| 4756732 | Zhang Yunjun | 19 October 2022, 21:05:08 UTC | add `pre-commit` to dependency and contributing guideline (#873) * ptime.read_date_txt(): ignore invalid/empty lines * read_template: bugfix for `skip_chars` arg * deps: add pre-commit + add `pre-commit` to the following dependency files, so that it will be installed automatically in the development version. - docs/environment.yml - requirements.txt - setup.py + docs/CONTRIBUTING: add note to install `pre-commit` + github PR template: add selection box for pre-commit check. * Update CONTRIBUTING.md we need to run `pre-commit sample-config` to have a basic config file before running `pre-commit install`. Co-authored-by: Yuan-Kai Liu <55262505+yuankailiu@users.noreply.github.com> | 19 October 2022, 21:05:08 UTC |
| 868c27f | Bryan Marfito | 16 October 2022, 17:52:03 UTC | `writefile.write`: force `BANDS` to 2 for `.unw` file (#871) to ensure the consistency between output metadata and data with the 2-band format, because the input *.unw file may have only 1-band, as produced by `isce2/alosStack`. | 16 October 2022, 17:52:03 UTC |
| 1350ddf | Zhang Yunjun | 13 October 2022, 02:32:37 UTC | support `hyp3` `lv_phi` file as azimuth angle (#865) + prep_hyp3.add_hyp3_metadata(): set UNIT to radian for "lv_phi" file + objects.stackDict.geometryDict(): - convert hyp3 azimuthAngle input from gamma to mintpy/isce2 convention - convert no-data-value from 0 to nan for azimuthAngle and incidenceAngle + docs: add lv_phi file to the example dir structure for hyp3 | 13 October 2022, 02:32:37 UTC |
| 8c23297 | Zhang Yunjun | 11 October 2022, 04:25:55 UTC | ionex: split interp_3d_maps() out of get_ionex_value() for re-use (#867) | 11 October 2022, 04:25:55 UTC |
| 890a743 | pre-commit-ci[bot] | 11 October 2022, 01:06:11 UTC | [pre-commit.ci] pre-commit autoupdate (#866) | 11 October 2022, 01:06:11 UTC |
| e4c94d1 | Zhang Yunjun | 09 October 2022, 22:50:38 UTC | ut.add_attribute(): support binary file type (#864) + utils.utils1.add_attribute(): support binary file, by writing roipac RSC file, in addition to the existing HDF5 file | 09 October 2022, 22:50:38 UTC |
| b71a6cf | Zhang Yunjun | 07 October 2022, 21:11:10 UTC | sort ds_list to ensure `velocity` as first and `residue/intercept` as last (#860) + `utils.readfile`: - add sort_dataset_list4velocity() to ensure velocity are the first dataset, and intercept/residue are the last datasets - apply the above func in get_dataset/slice_list() for velocity file - replace var `k` with `ftype` for code readility + tests/smallbaselineApp: use *.tar.gz file, in addition to *.tar.xz file, if exists. + add `mintpy.objects.progress.FileProgressObject` class to show a progrerss bar during uncompressing | 07 October 2022, 21:11:10 UTC |
| 38a9891 | Zhang Yunjun | 01 October 2022, 20:51:44 UTC | rename `bulk_plate_motion` to `plate_motion` (#858) + rename `bulk_plate_motion` to `plate_motion`: including changes in: - `mintpy.plate_motion.py` - `mintpy.cli.plate_motion.py` - `mintpy.__main__` - `setup.py` + `utils.readfile.read()`: add `no_data_values` arg to be able to convert the no-data-value from one number to another number. + `utils.network`: del the obsolete `igram_perp_baseline_list()` function + use the Python context manager `with` statement to better control the HDF5 file handle/lock (#855). | 01 October 2022, 20:51:44 UTC |
| 5eb8857 | pre-commit-ci[bot] | 27 September 2022, 00:58:37 UTC | [pre-commit.ci] autoupdate pyupgrade: v2.37.3 → v2.38.2 (#856) updates: - [github.com/asottile/pyupgrade: v2.37.3 → v2.38.2](https://github.com/asottile/pyupgrade/compare/v2.37.3...v2.38.2) | 27 September 2022, 00:58:37 UTC |
| 8ccacd1 | Zhang Yunjun | 24 September 2022, 02:06:46 UTC | `smallbaselineApp`: replace workflow import w/ individual import (#854) + `smallbaselineApp`: bring back the individual module import (as proposed in the lazy import PR #828), to replace the workflow import, for better speed and robustness. + `workflow/__init__.py`: fix the UnboundLocalError of 'mintpy' + `info`: support `--compact` output to `--date / --num` options + general Codacy style suggestions | 24 September 2022, 02:06:46 UTC |
| 9ca4adc | Zhang Yunjun | 23 September 2022, 01:46:27 UTC | readfile.read_isce_xml: bugfix when v_first=0 (#853) | 23 September 2022, 01:46:27 UTC |
| 7e36e6a | Zhang Yunjun | 22 September 2022, 21:54:14 UTC | setup `pre-commit` hook + initial run against all files (#852) + install pre-commit GitHub Apps + add `.pre-commit-config.yaml` + changes from the initial run of pre-commit against all files - end-of-file-fixer - trailing-whitespace - sort imports via isort - modernize python via pyupgrade + info: printout h5 dataset compression info + tests: consistent script header comments + utils.readfile: use MACRO_CASE global var - replace standardMetadataKeys with STD_METADATA_KEYS | 22 September 2022, 21:54:14 UTC |
| 73f4e28 | Zhang Yunjun | 22 September 2022, 06:32:41 UTC | support azimuth output for `solid_earth_tides` and `bulk_plate_motion` (#851) + solid_earth_tides.py: - add --comp enu2los / en2az to switch between range / azimuth direction output - use ut.get_unit_vector4comp_of_interest() for --comp projection - support date_list text file as input, as an alternative to the TS HDF5 file - change set_file as optional arg in calc_solid_earth_tides_timeseries() + bulk_plate_motion.py: - add --comp enu2los / en2az to switch between range / azimuth direction output - use ut.get_unit_vector4comp_of_interest() for --comp projection - use lower case "enu" and/or "az" for default output filename - set pmm_file as optional arg in calc_bulk_plate_motion() + utils.utils0.py: - add Coordinate / Orbit sub-section to simplify the Geometry sub-section - add definition with example values for the following angles: los_inc_angle, los_az_angle, orb_az_angle, head_angle - add los2orbit_azimuth_angle() - add azimuth2heading_angle(look_direction) and heading2azimuth_angle(look_direction) - add en2az() - add get_unit_vector4comp_of_interest() - add misregistration2coherence() based on Just & Bamler (1994) + utils.utils.prepare_geo_los_geometry(): change the output from head_angle to los_az_angle. + objects.ionex: move plotting-related modules inside plot_ionex() for more independency + objects.stack/giant: use MACRO_CASE for the global variables and update their usages throughout the repo. + objects.timeseries.read(): use single indexing to speedup IO + smallbaselineApp.plot_result: rm '-u cm' for velocity, as it now has datasets with different units, thus, '-u cm' won't work anymore. + tsview: fix the mpl.figure.canvas.set_window_title() bug, as reported and fixed by Jiawei Li + view: update example usage in the comments for (cli)/view.py + dependency: add `rich` to the formal dependency list, as it's lightweight and prints colorful template content, and plan to be used more. + del simulation/configSenDesc.txt, as it's not used in the code anymore. | 22 September 2022, 06:32:41 UTC |
