| 4c8e9fd | Zhang Yunjun | 28 April 2020, 02:29:46 UTC | Update fallback version number/date in version.py for the new release | 28 April 2020, 02:59:38 UTC |
| 40e64af | Zhang Yunjun | 28 April 2020, 02:26:07 UTC | add QGIS doc from wiki to readthedocs | 28 April 2020, 02:59:38 UTC |
| 2f28021 | Zhang Yunjun | 23 April 2020, 05:08:14 UTC | install: recommend conda env for installation * install: + remove max version constraint in conda_env.yml for dask + use tools instead of python for example directory name + update links for miniconda and vim * README: + update badge version number to 1.2.2 + add link to FRInGE | 28 April 2020, 02:59:38 UTC |
| 90ea2f1 | sssangha | 26 April 2020, 04:07:30 UTC | bugfix in prep_aria (#329) + fix bugs addressed in ARIA-tools issue 147 (aria-tools/ARIA-tools#147). Specifically, prep_aria crashes when one IFG passed (relevant for unit tests). | 26 April 2020, 04:07:30 UTC |
| a0aee9a | Forrest Williams | 26 April 2020, 01:42:47 UTC | prep_fringe: ingest FRInGE outputs into MintPy (#327) * Update prep_isce.py so that it can prepare metadata for non-multilooked files generated by the sentinelStack SLC workflow. if *.rdr geometry files are not found, *.rdr.full geometry files are used instead; if DATE12 contains only one date, the master date from the input metadata file (IW*.xml) is used as the first date * Create prep_fringe.py based on prep_aria.py to convert the output of FRInGE to timeseries.h5 and temporalCoherence.h5 files and creates a geometryRadar.h5 file clipped to the boundary box used by FRInGE. More work could be done, but this is workable. * Explicitly set first time series entry * convert time-series unit from phase to meter and add UNIT metadata Co-authored-by: Zhang Yunjun <yunjunz@users.noreply.github.com> | 26 April 2020, 01:42:47 UTC |
| 8d74c24 | ehavazli | 26 April 2020, 01:32:31 UTC | add scikit-learn to the dependency for bootstrapping (#328) * Time bug fix from ARIA products * add new dependency for boot_strap.py - scikit-laern added to dependency * Update ports.txt * revert the time format fix Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> | 26 April 2020, 01:32:31 UTC |
| 5945b9c | Zhang Yunjun | 20 April 2020, 00:22:18 UTC | fix link for example dset in README unw_err_phase_closure: matplotlib backend setting update | 20 April 2020, 23:05:49 UTC |
| 789e844 | Zhang Yunjun | 19 April 2020, 22:25:57 UTC | add numNonzeroIntClosure to routine workflow in quick_overview step + add `quick_overview` to routine workflow: - rename step `stack_interferograms` to `quick_overview` and move it from after correct_unwrap_error to before correct_unwrap_error - call unwrap_error_phase_closure.main() to calculate number of triplets with non-zero integer ambiguity of closure phase to show the distribution of phase unwrapping errors + add import unwrap_error_* in workflow/__init__.py because 1) they are now used multiple times; 2) installing skimage and cvxopt seems to work fine + update integer ambiguity functions in unwrap_error_phase_closure: - output default filename as "numNonzeroIntClosure.h5" - plot the distribution and histogram of the integer ambiguity same as the paper, but: 1) use RdBu_r colormap 2) plot reference point - enable the update mode - add template text from quick_overview step as well + view.py and utils/plot.py: use %(default)s in options help message | 20 April 2020, 00:04:13 UTC |
| 6a5c051 | Zhang Yunjun | 19 April 2020, 05:08:00 UTC | add reference link for scientific colormap | 20 April 2020, 00:04:13 UTC |
| 5588d58 | Zhang Yunjun | 19 April 2020, 03:45:08 UTC | support wildcard dset input in view.py + support input wildcard pattern for dataset input in view.py, for a more powerful search to plot a subset of images + support masking using the connected components from ifgramStack, works only for one interferogram because it read the date12 from the first dataset slice, and will not make sense if one use it while plotting mulitple pairs + rename the following functions to be more intuitive: - check_input_file_info --> read_input_file_info - check_dataset_input --> search_dataset_input + rename --no-glob option to --nosearch option. + update example usage. | 20 April 2020, 00:04:13 UTC |
| c96cdca | Zhang Yunjun | 16 April 2020, 23:32:34 UTC | calc # of non-zero closure phase unwrap_error_phase_closure.py + add --action option to calculate the number of non-zero integer ambiguity of closure phase only + add file writing to calc_num_nonzero_closure_phase() + add hist_num_nonzero_closure_phase() for plotting Fig. 3e in Yunjun et al. (2019). smallbaselineApp.py: update the usage of unwrap_error_phase_closure.py smallbaselineApp.cfg: more detailed section info in the paper for further reading | 20 April 2020, 00:04:13 UTC |
| 992d3c1 | ehavazli | 16 April 2020, 04:12:31 UTC | Bug fix in tsview.py for the coord_unit (#322) * Bug fix: - Output filename option works now * tsview.py bug fix: - Fixed coordiante unit bug reading in tsview.py * Update tsview.py in case Y_UNIT does not exists Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> | 16 April 2020, 04:12:31 UTC |
