''
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if stack.gridFrame is not None:
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cmd += ' -ref_frame {}'.format(stack.gridFrame)
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extraArguments += ' -ref_frame {}'.format(stack.gridFrame)
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if stack.gridSwath is not None:
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cmd += ' -ref_swath {}'.format(stack.gridSwath)
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extraArguments += ' -ref_swath {}'.format(stack.gridSwath)
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if insar.doIon:
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cmd += ' -subband'
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extraArguments += ' -subband'
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cmd += header('resample to a common grid')
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cmd += parallelSettings('dates')
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cmd += '''for ((i=0;i<${{#dates[@]}};i++)); do
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{extraCommands}
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{script} -idir {datesProcessingDir} -odir {datesResampledDir} -ref_date {dateReferenceStack} -sec_date ${{dates[i]}} -nrlks1 {numberRangeLooks1} -nalks1 {numberAzimuthLooks1}{extraArguments}
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done'''.format(extraCommands = parallelCommands,
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script = os.path.join(stackScriptPath, 'resample_common_grid.py'),
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datesProcessingDir = stack.datesProcessingDir,
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datesResampledDir = stack.datesResampledDir,
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dateReferenceStack = stack.dateReferenceStack,
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numberRangeLooks1 = insar.numberRangeLooks1,
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numberAzimuthLooks1 = insar.numberAzimuthLooks1,
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extraArguments = extraArguments)
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cmd += '\n'
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cmd += '\n'
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cmd += '\n'
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@ -421,8 +503,10 @@ def createCmds(stack, datesProcess, pairsProcess, pairsProcessIon, mode):
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cmd += ' -ref_swath {}'.format(stack.gridSwath)
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cmd += '\n'
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cmd += '\n'
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cmd += '\n'
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else:
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cmd += '\n'
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cmd += '\n'
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#compute lat/lon/hgt
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@ -441,23 +525,36 @@ def createCmds(stack, datesProcess, pairsProcess, pairsProcessIon, mode):
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cmd += 'cd ../../'
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cmd += '\n'
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cmd += '\n'
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cmd += '\n'
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#compute geometrical offsets
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if datesProcessSecondary != []:
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cmd += header('compute geometrical offsets')
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for x in datesProcessSecondary:
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date_par_dir = os.path.join('../../', stack.datesProcessingDir, x)
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lat = '../{}/insar/{}_{}rlks_{}alks.lat'.format(stack.dateReferenceStack, stack.dateReferenceStack, insar.numberRangeLooks1, insar.numberAzimuthLooks1)
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lon = '../{}/insar/{}_{}rlks_{}alks.lon'.format(stack.dateReferenceStack, stack.dateReferenceStack, insar.numberRangeLooks1, insar.numberAzimuthLooks1)
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hgt = '../{}/insar/{}_{}rlks_{}alks.hgt'.format(stack.dateReferenceStack, stack.dateReferenceStack, insar.numberRangeLooks1, insar.numberAzimuthLooks1)
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cmd += 'cd {}\n'.format(os.path.join(stack.datesResampledDir, x))
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cmd += os.path.join(stackScriptPath, 'geo2rdr.py') + ' -date {} -date_par_dir {} -lat {} -lon {} -hgt {} -nrlks1 {} -nalks1 {}'.format(x, date_par_dir, lat, lon, hgt, insar.numberRangeLooks1, insar.numberAzimuthLooks1)
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extraArguments = ''
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if insar.useGPU:
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cmd += ' -gpu'
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extraArguments += ' -gpu'
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cmd += header('compute geometrical offsets')
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cmd += parallelSettings('dates2')
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cmd += '''for ((i=0;i<${{#dates2[@]}};i++)); do
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{extraCommands}
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cd {datesResampledDir}
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{script} -date ${{dates2[i]}} -date_par_dir {datesProcessingDir} -lat {lat} -lon {lon} -hgt {hgt} -nrlks1 {numberRangeLooks1} -nalks1 {numberAzimuthLooks1}{extraArguments}
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cd ../../
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done'''.format(extraCommands = parallelCommands,
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script = os.path.join(stackScriptPath, 'geo2rdr.py'),
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datesResampledDir = os.path.join(stack.datesResampledDir, '${dates2[i]}'),
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datesProcessingDir = os.path.join('../../', stack.datesProcessingDir, '${dates2[i]}'),
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lat = '../{}/insar/{}_{}rlks_{}alks.lat'.format(stack.dateReferenceStack, stack.dateReferenceStack, insar.numberRangeLooks1, insar.numberAzimuthLooks1),
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lon = '../{}/insar/{}_{}rlks_{}alks.lon'.format(stack.dateReferenceStack, stack.dateReferenceStack, insar.numberRangeLooks1, insar.numberAzimuthLooks1),
