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Changelog

0.42.0 - 2025-08-19

Added

Changed

  • Update workflow defaults for larger half-window and nearest-3 (#634)

Fixed

  • Fixed JAX CRLB outputs for singular matrix cases
  • Updated docs/sample_dolphin_config.yaml for newer structure
  • Fix defaults in dolphin config CLI for interferogram_network settings (#636)

0.41.0 - 2025-08-11

Added

  • stitching.py: Add support for specifying output projection by @scottstanie in #607
  • Added Cramér–Rao lower bound (CRLB) estimation output to phase linking results by @scottstanie in #577
  • Add UAVSAR_WAVELENGTH to constants by @scottstanie in #620
  • Add sequential closure phase rasters to phase linking output by @scottstanie in #618
  • Add apply_mask_to_timeseries to set masked pixels to nodata in outputs by @scottstanie in #627
  • Stitch and output all per-ministack temporal_coherence_ and similarity_ files by @scottstanie in #615

Changed

  • Fix numerical issues with CRLB calculation by @scottstanie in #626

Fixed

  • Fix hardcoded port 5000 for moto tests by @scottstanie in #617
  • masking.py: Raise MaskingError after creating an empty mask by @scottstanie in #619

0.40.0 - 2025-06-30

Added

  • Added Cramér-Rao Lower Bound (CRLB) estimate rasters in https://github.com/isce-framework/dolphin/pull/577

0.40.0 - 2025-06-

Fixed

  • Throw a better error for dolphin without any args

Changed

  • Remove avg_coh from optional phase linking outputs
  • unwrap.py: Combine sliding window mask with similarity mask for masking / interpolation

0.39.0 - 2025-06-09

Largest visible change: Switch CLI to use tyro by @scottstanie in https://github.com/isce-framework/dolphin/pull/578 This involves multiple fixes and some breaking changes:

  • Fixed
  • Missing arguments that were not configurable via the command line
  • dolphin unwrap and dolphin timesries has several issues resulting from the function API being out of sync with the argparse API
  • config Changes:
  • Strides must be specified as --sx 6 --sy 3, not --strides 6 3
  • Several worker settings options like --threads-per-worker are not longer top-level command line options; you can specify them with --worker-settings.threads-per-worker

Added

  • Parallelize phase linking for single-swath case in single.py by @scottstanie in https://github.com/isce-framework/dolphin/pull/576
  • DOC: Add phase linking theory notebook to docs by @scottstanie in https://github.com/isce-framework/dolphin/pull/597
  • Add Github link to docs by @scottstanie in https://github.com/isce-framework/dolphin/pull/575
  • Add script to read GAMMA .rslc binary SLCs by @scottstanie in https://github.com/isce-framework/dolphin/pull/569
  • Add keep_bits to BackgroundBlockWriter API so writers can round_mantissa by @scottstanie in https://github.com/isce-framework/dolphin/pull/536

Changed

  • Make reference optional for velocity fitting by @scottstanie in https://github.com/isce-framework/dolphin/pull/571
  • Allow Iterator[Filename] to all readers with .from_file_list by @scottstanie in https://github.com/isce-framework/dolphin/pull/579
  • Fix to be Iterable, not Iterator API change for _readers from #579 by @scottstanie in https://github.com/isce-framework/dolphin/pull/582
  • Simplify reference index logic for ALWAYS_FIRST in stack.py, cut FIRST_PER_MINISTACK by @scottstanie in https://github.com/isce-framework/dolphin/pull/588
  • Remove single-burst special case in phase linking outputs by @scottstanie in https://github.com/isce-framework/dolphin/pull/574
  • Add fmt=file_date_fmt to all get_dates call to avoid file format assumptions by @scottstanie in https://github.com/isce-framework/dolphin/pull/585

Fixed

  • Run fix_typos.sh on repo by @scottstanie in https://github.com/isce-framework/dolphin/pull/572
  • Remove per-burst phase linking dirs that are empty by @scottstanie in https://github.com/isce-framework/dolphin/pull/595
  • stitching.py: fix strides check for either x or y by @scottstanie in https://github.com/isce-framework/dolphin/pull/596
  • Pass through timeseries_options.reference_point during displacement.py workflow by @scottstanie in https://github.com/isce-framework/dolphin/pull/602
  • unwrapping.py: fix comparison to avoid mask warping by @scottstanie in https://github.com/isce-framework/dolphin/pull/600

Removed

  • Remove unused _utils helper functions by @scottstanie in https://github.com/isce-framework/dolphin/pull/581
  • OutputOptions: Only require bounds_epsg if specifying bounds, cut resolution by @scottstanie in https://github.com/isce-framework/dolphin/pull/591
  • Remove old glrt_cutoffs.csv from MANIFEST.in by @scottstanie in https://github.com/isce-framework/dolphin/pull/573

