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e60940b version: bug fix when no new commit after last release 14 May 2019, 19:04:10 UTC
5cbe914 docs: update (#62) * update label in figures of example datasets * update acronym and the version number in 14 May 2019, 17:54:29 UTC
4c2b6f8 rename PySAR to MintPy (#61) $PYSAR_HOME --> $MINTPY_HOME #used in installation and documentations. PySAR --> MintPy #for names in comments and text mostly. pysar --> mintpy #for module import --> sh/ --> sh/ #shell script to plot results of defaults/pysarApp.cfg --> smallbaselineApp_auto.cfg #files of specific option value for all "auto" in sbasApp.cfg pysar.load.unwFile --> mintpy.load.unwFile objects rename giantobj --> giant insarobj --> stackDict pysarobj --> stack update file/dir structure /PYSAR --> /mintpy /GEOCODE --> /geo #files after runing geocoding (for dataset in radar coordinates only as dataset in geo coordinates won't need to run /INPUTS --> /inputs #input files folder, so that one can move/copy this folder and re-generate everything afterwards. /PIC --> /pic #for figures, kmz files, etc. adjust all related documents, comments, notebooks 12 May 2019, 16:56:25 UTC
db9dfa5 update comments (#60) + docs/paper: update link for nbviewer + add temp-c custom colormap cpt file + add -s besides --start-date and -e besides --end-date for + asc_desc2horz_vert: add example to prepare asc/desc data 09 May 2019, 02:59:04 UTC
a9ec91b geocode: add OMP_NUM_THREADS control + add geocode/check_num_processor() to check OMP_NUM_THREADS if it's defined in environment variable and use it if --nprocs is not specified. + set default --nprocs to 1 because 1) bonding between pykdtree and openmp is not clear yet and 2) the speedup is negligible for macport install and slows down for conda install + change default nprocs value to 1 in objects/ + detect lookup table file in current directory besides the INPUTS directory. 03 May 2019, 00:25:36 UTC
406c823 geocode: fix typo in help (#57) fix typo in and objects/ 01 May 2019, 17:19:31 UTC
3caeaea pysarApp: more compatiable with py2-pyaps (#55) * Update * pysarApp: more compatiable with py2-pyaps calling as an executable script using subprocess.Popen() to make works with py2-pyaps from caltech. The current way of importing tropo_pyaps as an sub-module is preferred but it failed to import python2 sub-modules in python3 environment. 30 April 2019, 20:55:53 UTC
d62d1b3 bug fix for data reading for single dataset files (#53) * added read data line for all file types of single datasets 30 April 2019, 20:28:39 UTC
bd67db3 test/test_pysarApp: add argument parsing + add argument parsing functions to be more user friendly. + add --dir to be able to change test directory + add --nofresh to be able to start processing not from the scratch, suitable for testing bugs in the middle of processing. 30 April 2019, 20:09:42 UTC
b3a4176 timeseries_rms: bug fix for plotting (#52) * bug fixed for timeseries_rms * Update 30 April 2019, 15:32:31 UTC
b54877d bugs fix for unwrap error correction (#51) docs/examples/input_files/GalapagosSenDT128.template: add pysar.load.waterMaskFile generated by ISCE pysar.unwrapError.waterMaskFile: change default value to waterMask.h5 or no if waterMask.h5 is not found; to be the same as and pysar.networkInversion.waterMaskFile dem_error: bug fixed for 3D bperp reading when it has different number of acquisitions from the time-series file get rid of string yunjunz from the code in objects/ and unwrap_error_phase_closure: fix bugs when there are interferograms excluded in ifgramStack.h5 file utils/writefile: fix bug in remove_hdf5_dataset() when input fname is not just basename. version: move code into get_release_info() Update 29 April 2019, 15:27:40 UTC
18f11e4 version: auto grab code version and date + do not install pykml through conda channel, which will cause error; install py2/3-pykml from yunjunz through Anaconda's pip + remove openmp from requirements.txt as it's not directly used by pysar, it's used by pyresample implictly 27 April 2019, 03:06:10 UTC
eb222bb info: rename --nodrop to --show-ifgram info: + rename previous --nodrop option to --show / --show-ifgram option to avoid confusion + bug fixed for --num option when show kept interferograms only. + simplified code plot/select_network: rename --nodrop to --show-kept to avoid confusion. 26 April 2019, 20:06:07 UTC