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hgt = '../{}/insar/{}_{}rlks_{}alks.hgt'.format(stack.dateReferenceStack, stack.dateReferenceStack, insar.numberRangeLooks1, insar.numberAzimuthLooks1),
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numberRangeLooks1 = insar.numberRangeLooks1,
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numberAzimuthLooks1 = insar.numberAzimuthLooks1,
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extraArguments = extraArguments)
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cmd += '\n'
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cmd += 'cd ../../\n'
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cmd += '\n'
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@ -473,6 +570,7 @@ def createCmds(stack, datesProcess, pairsProcess, pairsProcessIon, mode):
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cmd += '#########################################################################\n'
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cmd += '#set the environment variable before running the following steps\n'
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cmd += 'insarpair=({})\n'.format(' '.join(pairsProcess))
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cmd += 'dates2=({})\n'.format(' '.join(datesProcessSecondary))
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cmd += '#########################################################################\n'
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cmd += '\n\n'
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else:
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@ -486,12 +584,17 @@ def createCmds(stack, datesProcess, pairsProcess, pairsProcessIon, mode):
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cmd += os.path.join(stackScriptPath, 'pair_up.py') + ' -idir1 {} -idir2 {} -odir {} -ref_date {} -pairs {}'.format(stack.datesProcessingDir, stack.datesResampledDir, stack.pairsProcessingDir, stack.dateReferenceStack, ' '.join(pairsProcess))
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cmd += '\n'
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cmd += '\n'
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cmd += '\n'
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#form interferograms
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if pairsProcess != []:
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cmd += header('form interferograms')
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cmd += parallelSettings('insarpair')
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cmd += '''for ((i=0;i<${{#insarpair[@]}};i++)); do
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{extraCommands}
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IFS='-' read -ra dates <<< "${{insarpair[i]}}"
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ref_date=${{dates[0]}}
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sec_date=${{dates[1]}}
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@ -500,18 +603,25 @@ def createCmds(stack, datesProcess, pairsProcess, pairsProcessIon, mode):
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cd ${{insarpair[i]}}
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{script} -ref_date ${{ref_date}} -sec_date ${{sec_date}} -nrlks1 {nrlks1} -nalks1 {nalks1}
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cd ../../
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done'''.format(script = os.path.join(stackScriptPath, 'form_interferogram.py'),
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done'''.format(extraCommands = parallelCommands,
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script = os.path.join(stackScriptPath, 'form_interferogram.py'),
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pairsProcessingDir = stack.pairsProcessingDir,
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nrlks1 = insar.numberRangeLooks1,
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nalks1 = insar.numberAzimuthLooks1)
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cmd += '\n'
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cmd += '\n'
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cmd += '\n'
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#mosaic interferograms
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if pairsProcess != []:
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cmd += header('mosaic interferograms')
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cmd += parallelSettings('insarpair')
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cmd += '''for ((i=0;i<${{#insarpair[@]}};i++)); do
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{extraCommands}
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IFS='-' read -ra dates <<< "${{insarpair[i]}}"
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ref_date=${{dates[0]}}
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sec_date=${{dates[1]}}
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@ -520,13 +630,16 @@ done'''.format(script = os.path.join(stackScriptPath, 'form_interfe
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cd ${{insarpair[i]}}
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{script} -ref_date_stack {ref_date_stack} -ref_date ${{ref_date}} -sec_date ${{sec_date}} -nrlks1 {nrlks1} -nalks1 {nalks1}
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cd ../../
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done'''.format(script = os.path.join(stackScriptPath, 'mosaic_interferogram.py'),
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done'''.format(extraCommands = parallelCommands,
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script = os.path.join(stackScriptPath, 'mosaic_interferogram.py'),
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pairsProcessingDir = stack.pairsProcessingDir,
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ref_date_stack = stack.dateReferenceStack,
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nrlks1 = insar.numberRangeLooks1,
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nalks1 = insar.numberAzimuthLooks1)
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cmd += '\n'
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cmd += '\n'
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cmd += '\n'
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#estimate residual offsets between radar and DEM
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@ -558,26 +671,42 @@ done'''.format(script = os.path.join(stackScriptPath, 'mosaic_inter
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cmd += '\n'
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cmd += 'cd ../../\n'
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cmd += '\n'
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cmd += '\n'
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#rectify range offsets
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if datesProcessSecondary != []:
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cmd += header('rectify range offsets')
