v1.4.0

What's Changed

• add support for Mac OS (Apple Silicon chips) again by @carsten-forty2, @andieie & @florian-wagner
• update gimliuses.bib by @aurorec in #495 and other new papers
• separat VES related stuff from physics.ERT as own module physics.VES
• switch several tutorials (VES, Polyfit, DC+EM joint inversion) to modern (pg>1.2) framework styles
• new example additional Constraints (example layer interface in VES)
• three new ERT examples on 2D crosshole, 3D surface and 3D crosshole geometries
• new function extract2dSlice for slicing 3D models into 2D meshes by using PyVista
• widely avoid use of pg.core functions by sorting them into math, matrix etc.
• simplify passing keyword arguments to inversion (e.g. C=, Ctype=)
• extended docstrings and doctests, improvements of webpage
• lots of bug fixes (e.g. loading duplicate sensors) and new tests to prevent bugs
• fix error in FDEM modelling for small distances and large elevations

New Contributors

• @aurorec made their first contribution in #495

Full Changelog: v1.3.1...v1.4.0

v1.3.1

What's Changed

• Add scooby-report as pg.Report() by @prisae in #445
• update of CSS styles and sphinx themes for website
• add 3D magnetics modelling and inversion with example
• new tutorials on meshes, datacontainers, regularization, region control and prior data (from Transform 2022)
• re-structure examples, e.g. induced polarization in own section
• update of several examples to modern styles
• add some 3D slicing functions by using pyVista
• fix matplotlib>3.5 bugs by enabling Vector[np.newaxis
• lots of bug fixes
• improvement of documentation and test coverage

New Contributors

• @prisae made their first contribution in #445

Full Changelog: v1.3.0...v1.3.1

v1.3.0

What's Changed

• change release schedule (version numbering) so that core updates are MAJOR.MINOR.0 and pure Python updates are counting the patch number
• add jupyter backend panel for 3D pyvista plots in Jupyter Notebook by @andieie in #364
• add several logical matrices: TransposeMatrix, SquaredMatrix, SquaredTransposeMatrix additionally to horizontally, vertically or diagonally combined matrices
• add Python-based inverse solvers such as LSQR, CGLS, RRLS
• introduce LSQR-based inversion framework for including parameter constraints (Wagner et al. 2019)
• cleanup frameworks to follow v1.2 API
• improve traveltime manager for gradient models under topography and extracting raypaths
• add more functionality for 3D mesh generation using pg.meshtool.createParaMeshPLC3D
• add more synthetic sugar like pg.show(mesh, "property"),
• add more examples, particularly involving 3D plots, improve and cleanup existing examples
• improve docstrings and test coverage
• fix lots of minor and some major bugs
• improve code readability

Full Changelog: v1.2.6...v1.3.0

v1.2.6

General

• lots of bug fixes and minor improvements
• extend documentation and test coverage
• fix problems with matplotlib versions >= 3.5
• allow negative indices into pg Vectors
• symlog transformation pg.trans.TransSymLog (for signed logarithmically distributed data)

Inversion

• clearer starting model behavious
• clarify reference model behaviour by invert(isReference=True) (by default False! before accidentially True)
• regularization API: inv.setRegularization()
• geostatistical regularization by using correlationLengths=[Ix, Iy, Iz] (so far only global) regularization

Modelling

• PriorModelling class for both demonstration purposes and incorporation of prior data
• LinearModelling based on pg.Modelling for linearized problems

Matrices

• RepeatVMatrix, RepeatHMatrix, RepeatDMatrix for vertically/horizontally/diagonally repeated block matrices
• FrameConstraintMatrix for regularizing (spatially, temporally or spectrally) constraints in frame (multiple models) inversion

Frameworks

• Multi-frame (e.g. timelapse) framework pg.frameworks.MultiFrameModelling

SIPSpectrum: double Coule-Cole fit with various options (resistivity/Pelton vs. conductivity, tau definition, add vs. mult)
ERT: generateDataPDF

Full Changelog: v1.2.5...v1.2.6

Version used at Transform2021

v1.2.1

Version presented at Transform 21

v1.1.1

API change

• [API change] Restructuring / API / default changes for 1.1 #124
• [API change] Move pg.mplviewer to pg.viewer.mpl #121

building and distribution

• [building and distribution][documentation] Python 3.6 Win64 1.0.12 Wheel missing #214
• [building and distribution][testing] New structure for testdata #62

closed

• [closed] Save results of seismic tomography inversion #264
• [closed] traveltime tomography with close geometry #258
• [closed] how to display pseudosection and phiM and phiD curves and tikhonov curves in ERT #257
• [closed] Jacobian matrix for homogeneous model in ERT #252
• [closed] petrophysical joint inversion of ERT and SRT #251
• [closed] error installing pyBERT on python notebook #249
• [closed] Pygimli and seismic reflection #248
• [closed] [QUESTION] complex resistivity inversion #247
• [closed] ERT inversion with geostatistical regularization #246
• [closed] Missing Method in Update to 1.1 #244
• [closed] Cannot add data to VTK export #242
• [closed] [Question] ERT simulate - values in the data container #240
• [closed] Is it possible to use the c++ core in c++ programming #238
• [closed] how to set b as a velocity field in the solveFiniteElements module #237
• [closed] ERT Field Data With Topography #236
• [closed] New to Git Hub: Issues with Update from 1.0 to 1.1 #235
• [closed] Trivel-time / distance plot #234
• [closed] Refraction Result to pyqtgraph #233
• [closed] pygimli.viewer.mpl not found #231
• [closed] TravelTimeManager in pg1.1 #230
• [closed] Data not shown #229
• [closed] Conda packages for Mac OS? #201
• [closed] not able to import gmsh file in pygimli #197

enhancement

• [enhancement][feature request] Basic pg.viewer support for 3D visualizations #15

v1.1.0

Release presented at EGU2020: https://doi.org/10.5194/egusphere-egu2020-18751

conda install -c gimli -c conda-forge pygimli=1.1.0 # Win, Linux and Mac!