| eec16ba | Antonio Valentino | 21 September 2022, 19:12:11 UTC | lazy import via `mintpy.cli` for more responsive CLI (#828) NOTE: re-installation is required after this update, using pip or path setup, as described in docs/installation.md. + add `mintpy.cli`: split all CLI scripts in root module `mintpy` into two parts: core functionality (still in `mintpy`), and CLI-related functionalities (into a new sub-module `mintpy.cli`). The `mintpy.cli` module includes the following functions; and enables lazy improts (fast responsive CLI) to the `mintpy` command. - create_parser() - cmd_line_parse() - read_template2inps() - main() - __main__ - other very simple sub-functions + `mintpy.cli`: use `parse -> import -> run / check / default` order to expand the lazy imports to all the individual *.py commands. + `mintpy.__main__`: use absolute imports + `mintpy.workflow.__init__`: update the dynamic import to `mintpy.cli`. + setup.py: add extras_require field + create an overall processing function for the following scripts, to allow for simple main() call in `mintpy.cli`: - bulk_plate_motion.py - closure_phase_bias.py - dem_gsi.py - generate_mask.py - ifgram_inversion.py - info.py - iono_tec.py - load_data.py - lookup_geo2radar.py - modify_network.py - smallbaselineApp.py + ifgram_inversion: remove the unavailable and unused "mintpy.networkInversion.residualNorm" option, to simplify the code. + load_data: use `importlib` to import prep_module + objects.timeseries(): - add temporal_derivative() from temporal_derivative.py - add temporal_filter() from temporal_filter.py + objects.insar_vs_gps: refactor to replace `dateutil` with `datetime` to remove the `dateutil` dependency + smallbaselineApp.TimeSeriesAnalysis(): remove all unused `return` statement + tropo_gacos: keep only the JGR paper, to accurately reflect the fact that gacos website produced products do not include the GNSS info, as shown in Yu's other papers. + utils.utils1.run_or_skip(): rename check_readable to readable, to shortern its calls + view: remove unused `PLOT_TEMPLATE` and `--plot-setting` option. This was for insarmaps website, but does not seems to be used. Remove for code simplification. + remove the followings scripts, as they are aborted into `mintpy.cli` or `mintpy.objects.stack.timeseries`: - prep_snap.py - remove_hdf5_dset.py renamed from remove_hdf5_dataset.py - remove_ramp.py - spatial_average.py - temporal_average.py - temporal_derivative.py - temporal_filter.py + docs/installation.md: update the instruction to install mintpy via path setup + adjust to make path setup method working on cmd: - add `#!/usr/bin/env python3` to the top of all cli/[a-z]*.py scripts - run `chmod +x` to all `cli/[a-z]*.py` scripts - run `chmod -x` to all `mintpy/[a-z]*.py` scripts, except for two (add_attribute.py and multi_transect.py). Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> Co-authored-by: Antonio Valentino <Antonio.Valentino@ext.esa.int> | 21 September 2022, 19:12:11 UTC |
| 414cb65 | Zhang Yunjun | 17 September 2022, 00:03:01 UTC | bugfix in ionex.dload_ionex() (#849) | 17 September 2022, 00:03:01 UTC |
| 726fa70 | Zhang Yunjun | 13 September 2022, 04:11:09 UTC | del obsolete mintpy/legacy/gui folder (#846) + delete the obsolete `mintpy/legacy/gui` folder, as 1) they are not working nor maintained anymore, 2) they are causing problems while trying pre-commit hooks + legacy/transect_legacy.py: update print() from py2 to py3 + utils/isce_utils.get_processor(): add `data.db` to the supported list of metadata files generated by stripmapStack + load_data.py: add more msg for aria if load_data failed | 13 September 2022, 04:11:09 UTC |
| d987950 | Bryan Marfito | 07 September 2022, 06:20:27 UTC | fix typo in `smallbaselineApp.cfg` for `stepDate` (#843) | 07 September 2022, 06:20:27 UTC |
| 4a0f2c5 | BB | 05 September 2022, 19:46:54 UTC | unmask ref pixel in ts2vel and tsview (#842) + timeseries2velocity.py: - include the reference point as valid pixels for calculation/inversion. - use np.full() instead of np.ones() for initiation with nan value. + tsview.py: bugfix for keeping the reference point in the valid pixel mask + utils/plot.auto_figure_title(): add "_" for the processing flag if not existed already. Co-authored-by: bbuzz31 <buzzanga@jpl.nasa.gov> Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> | 05 September 2022, 19:46:54 UTC |
| 3245008 | Scott Staniewicz | 01 September 2022, 16:32:36 UTC | readfile.read_attribute: allow ENVI files created with SUFFIX=ADD (#841) + readfile.read_attribute: allow ENVI files created by GDAL with `SUFFIX=ADD`, in additional to the current ones created with `SUFFIX=REPLACE`. | 01 September 2022, 16:32:36 UTC |
| fe2fc27 | Zhang Yunjun | 22 August 2022, 22:09:09 UTC | ts2vel: save `residue` & `intercept` (#835) + timeseries2velocity.py: - save `residue` for the overall fitting residues, a useful parameter to evaluate the fitting quality - save `intercept` for the Y-axis intercept of the polynomial function, to be able to reconstruct the time-series completely. + .github/workflows/pypi: publish the release to test-pypi as well | 22 August 2022, 22:09:09 UTC |
| 4fef13c | stackTom | 20 August 2022, 04:02:57 UTC | hdf5eos: calc `data_footprint` for radar-coded dataset (#833) + save_hdf5eos.py: support radar-coded dataset - calculate `data_footprint` for radar-coded files, based on geometry files from both isce and roipac style - check the incompatible --subset option with radar-coded dataset - add example cmd for radar-coded dataset + utils0.py: add `snwe_to_wkt_polygon()` Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> | 20 August 2022, 04:02:57 UTC |
| 36a0835 | Zhang Yunjun | 16 August 2022, 06:51:05 UTC | wrap up for version 1.4.1 (#829) + version: add Tag for version 1.4.1 + readfile.read_hdf5_file(): speedup the 3D matrix reading when slicing a small fraction of the 1st dimension, by using integer indexing for 3D h5 dataset, instead of 1D boolean array indexing. + view.read_data4figure(): bugfix for referencing unwrapPhase while plotting mixed dset types + move the following plotting functions to utils.plot.py for a more compact module import, to simplify the UNAVCO notebook: - unwrap_error_phase_closure.plot_num_triplet_with_nonzero_integer_ambiguity() - timeseries_rms.plot_rms_bar() - objects.insar_vs_gps.plot_insar_vs_gps_scatter() + plot.plot_insar_vs_gps_scatter(): add preliminary outlier detection | 16 August 2022, 06:51:05 UTC |
| 47bb7f6 | Zhang Yunjun | 12 August 2022, 18:12:49 UTC | automate PyPI publishing with GitHub Actions (#827) + version: replace version_num with version for easy re-use, and update its usage in __inti__.py + setup: use sys.path.append() to replace open() to grab version from version.py + add .github/workflows/publish-to-test-pypi.yml: - triggered for push event on insarlab/main branch - use "pip install" and "python -m build" to build the binary wheel and source tarball - use pypa/gh-action-pypi-publish action to push to PyPI and TestPyPI - push to PyPI only for released version and when owner is insarlab + repo setting: add github secrets from pypi, to support the above action | 12 August 2022, 18:12:49 UTC |
| 2e9e300 | Zhang Yunjun | 11 August 2022, 21:11:48 UTC | bugfix in `load_data` for empty path due to the new iono file in `auto_path` (#826) + load_data.py: bugfix when empty file path found, introduced in load iono stack PR 780, due to the additional new iono file path defined in defaults/auto_path.py. | 11 August 2022, 21:11:48 UTC |
| ef31de5 | Zhang Yunjun | 08 August 2022, 06:04:39 UTC | remove `openmp` from the dependency list (#825) + remove "openmp" from all the dependency files, as "conda install pyresample" will install openmp correctly (llvm-openmp for linux, libgomp for linux; https://conda-forge.org/docs/maintainer/knowledge_base.html#openmp) + version.py: remove the prefix "v" from the version number, to be consistent with styles from gdal/numpy + smallbaselineApp.generate_temporal_coherence_mask(): run plot_result() to populate pic folder before raising errors, to facilitate the trouble shooting + reference_point: support more flexible mask dataset name in the mask h5 file. | 08 August 2022, 06:04:39 UTC |