| b90bba4 | Zhang Yunjun | 15 April 2020, 19:02:02 UTC | add more links to example dir structure (#321) * add more links to example dir structure update ARIA template option as wildcard for geom files Update requirements.txt for the max version of dask align output msg | 15 April 2020, 19:02:02 UTC |
| 866abd1 | ehavazli | 14 April 2020, 20:16:30 UTC | Wildcard option to prep_aria.py and bug fix in spatial_filter.py (#320) * Tool to run boot strapping method to estimate velocity and uncertainty from MintPy time series file - input is time series file in MintPy format - output is bootstrap estimation of velocity and uncertainty in MintPy velocity file format * fixed url bug in GPS data download step * add defo area example figure * Option added: - incidence angle and azimuth angle files can be given as wildcards in the template - updated example to reflect the new option * Bug fix: - Output filename option works now * Update prep_aria.py * Update spatial_filter.py Co-authored-by: Zhang Yunjun <yunjunz@users.noreply.github.com> Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> | 14 April 2020, 20:16:30 UTC |
| a78b8d7 | Zhang Yunjun | 12 April 2020, 06:05:36 UTC | support `aria` processor in smallbaselineApp.py (#319) * support `aria` processor in smallbaselineApp.py + smallbaselineApp.py: support 'mintpy.load.processor = aria', this will call prep_aria.py instead of load_data.py to load the data. In this way, users do not need to run prep_aria.py manually, making the ARIA products the same experience with other products. + doc: add example ARIA data/directory structure with example template setup. + prep_aria.py: - add -t/--template option to input template file, together with read_template2inps() - add --update option to be able to skip re-writing if outputs exist and contains all info, together with run_or_skip() - replace -w with -o option to be more consistent with load_data.py - raise an error when gdal.Open() vrt file failed, which happens when the folder is moved and the file path in vrt file becomes invalid. This is fine as long as mintpy h5 files already exist. - add help message for i) example template and ii) updated usage + add docs/examples/input_files/SanFranSenDT42.txt and update the README.md file acoordingly. + more comments of mintpy.load.*File in the default template file. | 12 April 2020, 06:05:36 UTC |
| cca2bb8 | Zhang Yunjun | 03 April 2020, 03:25:38 UTC | bugfix for --scalebar-pad in view.py view: + fix broken option for --scalebar-pad introduced while replacing basemap with cartopy + use eval() to replace PROJECTION_NAME2OBJ to specify the map projection from cartopy for more generic supports with more projections. + update prep_slice() to use cartopy too utils/utils0: add highest_power_of_2() to find the highest power of 2 that is <= the input number more comments in: + objects/resample.py + tropo_pyaps3.py + defaults/smallbaselineApp.cfg with guidelines on reference point test/test_smallbaselineApp: add custom colormap for final velocit pop out | 09 April 2020, 01:08:43 UTC |
| e742fbc | BB | 08 April 2020, 23:53:21 UTC | bug fix for correct data in unwrapping corrections (#317) * bugfix for correct data in unwrapping corrections prior to fixing, mintpy would default to using corrected dataset in timeseries.h5 if unwrapping corrections were turned off after running them, this would not be reflected this obtains the name of the dataset from the input file | 08 April 2020, 23:53:21 UTC |
| 01ad0b2 | Joshua Zahner | 07 April 2020, 18:18:55 UTC | support dask configuration by config_name (#315) * Added support for specifying a dask configuration by config_name * Changed auto value of clusterConfig to 'no' to match other config styles * Implemented simple fallback logic for clusterConfig where the default configuation name is used if a user specified name is not found in the dask.yaml file * Updated dask.yaml with base SLURM configuration variables * Updated installation note with new information about dask * Update installation.md * Update smallbaselineApp.cfg * Update smallbaselineApp_auto.cfg * Update smallbaselineApp.cfg * fig_inv: more --config input checking into cmd_line_parse() * Fixed typo in inps * Removed cast of inps.config to lower in all cases, as config names do not have to be all lowercase * Removed erroneous print statements * Create dask.md * Rename dask.yaml to mintpy.yaml * Update installation.md * Removed case dependency when defining cluster type * Added function to reformat walltime parameter to proper format based on cluster style * Removed extra check for inps.config default value * Update installation.md * Update smallbaselineApp.cfg * Update smallbaselineApp_auto.cfg * Revert "Removed extra check for inps.config default value" This reverts commit 12058a5dcd2c7e00ace0db8e56c718bd1a6d0f4b. * Update cluster.py * Update ifgram_inversion.py * Update mkdocs.yml * Update cluster.py * Update ifgram_inversion.py * add cluster.check_config_name() + move the config_name checking from ifgram_inversion.cmd_line_parse() to objects.cluster.check_config_name() + rename format_walltime_for_cluster() to check_walltime_format() * Updated cluster.py * Removed and tested check in cluster object Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> Co-authored-by: Zhang Yunjun <yunjunz@users.noreply.github.com> | 07 April 2020, 18:18:55 UTC |