29311e4 Update 26 April 2019, 03:09:52 UTC
11cfce4 Update 26 April 2019, 03:06:28 UTC
8a84005 pysarApp: expose more parameters for empirical tropospheric delay correction (#46) * expose `pysar.troposphericDelay.minCorrelation` option. * pass `pysar.troposphericDelay.looks` from `` to `` 26 April 2019, 00:50:17 UTC
9cce2b9 docs/tutorials/pysarApp: update superlink 25 April 2019, 21:40:15 UTC
d067089 installation: more note on parallel setup 25 April 2019, 21:33:30 UTC
730c2e3 prep_gamma: add LAT/LON_REF1/2/3/4 info to geometry files + merge `extract_metadata4dem_geo()` and `extract_metadata4lookup_table` into `extract_metadata4geometry_geo()` + rename `extract_metadata4dem_radar()` to `extract_metadata4geometry_radar()` + searching for LAT/LON_REF1/2/3/4 info for geometry files in radar coordinates + move code inside prepare_metadata() into main() 25 April 2019, 19:18:56 UTC
f3eb60d docs/paper: add shell scripts 25 April 2019, 02:14:03 UTC
63a6ea8 add docs/paper Add `docs/paper` for the figures in Yunjun et al., 2019 24 April 2019, 02:14:39 UTC
30b3ada docs/examples/input_files: add template files for the paper Update 24 April 2019, 02:14:39 UTC
bb0f91f move examples to docs/examples 24 April 2019, 02:14:39 UTC
666612b docs: rename Notebooks to tutorials 24 April 2019, 02:14:39 UTC
1a7ad41 tropo_pyaps3: bug fix 24 April 2019, 02:14:39 UTC
8990a58 utils/ptime: add datenum2datetime + utils/ptime: add datenum2datetime() to convert Matlab datenum into Python datetime format + timeseries_rms: update usage in plot_rms_bar(). 24 April 2019, 02:14:39 UTC
1a48e97 save_roipac: support HDF_EOS5 file + objects/pysarobj: add HDFEOS.get_date_list() + utils/readfile: remove the following obsolete global variables for py2 psyar: - multi_group_hdf5_file - multi_dataset_hdf5_file - single_dataset_hdf5_file + save_roipac: - remove --ref-date option because it's not convenient to use - support date1_date2 input for timeseries and HDFEOS files to change reference date easily. - support HDF-EOS5 file, including the displacement, temporalCoherence and all geometry datasets. 19 April 2019, 22:23:24 UTC
fd15fd2 update docs for pyaps3 + update requirements for pyaps3 + update installation for pyaps3 and dask setup + simplify 19 April 2019, 22:22:02 UTC
e53f3a3 ifgram_inversion: add NUM_WORKERS back for dask 19 April 2019, 04:24:33 UTC
24c41a2 add for pyaps3 with ERA5 print message adjustment in and objects/ add in response to pyaps3 from Angelique Benoit on Github, compared with, there are several changes: 1. add support for ERA-5 dataset with hourly temporal resolution and ~32 km spatial resoluion. 2. use ERA5, ERAINT etc as weatherModel name instead of ECMWF, which is essential an organization name. 3. do not generate and remove ROIPAC style geometry files with rsc file anymore as the input of PYAPS is 2D array directly. 4. ERA5 support area subset download, instead of previously ERAI downloads the data for the entire world, saves a lot of space. 5. do not set minimum file size anymore as area subset file is very small. 6. merge radar/geo coordinates PyAPS objects into one, as the input of lat/lon does not distinguish radar or geo 19 April 2019, 04:24:33 UTC
07ebc84 add parallel option to template file 1. add the following two option into pysarApp_template.txt for parallel processing: + pysar.networkInversion.parallel with auto for no + pysar.networkInversion.numWorker with auto for 40 ifgram_inversion: + catch and print import error for dask modules + change minRedundancy variable type from float to int + support reading parallel options from input template file + remove obsolete option `skip_zero_phase` + rename the following two functions: - split_into_boxes() --> split2boxes() - subsplit_boxes_by_num_workers() --> subsplit_boxes4workers() + use inps.numWorker directly without NUM_WORKERS + rename variable number_of_splits to num_split 19 April 2019, 04:24:33 UTC
4ce81aa Revert "ifgram_inversion: import dask module for --parallel option only" This reverts commit d1499c7f17f7f63055554aa9c940641e6d007f13. 19 April 2019, 04:24:33 UTC
2fcff4e ifgram_inversion: import dask module for --parallel option only 19 April 2019, 04:24:33 UTC