| 68cdbbe | Zhang Yunjun | 04 August 2022, 20:01:49 UTC | wrap up for version 1.4.0 (#824) + version: add release tag for v1.4.0 + bulk_plate_motion: add ITRF2014_PMM global var for convenience and future options with PMM model name and plate name, instead of typing detailed values manually. + geocode.py: add checking for the imcompatible options between "--geo2radar" and "--bbox / --software scipy" + subset: replace try/except with if/else for more robustness + arg_group: add --title / --fig-title for --figtitle option as alternatives | 04 August 2022, 20:01:49 UTC |
| 537c4ef | Antonio Valentino | 04 August 2022, 08:18:55 UTC | Single entrypoint with sub-commands (#823) + add `__main__.py` for the initial implementation of the single-entrypoint script - add sub-parser grabbing functions `get_*_parser()` for all executable scripts - add `_autocomplete()` - add the main parser function `get_parser()` with groupped calls for sub-parsers - add `main()` with proper logging info and exit code + `utils.arg_utils.py`: - rename from `arg_group.py` to `arg_utils.py` - add `create_argument_parser()` to create parser with or without sub-parsers - call `create_argument_parser()` from all executable scripts in `mintpy` folder. + `setup.py`: add the following optional requirements: - argcomplete - platemotion and astropy + `timeseries2velocity.py`: rename `inps.step` to `inps.stepDate` to avoid weird initiation bug in sub-command mode. Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> | 04 August 2022, 08:18:55 UTC |
| 00dd106 | Zhang Yunjun | 28 July 2022, 04:19:07 UTC | various bugs-fix in `ts2vel.py --periodic` and `prep_hyp3` (#822) + `timeseries2velocity.py --periodic`: use `atan2()`, instead of `atan()`, to account for the 4 quadrant outcome of the arc tangent operation, while calculating the phase component of the periodic signals. + `prep_hyp3.py`: fix bug of `ORBIT_DIRECTION`. + `reference_point.py inputs/ifgramStack.h5 --write-data`: skip pixels with no-data-value (zero) while updating the `unwrapPhase` matrix. + `README.md` and `setup.py`: switch MintPy license from `GPLv3` to `GPLv3+`. | 28 July 2022, 04:19:07 UTC |
| 8d8d85d | BB | 27 July 2022, 22:57:49 UTC | return empty in `main()` to have error code of 0 for normal complete (#821) return empty/None in `main()` for all executable scripts, to avoid the conflict with having error code "0" for normal completion. Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> | 27 July 2022, 22:57:49 UTC |
| 47c9bcc | Yujie Zheng | 27 July 2022, 00:04:02 UTC | non-closure phase bias estimation (#765) This PR adds the bias time-series estimation introduced by the non-closure phase, as described in Zheng et al. (2022, TGRS), via `--action quick_estimate / estimate` options. Detailed changes are as below: + `utils.isce_utils.py` - add `guassian_kernel()` and `convolve()` for the complex interferogram filtering. - add `estimate_coherence()` and `unwrap_snaphu()` based on `isce2/topsStack` to re-unwrap the closure phase interferogram, to mitigate the PU error during closure phase bias estimation, including notes on SNAPHU from Piyush. + `objects.stack.ifgramStack`: - move `split2boxes()` from `ifgram_inversion.py` to here for more convenient re-use, add `dim0_size` option for more flexibility - add `get_closure_phase_index()` to return the indices of interferograms that forms the given connection level of closure loop - add `get_sequential_closure_phase()` for the 3D CP calculation and its temporal average. + `ifgram_inversion.estimate_timeseries()`: support `inv_quality_name = no` to turn OFF the calculation. + closure_phase_bias.py: - add `--action mask` for average CP and mask calculation, by refactoring the existing script. - add `compute_unwrap_closure_phase()` to compute the wrapped sequential closure phase, unwrap them using isce2 modules, and then calculate the cumulative unwrapped seq closure phase time-series via `cum_seq_unw_closure_phase_timeseries()`, with parallel support and auto-skip. - add `estimate_wratio()` and `estimate_wratio_all()` for the `W_r` estimation, a.k.a., the weighted closure phase history. - add `bandwidth2num_ifgram()` - add `estimate_bias_timeseries_approx()` for `--action quick_estimate` - add `estimate_bias_timeseries()` for `--action estimate` with parallel support using dask. - 2X speedup of `estimate_bias_timeseries()` via `ifgram_inversion.estimate_timeseries()` with `scipy.linalg`, instead of `np.linalg.pinv`, and auto-skip the zero/nan values in part of the interferograms among the stack. - 2X speed up via common design matrix operation, same as in `ifgram_inversion.py` Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> | 27 July 2022, 00:04:02 UTC |
| e17d1d3 | Zhang Yunjun | 23 July 2022, 22:07:35 UTC | tsview: add --no-show-img option (#820) + tsview: add --no-show-img option to hide the map-view figures + timeseries2velocity: re-organize the UQ comment in the code, for clarify + prep_giant: move to the legacy folder as it's not used; remove it from setup.py entry_points + docs/installation: update the Debian link to tracker.debian.org + setup: fix the license info inconsistency by removing the "license" option, the rest is all GPLv3. + setup: remove the unnecessary wrapper of `__main__` and `do_steup()` | 23 July 2022, 22:07:35 UTC |
| 43e2c8b | Scott Staniewicz | 14 July 2022, 22:50:24 UTC | readfile: fix gdal_read to accept Paths obj(#813) * readfile: fix gdal_read to accept Paths object. The `os.fspath` was recommended in the GDAL issue (https://github.com/OSGeo/gdal/issues/1613), as the GDAL Python bindings fail for Path objects. | 14 July 2022, 22:50:24 UTC |
| f8319ec | Antonio Valentino | 14 July 2022, 21:06:55 UTC | Add installation instructions for Debian (#812) * Add installation instructions for Debian | 14 July 2022, 21:06:55 UTC |
| d1aa094 | Yuan-Kai Liu | 13 July 2022, 23:33:33 UTC | gps: bugfix component string (#811) bugfix on the string for identifying the component mintpy/objects/gps.py | 13 July 2022, 23:33:33 UTC |
| 632a394 | Zhang Yunjun | 10 July 2022, 01:00:33 UTC | plate_motion: supp radar-coord geometry & ITRF14 as default fname (#808) + utils.utils0.get_lat_lon(): add ystep and xstep for more flexible output + utils.utils.py: add prepare_geo_los_geometry() from solid_earth_tides.py for easy re-use. + bulk_plate_motion.py: - support radar-coord geometry input via resample object to radar-code the PMM output - refactor pmm2enu_at() - replace scipy.interpolate with skimage.transform.resize - use ut.get_lat_lon() for coarse grid preparation - use ut.prepare_geo_los_geometry() and simplify the post-handling for unit and no-data value - remove the obsolete interp_2d3l(), get_geobox_width_length() - remove MORVEL56 example cmd, to avoid potential confusion - replace BulkPlateMotion.h5 with ITRF14.h5 for the default output file name. This may change in the future to other PMM names once they are auto determined with values auto grabbed. - use pmm internally in the code | 10 July 2022, 01:00:33 UTC |
| 0d3b715 | Zhang Yunjun | 07 July 2022, 18:33:20 UTC | plot: better handle the DEM range < contour level warning (#807) + `utils.plot.prepare_dem_background`: better handle the warning msg when the DEM range < contour levels + `objects.stackDict`: use enumerate for "for" loop & progressBar while writing HDF5 files + `scripts/jupyter_notebook_config.py`: replace NotebookApp with ServerApp for running docker + `bulk_plate_motion`: update comments by removing NNR-NUVEL1A as it seems obsolete compared with ITRF2014-PMM and NNR-MORVEL56. | 07 July 2022, 18:33:20 UTC |
| 6558a52 | Bryan Marfito | 06 July 2022, 22:37:14 UTC | prep_isce: typo fix in alosStack example usage (#805) | 06 July 2022, 22:37:14 UTC |