| 46da031 | bb | 06 April 2020, 19:57:27 UTC | correct optional argument name | 06 April 2020, 20:09:18 UTC |
| 3cd0b68 | Ovec8hkin | 04 April 2020, 22:47:04 UTC | Updated configuration files with mintpy.networkInversion.cluster option | 04 April 2020, 22:56:51 UTC |
| 5c0deab | Ovec8hkin | 04 April 2020, 22:09:42 UTC | Updated read_template2inps to read cluster parameter from template file | 04 April 2020, 22:56:51 UTC |
| 0b87d4b | Zhang Yunjun | 27 March 2020, 19:01:26 UTC | view: fix bug for referencing on the fly for unwrapPhase* dset + move data & figure link to the end of paper info. | 31 March 2020, 22:12:43 UTC |
| 390b716 | Zhang Yunjun | 27 March 2020, 01:23:15 UTC | bug fix in utils/plot.read_mask() (#312) utils/plot: * auto_adjust_xaxis_date(): support buffer_year=None -> keep the original x-axis range limit * bug fixed in read_mask() with more info regarding data size difference view: * add --title4sen for Sentinel-1. This option display the subplot title for S1A/B acquisition in blue/orange color, and show the IPF number. *check invalid input files | 27 March 2020, 01:23:15 UTC |
| 04392eb | Zhang Yunjun | 25 March 2020, 03:46:22 UTC | diff: support file2 without REF_DATE + check number of file2 inputed, it should be only one for timeseries and ifgramStack + support file2 without REF_DATE + use read_attribute() to get metadata for file1/2 because `timeseries` object will assign a default REF_DATE value even if it's not exsited. This interferences with the handling of REF_DATE as None for file2. + use read() to get data, just to be consistent with metadata handling, no specific reason. tropo_pyaps3.py + print out info on dry/wet/comb delay + return error if input file not exist. | 25 March 2020, 04:44:13 UTC |
| a608a4c | Zhang Yunjun | 23 March 2020, 23:11:02 UTC | tropo_pyaps3: save abs delay by default + save the absolute tropospheric delay by default, without referencing in space and time. - This works because diff.py can handle the different reference in space and time between two input files and this is used in both tropo_pyaps3.py and smallbaselineApp.py - This is more generic, suitable for both phase and offset time-series, the later does not have spatial reference. + more smart way for default output file name: delay file in the same dir as geom file; corrected ts file in the same dir as the input ts file + remove --ref-yx option to simplify the code + remove reference related metadata from delay h5 file. + comment out other models as they are currently not supported in pyaps3, to avoid confusion. + re-organized create_parser() for improved readability + clean up cmd_line_parse(): - check required options --file OR (--date-list and --hour) - ignore invalid h5 file inputs - grab default output files + split check_inputs() into read_inps2date_time() and get_grib_info() + more straight forward main() + more comments objects/stack.timeseris.write2hdf5(): fix a bug when output file directory does not exist. | 25 March 2020, 04:44:13 UTC |
| cac5c00 | Zhang Yunjun | 23 March 2020, 06:18:15 UTC | bug fix in ifgram_inversion.py | 23 March 2020, 06:30:21 UTC |
| e7f42ee | Zhang Yunjun | 23 March 2020, 05:45:40 UTC | refactor cmd_line_parse() and startup() in smallbaselineApp.py + add read_inps2run_steps() to simplify cmd_line_parse() + add get_the_latest_default_template_file() to simplify TimeSeriesAnalysis.startup() + update citation note in README.md + update ifgram_inversion.py following codacy suggestion | 23 March 2020, 06:12:51 UTC |
| 7eb384b | Zhang Yunjun | 22 March 2020, 18:33:50 UTC | writefile.write(): more generic writer without timeseries.write2hdf5() + remove the call of timeseries.write2hdf5() in order to: - merge the writing of time-series file with all the other HDF5 files. - more generic writing to time-series file, i.e. dataset that are not previsouly defined in original time-series object + clean up the info extraction from reference file + checking the required dataset for timeseries and ifgramStack file, which is 'date'. | 23 March 2020, 06:12:51 UTC |
| bd2cf8e | Zhang Yunjun | 22 March 2020, 00:47:14 UTC | tropo_pyaps3: use %(default)s in argparse help msg | 23 March 2020, 06:12:51 UTC |
| 8d0057c | Zhang Yunjun | 21 March 2020, 03:33:09 UTC | plot_smallbaline*: check dataset in h5 file before plotting + call `h5ls` command to check if the dataset exsits in the HDF5 file before calling view.py to plot, for a cleaner message output in plot_smallbaselineApp.sh. + plot phase-unwrapping error correction result if the dataset is available + fix a potetial bug in utils1.run_deramp() if the input mask file dataset name is not 'mask'. | 23 March 2020, 06:12:51 UTC |
