o ^sz.MiaplPyParser.out_load_slc..)formatrZisceTopsAutoPathZisceStripmapAutoPathZroipacAutoPathZ gammaAutoPath template_fileprint_example_template SystemExitr print_usageprintr3r4basename__file__sysexitabspath project_dir PROJECT_NAMEwork_dirr5makedirsr6out_file)rsinpsZDEFAULT_TEMPLATErr9rr*;s8    zMiaplPyParser.out_load_slccCs|}tjtjtjd}tjtjtjd}|jr&tt|d |j r/ttj j |j sYtj tj|sY|jsY|jt|d}|d7}|d7}t|t|j rtj|j |_ tj |j spt|j tj|j tj|kr|j |_d|_ ||}|S)Nzdefaults/miaplpyApp.cfgz!defaults/miaplpy_mintpy_print.cfgrz+ERROR: no template file found! It requires:z& 1) input a custom template file, ORzH 2) there is a default template 'miaplpyApp.cfg' in current directory.)r3r4r5dirnamer0rBprint_templater>openreadversionr customTemplateFileisfilerAgenerate_templaterr?r@rEFileNotFoundError templateFileread_inps2run_steps)rrKr,r-r<Ztemplate_file_printmsgrrrr+bs8    zMiaplPyParser.out_miaplpy_appcCs,dD]$}t||}|r&||jvr&|dks&d|}|d|j7}t|q|jr2|j|_|j|_|j|j}|j|j}||krPd|j|j}t||j||d|_|j r`g|_t dt |jdkrt |jdkryt t j jnt t j jt d tjt d tt d tjt|jt d |j|dd |jd ur|jrtj|j}|d|_ntj|j|_tj|j|_d |_|jrtj|jdkstjtj|jd|_t d|jn tjtj|j|_tj|jst|jt d|S)z(read/get run_steps from input arguments.) startStependStepdoStep multilookzInput step not found: {}z Available steps: {}z2input start step "{}" is AFTER input end step "{}"r/z2--------------------------------------------------rz --RUN-at-{}--zCurrent directory: {}z+Run routine processing with {} on steps: {}zRemaining steps: {}Nz/miaplpyzmiaplpyApp.cfgz Project name:) varsr(r; ValueErrorr[rYrZindexZ run_stepsrTr@lenr0rQversion_descriptionlogodatetimenowr3getcwdr4rArBworkDirrRrMrVrEZ projectNamesplitextexistsmkdir)rr-keyvaluerXidx0idx1Zpath1rrrrWsV      z!MiaplPyParser.read_inps2run_stepsc Csd}d}tjdtj|d|d}|jdddd d |jd d td ddd|jddtddd|jdddddd|jddtdhddd d!|jd"d#d$d%d&d |jd'hd(dd)d*|jd+d,dd-d |jd.d/td0d1gd2d3d4|S)5Natemplate: ########## 1. Load Data ## auto - automatic path pattern for Univ of Miami file structure ## load_slc.py -H to check more details and example inputs. ## compression to save disk usage for slcStack.h5 file: ## no - save 0% disk usage, fast [default] ## lzf - save ~57% disk usage, relative slow ## gzip - save ~62% disk usage, very slow [not recommend] miaplpy.load.processor = auto #[isce,snap,gamma,roipac], auto for isceTops miaplpy.load.updateMode = auto #[yes / no], auto for yes, skip re-loading if HDF5 files are complete miaplpy.load.compression = auto #[gzip / lzf / no], auto for no. miaplpy.load.autoPath = auto # [yes, no] auto for no miaplpy.load.slcFile = auto #[path2slc_file] miaplpy.load.startDate = auto #auto for first date miaplpy.load.endDate = auto #auto for last date ##---------for ISCE only: miaplpy.load.metaFile = auto #[path2metadata_file], i.e.: ./reference/IW1.xml, ./referenceShelve/data.dat miaplpy.load.baselineDir = auto #[path2baseline_dir], i.e.: ./baselines ##---------geometry datasets: miaplpy.load.demFile = auto #[path2hgt_file] miaplpy.load.lookupYFile = auto #[path2lat_file], not required for geocoded data miaplpy.load.lookupXFile = auto #[path2lon_file], not required for geocoded data miaplpy.load.incAngleFile = auto #[path2los_file], optional miaplpy.load.azAngleFile = auto #[path2los_file], optional miaplpy.load.shadowMaskFile = auto #[path2shadow_file], optional miaplpy.load.waterMaskFile = auto #[path2water_mask_file], optional