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CHANGELOG.md

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Changelog

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

[1.2.1] - 24-02-19

Fixed

  • Fixed broadcast error when checking for empty affine matrix or shape vector in the grid sampler.

[1.2.0] - 21-10-13

Added

  • Added rectangular electrodes for tDCS.

Fixed

  • Fixed field interpolation. Before, the only case in which field interpolation worked was when the field was aligned with the structural image used to generate the mesh. Now, it works no matter the orientation of the field.
  • Fixed template embedding in the package. It looks like, before, template files were not included in the package/not accessible.
  • Fixed moving file between different drives. Shamo now uses shutil to perform this action.
  • Fixed None mask in grid conversion.

Changed

  • All .nii files are now .nii.gz files.
  • HD-tDCS solutions now contain the raw GetDP results so that it is possible to regenerate the .pos files. This allows the user to only keep the files of interest while still having the ability to get the others back if needed.

[1.1.1] - 21-06-01

Fixed

  • Fixed structure parsing in mesh_from_surfaces to allow single child tissues.

[1.1.0] - 21-04-22

Added

  • Added logging support for subprocesses and C libraries via subprocess_to_logger and stream_to_logger context managers.
  • Added documentation on how to use the logging library with shamo.
  • Added the mesh_from_fem method to provide a way to generate a mesh from a previously built one by merging tissues together.
  • Added the mesh_from_surfaces method to provide a way to generate a mesh from a set of surface meshes.
  • Added SurrMaskedScalar and SurrMaskedScalarNii to enable more sensitivity analysis.
  • Added SurrMaskedScalarNiiJ, SurrMaskedScalarNiiMagJ and SurrMaskedScalarNiiV for tDCS.

Changed

  • Moved GetDP logging to the new logging subprocess_to_logger context manager.

[1.0.0] - 20-12-16

Added

  • Added ObjABC, ObjFile and ObjDir classes to provide a base for any savable/loadable object.
  • Added Group, Tissue, Field, Sensor, PointSensor and FEM classes to provide a way to generate realistic finite element model based on labelled volumes.
  • Added ProbABC, CompABC, CompFilePath, CompGridSampler, CompSensors, CompTissueProp, CompTissues and ProbGetDP classes to define any problem.
  • Added SolGetDP class to store information about the solution of a ProbGetDP problem.
  • Added DistABC, DistConstant, DistNormal, DistTruncNormal and DistUniform to model random parameters for parametric problems.
  • Added ProbParamABC, CompParamTissueProp, CompParamValue, and ProbParamGetDP classes to define any parametric problem.
  • Added SolParamABC and SolParamGetDP classes to store information about the solution of a ProbParamABC problem.
  • Added ProbEEGLeadfield and SolEEGLeadfield classes to solve the EEG forward problem.
  • Added ProbParamEEGLeadfield, SolParamEEGLeadfield and SurrEEGLeadfield classes to solve the parametric EEG forward problem. Also added SurrEEGLeadfieldToRef class to evalaute the sensitivity of the EEG leadfield matrix.
  • Added ProbHDTDCSSim and SolHDTDCSSim classes to simulate a HD-tDCS.
  • Added ProbParamHDTDCSSim and SolParamHDTDCSSim classes to simulate a parametric HD-tDCS.
  • Added SurrogateABC class to define any surrogate model based on a SolParamABC.
  • Added SurrScalar class to define any surrogate model returning a scalar to perform sensitivity analysis.
  • Added shamo-report command to facilitate bug report.
  • Added automated full reference with sphinx autosummary.