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554f211 Merge branch 'main' into sss_rerefGPS 09 February 2023, 10:00:11 UTC
67ec693 fix bug while geocoding complex wrapped interferogram (#957) 09 February 2023, 09:41:27 UTC
47fa905 `view`: fix referencing error while read unwrapPhase* in 2D w/ multilook (#956) + view: fix the bug while referencing unwrapPhase* 2D matrix with multilook number>1 + requirements: pin scipy<1.10 to avoid interpolate error [temporary] + circleci: unset strict conda channel priority + ionex: update the link 09 February 2023, 09:05:51 UTC
1a3e85d build(deps): bump docker/build-push-action from 3 to 4 (#954) Bumps [docker/build-push-action]( from 3 to 4. - [Release notes]( - [Commits]( --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]> 06 February 2023, 13:45:27 UTC
737579d Generalize and clean-up Before the updated CSV file was only generated if a reference GPS station were specified. Now, this file is generated and captures at least the unit factor conversion regardless of the specification of a reference GPS station. 03 February 2023, 03:14:10 UTC
dd7e5e9 Export supplemental gps CSV file When plotting GPS stations and specifying a specific GPS reference station, it would be convenient if an additional CSV file (e.g. reref_gps_X.csv) would be created which tracks the rereferenced velocity values and accounts for any potential unit factor changes. This would make it easier to make separate, supplemental plots independent of MintPy. For example, in this case, station 70DM is the reference station and I wish to convert the velocities to cm/yr: (mintpy) [ssangha@leffe reref]$ more gps_enu2los.csv Site,Lon,Lat,Displacement,Velocity 7ODM,-117.09358508816442,34.11640732493536,-0.13098726,-0.010960488 BBRY,-116.88515702033878,34.26427837432715,-0.04806125,-0.0043038945 P613,-117.04706501804391,34.19618514313232,-0.05000028,-0.0059998427 (mintpy) [ssangha@leffe reref]$ (mintpy) [ssangha@leffe reref]$ more reref_gps_enu2los.csv Site,Lon,Lat,Displacement,Velocity 7ODM,-117.09358508816442,34.11640732493536,0.0,0.0 BBRY,-116.88515702033878,34.26427837432715,0.08292601,0.66565935 P613,-117.04706501804391,34.19618514313232,0.08098697999999999,0.49606452999999995 02 February 2023, 04:43:57 UTC
092a199 [] pre-commit autoupdate (#951) 01 February 2023, 14:38:46 UTC
86b8116 README/badge: flat-square style + docker status + conda download (#948) + docs/README/badge: - switch the style from flat to flat-square - add a badge for the github docker constainer build status - add a badge for the conda-forge download + scripts/load_data_aoi: save DEM as HDF5 file, instead of binary, to reduce the number of generated files. + cli/save_kmz: clarify -u/--unit help msg 21 January 2023, 03:55:02 UTC
ed3ce70 `utils.plot`: fix `_tkinter.TclError` via `plt.switch_backend('Agg')` (#947) Fix the `_tkinter.TckError: couldn't connect to display "localhost:38.0"` error by setting the matplotlib backend to Agg, in the following two functions, when saving figures without displaying: + `plot_num_triplet_with_nonzero_integer_ambiguity()`, used in the ` --dostep quick_overview` step + `plot_timeseries_rms()`, used in the ` --dostep timeseries_RMS` step Co-authored-by: Zhang Yunjun <> 20 January 2023, 06:04:36 UTC
ce1aed0 `euler_pole`: add PMM plotting functions (#935) * add PMM plotting functions + add plate boundary files from GSRMv2.1 and MORVEL56 + functions to read the boundary files and plot * updates * + ITRF2014_PMM use full names as keys + Consistent NNR model file: - src/mintpy/data/plate_boundary/GSRMv2.1/nnr.csv - src/mintpy/data/plate_boundary/MRVL56/nnr.csv - use camelCase plate names (but caplitalize the first character) + Consistent plate boundary file: - src/mintpy/data/plate_boundary/GSRMv2.1/plate_outlines.txt - src/mintpy/data/plate_boundary/MRVL56/plate_outlines.txt - use '> ' before plate abbv. names, good for GMT - use longitude, latitude for the columns, good for GMT + remove useless script: src/mintpy/data/plate_boundary/GSRMv2.1/ + update full reference in under src/mintpy/data/plate_boundary/ + update read_plate_attributes() read_plate_outlines() * bugfix