| 3e807ec | Zhang Yunjun | 16 March 2020, 06:25:28 UTC | Update tropo_pyaps3.py and README.md | 23 March 2020, 06:12:51 UTC |
| de61e20 | Zhang Yunjun | 13 March 2020, 05:36:42 UTC | add --cm-vlist optoin to view.py | 23 March 2020, 06:12:51 UTC |
| 2b6f7f5 | Zhang Yunjun | 06 March 2020, 23:26:31 UTC | diff: support file1/2 both without REF_X/Y | 23 March 2020, 06:12:51 UTC |
| 8705a0a | Zhang Yunjun | 06 March 2020, 23:21:52 UTC | load_data: support offset call for prep_isce.py | 23 March 2020, 06:12:51 UTC |
| da2f7bd | Zhang Yunjun | 06 March 2020, 01:46:44 UTC | smallbaselineApp for offset until modify_network adjust smallbaselineApp.py workflow for offset observations to work until the end of modify_network step. | 23 March 2020, 06:12:51 UTC |
| d56ee49 | Zhang Yunjun | 06 March 2020, 00:52:37 UTC | use argparse for temporal_derivative.py ifgram_inversion: + enable skip reference by default if input observation dataset is offset + do not skip zero value for offset while calc mask | 23 March 2020, 06:12:51 UTC |
| 466dfbc | Zhang Yunjun | 05 March 2020, 21:45:18 UTC | plot_network: support offsetSNR plot_network.py: + add --dset/-d option to change the dataset used for average quality calculation. + add -v/--vlim to be able to change default display range + objects/stack.py and utils/utils1.py: calculate spatial median instead of spatial mean for offset dataset | 23 March 2020, 06:12:51 UTC |
| 2740ddb | Zhang Yunjun | 05 March 2020, 01:59:52 UTC | support offset time-series inversion + add the following template option for offset dataset and the corresponding changes in load_data.py - mintpy.load.azOffFile - mintpy.load.rgOffFile - mintpy.load.offSnrFile - mintpy.networkInversion.maskDataset = offsetSNR ifgram_inversion.py: + re-organize argparse to more groups + auto output file name based on phase / offset input + support masking based on input offset SNR with threshold + turn OFF skip zero value for offset inversion prep_isce.py: + rename argument names to be more generic, regardless of phase or offset input | 23 March 2020, 06:12:51 UTC |
| badaaca | Zhang Yunjun | 05 March 2020, 00:07:04 UTC | multilook: add --margin option + add --margin option to be able to ignore/skip pixels on the bounaries during multilooking, which is usually the case of window matching operations, such as cross correlation during pixel tracking. + add more comments on multilook_file() + remove obsolete --no-parallel option. writefile: + add write_real_float64() + support BIL 2 band writing readfile: translate DATA_TYPE in read_attribute() | 23 March 2020, 06:12:51 UTC |
| a445d99 | Zhang Yunjun | 23 March 2020, 00:40:59 UTC | add defaults.template module + add `mintpy.defaults.template` sub-module, to remove the duplicated template content in the utility scripts - move STEP_LIST from smallbaselineApp.py to here - add `get_template_content()` to grab the related template option, given an step name - update docs/api/module_hierarchy.md + update defaults/smallbaselineApp.cfg to facilitate the template.get_template_content() + replace the large string in the following scripts with a call to get_template_content(). - dem_error.py - geocode.py - ifgram_inversion.py - load_data.py - modify_network.py - select_network.py - reference_date.py - reference_point.py - save_hdfeos5.py - timeseries2velocity.py - timeseries_rms.py - unwrap_error_bridging.py - unwrap_error_phase_closure.py + remove TEMPLATE string variable in the following scripts because they don't have -t/--template option, thus it's not needed. - remove_ramp.py - tropo_pyaps3.py - tropo_pyaps.py + add more argparse group in ifgram_inversion.py to improve the readability. + bug fix in select_network.py + remove the obsolete `defaults/file_structure.py` as it's already in `docs/dir_structure.md` | 23 March 2020, 01:14:48 UTC |
| 9ad6e95 | Joshua Zahner | 22 March 2020, 04:01:18 UTC | remove Dask version constraint for installation? (#307) * Update conda.txt Removed version dependencies for dask and dask-jobqueue * Update conda.txt Reimplemented minimum version numbers | 22 March 2020, 04:01:18 UTC |
| 6f332ba | Joshua Zahner | 22 March 2020, 01:30:40 UTC | Cluster (#306) * Created custom Cluster object to facilitate switching between different Dask cluster objects * Updated ifgram_inversion.py to switch between cluster types based on user preferences * Replace Cluster object with simple function * ifg_inv: update parallel option names Co-authored-by: Zhang Yunjun <yunjunz@users.noreply.github.com> | 22 March 2020, 01:30:40 UTC |
| a806c13 | Zhang Yunjun | 21 March 2020, 23:25:37 UTC | ref_point: turn ON --write-data for non-ifgramStack file | 21 March 2020, 23:36:37 UTC |
