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

v1.0.9

conda install -c gimli pygimli=1.0.9 # currently Linux only

New functionality

• Support for secondary nodes in traveltime calculations (following Giroux & Larouche, 2013; http://dx.doi.org/10.1016/j.cageo.2012.12.005)

  • New mesh method mesh.createSecondaryNodes(numberOfSecNodes)
  • New argument when setting mesh in RefractionManager rst.setMesh(mesh, numberOfSecNodes)

• New method to visualize raypaths: rst.showRayPaths() (a89eb2c, API Doc)

Other changes

• Fix RValue conversion bug (172c31f)
• Automatic detection of inline backend (improves pg.show() usage in Jupyter Notebooks) (207680e)
• Allow for cmap and other kwargs in rst.showVA() (096d02d)
• Fix compatibility issue with pytest 3.8 (ba59307)

v1.0.8

New functionality

• automatic type conversion for Numpy scalars (34041b0)
• automatic type conversion numpy.ndarray to BVector
• expose abs(RVector), abs(R3Vector) and abs(CVector). No need for pg.abs anymore.
• expose log(RVector). No need for pg.log anymore.
• add STL reading support for multiple soldis
• add basic operatores +/- for IVector

Closed

• [closed] pygimli.frameworks.harmfit does not work with numpy integers for nc #143

Changes

• mt.mergePLC recognize node on edge touching (not vice versa)
• show now checks for used 2d coordinates (x,y) or (x,z)
• mesh.createNodeWithCheck can now check for edge touching and split the edge on hit
• renamed: mesh.extract to mesh.createSubMesh

v1.0.7

bug

• [bug] Zero or one-based sensor indexing for traveltime data container? #141

closed

• [closed] Retrieve pyGIMLi version is 'untagged' #137
• [closed] marker view with pg.show() #135

fixes:

• pure singe region now build correct interregion constraints without region file
• passive body cem problem in bert fop
• *Vector < operator
• mesh bounding box problem for post createNode

add:

• repr for pg.Node.
• pg.load for *.collect files
• circular flag for patchValMap
• DataContainer.remove(BVector)
• showNodes flag to drawPLC
• boundingbox syntax sugar

remove:

• DataContainer.filter