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aff = os.path.join('../../', stack.dateReferenceStack, 'insar', 'affine_transform.txt')
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for x in datesProcessSecondary:
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rgoff = '{}_{}rlks_{}alks_rg.off'.format(x, insar.numberRangeLooks1, insar.numberAzimuthLooks1)
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rgoffRect = '{}_{}rlks_{}alks_rg_rect.off'.format(x, insar.numberRangeLooks1, insar.numberAzimuthLooks1)
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cmd += 'cd {}\n'.format(os.path.join(stack.datesResampledDir, x, 'insar'))
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cmd += os.path.join(stackScriptPath, 'rect_range_offset.py') + ' -aff {} -input {} -output {} -nrlks1 {} -nalks1 {}'.format(aff, rgoff, rgoffRect, insar.numberRangeLooks1, insar.numberAzimuthLooks1)
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cmd += parallelSettings('dates2')
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cmd += '''for ((i=0;i<${{#dates2[@]}};i++)); do
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{extraCommands}
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cd {datesResampledDir}
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cd ${{dates2[i]}}
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cd insar
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{script} -aff {aff} -input ${{dates2[i]}}_{nrlks1}rlks_{nalks1}alks_rg.off -output ${{dates2[i]}}_{nrlks1}rlks_{nalks1}alks_rg_rect.off -nrlks1 {nrlks1} -nalks1 {nalks1}
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cd ../../../
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done'''.format(extraCommands = parallelCommands,
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script = os.path.join(stackScriptPath, 'rect_range_offset.py'),
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datesResampledDir = stack.datesResampledDir,
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aff = os.path.join('../../', stack.dateReferenceStack, 'insar', 'affine_transform.txt'),
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nrlks1 = insar.numberRangeLooks1,
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nalks1 = insar.numberAzimuthLooks1)
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cmd += '\n'
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cmd += '\n'
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cmd += 'cd ../../../\n'
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cmd += '\n'
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#diff interferograms
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if pairsProcess != []:
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cmd += header('diff interferograms')
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cmd += parallelSettings('insarpair')
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cmd += '''for ((i=0;i<${{#insarpair[@]}};i++)); do
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{extraCommands}
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IFS='-' read -ra dates <<< "${{insarpair[i]}}"
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ref_date=${{dates[0]}}
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sec_date=${{dates[1]}}
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@ -586,7 +715,9 @@ done'''.format(script = os.path.join(stackScriptPath, 'mosaic_inter
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cd ${{insarpair[i]}}
|
||||
{script} -idir {idir} -ref_date_stack {ref_date_stack} -ref_date ${{ref_date}} -sec_date ${{sec_date}} -nrlks1 {nrlks1} -nalks1 {nalks1}
|
||||
cd ../../
|
||||
done'''.format(script = os.path.join(stackScriptPath, 'diff_interferogram.py'),
|
||||
|
||||
done'''.format(extraCommands = parallelCommands,
|
||||
script = os.path.join(stackScriptPath, 'diff_interferogram.py'),
|
||||
pairsProcessingDir = stack.pairsProcessingDir,
|
||||
idir = os.path.join('../../', stack.datesResampledDir),
|
||||
ref_date_stack = stack.dateReferenceStack,
|
||||
|
|
@ -594,13 +725,18 @@ done'''.format(script = os.path.join(stackScriptPath, 'diff_interfe
|
|||
nalks1 = insar.numberAzimuthLooks1)
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
|
||||
|
||||
#look and coherence
|
||||
if (pairsProcess != []) or processDateReferenceStack:
|
||||
cmd += header('look and coherence')
|
||||
if pairsProcess != []:
|
||||
cmd += parallelSettings('insarpair')
|
||||
cmd += '''for ((i=0;i<${{#insarpair[@]}};i++)); do
|
||||
|
||||
{extraCommands}
|
||||
|
||||
IFS='-' read -ra dates <<< "${{insarpair[i]}}"
|
||||
ref_date=${{dates[0]}}
|
||||
sec_date=${{dates[1]}}
|
||||
|
|
@ -609,7 +745,9 @@ done'''.format(script = os.path.join(stackScriptPath, 'diff_interfe
|
|||
cd ${{insarpair[i]}}
|
||||
{script} -ref_date ${{ref_date}} -sec_date ${{sec_date}} -nrlks1 {nrlks1} -nalks1 {nalks1} -nrlks2 {nrlks2} -nalks2 {nalks2}
|
||||
cd ../../
|
||||
done'''.format(script = os.path.join(stackScriptPath, 'look_coherence.py'),
|
||||
|
||||
done'''.format(extraCommands = parallelCommands,
|
||||
script = os.path.join(stackScriptPath, 'look_coherence.py'),
|
||||
pairsProcessingDir = stack.pairsProcessingDir,
|
||||
nrlks1 = insar.numberRangeLooks1,
|
||||
nalks1 = insar.numberAzimuthLooks1,
|
||||
|
|
@ -652,6 +790,7 @@ done'''.format(script = os.path.join(stackScriptPath, 'look_coheren
|
|||
cmd += os.path.join(stackScriptPath, 'pair_up.py') + ' -idir1 {} -idir2 {} -odir {} -ref_date {} -pairs {}'.format(stack.datesProcessingDir, stack.datesResampledDir, stack.pairsProcessingDirIon, stack.dateReferenceStack, ' '.join(pairsProcessIon))
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
|
||||
|
||||
#subband interferograms
|
||||
|
|
@ -662,7 +801,11 @@ done'''.format(script = os.path.join(stackScriptPath, 'look_coheren
|
|||
snapArgument = ''
|
||||
|
||||
cmd += header('subband interferograms')
|
||||
cmd += parallelSettings('ionpair')
|
||||
cmd += '''for ((i=0;i<${{#ionpair[@]}};i++)); do
|
||||
|
||||
{extraCommands}
|
||||
|
||||
IFS='-' read -ra dates <<< "${{ionpair[i]}}"
|
||||
ref_date=${{dates[0]}}
|
||||
sec_date=${{dates[1]}}
|
||||
|
|
@ -671,7 +814,9 @@ done'''.format(script = os.path.join(stackScriptPath, 'look_coheren
|
|||
cd ${{ionpair[i]}}
|
||||
{script} -idir {idir} -ref_date_stack {ref_date_stack} -ref_date ${{ref_date}} -sec_date ${{sec_date}} -nrlks1 {nrlks1} -nalks1 {nalks1}{snapArgument}
|
||||
cd ../../
|
||||
done'''.format(script = os.path.join(stackScriptPath, 'ion_subband.py'),
|
||||
|
||||
done'''.format(extraCommands = parallelCommands,
|
||||
script = os.path.join(stackScriptPath, 'ion_subband.py'),
|
||||
pairsProcessingDir = stack.pairsProcessingDirIon,
|
||||
idir = os.path.join('../../', stack.datesResampledDir),
|
||||
ref_date_stack = stack.dateReferenceStack,
|
||||
|
|
@ -680,6 +825,7 @@ done'''.format(script = os.path.join(stackScriptPath, 'ion_subband.