| ee43222 | BB | 06 July 2022, 22:33:44 UTC | bugfix in `prep_aria.py` multilook method option (#806) + prep_aria: add default values for multilooking options (x/ystep, method) when no template file is given + prep_fringe: use ptime.yyyymmdd_date12() for more robust info extraction + utils0.py: add print_command_line() to add "" for arguments containing *, for improved usability. + load_data.prepare_metadata(): use ut.print_command_line() to facilitate debugging. Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> | 06 July 2022, 22:33:44 UTC |
| 6e741da | Yuan-Kai Liu | 30 June 2022, 21:41:35 UTC | smallbaselineApp: get ionStack file & add metadata from custom template file (#802) + smallbaselineApp.py: - run_load_data(): add metadata to ionStack.h5 file from custom template file, to be consistent with ifgramStack.h5 and geometry*.h5 files - run_load_data(): remove load_complete, as it's not used. - plot_result(): add ion_file to plot_result() - update usage for check_loaded_dataset() throughout the script + utils.check_loaded_dataset(): - check and return ionStack.h5 file if it's valid - remove load_complete in returned values, as it's not used at all, for simplification - refactor Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> | 30 June 2022, 21:41:35 UTC |
| b13e409 | Yuan-Kai Liu | 29 June 2022, 21:42:38 UTC | bulk_plate_motion.py (#769) + Estimate the bulk motion of tectonic plates in the reference frame of the satellite. - bulk_plate_motion.py is the major new function that takes the geometry file and the user-input Euler pole vector to compute the plate motion velocity projected to the LOS in the SAR scene. - setup.py: add entry_points for bulk_plate_motion.py - add a reference to our paper, Stephenson et al., 2022, about this plate motion correction - add a brief description of each of the PMMs, including the reference + Applying the correction of the bulk motion of tectonic plates from the input velocity file: - diff.py: modified to take care of the velocity field subtraction - reference_point.py: use FILE_TYPE for velocity dataset name Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> | 29 June 2022, 21:42:38 UTC |
| 719c2b4 | Joseph H Kennedy | 28 June 2022, 18:42:19 UTC | Automatically build and push a docker image (#696) + update Dockerfile - move to the top-level - build from the local repo and include jupyter, gdal and isce2 - use micromamba user name - provide an easy access to Jupyter via ./scripts/jupyter_notebook_config.py - pin the python version to 3.9 + add dockerize github workflow to auto build/push the docker image to the github container registry - tag 'latest' to the latest released version - tag 'develop' to the latest development version + dependency files: pin pyaps3 >= 0.3 + update the documentation related to docker in installation.md and docker.md | 28 June 2022, 18:42:19 UTC |
| 340062d | Yuan-Kai Liu | 22 June 2022, 06:38:04 UTC | load_data: add `mintpy.multilook.method` for mean/median (#797) + add `mintpy.multilook.method = nearest / mean / median` to use different interpolation methods while loading stacks of observations. - mv mintpy.subset.* in front of mintpy.multilook.* to be more consistent with the order of execution in the code - update the following scripts to support this functionality: - load_data.py - objects/stackDict.py - defaults/smallbaselineApp.cfg - defaults/smallbaselineApp_auto.cfg - prep_aria.py + [BREAKING CHANGES] rename the following template options: - mintpy.load.ystep --> mintpy.multilook.ystep - mintpy.load.xstep --> mintpy.multilook.xstep - update files in `tests/configs` accordingly + utils.attribute.py: add `update_attribute4resize()` and simplify its usage in `prep_isce.prepare_stack()` and `stackDict.ifgramStackDict.write2hdf5()` + fix the metadata bug for ionosphere stack due to resizing Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> | 22 June 2022, 06:38:04 UTC |
| c50a231 | Zhang Yunjun | 21 June 2022, 23:46:43 UTC | tests: remove "test_" prefix + smaller zenodo file sizes (#799) + tests: remove the "test_" prefix for: - asc_desc2horz_vert.py - smallbaselineApp.py + tests/smallbaselineApp.py: update zenodo link for smaller sizes for the following 2 datasets, to avoid overburden zenodo/circle CI - SanFranSenDT42: 410 MB --> 280 MB - WCapeSenAT29: 520 MB --> 240 MB | 21 June 2022, 23:46:43 UTC |
| d17c7d9 | Zhang Yunjun | 19 June 2022, 01:26:42 UTC | tsview: update to the latest timeseries2velocity (#798) + tsview: - update its model/time func usage to the latest timeseries2velocity/time_func - remove the unnecessary np.array() call while updating image array + load_data: align the long global variable names, for readability | 19 June 2022, 01:26:42 UTC |
| f0a8038 | Zhang Yunjun | 17 June 2022, 21:24:52 UTC | load multiple stack files + resize ionosphere on the fly (#796) + utils.isce_utils.extract_geometry_metadata(): - extract LENGTH & WIDTH, as reference for the A/RLOOKS - update attribute if box is not None - simplify its usage in prep_fringe.py + prep_isce.py: simplify and support multiple obs files w/ different resolutions - prepare_stack(): update A/R/NCORRLOOKS & AZ/RG_PIXEL_SIZE if the input obs file has a different size than the stack.rsc file, to better reflect the truth, e.g. for low-resolution iono file. - Note that LENGTH/WIDTH/Y/X_FIRST/STEP is already extracted from the obs file, thus, no need for checking or updating to reflect the truth. - replace the combination of `-f/-d` with the single `-f` option for a simpler and more robust logic to grab all data files in a given path pattern. + objects.stackDict.py: - ifgramStackDict.get_size(): add geom_obj arg to be able to use the size from the reference geometry file, for the low-resolution ion file, needed for run_or_skip() checking in load_data.py - ifgramStackDict.write2hdf5(): add geom_obj arg, to auto detect the low-reso ion file, for resizing on the fly - ifgramDict.read(): add resize2shape arg to resize on the fly using skimage.transform.resize(), and make it compatible with the exiting subset and resampling options. + load_data.py: support multiple stack files loading in one command line, which is more flexible and simpler - remove the obsolete --ion option, as it's not needed anymore - remove the rarely used --output options, and use the hardwired values in the code, for simplification - code refactoring - update to the latest usage of prep_isce.py, to support loading regular and ion interferograms at the same command line call - use a for loop to load the following multiple stack HDF5 files: - ifgramStack.h5 - ionStack.h5 - offsetStack.h5 + diff.py: light refactoring | 17 June 2022, 21:24:52 UTC |
| 8ed98c1 | Zhang Yunjun | 17 June 2022, 20:29:06 UTC | integrate advanced time func with UQ into the routine workflow (#795) * ts2vel: add uncertaintyQuantification & timeSeriesCovFile option + add the following two new template options into smallbaselineApp.cfg - mintpy.velocity.uncertaintyQuantification = residue / covariance / bootstrap, to replace the previous mintpy.velocity.bootstrap option - mintpy.velocity.timeSeriesCovFile with the default value of no + timeseries2velocity: re-use arg_group.add_reference_argument(plot=False) in timeseries2velocity.py + load_data: write S1A/B_date.txt file from SAFE_files.txt file if the latter exists in its default location (same level as reference folder) * ts2vel: add timeFunc.