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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

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

Unreleased

[4.3.0] - 2020-08-20

  • Updates:
    • pytorch to 1.6
    • pykeops to 1.4.1

[4.2.0] - 2019-04-15

=======

  • Improved deformetrica package importing. Example: import deformetrica as dfca
  • Bugfix: GUI toggle button values
  • Updates:
    • pytorch to 1.1.0
    • pykeops to 1.1.1

[4.2.0] - 2019-04-18

dev

  • Use a more efficient _squared_distances method in AbstractKernel. This highly increases performance. contributes to #39
  • Improve TorchKernel
  • Upgrades: Closes #45
    • pytorch to 1.0.1
    • pykeops to 1.0.1
    • numpy to 1.16
    • nibabel to 2.3.3
    • matplotlib to 3.0
    • pillow to 5.4
    • psutil to 5.4
  • Better multiprocessing. high increases in performance. contributes to #39
  • Multi-GPU support. contributes to #39
  • Better OMP_NUM_THREADS management
  • Fix image intensity normalization
  • Add a check when working with meshes, to detect null area. fixes #41
  • Add set_seed() method to the API
  • Bugfix: Multiprocessing pool cleanup
  • Python 3.7 compliant. Closes #40
  • add dtype option to model_options in api and xml configuration file
  • re-activate keops kernel on macos
  • Bugfix: problem with image deformation
  • Smarter kernel factory. Closes #37
  • Better logger with console and file output. Closes #54
  • Functional tests now pass with 1e-10 precision
  • Added the longitudinal atlas model, along with functional tests. Closes #51.
  • Added the MCMC-SAEM estimator, along with its own save-state system, and corresponding functional tests. Closes #19, #32.
  • Refactoring of the deformable object class, now more robust.
  • New VTK reader, based on the conda-available VTK library (v8). Closes #50.
  • Generalized and harmonized use of the logger, along with automatic txt file dump. Closes #54.
  • Renamed number-of-threads to number-of-processes to better reflect reality
  • Replace use_cuda boolean with gpu_mode enum. Available gpu_modes are: auto, full, none, kernel

[4.1.0] - 2018-09-14

Added

  • New API: deformetrica can now be instantiated from python
  • Automatic dimension detection from input file
  • Allow to use different kernel types for the "shoot" and "flow" operations. Exponential class can now specify shoot_kernel and/or flow_kernel. resolves #10
  • Allow device selection when instantiation a kernel. 'device' kwarg is now available when using the kernel factory and 'device-device' is now available when using the xml configuration file. resolves #13
  • New Python (PyQt5) GUI. Allows the configuration and run of a 'deterministic atlas'. This is an alpha-release
  • Update Pykeops to version 0.0.14
  • Bugfix: Gradients not computed when number_of_processes>1 and tensor_scalar_type is a FloatTensor. resolves #27
  • Bugfix: Memory leak when using estimate_longitudinal_atlas due to pytorch's autograd graph. resolves #33

Changed

  • Split CLI commands into 2 groups: estimate and compute. resolves #6

[4.0.2] - 2018-08-23

  • Corrects the sobolev gradient in the multi-object case

[4.0.1] - 2018-06-27

  • Add different polyline VTK format

[4.0.0] - 2018-06-14

Added

  • Bugfix: version file not found. issue #24
  • Easy install with conda install -c pytorch -c conda-forge -c anaconda -c aramislab deformetrica, without any manual compilation.
  • All existing deformetrica functionalities now work with 2d or 3d gray level images.
  • A L-BFGS optimization method can now be used for registration, regression, deterministic and bayesian atlases.
  • Gradients are now automagically computed using PyTorch's autograd.
  • It is now possible to perform all computations on the gpu through the use-cuda option.

Changed

  • C++ is replaced by Python.
  • The "exact" kernel is now named "torch"; the "cudaexact" kernel is now named "keops".
  • The "deformable-object-type" xml entry is now split in two entries: "deformable-object-type" and "attachment-type". With this renamming, "NonOrientedSurfaceMesh" becomes a "SurfaceMesh" with a "Varifold" attachment (and an "OrientedSurfaceMesh" a "SurfaceMesh" with a "Current" attachment).

Removed

  • The Nesterov scheme for the gradient ascent optimizer (which was named "FastGradientAscent") is not available anymore. L-BFGS is more efficient though!