for codacy and unit_test checks * ionex: attempt to fix the unit test attempt to fix the unit test error below: ``` Testing /root/tools/MintPy/tests/objects/ Traceback (most recent call last): File "/root/tools/MintPy/tests/objects/", line 110, in <module> test_get_ionex_value() File "/root/tools/MintPy/tests/objects/", line 93, in test_get_ionex_value tec_val = ionex.get_ionex_value( File "/root/tools/miniconda3/lib/python3.10/site-packages/mintpy/objects/", line 102, in get_ionex_value tec_val = interp_3d_maps( File "/root/tools/miniconda3/lib/python3.10/site-packages/mintpy/objects/", line 184, in interp_3d_maps tec_val = interpolate.interpn( File "/root/tools/miniconda3/lib/python3.10/site-packages/scipy/interpolate/", line 654, in interpn return interp(xi) File "/root/tools/miniconda3/lib/python3.10/site-packages/scipy/interpolate/", line 331, in __call__ indices, norm_distances = self._find_indices(xi.T) File "/root/tools/miniconda3/lib/python3.10/site-packages/scipy/interpolate/", line 499, in _find_indices return find_indices(self.grid, xi) File "_rgi_cython.pyx", line 95, in scipy.interpolate._rgi_cython.find_indices File "stringsource", line 660, in View.MemoryView.memoryview_cwrapper File "stringsource", line 350, in View.MemoryView.memoryview.__cinit__ ValueError: ndarray is not C-contiguous ``` * ionex: bugfix attempt no. 2 * test git rename via jupyter * Revert "test git rename via jupyter" This reverts commit b62d7487ca8c23a884ba6943b9a0395ea600a763. * Revert "ionex: bugfix attempt no. 2" This reverts commit 22f88ba496d453b876f2e311c87086f6e2484e88. * Revert "ionex: attempt to fix the unit test" This reverts commit 5e491abe9251cfd628c3f2421fd42b331981caa5. * remove the unnecessary plate name abbreviation in ` -h` * filenames and variable changes: + read GSRM and MORVEL56 model parameters (abbrev) from built-in dictionary + GSRM and MORVEL56 PMM files (csv) are not in used, but keep them for bookkeeping + folder names hosting plate boundaries are modified + use original file names for plate boundaries files (consistent with the source) * structure changes refer to: + put pmm definitions here, plate abbv are upper case + cli/ remove pmm definitions + plate_boundary/*/nnr.csv: delete them + to-do: move --plate to --om-cart from mintpy.cli.plate_motion to mintpy.plate_motion * move ITRF2014_PMM dependent codes to src/mintpy/ src/mintpy/cli/ will not need this dictionary * src/mintpy/ from mintpy.objects.euler_pole import ITRF2014_PMM * fix import in tests/objects/ * plate_boundary dir/file rename with shell cmds to reproduce + use `MORVEL` instead of `MORVEL56` for the folder name, as it's generic for MORVEL and NNR-MORVEL56, to be consistent of using GSRM, instead of GSRMv2.1 + rename both data files as `plate_outlines.gmt` with shell commands in the README for easy produce + euler_pole: - update data file path from above changes - use `GSRM_V21_PMM` and `NNR_MORVEL56_PMM` for more precise info * codacy fix * euler_pole refactor - part 1 * codacy fix * euler_pole refactor part 2 + use center_lalo to replace center_lat/lon + use satellite_height directly, instead of zoom + map center priority: direct input arg > pts_lalo > polygon centroid + remove vu as it's not used * updates to the plate boundary files: + use the original downloaded files + extensions as .lalo or .lola + modify accordingly * update * read_plate_outline: return as shapely object Co-authored-by: Zhang Yunjun <> 15 January 2023, 23:51:51 UTC
e2b6a47 `utils0.median_abs_deviation()`: divide by `scale` instead of multiply (#946) The "scale" parameter in the `median_abs_deviation` function should be a divisor for MAD calculation, namely `np.nanmedian(...) / scale`, instead of `np.nanmedian(...) * scale`, in order to derive a cutoff value comparable to the 1-2-3-sigma rule. Co-authored-by: Zhang Yunjun <> 13 January 2023, 19:53:13 UTC
4e88f08 add version 1.5.1 tag (#945) 04 January 2023, 04:51:02 UTC