miaplpy.load.bperpFile = auto #[path2bperp_file], optional ##---------subset (optional): ## if both yx and lalo are specified, use lalo option unless a) no lookup file AND b) dataset is in radar coord miaplpy.subset.yx = auto #[y0:y1,x0:x1 / no], auto for no miaplpy.subset.lalo = auto #[S:N,W:E / no], auto for no aexample: load_slc.py -t PichinchaSenDT142.txt load_slc.py -t miaplpyApp.cfg load_slc.py -t PichinchaSenDT142.txt --project_dir $SCRATCH/PichinchaSenDT142 load_slc.py -H #Show example input template for ISCE/ROI_PAC/GAMMA products z0Saving a stack of Interferograms to an HDF5 file r formatter_classepilog-Hr=r z1Print/Show the example template file for loading.destrr-t --template+r<zTemplate file with path info.)typenargsrtrz-pjz --project_dirrFz-Project directory of SLC dataset to read fromrxrtr-d --work_dirrHz0Working directory of miaplpy (default ./miaplpy)rtdefaultrz-prz --processor processor>roipaciscegammazFInSAR processor/software of the file (This version only supports isce)r)rxrtchoicesrr~z --enforce-f updateMode store_falsezADisable the update mode, or skip checking dataset already loaded.z --compression>gzipNlzfz@Compress loaded geometry while writing HDF5 file, default: None.)rr~rz--no_metadata_checkZno_metadata_checkz:Do not check for rsc files, when running via miaplpyApp.py-o--outputrJ)z slcStack.h5zgeometryRadar.h5zgeometryGeo.h5zOutput HDF5 file)rxryrtr~r)rrRawTextHelpFormatterrstr)TEMPLATEr,rrrrr sJ$        zMiaplPyParser.load_slc_parsercCsB|j}|d}|jddtddd|jddtd d d d |jd dtdd dd |jddtdddd |jddtdddd |jddtdddd |jd d!td"dd#d |jd$d%td&d'dd |jd(d)td*dd+d |jd,d-td.d/d|jd0d1td2d3d4d |jd5d6d7td8d9d:|jd;dd:|jd?d@dAdBdCdD|S)ENzPhase inversion option-wr|rHWorking directory (miaplpy)rz-rz--range_window range_windowz!Range window size for shp findingrxrtr~r-az--azimuth_windowazimuth_windowz#Azimuth window size for shp finding-mz--methodZinversion_methodZEMIz5Inversion method (EMI, EVD, PTA, sequential_EMI, ...)z-lz --time_lagZtime_lag zTime lag in case StBAS is usedruz--testZshp_testksz$Shp statistical test (ks, ad, ttest)z-psnz --ps_num_shpZps_shpz Number of SHPs for PS candidates-pz --patch_sizeZ patch_sizez-mssz--mini_stack_sizeZministack_sizez#Number of images in each mini stack-sz --slc_stack slc_stackzSLC stack filez-ms--mask mask_fileNonezmask file for inversionz-nz --num_worker num_workerr/z%Number of parallel tasks (default: 1)rtrxr~r-iz--index sub_indexzd:d?d<|jd@dAd:dBd<|S)CNzUnwrap using snaphurrz--ifgZ input_ifgTzInput wrapped interferogram)rtrxrrrz --coherenceZ input_corzInput coherence filez-uz--unwrapped_ifgZ unwrapped_ifgzOutput unwrapped interferogramrrZ unwrap_maskrz-swz--widthZ ref_widthzWidth of Reference .h5 filez-slz--lengthZ ref_lengthzLength of .h5 filerz --wavelength wavelength Wavelengthz-htz--heightheightzAltitude of satellitez-erz--earth_radius earth_radiusz Earth Radiusrz --init_methodZ init_methodMSTz*Unwrap initialization algorithm (MST, MCF)r{z--max_discontinuityZdefo_maxg333333?z+Maximum abrupt phase discontinuity (cycles)z-ntz --num_tilesZ num_tilesr/z*Number of tiles for Unwrapping in parallelz --two-stageZ unwrap_2stager z"Use 2 stage unwrapping (from ISCE)rsz --rmfilterZremove_filter_flagzRemove filtering after unwrap--tmp copy_to_tmpCopy and process on tmprrrrrr$`sZ   zMiaplPyParser.unwrap_parsercCs8tjdd}|jddtdddd|jd d d d d |S)N"Convert phase to range time seriesrr{r|rHTrr --shadow_mask shadow_maskr %use shadow mask to mask final resultsrsrrrrrr%s  z0MiaplPyParser.generate_temporal_coherence_parserc Cstjdd}|jddd|jddtdd d d |jd d dtddd|jdddddd|jdddddtddd|jddd dd!