0.38.0 - 2025-04-15

Added

  • demo-filtering-sizes.ipynb for high-pass filtering cutoff demo by @scottstanie in https://github.com/isce-framework/dolphin/pull/561

Changed

  • Breaking change: Split corrections, remove raider pulled modules by @scottstanie in https://github.com/isce-framework/dolphin/pull/531

Fixed

  • Use is_symlink when checking for existing scratch files in spurt by @scottstanie in https://github.com/isce-framework/dolphin/pull/568

0.37.0 - 2025-03-27

Changed

  • filtering.py: Change default sigma calculation, add docstring explanation by @scottstanie in https://github.com/isce-framework/dolphin/pull/560

0.36.2 - 2025-03-25

Fixed

  • Update notebook walkthrough for new output structure by @scottstanie in https://github.com/isce-framework/dolphin/pull/558
  • Adding subdataset as input arguments because it is different for S1 and NISAR by @mirzaees in https://github.com/isce-framework/dolphin/pull/559

0.36.1 - 2025-03-06

Fixed

  • Fix ionosphere reading and delay computation by @scottstanie in https://github.com/isce-framework/dolphin/pull/554
  • Let amp_dispersion_threshold be 0 to select no PS points by @scottstanie in https://github.com/isce-framework/dolphin/pull/553
  • Move WriteArray calls after SetNoDataValue calls by @scottstanie in https://github.com/isce-framework/dolphin/pull/555

Added

  • Add nisar wavelengths to constants by @mirzaees in https://github.com/isce-framework/dolphin/pull/551

0.36.0 - 2025-02-21

Added

  • utils.grow_nodata_region to remove bad borders from images

Changed

  • timeseries.py: Auto reference point selection
  • Picks the center of mass instead of arbitrary argmax result
  • Rename condition_file to quality_file
  • Convert glrt SHP method to use JAX instead of Numba
  • Remove import for goldstein and filtering from top level __init_.py

Removed

  • Removed condition parameter in timeseries reference point functions
  • Removed CallFunc enum

Fixed

  • docs: Fix mathjax render, fix broken DateOrDatetime error
  • Replace __name__ with "dolphin" in getLogger to fix missing log entries from .jsonl log files
  • Used utils.grow_nodata_region to remove bad borders from shp_counts.tif

0.35.1 - 2025-01-15

Fixed

  • filtering.py Fix in_bounds_pixels masking, set default to 25 km
  • Set output_reference_idx separately from compressed_reference_idx during phase linking setup

0.35.0 - 2025-01-09

Added

  • Compute timeseries inversion and save to rasters
  • use_seasonal_coherence parameter to simulate.py

Changed

  • keepdims options to reader classes to avoid squeezing singleton dims
  • Using L1 inversion by default for timeseries
  • Using most recent compressed SLC as output for LAST_PER_MINISTACK
  • Adapted short wavelength filter to use gdal_fillnodata for edge effects mitigation
  • Removed Numba dependency from simulate.py

Fixed

  • Documentation grammar on VRT size check

0.34.0 - 2024-11-26

Added

  • --use-evd option to dolphin config CLI
  • CITATION.cff file for better zenodo parsing

Changed

  • Spurt changes
  • Logging redirect, add a log file, multiprocess during final interpolation
  • Improved speed of post-spurt 2-pi ambiguity interpolation
  • Default ministack_size changed to 15 in PhaseLinkingOptions
  • Using nearest sampling for stitching static layers

Fixed

  • Unit string written to velocity.tif
  • extra_reference_date logic for single reference unwrapping
  • Missing annotations for Python 3.9 compatibility
  • Pinned mkdocs-jupyter to 0.25.0
  • Make --condition-file not required for dolphin timeseries
  • Removed .flake8

0.33.0 - 2024-11-07

Added

  • fill_value parameter to filter_long_wavelength
  • Function to create counts of valid unwrapped outputs (create_nonzero_conncomp_counts)

Changed

  • Modified logging capture from spurt to be more selective

0.32.0 - 2024-11-05

Fixed

  • Merge documentation improvements from joss branch
  • Add a retry to spurt for BrokenProcessPools

0.31 - 2024-11-03

Changed

  • Skip nodata values of interferograms when interpolating

0.30 - 2024-11-01

Added

  • Support for specifying output bounds as WKT
  • Ability to calculate similarity using nearest-3 interferograms
  • Add configuration option for single tile reoptimize functionality for snaphu-py. Turn off by default.
  • Support for layover shadow mask files to mask pixels during wrapped phase
  • Zero correlation threshold parameter for phase linking
  • Censored least squares solving capability for missing data
  • Support for reading from S3 using osgeo.gdal with /vsis3 conversion