cc27078 temporal_filter: add median filter from scipy with -f option + cli.temporal_filter: - add -f option to specify the filter type - change the default filter from gaussian to median + objects.stack.timeseries.temporal_filter(): - add `filter_type` argument - support median filter via scipy.ndimage.median_filter() - more informative default output file name + minor message/comment update in and utils.utils1.add_attribute() 01 January 2023, 22:34:04 UTC
0247168 fix codacy issues + tsview legend for multi-file + fix various codacy detected issues + bugfix in tsview legend for multiple input files + delete the unused legacy/ 01 January 2023, 22:34:04 UTC
aa390d2 `(ts)view`: auto-adjust lat/lon decimal places + ignore ex date for time func fit (#942) + ``: add `get_lalo_digit4display()` to calculate the appropriate decimal places for the lat/lon coordinates for displaying purposes, based on the pixel size info in the metadata. - `view.plot_slice()`: call `ut.get_lalo_digit4display()` and use it in `format_coord()` for the status bar. - `tsview`: call `ut.get_lalo_digit4display()` in `read_init_info()` and use it in `get_point_coord_str()` for the figure title and saved txt file. + `tsview`: ignore the excluded dates while fitting the time-functions + `tsview`: print out the specified command if `--noverbose`, similar to + `plot_network`: auto-adjust the fig size / dpi for long time-series stack + `scripts/load_data_aoi`: add `ionStack.h5` file crop/geocode 31 December 2022, 01:48:54 UTC
04793a5 `resample`: fix discrepancy between `num_box` and `dest_box_list` (#940) + `objects.resample.prepare_geometry_definition_radar()`: update the initially guessed `num_box` value, based on the later-on-calculated actually-used `dest_box_list`. These two could occasionally be different when the input file is large. + use `use scipy.interpolate.RegularGridInterpolator` without `as RGI` in the following scripts, as suggested by codacy. - - - + `.github./dependabot.yml`: fix typo introduced in #939 28 December 2022, 06:14:12 UTC
c7400f9 docs/installation: switch syntax from markdown to html (#939) + docs/installation: - switch syntax from markdown to html, for elements within the html `<section>` tag, as they do not work on readthedocs: - links with `<a>` tag - code block with `<code>` and `<pre>` tags - lists with `<ul>` and `<li>` tags - use `<p>` tag to fine-tune the spacing between paragraphs - keep markdown syntax for titles, as much as possible (outside of any html tags), as it provides links for precise (sub)-sections - remove the unnecessary link to section 3 "post-installation setup" + `.github/dependabot.yml`: ignore patch updates for all dependencies to reduce the PR frequency + `utils.readfile.get_hdf5_dataset_attrs()`: return None, instead of raising an error, if the input file is not hdf5, for more compatibility 28 December 2022, 02:38:11 UTC
61177bb pre-commit/PyCQA/isort: v5.11.3 → 5.11.4 (#937) [] pre-commit autoupdate updates: - [ v5.11.3 → 5.11.4]( Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]> 27 December 2022, 03:27:02 UTC
1c7d22a image_math: support multi-file + overwrite (#936) + cli.image_math: support multiple input files + cli.image_math: add --overwrite option + cli.asc_desc2horz_vert: check input file types, to give meaningful error msg if not pass + simulation.iono.iono_incidence2refraction_angle: support 3D output + utils.utils0: add diff_wrapped_phase() 23 December 2022, 23:23:52 UTC
541f33c isort: 5.11.1 --> 5.11.3 (#931) updates: - [ 5.11.1 → v5.11.3]( 21 December 2022, 02:40:55 UTC
85d8e25 update numpy expired deprecations (#934) 21 December 2022, 01:55:41 UTC
f9b1970 [] pre-commit autoupdate (#929) 13 December 2022, 02:58:54 UTC
99ae8ec [] pyupgrade: v3.2.2 → v3.3.0 (#924) updates: - [ v3.2.2 → v3.3.0]( 06 December 2022, 02:26:44 UTC
baed904 closure_phase_bias: use `wrapPhase` if available (#922) + update `objects.stack.ifgramStack.get_sequential_closure_phase()`: - prefer the use of wrapped phase, only use unwrapped phase when no wrapped phase is found - eliminates the need for a reference point for the computation of the wrapped closure phase + closure_phase_bias: give some info regarding the necessity of a reference point for action quick_estimate and estimate. + docs/install: fix the order of `conda activate mintpy` and `mamba install isce2` 02 December 2022, 23:05:52 UTC