| 4d7184f | Zhang Yunjun | 21 March 2020, 03:15:27 UTC | fix bug for remove_ramp.py ifgramStack.h5 (#301) + remove_ramp: diable update mode if the outfile option is missing, in order to use the default output filename from ut.run_deramp() when --update is not specified. + utils1.run_deramp(): put out_file the same as input file if the input file is ifgramStack + view: support spatial referencing on the fly for unwrapPhase* dataset + tropo_pyaps3: save abs delay in ERA5 file for more generic usage. Since diff.py can handle different reference date, this change does not affect smallbaselineApp.py | 21 March 2020, 03:15:27 UTC |
| b460abb | BB | 18 March 2020, 22:06:48 UTC | Read list of dates in textfile for mintpy.network.referenceFile (#300) + use utils.network.get_date12_list() instead of ifgramStack().get_date12_list() for mintpy.network.referenceFile option. + bug fix for utils.network.get_date12_list() | 18 March 2020, 22:06:48 UTC |
| edcd0b1 | Zhang Yunjun | 10 March 2020, 19:01:03 UTC | add module_hierarchy.md to API document + move module hierarchy info from __init__.py to readthedocs + update CONTRIBUTING.md | 11 March 2020, 00:36:36 UTC |
| b2849a3 | Zhang Yunjun | 05 March 2020, 02:10:47 UTC | temp coh mask: do not change input min temp coh of 0 | 05 March 2020, 03:02:26 UTC |
| 87eb5a6 | Zhang Yunjun | 02 March 2020, 03:03:25 UTC | add defo area example figure | 02 March 2020, 03:15:56 UTC |
| a63917f | Zhang Yunjun | 01 March 2020, 22:55:16 UTC | bug fixed for print message in gps.py | 01 March 2020, 23:13:10 UTC |
| 98614e2 | Zhang Yunjun | 28 February 2020, 03:28:23 UTC | fix bug in plotting DEM background utils/plot.plot_dem_background(): + calculate extent in geo coordinates + add extent for ax.imshow() for both shaded relief and contour + remove obsolete latlon argument from contour() | 28 February 2020, 03:39:36 UTC |
| f6ea222 | Zhang Yunjun | 28 February 2020, 01:24:23 UTC | default UNR GPS version IGS08 to IGS14 objects/gps.py: + add min_num_solution argument to search_gps() to discard stations with too few solutions, which can be too little for velocity calculation. + update the default GPS solution version from IGS08 to IGS14 because the later contains more data and is consistent with the station list file. The original IGS08 data is still supported. utils/plot.py: simplify the CSV file writing code | 28 February 2020, 01:35:51 UTC |
| e7ff998 | Zhang Yunjun | 20 February 2020, 04:12:56 UTC | plot_smallbaselineApp: add connectComponent | 28 February 2020, 00:26:51 UTC |
| 6ca47f8 | Zhang Yunjun | 22 February 2020, 02:29:17 UTC | view: support data operation for undefined binary files (#284) + view: support data operation for undefined binary files + Update README.md | 22 February 2020, 02:29:17 UTC |
| ec3fb37 | Zhang Yunjun | 20 February 2020, 03:31:56 UTC | bugs fix in plot_network (#283) + plot_network: fix bug when the input coherence cut value is smaller than the default 0.2 for start. + ifgram_inversion.py: turn off the minNormVelocity, to be consistent with smallbaselineApp_auto.cfg file. | 20 February 2020, 03:31:56 UTC |
| 080196c | Zhang Yunjun | 18 February 2020, 00:18:43 UTC | smallbaselineApp: able to skip plot_network Add support to use --noplot or mintpy.plot = no in template file to skip plotting the network. | 18 February 2020, 00:33:01 UTC |
| d5259e5 | Zhang Yunjun | 14 February 2020, 07:28:39 UTC | update comment: replace ECMWF with ERA5 | 18 February 2020, 00:33:01 UTC |
| f85a1d7 | Zhang Yunjun | 13 February 2020, 02:37:16 UTC | bug fixed for save_gmt.py | 13 February 2020, 02:43:01 UTC |
| a56c43c | Zhang Yunjun | 12 February 2020, 04:12:16 UTC | bug fix for sensor.project_name2sensor_name() fix bug when the custom project name don't have the sensor in Capitalize style | 12 February 2020, 05:05:09 UTC |
| 1d63c98 | Zhang Yunjun | 12 February 2020, 01:06:59 UTC | fractal: more comments on regime argument regime argument determines the energy distribution of the simulation each power-law components, each corresponds to different ranges of spatial scale. | 12 February 2020, 05:05:09 UTC |
| f4712fc | Zhang Yunjun | 11 February 2020, 19:37:40 UTC | timeseries obj: turn off squeeze while calc temporal_average | 11 February 2020, 19:49:58 UTC |
| a30819b | Zhang Yunjun | 11 February 2020, 07:05:52 UTC | fractal: add recon_power_spectral_density() | 11 February 2020, 08:16:37 UTC |
| 105d539 | Zhang Yunjun | 11 February 2020, 07:03:39 UTC | bugs fix for writing timeseries file in asc_desc2horz_vert adjust the rounded decimal digits from 4 to 3 | 11 February 2020, 08:16:37 UTC |
| a15d459 | Zhang Yunjun | 10 February 2020, 01:33:38 UTC | keep single date timeseries as 3D for common IO For timeseries FILE_TYPE dataset, keep the data as 3D matrix when there is only one acuiqisiotn (readfile.read() will squeeze it to 2D by default). To be consistent with the data structure definition and geocode.py | 10 February 2020, 01:55:20 UTC |
