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Add computation of gravitational tensor components for point sources #288

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merged 17 commits into from
May 3, 2022

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@santisoler santisoler commented Nov 24, 2021

Add new kernel functions to compute gravity tensor components generated by
point sources. Add test functions for the new feature: check that the diagonal
elements satisfy the Laplace equation, compare all components against finite
difference computations from the gravity acceleration. Add test class for
checking the symmetry of tensor components. Refactor old test functions for
point gravity: merge some functions into single ones through pytest
parametrizations. Avoid using "gradient" for specifying the gravity
acceleration vector: the "gravity gradient" is usually used to refer to the
tensor.

Reminders:

  • Run make format and make check to make sure the code follows the style guide.
  • Add tests for new features or tests that would have caught the bug that you're fixing.
  • Add new public functions/methods/classes to doc/api/index.rst and the base __init__.py file for the package.
  • Write detailed docstrings for all functions/classes/methods. It often helps to design better code if you write the docstrings first.
  • If adding new functionality, add an example to the docstring, gallery, and/or tutorials.
  • Add your full name, affiliation, and ORCID (optional) to the AUTHORS.md file (if you haven't already) in case you'd like to be listed as an author on the Zenodo archive of the next release.

Add kernel functions for computing the diagonal components of the
gravitational effect of point sources on Cartesian coordinates.
Mix a few test functions into single ones by applying some pytest
parametrizations.
Improve some function names and create a function to compute the
gradient components from finite differences.
The acceleration vector is defined as the gradient of the gravitational
potential, but the gravity gradient is used to specify the tensor.
Using "gradient" ambiguously could create confusions.
Add test function that compares tensor components against finite
difference computations.
@santisoler
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@leouieda I finally found a very good opportunity to add a test class! The tests for tensor components symmetry has a few different cases that were hard to cover with just a few pytest parameters. So I decided it would be better to define a class for it, with different methods for each one of these cases. Let me know what do you think.

Remove test over diagonal components with mirrored computation points:
the test was equivalent to the one over opposite computation points
because they were modified along a single direction.
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Looks good to me! I had never used a class for this before. Is the advantage only being able to hold values as attributes? Not complaining, just curious 🙂

Caught a little typo but otherwise merge away!

@santisoler
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I had never used a class for this before. Is the advantage only being able to hold values as attributes? Not complaining, just curious

Neither do I. I saw that xarray uses classes in their tests, mostly to group and keep tests organized and use inheritance to avoid repeating themselves. I thought that here this new class would work in that sense: group all tensor symmetry related fixtures, parameters and functions (methods now) under the same structure. I think the current scheme improves readability. Pytest parametrizations are nice to avoid repetition and buggy for loops inside test functions, but for some multi parameters cases, they fell short and create harder to read code.

To finish this PR I would:

  • Add an example (or wait for the improvement of the docs and add it as a part of the User Guide)
  • Check if passing g_ne is the same as passing g_en. If not, maybe add a utils function to sanitize tensor component names (we will probably use it in other forward modelling functions).

@santisoler santisoler added this to the v0.5.0 milestone Apr 23, 2022
@santisoler santisoler merged commit d132abb into main May 3, 2022
@santisoler santisoler deleted the point-gravity-tensor branch May 3, 2022 15:47
LL-Geo added a commit to LL-Geo/harmonica that referenced this pull request Jun 23, 2022
commit 54c3cbe52bd33a94ccbb5bb44f2958bb3afc9330
Author: LL-Geo <[email protected]>
Date:   Thu Jun 23 21:36:23 2022 +0800

    Update filter

    Add more filter

commit 4a5d6f1
Author: Santiago Soler <[email protected]>
Date:   Thu Jun 16 18:00:32 2022 -0300

    Avoid checking floats in tesseroid doctests (fatiando#326)

    Remove expected results for tesseroid calculations in docstring examples.
    Printing floats in forward modelling examples isn't that meaningful and often
    creates failures when running doctests: small differences between the expected
    and the got value could occur under some dependency and OS combinations.