4fcc33d install: rm pip non-editable mode (#923) + docs/installation: remove note for the regular `pip install` in non-editable mode, as this is not really useful for development version, because one needs to frequently git pull, and re-install to keep up with updates + docs/installation: add `mamba install isce2` note for `conda env create -f environment.yml` dependency installation + readfile.read_attribute: enforce lower case for metadata file extension for more robust detection against TIF file with an upper case file extension. 02 December 2022, 22:11:08 UTC
d8b74c6 pre-commit: v4.3.0 → v4.4.0 (#921) updates: - [ v4.3.0 → v4.4.0]( 29 November 2022, 01:11:04 UTC
9941b20 build(deps): bump akhilerm/tag-push-action from 2.0.0 to 2.1.0 (#917) 28 November 2022, 17:06:45 UTC
89fc646 save_gbis: support non-velocity dataset from the velocity file (#916) * Ability to extract other datasets from the velocity files 24 November 2022, 23:33:49 UTC
143fef5 deps: drop `defusedxml` (#915) * deps: drop `defusedxml`. revert back the ElementTree usage from `defusedxml` to the native `xml.etree` module, to drop this extra dependency, because there are only two use cases in the code: parse known XML files from ISCE and SNAP. #340 * del add_attribute from and * ionex.get_ionex_value(): rotate TEC map by default * closure_phase_bias: add link to notebook 23 November 2022, 01:15:16 UTC
1edce64 save_kite: typo fixed on `capitalize()` (#914) 21 November 2022, 21:08:20 UTC
93d769b docs: add <details> tag to shorten installation note + version 1.5.0 tag (#912) * docs/install: add <details> tag to shorten the default instruction * version: add tag for version 1.5..0 18 November 2022, 19:53:12 UTC
a28fc2c mv `constants` from `mintpy.objects` to `mintpy` level (#911) + move the `constants` from the `objects` directory to the root directory, to simplify its usage. + update all existing usage of `mintpy.constants` sub-module 17 November 2022, 03:55:03 UTC
7181dec `plate_motion`: add `--plate` option to use built-in tables (#906) * move to legacy dir move `mintpy/` to the `mintpy/legacy` directory because: 1. it's rarely used (it was designed as a quick hack to fix unexpected metadata problems) 2. it does not have the argparse usage to be included in the "mintpy/cli" sub-module, making it inconvenient to maintain 3. its functionality can be covered in Python using `mintpy.utils.utils.add_attribute()` API and in command line by adding extra metadata in the custom template file during data loading process. * plate_motion: add --plate option to use built-in tables add --plate option to grab the built-in rotation parameters from ITRF2014-PMM (Altamimi et al., 2017), for easy usage. 17 November 2022, 00:43:57 UTC
e00074a copy dataset units in `` (#910) + `utils.readfile`: add `get_hdf5_dataset_attrs()` to extract a given attribute from all top-level datasets of the input HDF5 file. + ``: copy over the dataset unit from input file to output file, e.g. for the velocity.h5 file. - call `readfile.get_hdf5_dataset_attrs()` - pass to `writefile.layout_hdf5(ds_unit_dict)` 16 November 2022, 07:32:11 UTC
27f8924 [] pyupgrade: v3.2.0 → v3.2.2 (#907) updates: - [ v3.2.0 → v3.2.2]( Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]> 15 November 2022, 03:02:28 UTC
16f4596 `dem_error` w/ phase velocity: rm all-zero column in design matrix (#905) + --phase-velocity: remove the all-zero column in the design matrix G and the all-one column in the design matrix G0, as the constant intercept term is not estimated in the phase velocity minimization scenario. Including this all-zero column in G could sometimes introduce abnormally large eigenvalues in the least-squares inversion, resulting in unrealistic TS residual. 12 November 2022, 06:16:38 UTC
0b0a8eb switch to `src` layout (#903) + switch `mintpy` to the standard `src/mintpy` layout for the source code + move/rename `mintpy/data/input_files` to `docs/templates` + update links and paths for 1) the src layout, 2) the renamed template dir and 3) $MINTPY_HOME usage: - docs/api/ - docs/api/ - docs/ - docs/ - docs/ - docs/ - docs/ - docs/ - mkdocs.yml + update ``: - update "version" and "packages" settings for the new `src` layout - remove "data/input_files" from the package data section + `version`: use ".postX" convention to be consistent with pip 09 November 2022, 21:14:57 UTC
