Arbitrarily shaped sources

• fields.get_source_field:

  • Arbitrarily shaped sources (and therefore also loops) can now be created by
    providing a src that consists of x-, y-, and z-coordinates of all
    endpoints of the individual segments.

  • Simple "magnetic dipole" sources can now be created by providing a point
    dipole ([x, y, z, azm, dip]) and set msrc=True. This will create a
    square loop of lengthxlength m perpendicular to the defined point
    dipole, hence simulating a magnetic source. Default length is 1 meter.

  • Point dipoles and finite length dipoles were before treated differently.
    Point dipoles are new converted into finite length dipoles of provided
    length (default is 1 meter), and treated as finite length dipoles. This is
    backwards incompatible and means that the source field for point dipoles
    might not be exactly the same as before. However, in any properly set-up
    simulation this should have no influence on the result.

  • Bugfix: Fix floating point issue when the smaller coordinate of a finite
    length dipole source was very close to a node, but not exactly. This is
    done by rounding the grid locations and source position, and the precision
    can be controlled via decimals; default is micrometer.

• fields: Values outside the grid in get_receiver and
  get_receiver_response are new set to NaN's instead of zeroes.
  Additionally, the first and last values in each direction of the fields are
  ignored, to avoid effects form the boundary condition (receivers should not
  be placed that close to the boundary anyway).

• simulations:

  • Within the automatic gridding the properties are estimated much more
    conservative now, if not provided: before the log10-average of the last
    slice in a given direction was used; now it uses the maximum resistivity.
    This is usually the air value for x/y and positive z. This is very
    conservative, but avoids that users use too small computational domains in
    the case of land and shallow marine surveys. The downside is that it
    heavily over-estimates the required domain in the deep marine case.
    However, slower but safe is better in this case.
  • New method print_grids, which prints the info of all created grids.
    This is also used for logging in the CLI interface.

• maps: interp3d takes a new keyword cval, which is passed to
  map_coordinates.

Move to EMSiG

Various small things, mostly related to the automatic meshing.

• New parameter distance for get_origin_widths, as an alternative for
  domain and vector: distance defines the survey domain as distance
  from the center. This is then also available in construct_mesh and
  Simulation, including the CLI.
• Removed precision from skin_depth, wavelength,
  min_cell_width; all in meshes. It caused problems for high
  frequencies.
• All data is stored in the Survey, not partly in Survey and partly
  in Simulation.
• Deprecated collect_classes in io.
• Expanded the what-parameter in the Simulation-class to include
  properties related to the gradient.
• Moved from github.com/empymod to github.com/emsig.

Fix deploy; take 2

v0.15.2

Fix deploy; take 2

Bugfix deploy

Small bugfix release, as v0.15.0 never got deployed.

• Fix CI deploy script.
• Makefile for the most common dev-tasks.

discretize restructure

The package discretize went through a major restructuring with many name
changes and consequent deprecations (see below for a list of affected
mesh-properties for emg3d). This version updates emg3d to be compatible
with discretize>=0.6.0 in the long run. It also means that emg3d will, from
emg3d>=0.15.0 onwards, only work with discretize>=0.6.0.

Other notable changes:

• Bug fix re storing/loading synthetics
• Moved from Travis CI to GitHub Actions.

The relevant aliases and deprecations for emg3d are (consult the release
notes of discretize for all changes):

Aliases: Aliases (left) remain valid pointers to the new names (right).

• x0 => origin
• nC => n_cells
• vnC => shape_cells
• nN => n_nodes
• vnN => shape_nodes
• nE => n_edges
• nEx => n_edges_x
• nEy => n_edges_y
• nEz => n_edges_z
• vnE => n_edges_per_direction
• vnEx => shape_edges_x
• vnEy => shape_edges_y
• vnEz => shape_edges_z

Deprecations: Deprecated properties (left) raise a deprecation warning and
will be removed in the future. Currently, they still work and point to the new
names (right).

• hx => h[0]
• hy => h[1]
• hz => h[2]
• nCx => shape_cells[0]
• nCy => shape_cells[1]
• nCz => shape_cells[2]
• nNx => shape_nodes[0]
• nNy => shape_nodes[1]
• nNz => shape_nodes[2]
• vectorNx => nodes_x
• vectorNy => nodes_y
• vectorNz => nodes_z
• vectorCCx => cell_centers_x
• vectorCCy => cell_centers_y
• vectorCCz => cell_centers_z
• vol => cell_volumes

Bug fix discretize

• Bug fix for discretize>=0.6.0.

Bug fix

• Bug fix for Windows affecting good_mg_cell_nr (int32 issue).

Bug fix

• Fix for h5py>3.0.
• Improved docs re automatic gridding.

Automatic gridding

The simulation class comes new with an automatic gridding functionality, which should make it much easier to compute CSEM data. With that the entire optimization routine was improved too. See the API docs for more info of the relevant implementation.

• simulation:

  • Simulation: New gridding options 'single', 'frequency', 'source', and 'both'; new default is 'single'.
  • compute() takes a new argument, min_offset. If observed=True, it will add Gaussian random noise according to the standard deviation of the data; it will set receivers responses below the minimum offset to NaN.
  • There is no longer a reference model.
  • misfit and gradient can now handle observations with NaN's.

• survey: A Survey has new attributes standard_error, noise_floor, and relative_error.

• optimize: Completely changed misfit and data-weighting to more sensible functions.

• cli:

  • As a consequence of the changes the data_weight_opts got removed.
  • New sections [data] to select the wanted data and [gridding_opts] for options of the automatic gridding.
  • Section [simulation] has a new parameter min_offset (for creating observed data).
  • Output has a new parameter n_observations if misfit or gradient were called, which is the number of observations that were used to compute the misfit.

• meshes:

  • New functions construct_mesh, get_origin_widths, good_mg_cell_nr and other, smaller helper routines.
  • Deprecated the old meshing routines get_hx_h0, get_cell_numbers, get_stretched_h, get_domain, get_hx; they will be removed in the future.
  • Default of good_mg_cell_nr changed, and the documentation (and verbosity) with regards to «good» number of cells was improved.

• Bug fixes:

  • maps: Fixed the mapping of the gradients (Conductivity is the only mapping that was not affected by this bug).

• Removed deprecated features:

  • models.Model: Removed parameters res_{x;y;z}.
  • io.save: Removed deprecated parameter backend.
  • io.save: Removed default, file extension has to be provided.

CLI

• New Module cli for command-line interaction:

  The command-line interface can currently be used to forward model an entire Simulation, and also to compute the misfit of it with respect to some data and the gradient of the misfit function. See the section "CLI interface" in the documentation for more info.

Note that, while cli (v0.13.0) and optimize (v0.12.0) are implemented, they are still in development and are likely going to change throughout the next two minor releases or so.

• Other changes:

  • solver: Changes in verbosity for emg3d.solve:

    • New default verbosity is 1 (only warnings; before it was 2).
    • Verbosities {-1;0;1} remain unchanged.
    • Verbosities {2;3;4} => {3;4;5}.
    • New verbosity 2: Only shows a one-liner at the end (plus warnings).

  • survey and simulation: to_file and from_file have new a parameter name, to store and load with a particular name instead of the default survey/simulation (useful when storing, e.g., many surveys in one file).

  • survey: stores new also the reference-data; different data (observed, reference) is contained in a data-dict when storing.

  • simulation: takes new a verb parameter.

  • optimize:

    • Gradient now possible for arbitrarily rotated sources and receivers.
    • Falls back to synthetic instead of observed now if reference not found.

  • io: np.bool_ are converted back to bool when loading.

  • Re-arrange, improve, and update documentation.