Changed

  • Updated dolphin timeseries CLI for new options, using L1 by default
  • Increased spurt max_tiles default to 49 for smaller MCF problems
  • Modified compressed_reference_idx with relative index fix
  • Replaced CSVs with chi2.ppf for GLRT test
  • Lowered min_conncomp_frac default to 0.001
  • Using output_reference_idx as default for creating compressed SLCs with ALWAYS_FIRST
  • Increased buffer_pixels when making OPERA CSLC mask
  • Refactored repack_raster to work in blocks for lower memory usage

Fixed

  • Fixed ministack output and compressed SLC indexing
  • Fixed in_trim_slice size for non-overlapping blocks
  • Fixed units passthrough during timeseries._redo_reference
  • Improved spurt subprocess handling to avoid fork issues
  • Fixed block_shape passthrough to create_similarities after phase linking

0.29.0 - 2024-10-14

Added

  • Sample dolphin_config.yaml to the documentation
  • Stitched phase cosine similarity raster to outputs
  • Post-processing step to fill NaN gaps after running spurt
  • Outside input range options to get_nearest_date_idx

Changed

  • Set EVD input to be weighted by correlation
  • Using dataclasses instead of NamedTuple for displacement and stitched outputs
  • Passing through phase_linking.output_reference_idx to avoid reference resets

Fixed

  • Added logic to reset extra_reference_date after network unwrapping
  • Applied nan/0 mask to output of goldstein filter
  • Added references/url fixes from JOSS branch

0.28.0 - 2024-09-19

Added

  • num_parallel_tiles and num_parallel_ifgs to SpurtOptions
  • L1-norm-based inversion to timeseries
  • Config option to avoid PS pixels during phase linking
  • block_shape to timeseries parameters
  • wavelength attribute to workflow to convert rasters to meters
  • Larger N rows to computed GLRT cutoffs
  • Logic for manually specifying reference dates mid-stack
  • ADMM to minimize L1-norm of Ax - b
  • Instructions for building Docker image in documentation
  • Link to notebook in simulate-demo function
  • Printing of unwrapping options in show_versions
  • Update walkthrough notebook for docs
  • Add clarifications and suggested changes to documentation

Changed

  • Remove transposed versions of functions in covariance
  • Set use_slc_amp default to False during phase linking
  • Use the same mask for unwrapping and conncomp regrowing steps
  • Turn off correlation weighting for velocity by default
  • Use less memory for L1 inversion
  • Include layover shadow mask when stitching in prepare_geometry
  • Create .conncomp files for spurt from temporal coherence
  • Add like_filename for spurt connected components

Fixed

  • Fix plotting/imports for walkthrough
  • Fix displacement.run to avoid troposphere computation with empty list
  • Pass through EPSG code to _get_mask
  • Fix n_parallel_tiles to be an integer, not float
  • Skip combine_mask_files if the output already exists
  • Fix typos in walkthrough configuration
  • Fix simulate-demo function usage
  • Fix mismatching docs and missing log statements
  • Pass through add_overviews, run even if single-reference network
  • Add ignore_errors=True to rmtree for scratch removal
  • Setup gaussian_filter_nan in utils, use in estimate_correlation_from_phase
  • Fix Apache end template
  • Fix ionospheric date parsing and grouping
  • Fix handling of nodata during timeseries conversion to meters

0.27.1 - 2024-08-12

Changed

  • Set the default input_conventions to be same as output_conventions

0.27.0 - 2024-08-12

Added

  • Ability to mask a subset of input SLCs

Changed

  • Temporarily removed resampling during stitching final crop

0.26.0 - 2024-08-02

Added

  • map option for DummyProcessPoolExecutor
  • PR template
  • dolphin filter CLI to run a long wavelength filter on a set of rasters

Changed

  • Changed datetime format for reading tropospheric corrections
  • Copy over unwrapped to timeseries/ even with 1 file
  • Removed atmosphere imports from the main path

0.25.0 - 2024-08-01

Changed

  • Moved reference point selection back to always be run if not specified
  • Reference correction outputs to a point in space and convert to meters

Fixed

  • Fixed timeseries to mkdir right away

0.24.0 - 2024-08-01

Added

  • Skip correlation estimate for files that exist
  • Save ReferencePoint into file in timeseries/ folder

Changed

  • Clip nlooks to a max of 20 for whirlwind
  • Refactor filter_long_wavelength to avoid boundary issues for images with lots of no data region
  • Skip zero raster output by timeseries inversions