Main changes:

• repository restructuring (Python part now at root level)
• improved API documentation and website
• improved and cleaned frameworks: https://www.pygimli.org/pygimliapi/_generated/pygimli.frameworks.html
• 3D viewer based on PyVista: https://www.pygimli.org/pygimliapi/_generated/pygimli.viewer.pv.html

API renaming & namespace clean-up

• pg.mplviewer - > pg.viewer.mpl
• pg.RVector -> pg.Vector
• pg.RMatrix -> pg.Matrix
• new module pg.math (cos, cot, sin, det, exp10, median, randn, rms, etc.)
• new module pg.matrix (Vector, BlockMatrix, etc.)
• core (C++) members now explicitly in pg.core.coreMember instead of pg.coreMember

Default changes in viewer

• logScale=False
• colorBar=True

New syntactic sugar

• pg.physics.ert.simulate
• pg.physics.ert.createGeometricFactors
• pg.fit: run curvefit with ParameterInversion.
  Provide function for a curve, data and dataspace and the curve will be fitted with some automagic
• expose abs to pg.core objects. e.g. abs(pg.Vector), abs(CVector), abs(R3Vector)
• pg.x(obj), pg.y(obj), returns x coordinates for obj (Mesh, DataContainer, R3Vector .. everywhere where we think it can be useful)

Meshtools

• Spline interpolation in createPolygon
• support for 3D PLC (may replace bert.polytools (out-of-core))
  e.g., meshtools.polytools.createCube, createCyinder, extrude, createFacet, createMesh(3dplc)
• mergePLC works with 3D objects too .. only touching a smaller on a bigger object for now
• nice pyVista target if calling pg.show with 3D objects (mesh, PLC)
• object conversion from meshio meshes (https://pypi.org/project/meshio/)

Frameworks

• base classes pg.Inversion and pg.Modelling are now pure Python.
• main inversion loop now in Python
• rewritten Refraction as TravelTimeManager
• rewritten ERTManager to replace pybert.Resistivity

Config

• pg.rc dictionary for global-user specific settings
• basic support for appearance support:
  pg.unit(), pg.cmap() gives default names and default color maps for your desired physical parameters
  only res and vel for now ... will grow on demand

Logging

• colored terminal output
• pg.debug(), pg.info(), pg.error() and pg.critical(), the latter throws an exception, the other give colored output based on python logger class
• debug level can be set on command line argument --debug or -d

Caching

• on-disk cache for single functions with decorator @pg.cache
  e.g.:

    @pg.cache
    def func(args, **kwargs):
        return result

• cache hash depends on function body, pg.version, and hashable args and kwargs
• cached values are either single-returned hashable pg.core objects or multiple numpy objects
• hash values for some Python and pg.core objects
• you can turn off caching with command line --noCache

FE solver

• support for complex values and anisotropy matrix
• boundary conditions are now provided as dictionary

Misc

• print(Datacontainer) gives more output
• DataContainer and Mesh data values can and should be accessed with index operator
  e.g. t = data['t']or mesh['resistivity'] = model
• renamed all cmap arguments to cMap
• pg.wait() is obsolete at end of script, any pending MPL figures will be opened
  automatically if using a non-interactive backend based on qt or wx

Tests

• many new tests available

v1.0.12

conda install -c gimli -c conda-forge pygimli=1.0.12 # Win & Linux!

bug

• [bug] Problem using fatray #188
• [bug] pg.solver.solveFiniteElements(mesh, a=1.0, b=0...) does not work if b is set as a field #181

v1.0.11

conda install -c gimli -c conda-forge pygimli=1.0.11 # currently Linux only

bug

• [bug] Examples Raypaths, Layered Example not working #167

closed

• [closed] Trying the Field data inversion (“Koenigsee”) example #164
• [closed] Question -ModuleNotFoundError: No module named 'pygimli' #160

v1.0.10

Changes

• improved handling of region markers during mesh creation (PR #157 by @m-weigand)
• fixed marker bug for coverage mapping (145dbad)
• Matplotlib 3.0 support

Closed issues

bug

• [bug] drawField does not work for very small values #136
• [bug] potential wrong reference to const & RMatrix() const in python bindings #61

closed

• [closed] Parameter check in createRectangle #158
• [closed] Mesh creation: marker parameter not always honored #152

feature request

• [feature request] Support vtk STRUCTURED_GRID Dataset #87

Misc

fixes

• polyCreate* that does not use leftDirection.
• wrong Neumann BC scaling,

adds

• dataContainerERT.addFourPointData accept now also values
• pygimli/core/datacontainer.py for easy extentions
• createCylinder(OOC: polytools), createMesh() accecpt 3D PLC and now tries a systemcall for tetgen
• dataIndex(), dataContainer.sortSensorIndex() returns now sorting indieces.
• isGeometry flag for core.Mesh. If set meshtool automatic check for duplicated nodes.
• BlockMatrix to sparseMap conversion
• argument for solver.linSolver to change solving backend

doc

• slight changes to interpolation api docs