| 162d02c | Zhang Yunjun | 09 February 2020, 22:05:04 UTC | fix potential bug while reading isce baseline prep_isce.py: + add get_processor() + read_baseline_timeseries() ignore files with different reference date utils/utils1.py: add get_center_lat_lon() to extract the scene center lat/lon from geometry file. | 09 February 2020, 22:42:48 UTC |
| 49d89fb | Zhang Yunjun | 07 February 2020, 02:12:10 UTC | fix readthedocs issue due to cartopy remove cartopy from docs/requirements.txt for now because it causes errors in the complilation on readthedoc delete obsolete cartopy.ipynb | 09 February 2020, 01:23:06 UTC |
| e9aec27 | ehavazli | 07 February 2020, 01:57:44 UTC | Tool to run boot strapping method to estimate velocity and uncertainty from MintPy time series file (#267) - input is time series file in MintPy format - output is bootstrap estimation of velocity and uncertainty in MintPy velocity file format | 07 February 2020, 01:57:44 UTC |
| b54284c | Zhang Yunjun | 09 January 2020, 02:55:17 UTC | update fractal.py fractal_surface_atmos(): + cleanup power spectrum code + use wavelength1/2 in km to replace the previous regmine in percentage for the transition wavelength between regmine1/2/3. Bring argument regime back to specify the transition wavelength, instead of previous wavelength1/2, to avoid the over decorrelation of the simulated tropospheric turbulence in very high spatial frequency. simulation/fractal.py: + add radial_average_spectrum() + add freq0 argument in power_slope() to be able to calculate the power spectral density in any given reference frequency. + rename check_power_spectrum_1d() to get_power_spectral_density() + use `np.fft.fftfreq()` to prepare the sample freqencies instead of manually prepare. + use m for all length unit to replace the previous wavenumber of cycle / km with cycle / m. + use pyfftw.interfaces.numpy_fft to replace numpy.fft module for slight speedup + update plot details + fractal_surface_atmos(): constrain xx/yy to float32 for more robust performance utils/ptime.py: + add yyyymmdd2season() utils/utils1.py: + remove the amateur function get_residual_spectral_power_density() utils/readfile.py: + read_template: add ! for fortran style Update help for save_kmz_timeseries.py | 06 February 2020, 06:07:20 UTC |
| 3e935e0 | Zhang Yunjun | 04 February 2020, 07:13:53 UTC | demo dataset: replace ECMWF.h5 with ERA5.h5 + update link for all 3 datasets in zenodo + update template file settings for ERA5 in test directory + update data.rsc for Fernandina dataset with new fields from prep_isce.py + rename example_dataset.md to demo_dataset.md + Update references.md | 05 February 2020, 03:19:31 UTC |
| 237ffbe | Joshua Zahner | 04 February 2020, 01:23:26 UTC | Replace Basemap with Cartopy (#263) * Replaced BasemapExt scalebar with cartopy scalebar * Broken up scalebar definition and draw method * Reimplemented draw_lalo_labels in cartopy * Replaced BaseMapExt initializations with default cartopy GeoAxes object * Changed --coastline parameter to take coastline resolution in cartopy format `{scale}m` and display proper resolution coastline * Updated Scalebar to take length as a percentage of the dataset width * Moved scalebar plotting code to plot function * Removed all basemap imports and instances * Replaced two instances of BasemapExt with cartopy GeoAxes objects * clean up Matplotlib and cartopy import * codacy suggestion Fixing warning from codacy suggestion, although I do agree this version works as well. * fix more f"{}" occurrences * add return to draw_scalebar() and draw_lalo_label() * Update plot.py * Replace shapely computation of dataset width in km with pyproj computation * Reaplced use of 'm' as map variable with cartopy axis object * update import import multiple sub-modules in one line * add PROJECTION_NAME2OBJ * change default map_projection name * Update view.py * move code to utils/plot_map.py move all map/cartopy related code into plot_map.py to simplify utils/plot.py bugs fix * adjust old draw_scalebar() to be independent of basemap/cartopy utils/plot_map.py: + rename draw_scalebar() to draw_scalebar_cartopy() + add old draw_scalebar() back and adjust it to be independent of basemap and cartopy + draw_lalo_label() to plot ticks instead of gridlines, which was not possible in basemap but now possible through cartopy. objects/colors.py: move mplColors back to utils/plot.py in order to avoid "import as *" style, which is not recommende. utils/plot.py: + remove the obsolete --resolution argument, which is now part of --coastline option view.py: use cartopy projection ONLY when ALL the following 5 conditions met: 1. input file is geocoded 2. only one dataset is plotted 3. display coordinate is geo 4. input file length unit is degrees 5. --lalo-label is enabled. In this way, cartopy is only imported in the limited case. This is good because: 1. the new draw_scalebar() does not need basemap/cartopy anymore 2. draw_lalo_label() through cartopy can not re-plot the tick/labels while user zoom-in/out and pan through matplotlib toolbar. Thus, cartopy is only used for pretty figure generation, required by publication. * merge plot_map.py into plot.py * Update conda_env.yml * update installation note for cartopy * remove obsolete utils/plot_map remove utils/plot_map.py because the utils/plot.draw_scalebar() is only dependent of pyproj and independent of both basemap and cartopy. Another benefit is that, it allows plotting scalebar all the time without cartopy. This allows the adaptive lat/lon label when zooming and panning, when --lalo-label is not enabled. * Update plot.py * Update colors.py * Update view.py Co-authored-by: Zhang Yunjun <yunjunzgeo@gmail.com> | 04 February 2020, 01:23:26 UTC |