Fixed

  • Fixed reference point selection labels

0.23.0 - 2024-07-29

Added

  • whirlwind unwrapper
  • Option to redirect other loggers to same JSON file
  • Interleave GTiffs by band, not pixel

Changed

  • Updated show_versions to read importlib.metadata, use keep_bits instead of lerc
  • Made network formation staticmethods public
  • Shrunk nlooks for whirlwind
  • Improved code for transferring unwrapped phase ambiguities
  • Moved mask loading function into masking.py

Fixed

  • Fixed Spurt tests
  • Updated spurt imports for exported interface
  • Set the final_arr nodata to be same as original ifg mask
  • Fixed filtering ambiguity transfer for interp/goldstein
  • Fixed confusing name for scratchdirs

0.22.1 - 2024-07-17

Fixed

  • Fixed v0.22.0 imports

0.22.0 - 2024-07-16

Added

  • Output velocities in units per year in timeseries

Changed

  • Minor changes in spurt config to match its naming conventions
  • Vendored mdx_bib to avoid direct URL in docs/requirements.txt

0.21.0 2024-07-16

Added

  • Continuous deployment Github action workflow to publish to pypi
  • Conversion from NetCDF tropospheric correction files

Changed

  • Round mantissa bits instead of truncate, call the argument keep_bits for clarity

0.20.0 - 2027-07-08

Added

  • Functions in ps to combine amplitude dispersions from older rasters
  • truncate_mantissa option to repack functions for simple compression
  • band option to write_block and background writers
  • Option to run merge_dates and estimate_interferometric_correlations with thread_map for parallel processing
  • Baseline lag option for "STBAS" phase linking inversion

Changed

  • Logging now uses dictConfig and always logs JSON to a file for the Displacement workflow
  • Set modulus of compressed SLCs to be real SLC magnitude means
  • Updated Docker requirements and specfile
  • Delete intermediate unwrapping scratchdirs by default

Fixed

  • use_max_ps would occasionally fail with certain stride/window configurations
  • Unwrapped phase files did not always contain the right geographic metadata
  • Filenames in the timeseries/ folder were wrong
  • Set upsampled boundary to nan in compress
  • Unwrapped file output path

0.19.0 - 2024-06-21

Added

  • filtering module for filtering out long wavelength signals from the unwrapped phase
  • baseline module for computing the perpendicular baseline. Initial version has logic for OPERA CSLCs, uses isce3
  • Interface only for 3D unwrapping
  • Faster correlated noise simulation, along with 3d stack simulation with synthetic deformation
  • Added ability to read rasters on S3 using VRTStack object
  • Eigenvalue solver speedups of 3-9x
  • Initial version of 3D unwrapping using spurt

Removed

  • the KL-divergence SHP estimator has been removed. GLRT is recommended instead.

Fixed

  • reproject_bounds uses the rasterio version, which densifies points along edges for a more accurate bounding box
  • The output SHP rasters now output 0 if there was no valid input data
  • Logic for filling PS pixels, with and without setting the amplitudes to be the original SLC amplitudes
  • ReferencePointError during the displacement workflow now will fall back look only at the condition_file (i.e. choose the point with highest temporal coherence by default)

Changed

  • The configuration options for unwrapping have been refactored. Options unique to each unwrapper are grouped into subclasses.
  • Note that older dolphin_config.yaml files will error after this refactor.
  • Unweighted time series inversion will make one batch call, providing a large speedup over the vmap version for weighted least squares

0.18.0 - 2024-05-07

Added

  • dolphin timeseries command line tool for inverting unwrapped interferogram network and estimating velocity

Fixed

  • Parse the file names correctly to find compressed SLCs and read dates based on production file naming convention

0.17.0 - 2024-04-10

Added

  • Added Goldstein filtering for unwrapping
  • Added Interpolation for unwrapping
  • Added the regrow connected components for the modified phase
  • Added option to toggle off inversion
  • Added similarity module

Fixed

  • 3D readers would squeeze out a dimension for length one inputs (i.e. they would give an array with .ndim=2)
  • max_bandwidth config can now be 1 to specify only nearest neighbor interferograms.
  • Use the 'compressed' key term to find compressed slcs and regular slcs instead of number of dates in ionosphere
  • Consider the compressed SLCs have different naming convention with capital letters
  • Enforce consistency between jax and jaxlib
  • Disable corrections part of pytest, add one for timeseries