|
|||
snapArgument = snapArgument)
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
|
||||
|
||||
#unwrap subband interferograms
|
||||
|
|
@ -691,7 +837,11 @@ done'''.format(script = os.path.join(stackScriptPath, 'ion_subband.
|
|||
filtArgument = ''
|
||||
|
||||
cmd += header('unwrap subband interferograms')
|
||||
cmd += parallelSettings('ionpair')
|
||||
cmd += '''for ((i=0;i<${{#ionpair[@]}};i++)); do
|
||||
|
||||
{extraCommands}
|
||||
|
||||
IFS='-' read -ra dates <<< "${{ionpair[i]}}"
|
||||
ref_date=${{dates[0]}}
|
||||
sec_date=${{dates[1]}}
|
||||
|
|
@ -700,7 +850,9 @@ done'''.format(script = os.path.join(stackScriptPath, 'ion_subband.
|
|||
cd ${{ionpair[i]}}
|
||||
{script} -idir {idir} -ref_date_stack {ref_date_stack} -ref_date ${{ref_date}} -sec_date ${{sec_date}} -wbd {wbd} -nrlks1 {nrlks1} -nalks1 {nalks1} -nrlks_ion {nrlks_ion} -nalks_ion {nalks_ion}{filtArgument}
|
||||
cd ../../
|
||||
done'''.format(script = os.path.join(stackScriptPath, 'ion_unwrap.py'),
|
||||
|
||||
done'''.format(extraCommands = parallelCommands,
|
||||
script = os.path.join(stackScriptPath, 'ion_unwrap.py'),
|
||||
pairsProcessingDir = stack.pairsProcessingDirIon,
|
||||
idir = os.path.join('../../', stack.datesResampledDir),
|
||||
ref_date_stack = stack.dateReferenceStack,
|
||||
|
|
@ -712,6 +864,7 @@ done'''.format(script = os.path.join(stackScriptPath, 'ion_unwrap.p
|
|||
filtArgument = filtArgument)
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
|
||||
|
||||
#filter ionosphere
|
||||
|
|
@ -731,7 +884,11 @@ done'''.format(script = os.path.join(stackScriptPath, 'ion_unwrap.p
|
|||
filtArgument += ''.join([' -masked_areas '+' '.join([str(y) for y in x]) for x in insar.maskedAreasIon])
|
||||
|
||||
cmd += header('filter ionosphere')
|
||||
cmd += parallelSettings('ionpair')
|
||||
cmd += '''for ((i=0;i<${{#ionpair[@]}};i++)); do
|
||||
|
||||
{extraCommands}
|
||||
|
||||
IFS='-' read -ra dates <<< "${{ionpair[i]}}"
|
||||
ref_date=${{dates[0]}}
|
||||
sec_date=${{dates[1]}}
|
||||
|
|
@ -740,7 +897,9 @@ done'''.format(script = os.path.join(stackScriptPath, 'ion_unwrap.p
|
|||
cd ${{ionpair[i]}}
|
||||
{script} -idir {idir1} -idir2 {idir2} -ref_date_stack {ref_date_stack} -ref_date ${{ref_date}} -sec_date ${{sec_date}} -nrlks1 {nrlks1} -nalks1 {nalks1} -nrlks2 {nrlks2} -nalks2 {nalks2} -nrlks_ion {nrlks_ion} -nalks_ion {nalks_ion} -win_min {win_min} -win_max {win_max}{filtArgument}
|
||||
cd ../../
|
||||
done'''.format(script = os.path.join(stackScriptPath, 'ion_filt.py'),
|
||||
|
||||
done'''.format(extraCommands = parallelCommands,
|
||||
script = os.path.join(stackScriptPath, 'ion_filt.py'),
|
||||
pairsProcessingDir = stack.pairsProcessingDirIon,
|
||||
idir1 = os.path.join('../../', stack.datesResampledDir),
|
||||
idir2 = os.path.join('../../', stack.datesProcessingDir),
|
||||
|
|
@ -756,19 +915,26 @@ done'''.format(script = os.path.join(stackScriptPath, 'ion_filt.py'
|
|||
filtArgument = filtArgument)
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
|
||||
|
||||
#prepare interferograms for checking ionospheric correction
|
||||
cmd += header('prepare interferograms for checking ionosphere estimation results')
|
||||
if pairsProcessIon1 != []:
|
||||
cmd += parallelSettings('ionpair1')
|
||||