fcf5758 remove temporarily `import dask` (#40) 19 April 2019, 01:05:30 UTC
b043522 utils/readfile: bug fix while reading ISCE file with full in filename (#39) utils/readfile: + exclude `.full` while checking FILE_TYPE for ISCE binary files + more generic read_binary() by do not distinguish num_band utils/writefile: update comments 18 April 2019, 04:07:43 UTC
ba88a24 process_isce_stack: copy masterShelve to the root directory (#38) * process_isce_stack: add copy_masterShelve() * process_isce_stack: add --submit as an alternative to --bsub * utils/plot: use "1 km" instead of "1000 m" for scale bar * utils/plot: adjust parameter for DEM shaded relief min/max 16 April 2019, 21:23:33 UTC
4abe4c3 updated minimum dask_jobqueue version (#37) * updated minimum dask_jobqueue version 15 April 2019, 20:02:11 UTC
d3cac2b bug fix for tsview when reference point is outside of the display subset (#34) 14 April 2019, 16:56:55 UTC
c2cdc11 Lowered Dask memory config 13 April 2019, 17:39:38 UTC
5e3beda utils/utils: add win_size in read_timeseries_lalo/yx (#33) 11 April 2019, 23:57:56 UTC
ad15a88 Added Dask config defaults & fixed #31 (#32) * Updated Dask config and refactored Dask comments * Fix for #31 and fix cluster.close() throwing an exception * Added examples, added NUM_WORKERS to params, cleaned up subsplit() func * add par parser group for num_workers 10 April 2019, 15:18:16 UTC
dc776ac Included dask-jobqueue in the imports (#29) dask-jobqueue is the library used to run Dask on HPC. 09 April 2019, 21:50:08 UTC
15e6441 ifgram_inversion: bug fixed while runing in command line (#30) 09 April 2019, 19:43:23 UTC
ed5c794 save_roipac: drop all lower case keys for geodmod (#28) + save_roipac: drop all attributes with key name not all upper case, to better support geodmod + utils/readfile: add default value for num_band and band_interleave 08 April 2019, 23:57:34 UTC
d49789f examples: add notebook for GACOS (#27) * dem_gsi: add reference datum info + add reference datum info into xml file so that ISCE will not convert it again, as DEHM from GSi is already in ellipsoid. The indent needs to be adjusted, this should not be a problem for now. + change default output name to be consistent with ISCE convention: gsi10m.dem --> gsi10m.dem.wgs84 * ports: remove sundials and petsc due to gcc5 and 8 conflict * examples: add notebook for GACOS add example notebook to correct tropospheric delay using GACOS product for geocoded time-series file. 08 April 2019, 22:08:33 UTC
3b1b5ab Added requirements for using dask Conda installs all of dask with a simple `conda install dask`, however pip fails to install a dependency for Dask's distributed dashboard, `bokeh`. The `bokeh` requirement is included in the `requirements.txt` file but not in the `conda.txt` file. 08 April 2019, 17:31:05 UTC
803523b Moved `requirements.txt` to the base directory (#26) * Moved `requirements.txt` to the base directory It is a common practice amongst open source projects to have requirements.txt files in the base directory. This commit follows that practice. * Changed updated path of requirements file in 08 April 2019, 16:47:00 UTC
e9a8886 Update 06 April 2019, 22:23:46 UTC
b44d858 tropo velocity: adjust file name following Falk's suggestion (#25) + adjust the velocity file name of tropospheric delay time-series: use `velocityECMWF.h5` instead of `velocityEcmwf.h5`, to be more consistent with other file names. + fix bug related with the update mode of calling. adjust accordingly. 05 April 2019, 02:26:17 UTC
b4bda00 prep_gamma: support more flexible file naming (#24) * prep_gamma: more flexible file name pattern * fix bugs detected by codacy 03 April 2019, 05:05:47 UTC
3d162a8 Update 03 April 2019, 02:19:12 UTC
f2c11b5 installation: note to install pyhdf for macports 02 April 2019, 19:17:23 UTC
5792051 readfile: add DATA_TYPE for binary files utils/readfile: + add DATA_TYPE metadata for binary files in read() + comment the Exception statement to be able to read more files without fixed file extension, such as .ztd from GACOS, although this will skip error message for potential reading mistakes. 02 April 2019, 15:34:07 UTC