0.16.0 - 2024-03-03

Added

  • Added dolphin.timeseries module with basic functionality:
  • Invert a stack of unwrapped interferograms to a timeseries (using correlation weighting optionally)
  • Estimate a (weighted) linear velocity from a timeseries
  • Added inversion and velocity estimation as options to DisplacementWorkflow
  • Create DatasetStackWriter protocol, with BackgroundStackWriter implementation

Changed

  • Rename GdalWriter to BackgroundBlockWriter
  • Displacement workflow now also creates/returns a stitched, multi-looked version of the amplitude dispersion

Fixed

  • BackgroundRasterWriter was not creating the files necessary before writing
  • Allow user to specify more than one type of interferogram in Network configuration

0.15.3 - 2024-02-27

Changed

  • Return the output paths created by the ionosphere/troposphere modules to make it easier to use afterward

0.15.2 - 2024-02-27

Fixed

  • Fixes to ionosphere/troposphere correction in for DisplacementWorkflow and PsWorkflow
  • Correct the nodata value passed through to snaphu-py

0.15.1 - 2024-02-26

Fixed

  • PHASS now uses the Tophu wrapper to avoid isce3 inconsistencies between argument order

0.15.0 - 2024-02-16

Changed

  • Combine the nodata region with the mask_file to pass through to unwrappers
  • Update regions which are nodata in interferograms to be nodata in unwrapped phase
  • Use uint16 data type for connected component labels

Fixed

  • Intersection of nodata regions for SLC stack are now all set to nan during phase linking, avoiding 0 gaps between bursts

0.14.1 - 2024-02-15

Fixed

  • Changed snaphu-py tile defaults to avoid max secondary arcs error in #233
  • Fixed linalg.norm`` to be pixelwise inprocess_coherence_matrices` in #234

0.14.0 - 2024-02-13

Fixed

  • Temporal coherence and eigenvalue rasters were switched in their naming
  • Output a better estimator raster to see where we switched to EVD
  • Cap the max number of threads to the CPU count to avoid numba config errors

Changed

  • refactor temporal coherence calculation to use vmap
  • Allows us to start making a weighted temporal coherence metric
  • Turn off default beta=0.01 regularization now that CPL is in place
  • Removed InterferogramNetworkType from configuration.
  • You can add multiple types of network parameters and it includes all of them. Adding the name only decreased flexibility.

0.13.0 - 2024-02-09

Added

  • _overviews module, and workflow configuration to create overviews of the output stitched rasters
  • Configuration to use the snaphu-py wrapper, and drop using isce3.unwrap.snaphu

Fixed

  • Apply bounds even if only one image is passed to stitching (#210)
  • Allow take_looks to work with MaskedArrays without converting to np.ndarray

Dependencies

  • Move back to tqdm instead of using rich for progress bars.

0.12.0 - 2024-02-01

Added

  • Added DatasetWriter protocol
  • Added RasterWriter and BackgroundRasterWriter implementations of this protocol
  • Refactored phase linking
  • Covariance and EVD/MLE use jax
  • This combines the implementation of CPU/GPU, and removes the need for using pymp
  • Added utils.disable_gpu to stop the use ofr a GPU even if it's available

Changed

  • Internal module organization, including grouping IO modules into dolphin.io subpackage
  • Renamed io.Writer to io.GdalWriter to distinguish from RasterWriter
  • Removed the n_workers option from the configuration.
  • There is no more need to have two levels of parallelism (threads_per_worker and n_workers)
  • The name threads_per_worker is kept for consistency; it is still an accurate name for the multi-burst processing case.

Added

  • jax>=0.4.19
  • numpy=>1.23 (bump to minimum version that they're still supporting)
  • scipy>=1.9 (same reason)
  • numba>=0.54

Removed

  • pymp
  • cupy from optional GPU usage

0.11.0 - 2024-01-24

Added

  • Added ionospheric correction in dolphin.atmosphere.ionosphere
  • Included in DisplacementWorkflow if TEC files are provided

0.10.0 - 2024-01-22

Added

  • Create dolphin.unwrap subpackage to split out unwrapping calls, and post-processing modules.

Removed

  • the _dates module has been removed in favor of using opera_utils._dates

Fixed

  • stitching.merge_images will now give consistent sizes for provided bounds when strides is given

0.9.0 - 2024-01-10

Added

  • DatasetReader and StackReader protocols for reading in data from different sources
  • DatasetReader is for reading in a single dataset, like one raster image.
  • StackReader is for reading in a stack of datasets, like a stack of SLCs.
  • Implementations of these have been done for flat binary files (BinaryReader), HDF5 files (HDF5Reader), and GDAL rasters (RasterReader).

