Release v1.2

v1.2 release notes

The v1.2 release contains a new graphical user interface (GUI) plus incremental improvements and bug fixes.

Graphical User Interface

The GUI allows to intuitively build tailored reconstruction algorithms with minimal effort. The proficiency of the GlobalBioIm GUI is, once the objective function is defined, to automatically propose algorithms that are adapted to the built cost function. Finally, the MATLAB script corresponding to the pipeline is automatically generated. See more at
https://biomedical-imaging-group.github.io/GlobalBioIm/gui.html

Improvements

• improvement to save memory in ADMM
• in Opti classes, previous iterate xold is no longer stored when it is not necessary
• move (deprecated) SNR stuffs from OutpuOpti to OutputSNR
• add Element-wise function operator: OpEWfunc
• add Element-wise modulus operator: OpEWAbs
• add CostRobustPenalization (Andrews, Beaton-Tukey, Cauchy, Fair, Huber, Logistic, Talwar-Hinich, Welsch-Dennis)
• add the option to put weights in CostHyperBolic
• add constant cost : CostConst
• add option for Nesterov accelerated gradient descent in OptiGradDesc
• add L infinity cost function
• allow deep copy of objects
• make protected most Map/Linop/Cost properties
• add backtracking rule and reduced-step-size rule in OptiFBS
• add LinOpSelectorPlanes
• add memoize options in CostGoodRoughness (like in CostHyperBolic)
• add attribute first index in LinOpSelector

Bug Fixes

• fix bug in the adjoint computation of StackMap
• fix LinOpSum norm computation with multiple index
• fix bug OptiFGP when running on GPU
• fix issue in CostLinear with complex entries
• in OptiConjGrad set_b method : also set CostLinear b to new value
• fix pb to restart algorithms from the last iterate of the previous run

Release v1.1.2

v1.1.2 release notes

The v1.1.2 release does not contain any major changes but mainly incremental improvements and bug fixes.

Improvements

• New LinOpXRay for 2D radon transform (Note that the adjoint is not really the adjoint, but only an approximation (up to about 20 dB),
• LinOp compatibility with sparse matrices,
• Util/estimateNorm.m for estimation of the norm of an operator,
• New OutputOptiSNR to print SNR during optimization,
• Better summation and multiplication of Map objects with scalars,
• Rename OpEWSquareRoot to OpEWSqrt,
• Add some kind of unitary tests,
• CostHyperBolic: Epsilon can be a vector,
• non scalar step size in OptiFBS

Bug fixes

Many bug fixes, among them:

• Generalize Compiler option for C/C++ files and reactivate openmp for the Schatten norm
• Better handling of singletons dimensions.

Release v1.1.1

The v1.1.1 release does not contain any major changes but mainly incremental improvements and bug fixes.

Improvements

• Sfft functions: faster implementation, work with any dimension, new padding option argument.
• Merge LinOpDFT into LinOpSDFT. LinOpDFT remains now as an alias.
• Remove code duplication in SelectorLinOps.
• Add unitary tests (using the provided examples, see /Util/UnitTest/Script.m)
• Add subgradient in CostL1
• Add test for applyAdjointInverse method in checkMap
• Add property for real input in CostComposition. When activated, takes the real part after gradient computation.

Bug fixes

• Fix bug in applyHtH and applyHHt of LinOpSummation
• Fix a memory issue in Cost
• Fix bug in the computation of the Lipschitz constant of CostSummation.
• Fix index of the coefficients vetor in the plus method of LinOp
• Fix superclass constructor call in CostReals

v1.1 GPU functionality

v1.1 release notes

The v1.1 release contains a new functionality for GPU computation plus incremental improvements and bug fixes.

GPU functionality

• add the functions ones_, zeros_, useGPU, isGPU, gpuCpuConverter
• replace occurences of all() by sum( test)==0
• replace occurences of ones() and zeros() by ones_() and zeros_()
• update the 3D deconvolution example with GPU
• add a page in the documentation dedicated to GPU

Other changes

• fix a bug in OptiVMLMB compilation (you should recompile it by running installOptimPack.m)
• set saveXopt=false by default in OutputOpti
• add flag isSeparable for Cost classes. Generic implementation of applyProx_ for the sum of a separable cost with an indicator cost.
• add a direct prox computation for the composition of a CostL2 with a Downsampled Convolution
• add CostMixNorm21 a non negativity constrained version of CostMixNorm21
• ADMM can now take a Sum of CostL2Composition in the F0 argument
• remove OutputOptiADMM

## v1.0.1 release notes

v1.0.1 release notes

The v1.0.1 release does not contain any major changes but mainly incremental improvements and bug fixes.

LinOp

• New LinOpBroadcastMatrix
• fix pb in makeComposition of LinOpSum other cases in makeComposition btw LinOpDiag and LinOpConv
• LinOpHess is now working for any dimensions, with the choice of the index along which the hessian is computed (Like in LinOpGrad). The method makeHtH return the correct corresponding convolution when the boundary condition is circular
• Adapt MixNormSchatten to the new Hessian functionalities
• makeHtH in LinOpGrad works now for any number of dimensions. It also returns the correct LinOpConv if the gradient is applied to specific dimensions
• LinOpCpx is deprecated as it is not really a LinOp

Cost

• New CostLinear
• CostL2 now accept any linop as weighting (metric) operator
• Indicator functions: Move the size parameter at the first place according to what was done for all maps

Opti

• add methods computeCost and computeSNR in OutputOpti to facillitate deriving classes
• Fix copy on write side effect in OptiVMLMB
• Fix OptiVMLMB such that the returned value is the last accepted one
• Add OutputOptiADMM which evaluates the Lagrangian instead of the cost function
• OutputOpti can deal with both logical or scalar flags

Bug fixes other changes

• Improve doc
• Improve examples
• Faster operation when memoize is off
• Add Conjugate Gradient in Deconv_LS_NoReg

v1.0 milestone

Major Changes and improvements

• Remove deprecated LinOpScaling,
• Improve tests with CheckLinOp, CheckMap and `TestsSummationLinOp' functions
• implement methods makeAdjoint and makeInversion in LinOp
• more simplifications in Summation, Composition, Ìnversion for Map and hence LinOpand Cost
• New LinOpBroadcast linear operator
• Add ElementWiseOp non linear operators: OpEWSquareRoot, OpEWInverse and OpEWSSquaredMagnitude.
• New CostGoodRoughness cost function
• Introduce positivity constraint in CostL1
• New CostTV cost function
• Rework Opti optimization class
• Introduce several TestCvg classes to assess convergence of optimization according to different criteria
• Automatic download and compilation of OptimPackLegacy for OptiVMLMB
• OptiConjGradno longer takes a W parameter
• New ÒptiFGP` (Fast gradient proximal) optimization function

Bug fixes and minor changes

• Improve doc
• Implement function cmpSize to compare size of vectors
• Faster CostHyperBolic cost function- Automatic compilation of C files needed for CostMixNormSchatt1 cost function
• Better examples
• Add functions GenerateData and GenerateData to generate star phantom- More options in `LinOpConv'
• Implement make... methods in LinOpDFT
• Reworked OutputOpti printing class

Contributors

This release contains contributions from Mike Mc Cann, Thomas Debarre, Thanh-an Pham, Emmanuel Soubies and Ferréol Soulez