* options to smallbaselineApp.cfg + integrate the advanced time func fitting into smallbaselineApp.py, via the following template options: - mintpy.timeFunc.polynomial - mintpy.timeFunc.periodic - mintpy.timeFunc.step - mintpy.timeFunc.exp - mintpy.timeFunc.log + rename the following options for consistency **[BREAKING CHANGES]**: - mintpy.velocity.excludeDate --> mintpy.timeFunc.excludeDate - mintpy.velocity.startDate --> mintpy.timeFunc.startDate - mintpy.velocity.endDate --> mintpy.timeFunc.endDate - mintpy.velocity.uncertaintyQuantifiction --> mintpy.timeFunc.uncertaintyQuantification - mintpy.velocity.timeSeriesCovFile --> mintpy.timeFunc.timeSeriesCovFile - mintpy.velocity.bootstrapCount --> mintpy.timeFunc.bootstrapCount + utils.time_func.py: - add MODEL_EXAMPLE as the single-sourced example for the time function model/configuration setup - add inps2model() to parse/convert the namespace "inps" object into time function dict "model" object - add get_num_param() to estimate the num of unknown parameters from a given model dict object + utils.readfile.read_template(): add "skip_chars" argument to skip certain characters in the template values, e.g. the commonly template typo from users "[" and "]". This is to simplify the read_template2inps() functions. - leverage the new read_template() in following scripts: - dem_error.py - geocode.py - modify_network.py - reference_point.py - timeseries2velocity.py - the insarmaps-related code is removed, and they are messy and they can and should be implemented separately in insarmaps repo if needed. + utils.ptime.py: add get_exclude_date_list() from previous ts2vel.py + utils.arg_group.py: - add_time_func_argument(): fix typo and better alignment for comments to improve the readability - adjust indentation throughout the script + timeseries2velocity: support time function inputs from template files - add time function inputs into the config keys to be saved in the h5 file - remove the comments on contributing authors, as they are visible in the git commit history - merge init_exp_log_dicts() and read_inps2model() into utils.time_func.inps2model() - refactor and move read_exclude_date() into utils.ptime.get_exclude_date_list() - read_template2inps(): support the new time function template options - model2hdf5_dataset(): modify the periodic/exp/log dataset names, to be more clear on the time unit + move ifgram_reconstrunction.py to /legacy since it's not frequently used at all + move tropo_pyaps.py to /legacy since it's unavailable anymore (due to the takedown of EarthDef and Python2) and not actively used. | 17 June 2022, 20:29:06 UTC |
| c8ae9c7 | Zhang Yunjun | 06 June 2022, 23:43:42 UTC | add ionex.py with simplified IONEX file reading + add mintpy.objects.ionex sub-module to handle all the IONEX file download/reading - add ionex.py based on daniestevez notebook, to simplify the IONEX file reading - move the following functions from mintpy.simulation.iono, to be more independent: - dload_ionex() - get_ionex_value() - get_ionex_filename() - get_ionex_date() - get_ionex_height() - plot_ionex() - simulation.iono.py: remove the obsolete read_ionex_tec() + add unit test for objects/ionext.py: - add tests/objects/ionex.py - add tests/data/jplg3190.15i - update .circleci/config.yml + update simulation.iono.py and iono_tec.py accordingly + update docs: - add ionex to docs/api/module_hierarchy.md - update .gitignore against the latest github example for python | 17 June 2022, 03:42:28 UTC |
| d3f6be4 | Zhang Yunjun | 06 June 2022, 06:23:23 UTC | view: add --ylabel-rot option | 17 June 2022, 03:42:28 UTC |
| ba834f3 | Zhang Yunjun | 03 June 2022, 19:19:38 UTC | add utils.map module for lalo_label/scalebar + move draw_lalo_label() and draw_scalebar() from mintpy.utils.plot.py into a new sub-module mintpy.utils.map.py, for more independence. + refactor mintpy.utils.map.py + mv read_gmt_lonlat_file() from plot.py into readfile.py + remove unused plot.cmd_line_parse() + update module_hierarchiy accordingly. + mv constants from utils to objects | 17 June 2022, 03:42:28 UTC |
| da225ba | Zhang Yunjun | 14 June 2022, 06:51:52 UTC | ifg_inv: adjust default stack aux quality file for ionStack (#791) + ifgram_inversion.py: adjust the default stack quality file for ionStack, add size checking before using it for masking + load_data.run_or_skip(): bugfix for the in/out_size comparison, as suggested by @olliestephenson. + cluster.DaskCluster.close(): reverse client/cluster.close() order to better avoid the CancelledError. + multilook: replace average with mean + utils.plot.auto_fig_title(): add extra suffix for ionStack.h5 | 14 June 2022, 06:51:52 UTC |
| 3045089 | Yuan-Kai Liu | 12 June 2022, 21:24:51 UTC | load ionosphere stack from isce2/topsStack (#780) + load ionosphere stack from isce2/topsStack via `load_data.py --ion` - add the following new template options for iono file paths to smallbaselineApp.cfg - mintpy.load.ionUnwFile - mintpy.load.ionCorFile - mintpy.load.ionConnCompFile - add the mintpy.load.ion*File to auto_path.py to support mintpy.load.autoPath = True - split datasetName2templateKey into 4 dict objects, to help to distinguish between regular stack and ion stack, while setting the correct template key - add `load_data.py --geom` to load only the geometry files - set --ion / geom as mutually exclusive arg for more robust user typo checking - add Parameters/Returns comments for most functions - rename update_object() to run_or_skip() for consistency and a more intuitive name - run_or_skip(): add the checking of dataset list between in/out stack file/obj + ifgram_inversion.py: set default output file name based on ionStack.h5 filename + stackDict.ifgramStackDict: add get_dataset_list() + plot_network: auto handle ionStack.h5 and non-interruptive handle of no dataset found. + utils/ptime.py and prep_isce.py: add get_date12_from_path() to simplify code + utils/readfile: add .ion file ext to read_binary_file() and get_slice_list() + remove the obsolete `ionoPhase` related code and comments in the following files: - docs/api/data_structure.md - objects/stack.py - objects/stackDict.py Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> | 12 June 2022, 21:24:51 UTC |
| 4f77a83 | Zhang Yunjun | 02 June 2022, 03:26:53 UTC | add `s1ab_range_bias.py` for range offset time series (#787) + add s1ab_range_bias.py to calculate and correct for the S1A/B range bias in the range offset time series, as in Yunjun et al. (2022). - use --action to swith between compute / correct, to be able to compute from an TS file, and correct for it from another TS file. - add --save/nodisplay optiton, and remove --plot option, so that it works in the same way as plot_network.py + safe_list_file2sensor_list(): mv from isce_utils to s1_utils + update yunjun et al. (2022) bio info in relevant scripts: title syntax and vol num | 02 June 2022, 03:26:53 UTC |
| 1857814 | Zhang Yunjun | 31 May 2022, 21:12:49 UTC | save_kmz_ts: support non-mpl colormaps + save_kmz(_timeseries).py: - use inps.cmap_name for the str and inps.colormap for the mpl colormap object to better book keeping - more organized comments + save_kmz.py: bugfix for the placemark KMZ file when cbar is not shown after moving the file location + save_kmz_timseries.py: support custom non-mpl colormaps, similar to view/tsview.py | 31 May 2022, 21:45:46 UTC |
| 5e2a43a | Zhang Yunjun | 26 May 2022, 05:08:18 UTC | view: support --ref-lalo out of subset ext for 2D matrix + view: support --ref-lalo out of subset extent for 2D matrix input, similar to the existing support for 3D matrix + minor comments update in scripts below: - asc_desc2horz_vert.py - prep_fringe.py - objects/sensor: notes on az*_pix*_size for S1 | 31 May 2022, 21:45:46 UTC |
| 8b773be | Antonio Valentino | 30 May 2022, 01:05:34 UTC | Move shell scripts from mintpy/sh to scripts. (#785) + move shell scripts from `mintpy/sh` to `script`. + update setup.py as the shell scripts are no longer installed * update README.md for the link of the example shell script usage. | 30 May 2022, 01:05:34 UTC |
| 5111f33 | Bryan Marfito | 27 May 2022, 17:38:41 UTC | Fixed a minor typo on README.md and smallbaselineApp.py (#784) goodle --> google | 27 May 2022, 17:38:41 UTC |