| a7bc68f | rzinke | 10 January 2020, 04:28:41 UTC | Added geos and basemap as conda packages to conda_env.yml (#262) * Added basemap to conda_env.yml file and removed pip install basemap. These modifications intended to fix problems with pip finding geos libs. * add basemap to conda.txt * update installation.md with basemap from conda | 10 January 2020, 04:28:41 UTC |
| 67577b6 | Zhang Yunjun | 08 January 2020, 05:37:44 UTC | adjust cmy to green in center + adjust cmy colormap to be green in the center and orange for positive value by default. + update colormap file url + bugs fix + suppress matplotlib user warning in plot_network.py | 08 January 2020, 21:04:25 UTC |
| 3536098 | Zhang Yunjun | 08 January 2020, 01:54:15 UTC | add cyclic colormap - cmy | 08 January 2020, 05:35:27 UTC |
| 867b73a | Zhang Yunjun | 08 January 2020, 01:29:26 UTC | tropo_pyaps3: support delay calculation without ref_y/x diff.py: support the second input file without REF_X/Y info tropo_pyaps3.py: + change ref_y/x info optional for delay calculation. + add 'REF_DATE' to the delay file + rename 'trop_*' to 'tropo_*' for better readability. fractal.py: slight improvement on the speed. | 08 January 2020, 05:35:27 UTC |
| 52727ec | Zhang Yunjun | 07 January 2020, 02:01:52 UTC | prep_isce: use az/rgResolution from S1 product definition replace the previous hardwired S1 spaital resolution value with the value from the product definition, which results in a rg/az_fact value larger than 1. | 08 January 2020, 05:35:27 UTC |
| 1105593 | Zhang Yunjun | 06 January 2020, 06:42:19 UTC | auto fig title: keep binary file ext plot.auto_figure_title(): for binary file (non HDF5 file), use the full basename of input file, including the file extension, as the default output figure name, in order to better support isce binary file plotting. | 08 January 2020, 05:35:27 UTC |
| 8189ad1 | Zhang Yunjun | 06 January 2020, 03:12:48 UTC | readfile: easy read int/magnitude + support reading the magnitude of .int file through datasetName + more generic band1/2/3... in get_slice_list() + respect UNIT grab from manually input datasetName more than the existing UNIT metadata | 08 January 2020, 05:35:27 UTC |
| d2173b0 | Zhang Yunjun | 03 January 2020, 07:20:21 UTC | fractal: adaptive p0 scaling factor adapt p0 value internally instead of the previously fixed scale value so that the input p0 is equal to C0 from the check_power_spectrum(). check_power_spectrum_1d() use the square part of the input data with dimension as a power of 2, for more robust performance. | 04 January 2020, 01:08:35 UTC |
| d0259da | Zhang Yunjun | 01 January 2020, 01:23:55 UTC | update module dependency graph + update module dependency graph in mintpy/__init__.py + remove duplicated mintpy/utils/variance.py and keep mintpy/simulation/variance.py + reduce the dependency level for the following modules by using utils0/1 and coord directly instead of using utils + utils/utils1.py: add get_residual_spectral_power_density() + version: update from beta verion to stable release | 04 January 2020, 01:08:35 UTC |
| fd14b11 | Zhang Yunjun | 01 January 2020, 01:19:51 UTC | fractal: add crop_data_max_square() + handling input data with shape in odd number + use the portion with least zero values | 04 January 2020, 01:08:35 UTC |
| 2215dea | Zhang Yunjun | 31 December 2019, 02:12:17 UTC | smallbaselineApp: ignore no-data pixels in lat/lon while generating waterMask.h5 + update function comments in simulation modules | 04 January 2020, 01:08:35 UTC |
| f8fed62 | Zhang Yunjun | 31 December 2019, 21:57:06 UTC | init simulation/decorrelation.py (#256) * init simulation/decorrelation.py + merge all decorrelation noise related functions from ifgram_inversion.py and simulation/simulation.py into a level1 sub-module simulation/decorrelation.py + rename simulation/forward_model.py as simulation/defo_model.py and move mogi_deformation() from simulation.py to defo_model.py + update related __init__.py and README.md files | 31 December 2019, 21:57:06 UTC |
| 3741154 | Zhang Yunjun | 27 December 2019, 09:52:50 UTC | fix bugs/warnings found by Codacy | 27 December 2019, 20:59:02 UTC |
| 3fbc3bb | Zhang Yunjun | 20 December 2019, 02:25:46 UTC | update copyright year update copyright year to 2013 as the earliest available date remove obsolete legacy/tsview_dev_yunjun.py more the following unused scripts to `mintpy/objects/insarStack`: + insarPair.py + insarStack.py + loadData.py + reader.py | 27 December 2019, 20:59:02 UTC |