if (insar.numberRangeLooksIon != 1) or (insar.numberAzimuthLooksIon != 1):
|
||||
cmd += '''for ((i=0;i<${{#ionpair1[@]}};i++)); do
|
||||
|
||||
{extraCommands}
|
||||
|
||||
IFS='-' read -ra dates <<< "${{ionpair1[i]}}"
|
||||
ref_date=${{dates[0]}}
|
||||
sec_date=${{dates[1]}}
|
||||
|
||||
{script} -i {pairsProcessingDir}/${{ionpair1[i]}}/insar/diff_${{ionpair1[i]}}_{nrlks1}rlks_{nalks1}alks.int -o {pairsProcessingDirIon}/${{ionpair1[i]}}/ion/ion_cal/diff_${{ionpair1[i]}}_{nrlks}rlks_{nalks}alks_ori.int -r {nrlks_ion} -a {nalks_ion}
|
||||
done'''.format(script = os.path.join('', 'looks.py'),
|
||||
|
||||
done'''.format(extraCommands = parallelCommands,
|
||||
script = os.path.join('', 'looks.py'),
|
||||
pairsProcessingDir = stack.pairsProcessingDir.strip('/'),
|
||||
pairsProcessingDirIon = stack.pairsProcessingDirIon.strip('/'),
|
||||
nrlks1 = insar.numberRangeLooks1,
|
||||
|
|
@ -779,23 +945,34 @@ done'''.format(script = os.path.join('', 'looks.py'),
|
|||
nalks = insar.numberAzimuthLooks1 * insar.numberAzimuthLooksIon)
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
else:
|
||||
cmd += '''for ((i=0;i<${{#ionpair1[@]}};i++)); do
|
||||
|
||||
{extraCommands}
|
||||
|
||||
IFS='-' read -ra dates <<< "${{ionpair1[i]}}"
|
||||
ref_date=${{dates[0]}}
|
||||
sec_date=${{dates[1]}}
|
||||
|
||||
cp {pairsProcessingDir}/${{ionpair1[i]}}/insar/diff_${{ionpair1[i]}}_{nrlks1}rlks_{nalks1}alks.int* {pairsProcessingDirIon}/${{ionpair1[i]}}/ion/ion_cal
|
||||
done'''.format(pairsProcessingDir = stack.pairsProcessingDir.strip('/'),
|
||||
|
||||
done'''.format(extraCommands = parallelCommands,
|
||||
pairsProcessingDir = stack.pairsProcessingDir.strip('/'),
|
||||
pairsProcessingDirIon = stack.pairsProcessingDirIon.strip('/'),
|
||||
nrlks1 = insar.numberRangeLooks1,
|
||||
nalks1 = insar.numberAzimuthLooks1)
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
|
||||
|
||||
if pairsProcessIon2 != []:
|
||||
cmd += parallelSettings('ionpair2')
|
||||
cmd += '''for ((i=0;i<${{#ionpair2[@]}};i++)); do
|
||||
|
||||
{extraCommands}
|
||||
|
||||
IFS='-' read -ra dates <<< "${{ionpair2[i]}}"
|
||||
ref_date=${{dates[0]}}
|
||||
sec_date=${{dates[1]}}
|
||||
|
|
@ -804,7 +981,9 @@ done'''.format(pairsProcessingDir = stack.pairsProcessingDir.strip('/'),
|
|||
cd ${{ionpair2[i]}}
|
||||
{script} -ref_date ${{ref_date}} -sec_date ${{sec_date}} -nrlks1 {nrlks1} -nalks1 {nalks1}
|
||||
cd ../../
|
||||
done'''.format(script = os.path.join(stackScriptPath, 'form_interferogram.py'),
|
||||
|
||||
done'''.format(extraCommands = parallelCommands,
|
||||
script = os.path.join(stackScriptPath, 'form_interferogram.py'),
|
||||
pairsProcessingDir = stack.pairsProcessingDirIon,
|
||||
nrlks1 = insar.numberRangeLooks1,
|
||||
nalks1 = insar.numberAzimuthLooks1)
|
||||
|
|
@ -812,6 +991,9 @@ done'''.format(script = os.path.join(stackScriptPath, 'form_interfe
|
|||
cmd += '\n'
|
||||
|
||||
cmd += '''for ((i=0;i<${{#ionpair2[@]}};i++)); do
|
||||
|
||||
{extraCommands}
|
||||
|
||||
IFS='-' read -ra dates <<< "${{ionpair2[i]}}"
|
||||
ref_date=${{dates[0]}}
|
||||
sec_date=${{dates[1]}}
|
||||
|
|
@ -820,7 +1002,9 @@ done'''.format(script = os.path.join(stackScriptPath, 'form_interfe
|
|||
cd ${{ionpair2[i]}}
|
||||