ea5457f smallbaselineApp/dem_error: roll back "phase" minimization as default (#902) + mintpy/defaults/smallbaselineApp(_auto).cfg: roll back the default to `phase velocity` for topo resid + tests/dem_error: use model with step functions, which has better est. accuracy for complex deformation + mintpy/utils/time_func/*design_matrix4poly*: more comments on the math form of the polynomial equations 08 November 2022, 20:50:56 UTC
f24076b update circle CI + bugfix in save_gmt (#901) + .circleci/config.yml update: - use $BASH_ENV to set and share environment variable (PATH) among multiple run steps - rename to workflow/job to "unit-n-workflow-tests" + cli/ fix a typo in the module import + cli/load_data: check `-t smallbaselineApp.cfg` existence and print out error msg + tsview: show the reference index/date info on the slider as the title 08 November 2022, 07:17:03 UTC
64ffdef build(deps): bump docker/build-push-action from 2 to 3 (#899) Bumps [docker/build-push-action]( from 2 to 3. - [Release notes]( - [Commits]( --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <> 07 November 2022, 18:26:35 UTC
2ab0148 build(deps): bump docker/setup-buildx-action from 1 to 2 (#897) Bumps [docker/setup-buildx-action]( from 1 to 2. - [Release notes]( - [Commits]( --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <> Signed-off-by: dependabot[bot] <> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]> 07 November 2022, 18:25:48 UTC
fd368b4 build(deps): bump actions/checkout from 2 to 3 (#898) Bumps [actions/checkout]( from 2 to 3. - [Release notes]( - [Changelog]( - [Commits]( --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <> 07 November 2022, 07:29:31 UTC
7ce59a8 build(deps): bump akhilerm/tag-push-action from 1.0.0 to 2.0.0 (#896) Bumps [akhilerm/tag-push-action]( from 1.0.0 to 2.0.0. - [Release notes]( - [Commits]( --- updated-dependencies: - dependency-name: akhilerm/tag-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <> 07 November 2022, 07:29:06 UTC
f6695ac build(deps): bump actions/setup-python from 3 to 4 (#895) Bumps [actions/setup-python]( from 3 to 4. - [Release notes]( - [Commits]( --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <> 07 November 2022, 07:28:33 UTC
d55f781 build(deps): bump docker/login-action from 1 to 2 (#894) Bumps [docker/login-action]( from 1 to 2. - [Release notes]( - [Commits]( --- updated-dependencies: - dependency-name: docker/login-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <> 07 November 2022, 07:26:17 UTC
6167bc9 break publish-to-pypi into 2 jobs + add dependabot (#893) + build-n-publish-to-pypi.yml: - rename "publish-to-test-pypi.yml" to "build-n-publish-to-pypi.yml" - trigger for pull requests - split jobs into 2: "build-sdist-n-wheel" and "upload-to-pypi" - use upload/download artifacts to connect them, as used in pysolid + add `.github/dependabot.yml` for auto update 07 November 2022, 06:55:29 UTC
a199d92 dem_error: set `cond=1e-8` to fix abnormal fit residual + add unit test (#890) + `dem_error`: fix abnormal residual TS with default phase velocity mode - estimate_dem_error(): switch cutoff value of the least squares solution from 1e-15 to 1e-8, to avoid abnormal high TS residual value, when the phase velocity mode is turned ON by default. Tests (based on the new unit test script) shows this change has no impact on the estimation result at all, which is good. - set `debug_mode` as global variable to be test a specific pixel given Y/X easily. + add `tests/`, to test the DEM error estimation / correction in both scenarios (simple linear and complex non-linear) for one pixel. - add to circle CI testing + `ifgram_inversion`: rename/shortern the default output filenames for ionStack.h5 + `tropo_pyaps3`: improved auto-skip/run checks - skip dload if ERA5.h5 already exists - skip re-applying correction if corrected displacement exists and is newer - print out msg adjustment 06 November 2022, 06:48:19 UTC