Changed

  • The VRTStack no longer has an .iter_blocks method
  • This has been replaced with creating an EagerLoader directly and passing it to the reader argument

Dependencies

  • Added rasterio>=1.3

0.8.0 - 2024-01-05

Added

  • Ability to unwrap interferograms with the snaphu-py (not a required dependency)
  • Added ability to make annual ifgs in Network
  • Start of tropospheric correction support in dolphin.atmosphere using PyAPS and Raider packages
  • Expose the unwrap skipping with dolphin config --no-unwrap

Changed

  • The output directory for interferograms is now just "interferograms/" instead of "interferograms/stiched"
  • Even when stitching, the burst-wise interferograms would be in the named phase-linking subfolders.
  • Split apart the dolphin.workflows.stitch_and_unwrap module into stitching_bursts and unwrapping
  • Switched output filename from tcorr to temporal_coherence for the temporal coherence of phase linking.
  • Also added the date span to the temporal_coherence output name
  • The default extension for conncomps is now .tif. Use geotiffs instead of ENVI format for connected components.
  • Using ruff instead of pydocstyle due to archived repo

0.7.0 - 2023-11-29

Added

  • MiniStackPlanner and MiniStackInfo class which does the planning for how a large stack of SLCs will be processed in batches.
  • Previously this was done at run time in sequential.py. We want to separate that out to view the plan in advance/allow us to dispatch the work to multiple machines.
  • CompressedSlcInfo class added to track the attributes of a compressed SLC file created during the workflow.
  • This has the reference_date as an attribute, which allows us to know what the base phase is even without starting from the first SLC in the stack (i.e. if we have limited the number of compressed SLCs)
  • Added better/more complete metadata to the compressed SLC Geotiff tags, including the phase reference date
  • Before we were relying on the filename convention, which was not enough information
  • config: phase_linking.max_compressed_slcs to cap the number of compressed SLCs added during large-stack sequential workflows
  • interferogram: Add ability to specify manual dates for a Network/VRTInterferogram, which lets us re-interfere the phase-linking results

Changed

  • Date functions have been moved from dolphin.utils to dolphin._dates. They are accessible at dolphin.get_dates, etc
  • get_dates now uses datetime.datetime instead of datetime.date.
  • This is to allow for more flexibility in the date parsing, and to allow for the use of datetime.date or datetime.datetime in the output filenames.
  • VRTStack has been moved to _readers.py. The minstack planning functions have been removed to focus the class on just reading input GDAL rasters.

Fixed

  • When starting with Compressed SLCs in the list of input SLCs, the workflows will now recognize them, find the correct reference date, and form all the correct interferograms

Removed

  • Extra subsetting functions from VRTStack have been removed, as they are not used in the workflow and the reimplmenent simple GDAL calls.
  • CPURecorder and GPURecorder have been removed to simplify code. May be moved to separate repo.

0.6.1 - 2023-11-13

Removed

  • dolphin.opera_utils now lives in the separate package

Dependencies

  • Added opera_utils

0.6.0 - 2023-11-07

Added

  • opera_utils.get_missing_data_options to parse the full list of SLCs and return possible subsets which have the same dates used for all Burst IDs
  • PsWorkflow class for running just the PS estimation workflow
  • asv benchmark setup to measure runtime across versions
  • @atomic_output decorator for long running write processes, to avoid partially-written output files

Changed

  • removed minimum_images as an argument from opera_utils.group_by_burst. Checking for too-few images now must be done by the caller
  • opera_utils.group_by_burst now matches the official product name more robustly, but still returns the lowered version of the burst ID.
  • The s1_disp workflow has been renamed to displacement, since it is not specific to Sentinel-1.
  • The configuration was refactored to enable smaller workflow
  • The Workflow config class has been renamed to DisplacementWorkflow.
  • A PsWorkflow config class has been added for the PS estimation workflow.
  • A WorkflowBase encompasses some of the common configuration options.

Maintenance

  • ruff has replaced isort/black/flake8 in the pre-commit checks

0.5.1 - 2023-10-10

Added

  • stitch_and_unwrap.run returns the stitch PS mask

0.5.0 - 2023-10-09

Added

  • CPURecorder class for fine grained benchmarking of the CPU/memory usage for

Changed

  • Docker specfile now builds with tophu

0.4.3 - 2023-10-06

Added

  • Ability to unwrap using isce3's PHASS
  • CorrectionOptions model for specifying the correction options in the Workflow config
  • Currently a placeholder for the files which will be used for tropospheric/ionospheric corrections
  • Ability to keep relative files in the Workflow config
  • This is useful for keeping the relative paths to the SLCs in the config, and then running the workflow from a different directory

Changed

  • Instead of specifying the unwrapping algorithm in dolphin unwrap as --use-icu, the option is not --unwrap-method
  • This let's us add --unwrap-method "phass", but also future unwrap methods without a --use-<name> for every one
  • Use spawn instead of fork for parallel burst multiprocessing
  • This leads to the error Terminating: fork() called from a process already using GNU OpenMP, this is unsafe. in certain situations, and does not happen with spawn. See https://pythonspeed.com/articles/python-multiprocessing/ for more details.