{script} -ref_date_stack {ref_date_stack} -ref_date ${{ref_date}} -sec_date ${{sec_date}} -nrlks1 {nrlks1} -nalks1 {nalks1}
|
||||
cd ../../
|
||||
done'''.format(script = os.path.join(stackScriptPath, 'mosaic_interferogram.py'),
|
||||
|
||||
done'''.format(extraCommands = parallelCommands,
|
||||
script = os.path.join(stackScriptPath, 'mosaic_interferogram.py'),
|
||||
pairsProcessingDir = stack.pairsProcessingDirIon,
|
||||
ref_date_stack = stack.dateReferenceStack,
|
||||
nrlks1 = insar.numberRangeLooks1,
|
||||
|
|
@ -829,6 +1013,9 @@ done'''.format(script = os.path.join(stackScriptPath, 'mosaic_inter
|
|||
cmd += '\n'
|
||||
|
||||
cmd += '''for ((i=0;i<${{#ionpair2[@]}};i++)); do
|
||||
|
||||
{extraCommands}
|
||||
|
||||
IFS='-' read -ra dates <<< "${{ionpair2[i]}}"
|
||||
ref_date=${{dates[0]}}
|
||||
sec_date=${{dates[1]}}
|
||||
|
|
@ -837,7 +1024,9 @@ done'''.format(script = os.path.join(stackScriptPath, 'mosaic_inter
|
|||
cd ${{ionpair2[i]}}
|
||||
{script} -idir {idir} -ref_date_stack {ref_date_stack} -ref_date ${{ref_date}} -sec_date ${{sec_date}} -nrlks1 {nrlks1} -nalks1 {nalks1}
|
||||
cd ../../
|
||||
done'''.format(script = os.path.join(stackScriptPath, 'diff_interferogram.py'),
|
||||
|
||||
done'''.format(extraCommands = parallelCommands,
|
||||
script = os.path.join(stackScriptPath, 'diff_interferogram.py'),
|
||||
pairsProcessingDir = stack.pairsProcessingDirIon,
|
||||
idir = os.path.join('../../', stack.datesResampledDir),
|
||||
ref_date_stack = stack.dateReferenceStack,
|
||||
|
|
@ -848,12 +1037,17 @@ done'''.format(script = os.path.join(stackScriptPath, 'diff_interfe
|
|||
|
||||
if (insar.numberRangeLooksIon != 1) or (insar.numberAzimuthLooksIon != 1):
|
||||
cmd += '''for ((i=0;i<${{#ionpair2[@]}};i++)); do
|
||||
|
||||
{extraCommands}
|
||||
|
||||
IFS='-' read -ra dates <<< "${{ionpair2[i]}}"
|
||||
ref_date=${{dates[0]}}
|
||||
sec_date=${{dates[1]}}
|
||||
|
||||
{script} -i {pairsProcessingDir}/${{ionpair2[i]}}/insar/diff_${{ionpair2[i]}}_{nrlks1}rlks_{nalks1}alks.int -o {pairsProcessingDir}/${{ionpair2[i]}}/ion/ion_cal/diff_${{ionpair2[i]}}_{nrlks}rlks_{nalks}alks_ori.int -r {nrlks_ion} -a {nalks_ion}
|
||||
done'''.format(script = os.path.join('', 'looks.py'),
|
||||
|
||||
done'''.format(extraCommands = parallelCommands,
|
||||
script = os.path.join('', 'looks.py'),
|
||||
pairsProcessingDir = stack.pairsProcessingDirIon.strip('/'),
|
||||
nrlks1 = insar.numberRangeLooks1,
|
||||
nalks1 = insar.numberAzimuthLooks1,
|
||||
|
|
@ -863,23 +1057,34 @@ done'''.format(script = os.path.join('', 'looks.py'),
|
|||
nalks = insar.numberAzimuthLooks1 * insar.numberAzimuthLooksIon)
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
else:
|
||||
cmd += '''for ((i=0;i<${{#ionpair2[@]}};i++)); do
|
||||
|
||||
{extraCommands}
|
||||
|
||||
IFS='-' read -ra dates <<< "${{ionpair2[i]}}"
|
||||
ref_date=${{dates[0]}}
|
||||
sec_date=${{dates[1]}}
|
||||
|
||||
cp {pairsProcessingDir}/${{ionpair2[i]}}/insar/diff_${{ionpair2[i]}}_{nrlks1}rlks_{nalks1}alks.int* {pairsProcessingDir}/${{ionpair2[i]}}/ion/ion_cal
|
||||
done'''.format(pairsProcessingDir = stack.pairsProcessingDirIon.strip('/'),
|
||||
|
||||
done'''.format(extraCommands = parallelCommands,
|
||||
pairsProcessingDir = stack.pairsProcessingDirIon.strip('/'),
|
||||
nrlks1 = insar.numberRangeLooks1,
|
||||