| 6e592f8 | Zhang Yunjun | 23 May 2022, 22:23:02 UTC | plot_transection: bugfix for `add_arrow()` (#778) + plot_transection.py: fix the "IndexError: index 2 is out of bounds for axis 0 with size 2" due to utils/plot.add_arrow() + utils/plot.plot_colorbar(): use len(unique_values) instead of cmap_lut while checking for discrete colorbar ticks + view: rm the useless plt.subplots(num), as it shows up in notebooks with %matplotlib widget + iono_tec: printout CENTER_LINE_UTC and local solar time + diff.check_reference(): simple refactor and bugfix when file1 is absolute w/o REF_DATE. + docs/installation: minor comment simplification | 23 May 2022, 22:23:02 UTC |
| 5405746 | Antonio Valentino | 22 May 2022, 18:47:49 UTC | use `sh` instead of `bash` in `load_data_aoi.sh` (#774) | 22 May 2022, 18:47:49 UTC |
| 8dd9390 | Antonio Valentino | 21 May 2022, 20:48:58 UTC | Fix spelling errors and typos (#775) * Fix spelling errors and typos in different files (mostly online help messages of the CLI). * Remove the unused `--no-parallel` opt for `subset/prep_roipac.py` Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> | 21 May 2022, 20:48:58 UTC |
| 7014b0b | Zhang Yunjun | 10 May 2022, 02:45:44 UTC | move `requirements.txt` to the root dir (#772) * mv requirements.txt to root dir for a shorter path + move requirements.txt from ./docs to ./ dir for a shorter path; update path in installations.md and circleci/config.yml + utils.utils1.update_template_file(): handle value2seach inside if check, to avoid unnecessary running * view: add --coastline-lw / --lalo-off / --lalo-fs + view: add 3 new options to customize plotting in geo-coordinates: - coastline-linewidth - lalo-offset - lalo-fontsize + asc_desc2horz_vert: - bugfix on the printout msg during REF_LAT/LON checking - bugfix on the output metadata in one output HDF5 fil + readfile: GDAL related metadata - DATA_TYPE_GDAL2NUMPY/NUMPY2GDAL: add cint16/32 for translation purpose - add ".tiff" to GDAL_FILE_EXTS | 10 May 2022, 02:45:44 UTC |
| 8b32b3c | Kang Liang | 07 May 2022, 22:00:04 UTC | bugfix for manually specified site_list_file in `gps.search_gps()` (#771) + objects.gps.search_gps(): fix a bug that `site_list_file` will not be downloaded when the user specifies the path to it, and pass `site_list_file` to `dload_site_list()`. | 07 May 2022, 22:00:04 UTC |
| 0344522 | Zhang Yunjun | 02 May 2022, 20:43:57 UTC | ut.update_template_file(): support "[]()" during option value search (#768) + utils.utils1.update_template_file(): - add "[]()" to the special symbol interpretation list while searching for template option values. - use "value2search" for "re.findall()" expression, without changing original value variable, for more robust replace() operation. | 02 May 2022, 20:43:57 UTC |
| 0718be9 | Zhang Yunjun | 02 May 2022, 04:36:45 UTC | tsview: bugfix for cartopy feature (#767) + tsview.py: bugfix for cartopy feature while initializing projection + timeseries2velocity.read_inps2model(): add print_msg + objects/sensor.SEN: fix antenna and PRF parameters + smallbaselineApp.py:_read_template(): align the print out "copy for backup" msg | 02 May 2022, 04:36:45 UTC |
| bbb2ce2 | Zhang Yunjun | 22 April 2022, 21:55:55 UTC | tsview: new "narrow" slider + tsview: switch to a new look of "slider" in tsview.py. The main changes are: 1. use a narrower slider on the Y-axis, for a more compact looking. 2. The slider is solely based on image number, instead of time, to be agnostic against TS files with different time gaps. 3. Plot the reference date as a "gray" dot on the slider, to be more visible. 4. use subplot() with tight_layout() to better scale the subplots + utils.ptime: add get_compact_isoformat() | 23 April 2022, 00:16:03 UTC |
| 479d308 | Zhang Yunjun | 22 February 2022, 06:02:14 UTC | use fig.canvas.draw_idle() to replace fig.canvas.draw() + replace fig.canvas.draw() with "fig.canvas.draw_idle()" and "fig.canvas.flush_events()", as recommended by matplotlib (https://matplotlib.org/stable/users/explain/interactive_guide.html). This fixed the non-resposive point TS plot, with the latest version of matplotlib version 3..5.1. It's unknown since which version of matplotlib that this behavior change started to happen. Involved scripts are: - tsview.py - plot_transection.py - plot_coherence_matrix.py + tsview: update bar() plot in the slider, to make sure the vertical lines are within the slider extent + utils.plot: add add_arrow() from stack overflow + plot_transection: plot the profile location as dashed arrow instead of dashed line, to indicate the profile direction, via plot.add_arrow(). | 23 April 2022, 00:16:03 UTC |
| 04bf0b2 | Zhang Yunjun | 10 April 2022, 05:10:14 UTC | plot_colorbar(): show the exact tick values for matrix w/ <=5 unique values + utils/plot.auto_adjust_colormap_lut_and_disp_limit(): add unique_values as the 3rd return arg & update its usage in save_kmz.py, view.py and tsview.py + utils/plot.plot_colorbar(): use unique_values to set tick locations if they are <=5 + utils/plot.read.gmt_lonlat_file(): ignore comment lines + utils/utils.read_timeseries_yx(): bugfix for dis_std unit conversion + objects/sensor: add a few paramters for the GaoFen-3 sensor + objects/gps.get_gps_los_obs(): bugfix when input site_names are not consistent with CSV file + add Yunjun et al. (2022) with DOI to the following files: - defaults/smallbaselineApp.cfg: SET option - iono_tec.py - solid_earth_tides.py - simulation/iono.py | 23 April 2022, 00:16:03 UTC |
| a390362 | Falk Amelung | 21 April 2022, 04:12:17 UTC | save_hdfeos5.py: allows for suffix in filename (#763) add --suffix option to allow for suffix in the filename. | 21 April 2022, 04:12:17 UTC |
| edebebd | Zhang Yunjun | 14 April 2022, 21:14:12 UTC | version: add version 1.3.3 tag (#761) | 14 April 2022, 21:14:12 UTC |
| fb88aa4 | Zhang Yunjun | 17 March 2022, 06:16:32 UTC | add iono ramp calc from GIM TEC products + add simulation/iono.py sub-module: - add iono mapping functions from Yunjun et al. (2022) - add JPL high resolution GIM I/O - add GIS low resolution GIM downloading, I/O and plotting + add iono_tec.py for high level usage - auto download IGS TEC files, similar to tropo_pyaps3.py - call simulation/iono.py to read and calculate iono ramps + add data/top_tec_perc_s1.py from Yunjun et al.. (2022) + update docs accordingly - docs/api/module_hierarchy.md: add simulation/iono - setup.py: add entry point for iono_tec.py | 23 March 2022, 19:52:52 UTC |
| 8edc973 | Zhang Yunjun | 19 March 2022, 21:41:46 UTC | plot very long TEC TS file + coord.geo2radar(): support file longitude exceeding 180 in both end, e.g. the GIM IONEX file + plot.auto_multilook_num(): turn OFF multilooking for small spatial size, even if the over size is large due to the large time dimension, to speed up the reading. Otherwise, it will do the epoch-by-epoch reading with indexing, which is slow. + tsview: for very long TS (> 1000 acquisitions), do not print out displacement TS in the terminal, reduce the default marker size by 10X. | 23 March 2022, 19:52:52 UTC |
| c0d6c3a | Zhang Yunjun | 21 March 2022, 03:53:09 UTC | asc_desc2horz_vert: speedup pixel-wise inversion via win-by-win (#756) + asc_desc2horz_vert.py: - use a window-by-window strategy to speedup the pixel-wised inversion - add get_design_matrix4east_north_up() for future 3D decomposition - bug fix for --oo option during file writing + gps.GPS.read_displacement(): add self.date_list member variable, for easy use + stack.timeseries: remove get_design_matrix4time_func, as it's not used anywhere in mintpy anymore, to avoid circular imports | 21 March 2022, 03:53:09 UTC |