commit cc697af
Author: Matt Tankersley <[email protected]>
Date:   Fri Jun 17 08:24:32 2022 +1200

    Add progressbar to prism forward gravity calculations (fatiando#315)

    Add optional `progressbar` flag to `prism_gravity` function and to the
    `gravity` method of the prism layer accesor to print a progress bar using
    `numba_progress`. Add `numba_progress` as optional dependency. Add test
    functions for the new feature.

commit 5a1c895
Author: Santiago Soler <[email protected]>
Date:   Tue Jun 14 13:20:39 2022 -0300

    Specify spherical latitude in point sources guide (fatiando#325)

    Replaces latitude for spherical latitude in another place of the
    `point.rst`. Fix typo on "Alternatively".

commit cb476b2
Author: Federico Esteban <[email protected]>
Date:   Tue Jun 14 11:33:22 2022 -0300

    Note that spherical and geodetic latitudes are equal in spherical ellipsoids (fatiando#324)

    Add sentence in the Coordinate Systems section of the User Guide noting that
    if the reference ellipsoid were a sphere both the spherical latitude and the
    geodetic latitude are equivalent.

commit 1256ff6
Author: Federico Esteban <[email protected]>
Date:   Mon Jun 13 11:35:02 2022 -0300

    Add Federico Esteban to AUTHORS.md (fatiando#323)

    Add his name, link to his GitHub account, affiliation and ORCID number.

commit 32de6e0
Author: Federico Esteban <[email protected]>
Date:   Thu Jun 9 15:44:48 2022 -0300

    Specify "spherical latitude" when describing coordinates of point masses (fatiando#321)

    Add "spherical" when describing the spherical latitude coordinate of point
    masses in the user guide. This way we differentiate it from the "latitude"
    geodetic coordinate.

commit 9667fab
Author: Santiago Soler <[email protected]>
Date:   Mon Jun 6 11:05:17 2022 -0300

    Fix small format errors in the user guide (fatiando#319)

    Fix link to EquivalentSources.predict method and fix superscripts in the docs.

commit 2f7fcb6
Author: Santiago Soler <[email protected]>
Date:   Fri Jun 3 11:17:51 2022 -0300

    Update docs and create a proper user guide (fatiando#305)

    Update Sphinx docs using sphinx-panels.
    Add a proper User Guide that will ultimately replace the gallery examples.
    Each page of the new User Guide is a .rst file that uses jupyter-sphinx to run example code blocks.
    Added pages for: Coordinate systems, Forward Modelling, Gravity corrections and Equivalent Sources.
    Added a new doc/versions.rst file with links to previous documentations.

commit cf4080c
Author: Santiago Soler <[email protected]>
Date:   Tue May 31 15:58:25 2022 -0300

    Compute upward derivative of a grid in the frequency domain (fatiando#238)

    Define a new derivative_upward function for computing the spatial upward
    derivative of a 2D grid in the frequency domain. The function makes use of
    xrft for handling Fourier transformations of xarray objects. Add a new
    filters subpackage that includes FFT filters: functions that take grids in
    frequency domain and return the desired filter also in frequency domain. Add
    fft and ifft wrapper functions of the xrft.fft and xrft.ifft ones. Add
    a new apply_filter function that takes a grid in the spatial domain, applies
    fft, the filter and ifft and returns the filtered grid also in spatial domain.
    Add tests for the new features and a gallery example for the upward derivative.
    Add netcdf4 as requirement for testing.

commit 6a30797
Author: Santiago Soler <[email protected]>
Date:   Fri May 27 16:22:18 2022 -0300

    Ditch soon-to-be deprecated args of equivalent sources grid method (fatiando#311)

    The grid() method of Verde gridders now take a coordinates argument with
    the coordinates of the target grid. The previous region, shape and
    spacing arguments will be deprecated in Verde v2.0.0. This change makes it
    easier for our equivalent sources classes: we don't need the extra upward
    argument, users can create the coordinates of the target grid using
    verde.grid_coordinates and pass them via coordinates argument. Ditch the
    upward, shape, spacing and region arguments from the equivalent sources
    gridders. Replace them for the new coordinates argument: users need to
    provide the coordinates of the target grid instead of building it through the
    grid method. Raise errors if any of those old arguments are being passed. Raise
    warnings if any kwargs are passed: they are being ignored and not passed to the
    BaseGridder.grid() method.