nalks1 = insar.numberAzimuthLooks1)
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
|
||||
|
||||
#check ionosphere estimation results
|
||||
cmd += header('check ionosphere estimation results')
|
||||
cmd += parallelSettings('ionpair')
|
||||
cmd += '''for ((i=0;i<${{#ionpair[@]}};i++)); do
|
||||
|
||||
{extraCommands}
|
||||
|
||||
IFS='-' read -ra dates <<< "${{ionpair[i]}}"
|
||||
ref_date=${{dates[0]}}
|
||||
sec_date=${{dates[1]}}
|
||||
|
|
@ -888,7 +1093,9 @@ done'''.format(pairsProcessingDir = stack.pairsProcessingDirIon.strip('/'),
|
|||
cd ${{ionpair[i]}}
|
||||
{script} -e='a*exp(-1.0*J*b)' --a=ion/ion_cal/diff_${{ionpair[i]}}_{nrlks}rlks_{nalks}alks_ori.int --b=ion/ion_cal/filt_ion_{nrlks}rlks_{nalks}alks.ion -s BIP -t cfloat -o ion/ion_cal/diff_${{ionpair[i]}}_{nrlks}rlks_{nalks}alks.int
|
||||
cd ../../
|
||||
done'''.format(script = os.path.join('', 'imageMath.py'),
|
||||
|
||||
done'''.format(extraCommands = parallelCommands,
|
||||
script = os.path.join('', 'imageMath.py'),
|
||||
pairsProcessingDir = stack.pairsProcessingDirIon,
|
||||
nrlks = insar.numberRangeLooks1*insar.numberRangeLooksIon,
|
||||
nalks = insar.numberAzimuthLooks1*insar.numberAzimuthLooksIon)
|
||||
|
|
@ -898,6 +1105,7 @@ done'''.format(script = os.path.join('', 'imageMath.py'),
|
|||
cmd += os.path.join(stackScriptPath, 'ion_check.py') + ' -idir {} -odir fig_ion -pairs {}'.format(stack.pairsProcessingDirIon, ' '.join(pairsProcessIon))
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
|
||||
|
||||
#estimate ionospheric phase for each date
|
||||
|
|
@ -910,14 +1118,17 @@ done'''.format(script = os.path.join('', 'imageMath.py'),
|
|||
cmd += ' -zro_date {}'.format(stack.dateReferenceStackIon)
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
|
||||
|
||||
#correct ionosphere
|
||||
if insar.applyIon:
|
||||
cmd += header('correct ionosphere')
|
||||
cmd += '#no need to run parallelly for this for loop, it is fast!!!\n'
|
||||
cmd += '''#redefine insarpair to include all processed InSAR pairs
|
||||
insarpair=($(ls -l {pairsProcessingDir} | grep ^d | awk '{{print $9}}'))
|
||||
for ((i=0;i<${{#insarpair[@]}};i++)); do
|
||||
|
||||
IFS='-' read -ra dates <<< "${{insarpair[i]}}"
|
||||
ref_date=${{dates[0]}}
|
||||
sec_date=${{dates[1]}}
|
||||
|
|
@ -927,6 +1138,7 @@ for ((i=0;i<${{#insarpair[@]}};i++)); do
|
|||
#uncomment to run this command
|
||||
#{script} -ion_dir {ion_dir} -ref_date ${{ref_date}} -sec_date ${{sec_date}} -nrlks1 {nrlks1} -nalks1 {nalks1} -nrlks2 {nrlks2} -nalks2 {nalks2}
|
||||
cd ../../
|
||||
|
||||
done'''.format(script = os.path.join(stackScriptPath, 'ion_correct.py'),
|
||||
pairsProcessingDir = stack.pairsProcessingDir,
|
||||
ion_dir = os.path.join('../../', stack.datesDirIon),
|
||||
|
|
@ -972,7 +1184,11 @@ done'''.format(script = os.path.join(stackScriptPath, 'ion_correct.
|
|||
extraArguments += ' -wbd_msk'
|
||||
|
||||
cmd += header('filter interferograms')
|
||||
cmd += parallelSettings('insarpair')
|
||||
cmd += '''for ((i=0;i<${{#insarpair[@]}};i++)); do
|
||||
|
||||
{extraCommands}
|
||||
|
||||
IFS='-' read -ra dates <<< "${{insarpair[i]}}"
|
||||
ref_date=${{dates[0]}}
|
||||
sec_date=${{dates[1]}}
|
||||
|
|
@ -981,7 +1197,9 @@ done'''.format(script = os.path.join(stackScriptPath, 'ion_correct.