0.4.2 - 2023-10-03

Added

  • use_evd option to force the use of eigenvalue decomposition instead of the EMI phase linking algorithm
  • Walkthrough tutorial notebook

Changed

  • Moved all OPERA_ variables to a new module dolphin.opera_utils.
  • Other OPERA-specific quirks have been moved to the separate disp-s1 repo, but the functions remaining are the ones that seem most broadly useful to sweets and other users working with burst SLCs.
  • Changed the burst regex to be able to match COMPASS and the official product name
  • Removed WorkflowName for separating stack vs single
  • The name didn't really provide benefit, as the real differences cam from other configuration options
  • Internals for which functions are called in sequential.py
  • Docker image now has tophu installed

0.4.1 - 2023-09-08

Dependencies

  • Added back isce3

0.4.0 - 2023-09-07

Changed

  • Split apart OPERA-specific needs from more general library/workflow functionality
  • Removed the final NetCDF product creation
  • Many rasters in the scratch/ folder are of general interest after running the workflow
  • Changed folder structure so that there's not longer a top-level scratch/ and output/ by default
  • Changed the required dependencies so the isce3 unwrapper is optional, as people may wish to implement their own custom parallel unwrapping

Dependencies

Dropped: - h5netcdf - pillow

Now optional: - isce3 (for unwrapping)

0.3.0 - 2023-08-23

Added

  • Save a multilooked version of the PS mask for output inspection

Changed

  • Pydantic models were upgraded to V2
  • Refactored the blockwise IO into _blocks.py.
  • The iteration now happens over the output grid for easier dilating/padding when using strides
  • New classes with BlockIndices and BlockManager for easier management of the different slices

Dependencies

  • pydantic >= 2.1

0.2.0 - 2023-07-25

Added

  • For OPERA CSLC inputs, we now read the nodata polygon and skip loading regions of the SLC stack which are all nodata.
  • This led to a reduction of 30-50% in wrapped phase estimation runtime for each burst stack.
  • Sample test data for the dolphin package loaded onto Zenodo.
  • Adds 3 methods of computing a variable statistically homogeneous pixel (SHP) window when estimating the covariance matrix:
  • Kolmogorov-Smirnov test (KS-test)
  • Generalized likelihood ratio test (GLRT)
  • Kullback-Leibler divergence/distance test (KLD)
  • "rect" is also an option for skipping any statistical test and using the full rectangular multilook window
  • Also included a script to view the window in an interactive matplotlib figure (matplotlib must be installed separately)
  • Added a simple method to check for adjacent-pixel unwrapping errors in unwrap.compute_phase_diffs
  • Adds a method utils.get_cpu_count which returns either os.cpu_count, or (if running in a Docker container) the number of CPUs allocated by Docker
  • If processing stacks from separate bursts, added option n_parallel_bursts to Workflow to run in parallel processes.
  • Created a script to test the incremental/near-real-time version of phase linking
  • Added a new CLI command dolphin unwrap to unwrap a single interferogram/a directory of interferograms in parallel.
  • Added ability to specify a glob pattern for input CSLC files in the YAML config
  • Saves a multilooked PS mask for the default workflow output
  • Allows the user to specify a desired bounds for the final stitched result

Changes

  • Default OPERA dataset is now within /data, reflecting the new COMPASS product spec since CalVal
  • Passing an existing file to VRTStack will no longer error unless fail_on_overwrite=True. The default just prints out the overwrite is happening. This prevents multiple runs in the same folder from errorings just for creating a reference to the SLC files.
  • The environment variable NUMBA_NUM_THREADS is set using the passed in config to prevent numba from using all CPUs during prange calls
  • The sequential.py module uses a different implementation of the sequential estimator to avoid the need for a datum adjustment.
  • The scratch directory holding unwrapped interferograms is named unwrapped instead of unwrap
  • Stitching files now can accept downsampled versions and product the correct geo metadata

Fixed

  • Calculating the nodata mask using the correct input geotransform
  • Trims the overlapped region of the phase linking step when iterating in blocks

Dependencies

  • shapely >= 1.8
  • Numba now supports Python 3.11, so we can drop the Python<3.11 version restriction.