e3b3d10 plot_coherence_matrix: support geo coded insar stack + plot_coherence_matrix: add support for geocoded ifgramStack.h5 + subset: bug fixed for -o/--output option + detect geometryGeo.h5 file if geometryRadar.h5 does not exists. 01 April 2019, 22:40:04 UTC
91b9f3e pysarApp: load waterMask from stripmapStack + add pysar.load.waterMaskFile to be able to load waterMask.rdr generated by ISCE/stripmapStack (Yunjun's version for now, plan to push to isce-framework later) + change the default value of pysar.networkInversion.waterMaskFile to waterMask.h5 if it's existed. waterMask.h5 will be automatically generated if it's loaded into geometry*.h5 + re-run if REF_Y/X are changed. + print warnings if ISCE meta file is not found. + pysarApp: add generate waterMask.h5 file from geometry* files remove_ramp: + add --update option for remote_ramp so that it will re-run if ramp type is changed. + remote multiple input files support for simplicity. utils/ + add get_geometry_file() back 01 April 2019, 16:50:21 UTC
f9fd0d7 sh/plot_pysarApp: move KMZ files to PIC folder 01 April 2019, 16:50:21 UTC
b9cc1bb update scripts for isce stack processing (#2) * mask: set int amp/pha to zero * process_isce_stack: add masterDate 01 April 2019, 16:50:21 UTC
572cbf7 remote CODEOWNERS remote docs/CODEOWNERS file, for now, to disable the automatic reviewers assignment of pull request as it's not really useful in the current scenario. 28 March 2019, 16:55:28 UTC
258f379 test: add Wells dataset + add WellsEnvD2T399 example dataset in test/test_pysarApp. + update DOI number for Fernandina dataset + use template files from code for the latest options, instead of the uploaded files in zenodo. + remove obsolete weatherDir setup in template files as WEATHER_DIR is detected. 28 March 2019, 16:51:07 UTC
b93944b remove joblib module requirement Remove joblib usage because it does not improve the runing speed much. Remove check_parallel() function calling in ``, `` and ``. update docs/requirements.txt and docs/conda.txt add usage example in the comments of check_parallel() in pysar/utils/ 28 March 2019, 16:51:07 UTC
eb80542 installation: more notes on PyAPS 28 March 2019, 15:34:22 UTC
cbe6692 nb/pysarApp: adjust for the order change of modify_network + update pysarApp_workflow + adjust pysarApp.ipynb 27 March 2019, 21:04:54 UTC
9af4d38 plot/plot_network: add disp_legend option (#1) 27 March 2019, 19:59:17 UTC
483990e docs: remote obsolete manual and template file + remote obsolete manual pdf/html + remote obsolete QR code image + remote pysarApp_template.txt fiel as it's now in pysar/defaults folder 27 March 2019, 19:59:17 UTC
c7f64f7 Add more reviewers in docs/CODEOWNERS + Update 27 March 2019, 19:59:17 UTC
a479c0a remove unused module import detected by codacy (#14) Fix issues detected by codacy, including: + remove unused module imports + remove unused variables + bugs fix 27 March 2019, 16:10:21 UTC
eca1fb7 Create (#15) 27 March 2019, 00:35:43 UTC
eb54bb7 add docs/CODEOWNERS (#13) * add docs/CODEOWNERS 26 March 2019, 17:57:50 UTC
fbe62f4 Merge pull request #12 from yunjunz/master README: remove FOSSA status checking 26 March 2019, 02:33:21 UTC
081ee54 README: remove FOSSA status checking 26 March 2019, 02:32:38 UTC
e5c58cc Merge pull request #11 from yunjunz/master update Github links from yunjunz to insarlab 26 March 2019, 01:20:44 UTC
2a75389 docs: update links to insarlab 26 March 2019, 01:19:34 UTC
190fa7d Github Page: update links 26 March 2019, 01:09:15 UTC
df98f37 Merge pull request #10 from yunjunz/master pull request before moving to insarlab organization 25 March 2019, 21:41:14 UTC
4f7d37a add WellEnvD2T399.txt 24 March 2019, 04:14:15 UTC
f60e23f Merge pull request #42 from yunjunz/dev Dev 24 March 2019, 03:45:55 UTC
ce2844a add figure for WellsEnvD2-gamma 24 March 2019, 03:43:56 UTC
4c8bc79 tropo_pyaps: check existed tropo_file size 22 March 2019, 18:29:48 UTC
e782cf0 modify_network: use waterMask.h5 as the primary default value switch auto value for step "modify_network" from "no" to "waterMask.h5" or "no" if waterMask.h5 does not exist. This will also fix the bug of not updating introduced by recent step order change of moving modify_network before reference_point modify_network: print out excluded dates 22 March 2019, 18:29:48 UTC