| 84421d5 | Zhang Yunjun | 19 March 2022, 22:50:47 UTC | readfile.read_snap_dim(): bugfix on WAVELENGTH unit (#755) + utils.readfile.read_snap_dim(): bugfix on WAVELENGTH unit + asc_desc2horz_vert: pass angles in deg instead of rad + utils.plot.auto_adjust_xaxis_date(): fix a bug introduced in https://github.com/insarlab/MintPy/pull/734 + local_oscilator_drift.get_relative_range_distance(): typo fix + docs/README: update aux links in Yunjun et al. (2019) | 19 March 2022, 22:50:47 UTC |
| 44dfae4 | zhurewitz | 19 March 2022, 03:44:32 UTC | get_design_matrix4time_func(): bugfix for `poly_order = 0` (#754) + utils.time_func.get_design_matrix4time_func(): resolves a bug that creates design matrices with columns of zeros, when the polynomial order is zero. | 19 March 2022, 03:44:32 UTC |
| bbbaf2b | Oliver Stephenson | 18 March 2022, 05:44:57 UTC | image_stitch - bugfix for bool / integer matrix (#751) Currently `image_stitch.py` can't correctly merge mask files. It puts the merged arrays into an array initialized as `np.nan`. Nans evaluates to `True`, meaning that we are left with blocks outside the data region that are set to `True`. + Adding a simple check to see if we're merging non-float arrays, then set the default values of `fill_value` to `0` instead of `np.nan` fixes the issue. + use vprint() to shorten the print() if check | 18 March 2022, 05:44:57 UTC |
| bd8795f | Yujie Zheng | 10 March 2022, 04:57:34 UTC | closure_phase_bias.py - mask for areas susceptible to closure phase bias (#740) + add a new script `closure_phase_bias.py`, to create a mask for areas susceptible to closure phase bias, based on Zheng et al. (2022, TGRS, under review). + setup.py: add entry point for the new script | 10 March 2022, 04:57:34 UTC |
| 6e39b67 | Sara Mirzaee | 08 March 2022, 20:50:54 UTC | ifg_inv: bugfix for design matrix w/ date1 > date2 & release memory occupied by covariance matrix (#750) + cluster.DaskCluster.collect_result(): support None in the output list, as an alternative to to numpy matrix, to be more flexible + stack.ifgramStack.get_design_matrix4timeseries(): - support non-sequential network (where the first date is not always the earlier date) - use the same reference date by default for a single reference network + ifgram_inversion.py: - estimate_timeseries(): comment out the B matrix inverrtability check, after correcting the B matrix bug above for non-sequential network - ifgram_inversion_patch(): set ts_cov = None if not calc_cov, to release memory from the huge 4D ts_cov matrix Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> | 08 March 2022, 20:50:54 UTC |
| 575f32b | Zhang Yunjun | 11 February 2022, 00:47:10 UTC | docs update for python 3.9 and 3.10 + remove "python<3.9" constraint from installation-related documents: - setup.py - docs/environment.yml - docs/requirements.txt + docs/installation.md: - add note on strict conda channel priority activation - remove the strict channel priority note, as it's currently not default in conda yet and NOT working all the time, especially when install mintpy together with isce2=2.6 + .circleci/config.yml: - activate the strict channel priority to avoid installation packages with conflicts versions - remove unnecessary cd command while runing testing on example datasets as it's done inside test scripts already + with the above changes, $MINTPY_HOME/tests/test_smallbaselineApp.py passed without errors on both python 3.9 and 3.10 environments + add mintpy.utils.constants module [preliminary] | 22 February 2022, 02:09:40 UTC |
| 8b15058 | Zhang Yunjun | 17 February 2022, 00:58:32 UTC | transection: support distance unit in pixel + plot_transection: - bugfix for the pip installed version - support transection with distance unit in pixel. + utils.utils.transect_yx(): add "distance_unit" to the output dict object, with default value of "m". In case there is not enough metadata to calculate the ground pixel size in meters, such as the raw isce-2 files, set "distance_unit = pixel" and continue. + utils.readfile.py: - read_snap_dim(): force int dtype for A/RLOOKS - remove TRACK_NUMBER from standardMetadata as it has not been tracked before, and has already been saved in the original snap metadata info. + simulation/variance.sample_data(): use np.random.default_rng() | 22 February 2022, 02:09:40 UTC |
| ef3d271 | Zhang Yunjun | 14 February 2022, 19:41:03 UTC | gps.get_gps_los_obs(): use meta / obs_type for args w/ example usage + utils/utils0.four_corners(): switch return order from WESN to SNWE, for consistency. Adjust its usage in the following scripts: - asc_desc2horz_vert.py - save_kmz.py - gps.py + gps.get_gps_los_obs(): - use "meta" and "obs_type" to replace "insar_file" for input arguments, for more explicit and straightforward usage. - add example function usage in the comments. - GPS.get_gps_los_velocity(): bugfix for more robust performance + utils.plot.plot_gps(): bugfix when no GPS found. | 22 February 2022, 02:09:40 UTC |
| 9d6d410 | Zhang Yunjun | 21 February 2022, 22:51:50 UTC | add test_asc_desc2horz_vert.py | 22 February 2022, 02:09:40 UTC |
| fe09fc3 | Zhang Yunjun | 30 January 2022, 05:49:47 UTC | asc_desc2horz_vert.py: add --geom-file option Support input geometry files for precise pixel-wised decomposition, which is important for large area analysis. + add -g / --geom-file option to specify the corresponding geometry files. + cmd_line_parse(): fix a bug while checking the reference point when two input files does not has the same spatial coverage, by using only Y/X_FIRST/STEP, without converting to REF_Y/X. + get_overlap_lalo(): support a list of attributes dicts >= 2 + get_design_matrix(): refactor to take matrix as inputs + asc_desc2horz_vert(): - refactor to take multi-dimension matrices as inputs directly. - for pixel-wise inversion, use a for loop + merge main(), asc_desc_files2horz_vert() and write_to_one_file() all into one function: run_asc_desc2horz_vert(). | 22 February 2022, 02:09:40 UTC |
| 23550ca | Zhang Yunjun | 30 January 2022, 06:13:07 UTC | image_stitch: support multi-dataset files + support input files with multiple datasets, e.g. geometry files. + If input files do not have the exact same list of datasets, only the common elements of datasets will be used. + For geometry files, ignore zero incidenceAngle pixels in the geometry file, so that one could feed them without masking in advance. + show all figures at the end, for a smoother experience | 22 February 2022, 02:09:40 UTC |
| 006f1f9 | Yuan-Kai Liu | 14 February 2022, 19:37:13 UTC | bugfix: timeseries2velocity `--save-res` excluded dates (#746) Save timeseries_res: instantiate the output hdf5 file accounting for the excluded dates Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> | 14 February 2022, 19:37:13 UTC |
| e9b0104 | Zhang Yunjun | 10 February 2022, 22:36:33 UTC | refactor prep_snap.py / add readfile.read_snap_dim() + rename prep_snap.get_ellpsoid_local_radius() to utils.utils0.xyz_to_local_radius() + utils.readfile: - add read_snap_dim() to read SNAP *.dim file with XML modules, instead of searching/parsing in text file in the old prep_snap.py, for simpler, more robust and faster performance. - read_isce_xml(): 1) add if check for coordinate1/2.delta/startingvalue; 2) force lower() case key names, to produce consistent output + significantly simplify prep_snap.py | 13 February 2022, 07:41:42 UTC |
| c316d32 | Zhang Yunjun | 08 February 2022, 07:49:40 UTC | improve *.unw file handling in mask/ref*_point/tropo_pyaps3.py + two 2-band *.unw file IO in the following scripts, instead of single band for phase only, to preserve the native *.unw file format: - mask.py - reference_point.py - tropo_pyaps3.py +ptime.(yy)yymmdd_date12(): support both str and list type inputs | 13 February 2022, 07:41:42 UTC |