ffefb7c bugfix for block-by-block resample & run/skip in load_data (#888) + objects.resample.prepare_geometry_definition_radar(): use abs() to ensure positive area calculation for both source/destination, before the adaptive source bbox calculation for block-by-block processing. + load_data.run_or_skip: check length/width only for ifgramStack to be able to skip re-loading if the existing ifgramStack file has more pairs than the input. + smallbaselineApp --plot: use relpath() for ionStack.h5 file 04 November 2022, 18:35:01 UTC
75012c5 docs/install: set env variables for more robust handling of HDF5 and GDAL VRT (#886) + docs/installation: add "3.c Extra environment variables setup" sub-section to setup three environment variables for more robust handling of HDF5 (for the file lock and version checking) and GDAL VRT (for dataset sharing in a multi-threading environment). Co-authored-by: Zhang Yunjun <> 04 November 2022, 06:39:19 UTC
2983a1a `tropo_pyaps3`: ensure 2 chars for `--hour` input (#883) + tropo_pyaps3: ensure 2 chars for --hour input + docs/module_hierarchy: add euler_pole + .circleci: use Unit/Workflow tests as names 02 November 2022, 17:57:35 UTC
24b1615 [] pre-commit autoupdate (#881) updates: - [ v3.1.0 → v3.2.0]( 31 October 2022, 23:45:15 UTC
930cbf4 `plate_motion` refactoring: remove pkg dependency (#868) + add ``: - create the `EulerPole` class/object based on `numpy` and `pyproj` (similar to - use matrix rotation to convert the cartesian frame to local ENU frame, to compute the plate motion - the above two remove the dependency on `astropy` and `platemotion` ( - add references to Pichon et al., 1973, Cox et al., 1986, ESA webpage - turn ON "ellipsoid" Earth calculation by default - `get_velocity_enu()`: set vu to 0 if assuming spherical Earth (ellps=False) + add `tests/objects/` for the unit tests: - test the EulerPole object initiation/conversion - test the plate motion calculation against the UNAVCO web calculator - add to the circle CI testing + `` and `cli/`: add published DOI to Stephenson, Liu, et al. (2022). + simplify the setup/install section for plate_motion in `` and `` + other minor features and bugfixes: - add get_azimuth_angle_from_east_north_obs() - utils.readfile.sort_dataset_list4velocity(): support velocity file without velocity dataset, e.g. ITRF14enu.h5 file. Co-authored-by: Zhang Yunjun <> 30 October 2022, 06:17:33 UTC
c15ad0f bugfix for ` --plot` option (#879) + smallbaselineApp: fix the bug of empty template file in _read_template(), which results in TypeError while running ` --plot` + tests/smallbaselineApp: use abspath() to fix the bug while using --dir for a different direction for testing + modify_network: print given ifg index number, instead of ordering number, to be more informative + setup: uncomment pysolid as it's now available on pypi 26 October 2022, 00:30:26 UTC
4275a94 `save_roipac`: support non-velocity dataset from the velocity file (#874) + `save_roipac.read_data()`: add an `if` check to skip the "velocity to displacement" conversion if the dataset of interest is not "velocity" + ``: add example usage for non-velocity datasets, e.g. step, annualAmplitude 23 October 2022, 03:58:22 UTC
a4a0780 `dem_error`: change default from phase to phase velocity (#875) + Change the default minimization option from "phase" to "phase velocity", based on the experiment of geolocation correction in the urban area. This is also more consistent with Fattahi & Amelung (2013, TGRS). + Fix matrix size bug for using phase velocity history during matrix operations. 22 October 2022, 18:55:23 UTC
4756732 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 - + docs/CONTRIBUTING: add note to install `pre-commit` + github PR template: add selection box for pre-commit check. * Update 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 <> 19 October 2022, 21:05:08 UTC
868c27f `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 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 ionex: split interp_3d_maps() out of get_ionex_value() for re-use (#867) 11 October 2022, 04:25:55 UTC