|jd"d#d$d%d!|jd&d'd(d(d)gd*d+|jd,d-d.d/d|jd0d1d2d3hd4d5d+|S)6NrrZifgramStackFilez(interferograms stack file to be inverted)rr{r|rHTrrrurvr<z-template file (default: smallbaselineApp.cfg)rz--tcohz --temp_cohtemp_cohrr}z --mask-thresz--mask-thresholdz--mtZ maskThresholdZNUMrzIthreshold to generate mask for temporal coherence (default: %(default)s).)rtmetavarrxr~rrrr rsz--min-norm-phaseZminNormVelocityrzoEnable inversion with minimum-norm deformation phase, instead of the default minimum-norm deformation velocity.z--norm residualNormL1L2z;Optimization mehtod, L1 or L2 norm. (default: %(default)s).)rtr~rrz--smooth_factorZL1_alphagMbP?z6Smoothing factor for L1 inversion [0-1] default: 0.01.rz --weight-funcZ weightFuncvar>cohrZfimnozfunction used to convert coherence to weight for inversion: var - inverse of phase variance due to temporal decorrelation (default) fim - Fisher Information Matrix as weightcoh - spatial coherence no - no/uniform weight)rrrrrrrrrr&s>      z&MiaplPyParser.network_inversion_parserc Cs\gd}d|dd|dd}d}tjdtj|d}|jdd d d |jd d dddd|jddddd|jddddd|jddddd|jddddd|jd d!dd"d|jd#d$dd%d|jd&d'dd(d|jd)d*dd+d|d,|}|jd-d.d/|dd0|dd1|jd2d3d4d/|d5d6|d5d1|jd7d8d/d9d:|||fS);N) load_datarZconcatenate_patchesZgenerate_ifgramZ unwrap_ifgramZ load_ifgramZifgram_correctionrZtimeseries_correctionagCommand line options for steps processing with names are chosen from the following list: {} {} In order to use either --start or --step, it is necessary that a previous run was done using one of the steps options to process at least through the step immediately preceding the starting step of the current run. raexample: miaplpyApp.py # run with default and custom templates miaplpyApp.py -h / --help # help miaplpyApp.py -H # print default template options # Run with --start/stop/step options miaplpyApp.py PichinchaSenDT142.txt --dostep load_data # run the step 'download' only miaplpyApp.py PichinchaSenDT142.txt --start load_data # start from the step 'download' miaplpyApp.py PichinchaSenDT142.txt --stop unwrap_ifgram # end after step 'interferogram' z(Routine Time Series Analysis for MiaplPyrorR?zUCustom template with option settings. ignored if the default miaplpyApp.cfg is input.)ryrz--dirz --work-dirrfz'Work directory, (default: %(default)s).r}rrTr z:Generate default template (if it does not exist) and exit.rsrrrNz)Print the default template file and exit.r r r rz --walltimeZ wall_timez+walltime for submitting the script as a jobz--queuequeuez Queue namez --jobfilesZ write_jobz*Do not run the tasks, only write job filesz --runfilesZrun_flagzCreate run files for all stepsrrrz#steps processing (start/end/dostep)z--startrYSTEPz/Start processing at the named step, default: {})rtrr~rz--endz--stoprZz-End processing at the named step, default: {}z--dostepr[z%Run processing at the named step only)rtrr)r;rrrrr)r(Z STEP_HELPr,rsteprrrr'sT             z MiaplPyParser.miaplpy_app_parser)NN)__name__ __module__ __qualname__rr.r*r+rW staticmethodr r!r#r"r$r%r&r'rrrrrs*  '(B K   "  r) rCrr0miaplpy.defaultsrr3rcZPathFindZpathObj CLUSTER_LISTrrrrrs