| 7e321b6 | Zhang Yunjun | 06 February 2022, 23:00:06 UTC | gen*_mask: add --vx/vy/vroipoly options + generate_mask.py: add --vs / vy / vroipoly options to specify the AOI for thresholding operations, the area outside will be untouched. This is usef to create an mask, without pixels on the fault, for phase unwrapping of co-seismic deformation. | 13 February 2022, 07:41:42 UTC |
| 592f186 | Zhang Yunjun | 02 February 2022, 07:18:59 UTC | view: add --no-data-value to manually specify the value to ignore + view.py: add --no-data-value option to manually sppecify the value to ignore, for plotting only + plot.plot_colorbar(): a more robust cbar extend style checking, to ignore the numerical precision level value leakage. | 13 February 2022, 07:41:42 UTC |
| 2499eeb | BB | 10 February 2022, 08:02:28 UTC | prep_fringe: write ifgramStack for connected components (#735) + add `--geom-only` option for only creating geometry (useful for making masks) + add `-r / --range` and `-a / --azimuth` option to specify looks (this is only for tracking metadata), if extra multilooking is applied after fringe processing. + create `inputs/ifgramStack.h5` file if *.unw.conncomp files exist. The non-first-date reference date is supported when writing ifgramStack to be more agnostic against the potential change in fringe output in the future. | 10 February 2022, 08:02:28 UTC |
| 80df178 | BB | 10 February 2022, 06:38:15 UTC | fix bool array index bug for `h5py>=3` (#743) + docs/requirements: remove `h5py<3` constrain + fix bool array index bug for `h5py>3` in the following scripts: - objects/stack.py - utils/readfile.py + timeseries2velocity: correct typo in example string | 10 February 2022, 06:38:15 UTC |
| 2acac3f | Marin Govorcin | 10 February 2022, 05:37:54 UTC | save_kite.py - convert to meters for UNIT in radians (#738) | 10 February 2022, 05:37:54 UTC |
| 569dd96 | BB | 06 February 2022, 03:59:20 UTC | resample: bugfix for auto_lat_lon_step_size() via merged src/lut_meta dict (#737) + merge `lut_meta` and `src_meta` and pass to `utils0.auto_lat_lon_step_size()` for a better chance of having enough metadata to calculate the pixel area constrained new lat/lon step. + fix the mis-functioned `try/except` fallback logic bug by using `except KeyError:` instead of `except AttributeError:`. | 06 February 2022, 03:59:20 UTC |
| b33fefc | Yuan-Kai Liu | 03 February 2022, 06:28:29 UTC | generic multi-dataset file (e.g. velocity) support in `add/diff` (#732) + `add.py` & `diff.py`: generic multi-dataset file support, by searching the common dataset list among all the input files, and doing a for loop for them. Ignore dataset names if all input files have one dataset, to support single dataset files with different dataset names, e.g. mask, mask and waterMask. In the later case, the 1st file dataset name will be used as the reference. + `utils1.run_deramp()`: when operating on velocity files, operate on velocity dset as default Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> | 03 February 2022, 06:28:29 UTC |
| 70d66d1 | Zhang Yunjun | 29 January 2022, 04:47:57 UTC | initial NO_DATA_VALUE support + add a new standard metadata: NO_DATA_VALUE + readfile.py: - read_attribute(): grab NO_DATA_VALUE with 'none' as default - add get_no_data_value() to get the value of the input file - add SPECIAL_STR2NUM() to facilitate no_data_value handling - read_isce_xml() / read_gdal_vrt(): grab NoDataValue if exists. + view.py: mask out pixels with no_data_value for single subplot + tests/config/*.txt: speedup testing by decrease plot.maxMemory to 2GB to use more parallel processes for plotting | 31 January 2022, 19:15:24 UTC |
| 7008581 | Zhang Yunjun | 28 January 2022, 19:36:03 UTC | refactor load2hdf5.py + rename `legacy/load_hdf5.py` to `legacy/load2hdf5.py` + refactor to be more flexible on the input/output file structure + add --sub-x/y + add --meta to add custom metadata + support --dname timeseries with "date" dataset added automatically + add DATA_TYPE_STR2OBJ to support most common numpy data types + check if the output file exists with --force option | 31 January 2022, 19:15:24 UTC |
| 04e4661 | Zhang Yunjun | 26 January 2022, 05:19:10 UTC | support plotting of SLC stack and GRACE time-series + identify SLC stack as "FILE_TYPE==timeseries" and "DATA_TYPE==complex(64/128)" + stack.timeseries.open): change CENTER_LINE_UTC from required to optional as SLC stack might not have it + readfile.read_attribute(): check SLC stack and reset UNIT to 1 + coord.geo2radar(): ensure the consistency between point longitude and source file, regardless of the source file convention in (-180, 180] or [0, 360) conventions. For geocoded files only. + plot: - auto_colormap_name(): use gray as default cmap for slc stack - auto_adjust_xaxis_date(): smart every_year/month for extra long time series, e.g. GRACE products. + view: - read_data4figure(): take abs() if data type is complex - move code to form check_map_projection() for easy re-use, e.g. in tsview.py + tsview: - pass `disp_unit` directly for the model estimation result display, for more simple and robust performance against input files that are not in the unit of meters, e.g. giant product or GRACE products. - grab WAVELENGTH if and only if wrap-range is 2 pi. This allows applying --wrap-range option to files w/o WAVELENGTH attributes, e.g. the GRACE products. - support cartopy map projection and its related features, e.g. --coastline, via view.check_map_projection() - take abs() if data is complex - bugfix for --flip-lr/ud options | 31 January 2022, 19:15:24 UTC |
| 18539d2 | Zhang Yunjun | 25 January 2022, 05:29:24 UTC | ref_point: add ref_lat value check + reference_point: add a validity checking for input `ref_lat` value + info: --num will turn ON --date - --num will turn ON --date, so that one can run info.py timeseries.h5 --num to print date list and number, without adding --date option, for conveniency. - remove --slice --num combo, as it's not used much, to simplify the code. + sensor: use rs1/rs2/rcm for radarsat series | 31 January 2022, 19:15:24 UTC |
| d219448 | Oliver Stephenson | 28 January 2022, 05:55:28 UTC | bugfix for `timeseries2velocity.py --bootstrap --save-res` (#733) When running `timeseries2velocity.py` with bootstrapping, we use the function `time_func.estimate_time_func` to repeatedly fit the time series data. This function returns the design matrix, `G`, however when bootstrapping we don't assign the design matrix to a variable, meaning that if we try to save the residual file we get the error `UnboundLocalError: local variable 'G' referenced before assignment` at line 702. If we want to output the residual when bootstrapping, we need to get the full design matrix. I've added a line of code to do this. | 28 January 2022, 05:55:28 UTC |
| cfa7991 | Oliver Stephenson | 26 January 2022, 05:41:51 UTC | image_stitch: bugfix & update plotting (#730) + fix the `AttributeError: 'AxesSubplot' error, because `fig` can not be used as return for subplot() anymore. + image_stitch: improved auto plot settings Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> | 26 January 2022, 05:41:51 UTC |
| 7dd7e1d | Zhang Yunjun | 25 January 2022, 00:03:56 UTC | bugfix in load_data.py & plot_network.py (#729) + load_data.py: fix a runtime bug when re-run after removing the ISCE stack processing folders + plot_network: fix the output file names bug + docs/install: a little bit more notes on dask | 25 January 2022, 00:03:56 UTC |
| f8a3fbe | Zhang Yunjun | 21 January 2022, 19:35:05 UTC | installation: add dask config to post-install setup (#727) | 21 January 2022, 19:35:05 UTC |