890a743 [] pre-commit autoupdate (#866) 11 October 2022, 01:06:11 UTC
e4c94d1 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 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 rename `bulk_plate_motion` to `plate_motion` (#858) + rename `bulk_plate_motion` to `plate_motion`: including changes in: - `` - `` - `mintpy.__main__` - `` + ``: add `no_data_values` arg to be able to convert the no-data-value from one number to another number. + ``: 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 [] autoupdate pyupgrade: v2.37.3 → v2.38.2 (#856) updates: - [ v2.37.3 → v2.38.2]( 27 September 2022, 00:58:37 UTC
8ccacd1 `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/`: 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 readfile.read_isce_xml: bugfix when v_first=0 (#853) 23 September 2022, 01:46:27 UTC
7e36e6a 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 support azimuth output for `solid_earth_tides` and `bulk_plate_motion` (#851) + - 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() + - 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() + - 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. + 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)/ + 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 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/ + 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`. + add extras_require field + create an overall processing function for the following scripts, to allow for simple main() call in `mintpy.cli`: - - - - - - - - - - - + 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 - add temporal_filter() from + 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`: - - renamed from - - - - - + docs/ 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 ( and Co-authored-by: Zhang Yunjun <> Co-authored-by: Antonio Valentino <> 21 September 2022, 19:12:11 UTC
414cb65 bugfix in ionex.dload_ionex() (#849) 17 September 2022, 00:03:01 UTC
726fa70 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/ update print() from py2 to py3 + utils/isce_utils.get_processor(): add `data.db` to the supported list of metadata files generated by stripmapStack + add more msg for aria if load_data failed 13 September 2022, 04:11:09 UTC
d987950 fix typo in `smallbaselineApp.cfg` for `stepDate` (#843) 07 September 2022, 06:20:27 UTC
4a0f2c5 unmask ref pixel in ts2vel and tsview (#842) + - include the reference point as valid pixels for calculation/inversion. - use np.full() instead of np.ones() for initiation with nan value. + 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 <> Co-authored-by: Zhang Yunjun <> 05 September 2022, 19:46:54 UTC
3245008 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 ts2vel: save `residue` & `intercept` (#835) + - 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 hdf5eos: calc `data_footprint` for radar-coded dataset (#833) + 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 + add `snwe_to_wkt_polygon()` Co-authored-by: Zhang Yunjun <> 20 August 2022, 04:02:57 UTC
36a0835 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 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 automate PyPI publishing with GitHub Actions (#827) + version: replace version_num with version for easy re-use, and update its usage in + setup: use sys.path.append() to replace open() to grab version from + 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 bugfix in `load_data` for empty path due to the new iono file in `auto_path` (#826) + bugfix when empty file path found, introduced in load iono stack PR 780, due to the additional new iono file path defined in defaults/ 11 August 2022, 21:11:48 UTC
ef31de5 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; + 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 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. + 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 Single entrypoint with sub-commands (#823) + add `` 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 + ``: - rename from `` to `` - add `create_argument_parser()` to create parser with or without sub-parsers - call `create_argument_parser()` from all executable scripts in `mintpy` folder. + ``: add the following optional requirements: - argcomplete - platemotion and astropy + ``: rename `inps.step` to `inps.stepDate` to avoid weird initiation bug in sub-command mode. Co-authored-by: Zhang Yunjun <> 04 August 2022, 08:18:55 UTC
