merge with latest xdem #11
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* adding gradientdescending coreg Zhihao * Linting and formatting * Adding xdem_pts to latest xdem NuthKaab also supports points and DEM coregistration. This is an implement by Zhihao. * error * error * update * confilcts sloved * bands into indexes of DEM class * bands into indexes * bands into index * move from fit to fit_pts * remove history * remove useless * for test * for test 2 * Test run * Test the half-pixel problem * - Fixed the half-pixel shift problem by making the area_or_point setting constant. - Added fit() (Raster) functionality for GradientDescending. - Parameterized test to debug and extend it more easily. * Revert "Half-pixel shift fix and other improvements" * add gitignore * To geoutils 0.0.12 * To geoutils 0.0.12 * to geoutils 0.0.12 * to geoutils 0.0.12 * Delete .vscode directory * to geoutils 0.0.12 * to geoutils 0.0.12 * Linting --------- Co-authored-by: Erik Mannerfelt <33550973+erikmannerfelt@users.noreply.github.com> Co-authored-by: Romain Hugonnet <romain.hugonnet@gmail.com>
….VerticalShift` (#158) * rename BiasCorr into VerticalShift, refactor all sources and adapt documentation * add biascorr, draft along/across track classes * update doc and NuthKaab with new VerticalShift variable naming * move ZScaleCorr to TerrainBias, wrap Along and Across into DirectionalBias * refactor post-merge biascorr tests with vshift naming * refactor remaining biascorr in vshift * improve with erik comments * draft structure bias corr * finish biascorr structure + start tests * advancing bias corr * Remove spatial_tools import * Fix linting errors * Fix flake8 * Incremental fixes on tests * Incremental commit on bias correction classes * Incremental commit on biascorr * Incremental commit on biascorr * Fix subsampling and parameter unpacking * Homogenize func parameter ungrouping, fix binning and continue tests * Finalize first round of tests * Linting all but mypy * Incremental commit on biascorr tests * Finalize bias correction tests * Finalize last test * Linting (including mypy!) * Move richdem to pip to force install * Add future annotation import in test_biascorr * Add basic documentation page and refactor coreg.Deramp into coreg.Tilt * Linting * Try to circumvent richdem issues * Linting * Skip or ignore new terrain error, opening issue * Add random state for all relevant tests * Linting * Use lambda functions that converge for the tests * Add bin_and_fit option * Linting * Fix dimensions in sumsin calculation to take any number of frequencies and input value array shape * Linting * Add draft gallery example and new methods to API * Linting * Fix test that randomly fails * Linting * Eriks comments * Linting * Fix residuals * Re-structure coreg module following discussed plan in PR comments * Linting * Fix documentation * Fix small indent warning * Linting
* Fix nearest neighbour and linear interpolant of interp_nd_binning * Linting * Increase samples for 2d bin in biascorr tests * Update doctest
…m in doc (#390) * Clarify Dowds variogram synergy with NMAD and put link into advanced examples * Add exception for Dowds variogram for scikit-gstat version lower or equal to 1.0.0 * Linting * Fix hyperlink in doc * Linting
* Revert back scikit-gstat on conda channels * Modify setup with coreg submodule and description
* Improved fit_pts tests. Fixed bug in NuthKaab pts implementation. * Fixed the old AREA_OR_POINT half pixel shift bug. Added _fit_func to GradientDescending. * Added fit_pts functionality for CoregPipelines * Fixed test to actually sample points. * Made default sampling strategy to center and simplified logic. * Fixed z_name to work as expected. Added geometry col parsing if no E/N cols exist. Fixed typo and cleaned test. * Added docstrings. * Added fit_pts functionality to ICP and disabled segfaulting test. * Linting * Changed DEM instantiations to Raster instantiations. * Added comments to ICP pixel shift test.
* Remove overwriting of nodata to None * Add test that nodata is preserved
#429) * Restructure environment file parsing across pip and conda, and versioning * Linting * Small fix * Try with this syntax * Update setup.py to remain only for backw-compat * Update install page * Fix dev env * Fix packages find given coreg submodule * Add wheel to build * Use setuptools_scm * Delete version.py file * Make opencv fully optional * Use the more common _version.py filename * Linting * Install opencv with base env in CI * Fix test deprecate with new versioning * Linting * Skip test failing due to SciPy * Linting * Add pull request template * Add warning on environment update * Linting * Move warning * Fix space * Update how-to-release with conda-forge explanations * Change license * Make dev-env and setup.cfg dev dependencies structure mirrored for clarity
* Rename pipelines in workflows and fix bias_vars bug * Restructure coreg tests * Linting * Add bias_var_name optional instantiation, checks in fit and apply and related tests * Write _parse_bias_vars logic for CoregPipeline and add tests * Linting * Import future annotations in new test modules
* Remove duplicate all_coregs * Rename master in main * Clarify how to install warning
* Update contributing guidelines * Fix typos * Linting* * Fix return to line * Small edit* * Slight edit again * Linting * Streamline further * Approval * Add contributing update line to PR template * Linting
* Add subsample to subclass init * Progress on subsampling in Coreg classes and pipelines * Finalize subsampling functionality * Add tests and minor fixes * Add test for get_subsample * Linting * Fix other tests * Get geoutils from git to check everything passes * Linting * Add exception in generate pip from conda script when pulling from repo directly * Change geoutils version required in advance * First commit for eriks comments * Finalize eriks comments * Linting
…asses (#439) * Use better default values and fix valid mask of Nuth and Kaab * Fix tests and lint * Fix values in example * Improve tests for subsampling in NuthKaab * Check with different rounding * Try to round c parameter as well * Check if the inconsistency is not arising because of SciPy * Like this? * COMME CA * Bon allez * Like this * Last try * Close to giving up * Next try * Next * Next * Try this * Like this? * ça va marcher oui * This * Like this * Change get yml script * Like this? * Again * Test CI like this * Test * Fix * Now? * Fix * Fixing version writing in env file * Add future annotations * Update python first * Try like this * Linting * Fix last tests * Linting * Unskip test
* Add kurtosis as metric to evaluate performance of standardization * Update workflow * Set for pre-release * Remove changes from kurtosis * Remove space * Update workflow
) * Fixed use of nearest-neighbour extrapolation when using interpolation_method='linear' in interp_nd_binning (#380) * Added possibility in fit_sum_model_variogram to pass a value for maxfev, which is passed on to curve_fit * Added possibility to save plots to file (variogram, 1d- and 2d-binning) * Add pd.interval reformatting to nd_binning plotting functions * Linting * Add test for fix * Tentative fix for plot1d and 2d binning with string pd.Interval --------- Co-authored-by: Romain Hugonnet <romain.hugonnet@gmail.com>
* Fix bug and remove _fit_func * Re-add the fit_pts func * Add test to check pipeline output consistency * Linting * Fix random states and increase tolerance * Increase tolerance of tilt test
* Fix rendering of sphinx-book-theme * Force pydata sphinx theme to fix doc
Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Romain Hugonnet <romain.hugonnet@gmail.com>
Co-authored-by: adehecq <3285905+adehecq@users.noreply.github.com>
Co-authored-by: Romain Hugonnet <romain.hugonnet@gmail.com>
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