| 0a47226 | Zhang Yunjun | 27 December 2019, 06:39:32 UTC | more robust coherence2variance calculation (#254) ifgram_inversion.py * bug fix for variance calculation while coherence is very close to 1 * handle all negative var in ifginv.phase_variance_ds() prep_isce.py: * calculate NCORRLOOKS from isce products * prep_isce: return warning message when no baseline file found * install basemap from native macport | 27 December 2019, 06:39:32 UTC |
| e83c09a | Zhang Yunjun | 19 December 2019, 02:49:12 UTC | replace zip command with zipfile module (#252) * replace zip command with zipfile module | 19 December 2019, 02:49:12 UTC |
| 0f6c3e1 | Zhang Yunjun | 05 December 2019, 02:55:41 UTC | save_kmz: add --cbar-loc option + add --cbar-loc option to modify the location of colorbar screen overlay + fix the not working issue of --cbar-bin-num and --cbar-label + remove the obsolete --cbar-height option | 05 December 2019, 05:30:59 UTC |
| b38a59c | Zhang Yunjun | 04 December 2019, 22:56:00 UTC | check/update reference point in asc_desc2horz_vert.py (#248) * check reference point and raise exception if the input files have different reference point. * remove obsolete 0 from np.array.flatten() * update REF_X/Y based on the REF_LAT/LON value | 04 December 2019, 22:56:00 UTC |
| 4193199 | Zhang Yunjun | 03 December 2019, 01:27:42 UTC | prep_aria: constain X/Y_STEP/FIRST as a 9 digits float to fix the potentially very slight inconsistency between the spatial resolution (posting size) between different ARIA GUNW products | 03 December 2019, 01:38:34 UTC |
| cd555fa | Zhang Yunjun | 02 December 2019, 22:33:09 UTC | support read/plot magnitude of .int file 1. objects.timeseries.get_design_matrix4average_velocity(): add optional refDate argument to specify the reference date 2. simulation.sample_decorrelation_phase(): more robust argument checking 3. utils.readfile.read_binary_file(): support reading (and plotting) magnitude of .int file | 03 December 2019, 01:38:34 UTC |
| 520b0ed | Zhang Yunjun | 27 November 2019, 20:03:48 UTC | utils.readfile: support 3 and 4 bands in binary files | 27 November 2019, 21:20:15 UTC |
| 9e6b1be | yunjunz | 27 November 2019, 00:28:52 UTC | support loading geometry only | 27 November 2019, 21:20:15 UTC |
| 7ce1392 | Zhang Yunjun | 26 November 2019, 05:31:00 UTC | update port to support ARIA-tools | 27 November 2019, 21:20:15 UTC |
| 0a861ac | Zhang Yunjun | 20 November 2019, 03:18:02 UTC | update conda install for basemap use the release version instead of git clone for faster install and smaller download, both in command line and conda_env.yml | 22 November 2019, 04:34:19 UTC |
| be4e50b | Zhang Yunjun | 04 November 2019, 02:40:25 UTC | update install via macports docs/ports.txt: 1. switch to +gcc7 except for atlas, which supports gcc5 only 2. switch default python from 3.6 to 3.7 3. remove hdf4 docs/installation.md: 1. use released archive of basemap from github, faster and smaller than git clone 2. use 'sudo -H' to solve the directory ownership issue. typo fixes Update default test directory in test_smallbaselineApp.py | 19 November 2019, 22:06:40 UTC |
| 022d08d | ehavazli | 19 November 2019, 21:10:19 UTC | plot.plot_gps: remove whitespace in site ID while saving to CSV (#243) change from column name 'Site ID' to 'SiteID' in GPSSitesVel.csv file. | 19 November 2019, 21:10:19 UTC |
| 14573cb | piyushrpt | 18 November 2019, 18:40:02 UTC | Save time-series in QGIS compatible format (#242) Adds support to export MintPy time-series in a QGIS ps-time-series plugin compatible shapefile format - https://plugins.qgis.org/plugins/pstimeseries/. Thanks @yunjunz for help with figuring out the directory structure. | 18 November 2019, 18:40:02 UTC |
| 990ad31 | Zhang Yunjun | 04 November 2019, 02:40:25 UTC | utils function for GSI F3 GPS daily solution (#239) utils/ptime: add yy2yyyy() objects/gps: + add read_pos_file() to read GSI F3 GPS solution generated by Bernese + add get_pos_years() to faciliate the file searching + add read_GSI_F3() as the generic reading function to extract info for specific GPS site with start/end_date sh/plot_smallbaselineApp.sh: copy *.txt file to pic folder | 04 November 2019, 02:40:25 UTC |
| d03fd45 | Zhang Yunjun | 03 November 2019, 19:02:30 UTC | copy cfg files to pic folder (#238) copy default/custom template files to inputs/pic folders for easy backup. more detailed info for the paper. | 03 November 2019, 19:02:30 UTC |
| d91e9e7 | ehavazli | 21 October 2019, 20:06:41 UTC | Write GPS LOS velocities to CSV file (#236) * write GPS velocities into a CSV file while plotting both InSAR and GPS velocities * return nan from GPS().get_gps_los_velocity() if no data | 21 October 2019, 20:06:40 UTC |
| 1f1e763 | Zhang Yunjun | 19 October 2019, 19:06:12 UTC | bugs fix for insar_vs_gps() | 19 October 2019, 19:11:37 UTC |