Added testing requirements: - pooch - pillow>=7.0

0.1.0 - 2023-03-31

  • First version of the _product.py module to output the combined NetCDF product file.
  • _pge_runconfig.py module to handle the separate PGE-compatible configuration, which translates to-from the Workflow object.
  • docker/build-docker-image.sh script to build the docker image.
  • Release scripts for generating documentation, script for validating output data by @gmgunter .
  • Use of a spatial correlation estimate for unwrapping purposes, rather than temporal coherence.
  • This is much more useful when the stack size is small (high temporal coherence), and snaphu is used for unwrapping.
  • masking.py module for masking the interferogram/combined multiple external masks of varying 1/0 conventions.
  • Ability to use existing amplitude mean/dispersion files for the PS portion of the workflow, skipping the step where we compute it using the SLC stack. Useful for small stack sizes
  • Added a create_only option to write_arr to create an empty file without writing data (e.g. to check the boundary results of stitching)

Changed

  • The YAML output/input functions are moved to a YamlModel class, which is a subclass of pydantic.BaseModel.
  • This allows us to use it in both config.py and _pge_runconfig.py.
  • Refactoring of the Workflow layout to more easily extract the input/output files for the PGE run.

Fixed

  • Compressed SLC outputs were getting corrupted upon writing when using strides > 1.
  • Single-update interferograms where the first SLC input is a compressed SLC was broken (using the wrong size raster).
  • Now the result will simply copy over the phase-linking result, which is already referenced to the first raster.

Dependencies

Added requirements:

  • h5netcdf>=1.1
  • Avoid HDF5 version 1.12.1 until NetCDF loading issue is fixed

0.0.4 - 2023-03-17

Added

  • Created first version of the single-update workflow, usable with dolphin config --single
  • _background.py module as the abstract classes for background input/output with EagerLoader and Writer.
  • from_vrt_file for the VRTInterferogram class.
  • Arbitrary interferogram index selection in Network class.
  • Parallel CPU eigenvector finding using scipy.linalg.eigh.
  • PS selection for strided outputs using the average PS phase within a window (that contains multiple PS).
  • Comments in the YAML file output by the dolphin config command.

Changed

  • The main workflow has been renamed to s1_disp.py to better reflect the workflow, since it can handle both single and stack workflows.
    • The sequential.py and single.py are where these differences are handled.
  • More uniform naming in io.get_raster_<X> functions.
  • The SLC compression is now done in _compress.py to declutter the mle.py module.
  • Replace tqdm with rich for progress bars.

  • The unwrap.py module now uses isce3 to unwrap the interferogram.

  • Docs are now using the mkdocs material theme.

Removed

  • utils.parse_slc_strings in favor of always using utils.get_dates.
  • io.get_stack_nodata_mask. This will be done using the nodata polygon, or not at all.

Dependencies

Added requirements:

  • rich>=12.0
  • threadpoolctl>=3.0
  • isce3>=0.8.0
  • pyproj>=3.3
  • Dropped support for Python 3.7

For docs: - mkdocs-material - pymdown-extensions

Removed requirements:

  • tqdm

0.0.3 - 2023-01-26

Added

  • Ability for VRTStack to handle HDF5 files with subdatasets.
    • The OPERA specific HDF5 files are now supported without extra configuration.
  • First stitching of interferograms in stitching.py.
    • Users can pass multiple SLC burst (like COMPASS bursts) per date, and the workflow will process per stack then stitch per date.
  • More features for load_gdal to load in blocks.

Changed

  • A small amount of regularization on the coherence matrix is done before inversion during phase linking to avoid singular matrices.
  • Renamed module to _log.py
  • workflows/wrapped_phase.py absorbed much logic formerly in s1_disp_stack.py.

0.0.2 - 2023-01-24

Added

  • Created first version of the s1_disp_stack.py workflow.
  • Created the modules necessary for first version of the sequential workflow, including
    • ps.py
    • sequential.py
    • io.py
    • interferogram.py
    • utils.py
    • unwrap.py
    • stitching.py
    • vrt.py
  • Created the phase_link subpackage for wrapped phase estimation.

Added requirements:

  • pyproj>=3.2
  • tqdm>=4.60

[0.0.1] - 2022-12-09

Added

  • Created the config module to handle the configuration of the workflows
  • Command line interface for running the workflows
  • Outline of project structure and utilities

Dependencies

Added requirements:

  • gdal>=3.3
  • h5py>=3.6
  • numba>=0.54
  • numpy>=1.20
  • pydantic>=1.10
  • pymp-pypi>=0.4.5
  • ruamel_yaml>=0.15
  • scipy>=1.5

Currently, Python 3.7 is supported, but 3.11 is not due numba not yet supporting Python 3.11.