f0c0191 tropo_pyaps: support ${WEATHER_DIR} add support of identifying environmental variable "WEATHER_DIR" for the default location of downloaded GAMs files. switch the default value for the weather directory to ${WEATHER_DIR] in both and Use the current directory "./" as the fallback value if WEATHER_DIR is not found and identified. 22 March 2019, 02:35:18 UTC
a33bb99 pysarApp: move modify_network before reference_point move the dynamic import from pysar/ to pysar/workflow/ to speed up the initiation of scripts used by pysarApp. pysarApp: + move modify_network before reference_point + move stack_interferograms after correct_unwrap_error + move avgSpatialCoh.h5 and maskConnComp.h5 generation to new function: TimeSeriesAnalysis.generate_ifgram_aux_file() + change default `` value from `maskConnComp.h5` to `no` and remove obsolete maskSpatialCoh.h5 file. + add missing return statement for run_*() utils/plot: change default mask file for avgPhaseVelocity.h5 to `None` instead of `maskSpatialCoh.h5` Do not update maskConnComp.h5 and avgSpatialCoh.h5 within as they are not relavent anymore. 20 March 2019, 23:08:20 UTC
39c3f4e add process_isce_stack add to run the recipe of ISCE stripmapStack processor. + it read job configuration from cfg file using configparser module + define the 1st version of isce processor option names + add reset_process_directory() to clean the directory before re-run. + add prepare_ALOS() for the SAR data preparation + add prepare_stack() to call + NOTE: DEM preparation is NOT included, as it is different in study areas in Japan. + add --bsub option, similar to remove obsolete split_jobs: switch job shell to tcsh to use the same environment as command line 20 March 2019, 05:00:19 UTC
8869798 add plot_coherence_matrix.ipynb 19 March 2019, 21:40:59 UTC
106967a Merge pull request #41 from yunjunz/dev notebook: add plot_coherence_matrix 19 March 2019, 21:39:24 UTC
301855c notebook: add plot_coherence_matrix utils/plot: add ratio argument in auto_figure_size() plot_coherence_matrix: + merge two figures into one with two subplots + add auto figure size calculation update and docs/Notebooks/ 19 March 2019, 21:36:30 UTC
83040e2 plot_coherence_matrix: add networkViewer object 19 March 2019, 21:00:49 UTC
56bdf12 sh/run_stripmap_stack: adjust to prepRawALOS in yunjunz/dev version bugs fix add pysarApp adjust to prepRawALOS in yunjunz/dev version 19 March 2019, 01:25:41 UTC
7b8abf9 move unwrap_error* module import inside run_unwrap_error_correction() 18 March 2019, 03:53:28 UTC
9c245a1 adjust for updated stripmapStack/dev 18 March 2019, 03:49:22 UTC
b43e257 Notebook (#40) * mask: update message * submit*stripmap_stack: update to new run_files 18 March 2019, 02:05:09 UTC
f291b47 adjust for updated FernandinaSenDT128 dataset adjustment for the new version of FernandinaSenDT128 dataset due to the re-calculated HEADING value from 17 March 2019, 22:52:55 UTC
d4787c5 Eliminate ALL subprocess calls for python scripts from (#34) * Refactored out easily modifiable subprocess calls * Removed status where possible * move plot result inside run_load_data() and run it if load_complete is False * bugs fixed in read_template2inps() in and 17 March 2019, 21:25:27 UTC
c6e16d9 update nb for stripmapApp_postprocessing 17 March 2019, 16:57:47 UTC
1f13a8f Merge pull request #39 from leixie-steven/patch-2 bug report for the azimuth angle in prep_isce 17 March 2019, 15:17:55 UTC
fa8281b bug report for the azimuth angle in prep_isce Reading the azimuth angle from the geom_file instead of incident angle for the heading angle conversion. 17 March 2019, 14:49:57 UTC
f5a5a5a utils/readfile: do not use "image_type" metadata from ISCE Do not use the "image_type" metadata from ISCE xml file for the FILE_TYPE metadata, because it is not robust (sometimes unw sometimes bil), use the file extension without rdr or geo, only, instead. 17 March 2019, 04:55:46 UTC
b21c850 bug fix in __init__ 16 March 2019, 22:27:13 UTC
67293c0 Merge pull request #37 from yunjunz/init_package_update Added automatic importing of modules when importing pysar 16 March 2019, 21:47:07 UTC
4695ed3 init: add geocode to __all__ 16 March 2019, 21:46:05 UTC
c37379f added automatic importing of modules when importing pysar 16 March 2019, 21:37:03 UTC
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