commit 51ceb7e
Author: Agustina <[email protected]>
Date:   Mon May 23 11:03:54 2022 -0300

    Remove deprecated point_mass_gravity function (fatiando#310)

    Remove point_mass_gravity function from harmonica because it was deprecated on
    PR fatiando#280. Remove related test functions.

commit f336aa8
Author: Santiago Soler <[email protected]>
Date:   Thu May 5 14:52:08 2022 -0300

    Drop support for Python 3.6 (fatiando#309)

    Remove the compatibility metadata, remove from the CI matrix, bump the
    python_requires to 3.7+.

commit d132abb
Author: Santiago Soler <[email protected]>
Date:   Tue May 3 12:47:22 2022 -0300

    Add computation of gravitational tensor components for point sources (fatiando#288)

    Add new kernel functions to compute gravity tensor components generated by
    point sources. Add test functions for the new feature: check that the diagonal
    elements satisfy the Laplace equation, compare all components against finite
    difference computations from the gravity acceleration. Add test class for
    checking the symmetry of tensor components. Refactor old test functions for
    point gravity: merge some functions into single ones through pytest
    parametrizations. Avoid using "gradient" for specifying the gravity
    acceleration vector: the "gravity gradient" is usually used to refer to the
    tensor.

commit eb71d54
Author: Santiago Soler <[email protected]>
Date:   Fri Apr 22 17:23:00 2022 -0300

    Add deprecations to datasets and synthetic modules (fatiando#304)

    Add FutureWarnings to public functions of the synthetic and dataset
    modules. Add tests for the new warnings. Both modules will be deprecated in
    Harmonica v0.6.0. Instead of providing sample datasets, Harmonica will depend
    on Ensaio for that. The synthetic surveys depend on some of the sample
    datasets, but those functions are intended to be used in methodology articles,
    so they should live somewhere else.

commit a4598ef
Author: Santiago Soler <[email protected]>
Date:   Fri Apr 22 17:06:43 2022 -0300

    Add conversion of prisms or a prism layer to PyVista objects (fatiando#291)

    Add a new visualization module that hosts prism_to_pyvista: a function to
    convert a set of prisms into a pyvista.UnstructuredGrid. Include the new
    module and this function in the API Reference. Add a new to_pyvista() method
    to the PrismLayer accessor that converts a prism layer into a pyvista grid,
    making it easier to plot it in 3D. The UnstructuredGrid has the information
    about each prism as hexahedrons, along with their physical properties as cell
    data. Add tests for the new features. Add pyvista and vtk as optional
    dependencies to environment.yml and setup.cfg. Add a new example for
    plotting a PrismLayer. Configure Sphinx to show pyvista plots in the gallery
    and to use the pyvista-plot directive in docstrings.

commit 762d210
Author: Santiago Soler <[email protected]>
Date:   Mon Apr 4 14:09:45 2022 -0300

    Update Black to its stable version (fatiando#301)

    Black has released a stable version: 22.3.0. Now the style check tests use this
    version. Fixes a bug on CI in which Black was trying to import a private module
    of click that doesn't exist anymore. Rerun black: now Black hugs simple
    power operators.

commit 10577fa
Author: Santiago Soler <[email protected]>
Date:   Mon Apr 4 14:00:42 2022 -0300

    Update Sphinx version to 4.5.0 (fatiando#302)

    Updates also sphinx gallery and sphinx book theme.
    This fixes a issue between latest jinja2 and Sphinx 3.5.*.

commit f880065
Author: Leonardo Uieda <[email protected]>
Date:   Fri Mar 18 13:34:51 2022 +0000

    Move configuration from setup.py to setup.cfg (fatiando#296)

    Make the move away from setup.py following the recommendations from the
    Python packaging guides. Moves the requirement listing to setup.cfg as
    well and will use a script to extract this for conda installing on CI.
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