00dd106 various bugs-fix in ` --periodic` and `prep_hyp3` (#822) + ` --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. + ``: fix bug of `ORBIT_DIRECTION`. + ` inputs/ifgramStack.h5 --write-data`: skip pixels with no-data-value (zero) while updating the `unwrapPhase` matrix. + `` and ``: switch MintPy license from `GPLv3` to `GPLv3+`. 28 July 2022, 04:19:07 UTC
8d8d85d 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 <> 27 July 2022, 22:57:49 UTC
47c9bcc 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: + `` - 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 `` 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. + - 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 `` Co-authored-by: Zhang Yunjun <> 27 July 2022, 00:04:02 UTC
e17d1d3 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 entry_points + docs/installation: update the Debian link to + 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 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 (, as the GDAL Python bindings fail for Path objects. 14 July 2022, 22:50:24 UTC
f8319ec Add installation instructions for Debian (#812) * Add installation instructions for Debian 14 July 2022, 21:06:55 UTC
d1aa094 gps: bugfix component string (#811) bugfix on the string for identifying the component mintpy/objects/ 13 July 2022, 23:33:33 UTC
632a394 plate_motion: supp radar-coord geometry & ITRF14 as default fname (#808) + utils.utils0.get_lat_lon(): add ystep and xstep for more flexible output + add prepare_geo_los_geometry() from for easy re-use. + - 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 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/`: 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 prep_isce: typo fix in alosStack example usage (#805) 06 July 2022, 22:37:14 UTC
ee43222 bugfix in `` 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 + 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 <> 06 July 2022, 22:33:44 UTC
6e741da smallbaselineApp: get ionStack file & add metadata from custom template file (#802) + - 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 <> 30 June 2022, 21:41:35 UTC
b13e409 (#769) + Estimate the bulk motion of tectonic plates in the reference frame of the satellite. - 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. - add entry_points for - 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: - modified to take care of the velocity field subtraction - use FILE_TYPE for velocity dataset name Co-authored-by: Zhang Yunjun <> 29 June 2022, 21:42:38 UTC
719c2b4 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/ - 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 and 28 June 2022, 18:42:19 UTC
340062d 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: - - objects/ - defaults/smallbaselineApp.cfg - defaults/smallbaselineApp_auto.cfg - + [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 + 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 <> 22 June 2022, 06:38:04 UTC
c50a231 tests: remove "test_" prefix + smaller zenodo file sizes (#799) + tests: remove the "test_" prefix for: - - + tests/ 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 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 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 + 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. + - 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 - ifgramStackDict.write2hdf5(): add geom_obj arg, to auto detect the low-reso ion file, for resizing on the fly - add resize2shape arg to resize on the fly using skimage.transform.resize(), and make it compatible with the exiting subset and resampling options. + 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, 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 + light refactoring 17 June 2022, 21:24:52 UTC
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