|
|||
cd ${{insarpair[i]}}
|
||||
{script} -idir {idir} -ref_date_stack {ref_date_stack} -ref_date ${{ref_date}} -sec_date ${{sec_date}} -nrlks1 {nrlks1} -nalks1 {nalks1} -nrlks2 {nrlks2} -nalks2 {nalks2} -alpha {alpha} -win {win} -step {step}{extraArguments}
|
||||
cd ../../
|
||||
done'''.format(script = os.path.join(stackScriptPath, 'filt.py'),
|
||||
|
||||
done'''.format(extraCommands = parallelCommands,
|
||||
script = os.path.join(stackScriptPath, 'filt.py'),
|
||||
pairsProcessingDir = stack.pairsProcessingDir,
|
||||
idir = os.path.join('../../', stack.datesResampledDir),
|
||||
ref_date_stack = stack.dateReferenceStack,
|
||||
|
|
@ -995,6 +1213,7 @@ done'''.format(script = os.path.join(stackScriptPath, 'filt.py'),
|
|||
extraArguments = extraArguments)
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
|
||||
|
||||
#unwrap interferograms
|
||||
|
|
@ -1003,7 +1222,11 @@ done'''.format(script = os.path.join(stackScriptPath, 'filt.py'),
|
|||
extraArguments += ' -wbd_msk'
|
||||
|
||||
cmd += header('unwrap interferograms')
|
||||
cmd += parallelSettings('insarpair')
|
||||
cmd += '''for ((i=0;i<${{#insarpair[@]}};i++)); do
|
||||
|
||||
{extraCommands}
|
||||
|
||||
IFS='-' read -ra dates <<< "${{insarpair[i]}}"
|
||||
ref_date=${{dates[0]}}
|
||||
sec_date=${{dates[1]}}
|
||||
|
|
@ -1012,7 +1235,9 @@ done'''.format(script = os.path.join(stackScriptPath, 'filt.py'),
|
|||
cd ${{insarpair[i]}}
|
||||
{script} -idir {idir} -ref_date_stack {ref_date_stack} -ref_date ${{ref_date}} -sec_date ${{sec_date}} -nrlks1 {nrlks1} -nalks1 {nalks1} -nrlks2 {nrlks2} -nalks2 {nalks2}{extraArguments}
|
||||
cd ../../
|
||||
done'''.format(script = os.path.join(stackScriptPath, 'unwrap_snaphu.py'),
|
||||
|
||||
done'''.format(extraCommands = parallelCommands,
|
||||
script = os.path.join(stackScriptPath, 'unwrap_snaphu.py'),
|
||||
pairsProcessingDir = stack.pairsProcessingDir,
|
||||
idir = os.path.join('../../', stack.datesResampledDir),
|
||||
ref_date_stack = stack.dateReferenceStack,
|
||||
|
|
@ -1023,6 +1248,7 @@ done'''.format(script = os.path.join(stackScriptPath, 'unwrap_snaph
|
|||
extraArguments = extraArguments)
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
cmd += '\n'
|
||||
|
||||
|
||||
#geocode
|
||||
|
|
@ -1033,7 +1259,11 @@ done'''.format(script = os.path.join(stackScriptPath, 'unwrap_snaph
|
|||
extraArguments += ' -bbox {}'.format('/'.format(insar.bbox))
|
||||
|
||||
cmd += header('geocode')
|
||||
cmd += parallelSettings('insarpair')
|
||||
cmd += '''for ((i=0;i<${{#insarpair[@]}};i++)); do
|
||||
|
||||
{extraCommands}
|
||||
|
||||
IFS='-' read -ra dates <<< "${{insarpair[i]}}"
|
||||
ref_date=${{dates[0]}}
|
||||
sec_date=${{dates[1]}}
|
||||
|
|
@ -1045,7 +1275,9 @@ done'''.format(script = os.path.join(stackScriptPath, 'unwrap_snaph
|
|||
{script} -ref_date_stack_track ../{ref_date_stack}.track.xml -dem {dem_geo} -input filt_${{insarpair[i]}}_{nrlks}rlks_{nalks}alks.unw -nrlks {nrlks} -nalks {nalks}{extraArguments}
|
||||
{script} -ref_date_stack_track ../{ref_date_stack}.track.xml -dem {dem_geo} -input filt_${{insarpair[i]}}_{nrlks}rlks_{nalks}alks_msk.unw -nrlks {nrlks} -nalks {nalks}{extraArguments}
|
||||
cd ../../../
|
||||
done'''.format(script = os.path.join(stackScriptPath, 'geocode.py'),
|
||||
|
||||
done'''.format(extraCommands = parallelCommands,
|
||||
script = os.path.join(stackScriptPath, 'geocode.py'),
|
||||
pairsProcessingDir = stack.pairsProcessingDir,
|
||||
ref_date_stack = stack.dateReferenceStack,
|
||||
dem_geo = stack.demGeo,
|
||||
|
|
|
|||
Loading…
Reference in New Issue