Code

Example for PET analysis#215

Code

Merged

jwboth merged 100 commits intomainpmgbergen/DarSIA:mainfrom pet-example-darsia-paperpmgbergen/DarSIA:pet-example-darsia-paperCopy head branch name to clipboardSep 21, 2023

+3,585-510

Commits

Commits on Jul 5, 2023

• EX: Initialize script for PET vs. simulation example included in DarSIA paper.

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• EX: USe suffix, add plot.

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Commits on Jul 6, 2023

• ENH: More control on plotting of W1-dist results.

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• EX: Add more advanced plots, and add 3d wasserstein.

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• EX: Fix plots and rename script.

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Commits on Aug 22, 2023

• ENH: init 3d version of wasserstein distance

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Commits on Aug 28, 2023

• ENH: Add restart and adaptive dimension to AA.

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• ENH: Add possibility to use restarted AA.

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• MAINT: Rename variables.

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• ENH: Extend plotting capabilities and convergence monitoring.

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• MAINT: rename edge -> face.

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• DOC: Improve documentation of connectivity infrastructure.

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Commits on Aug 29, 2023

• ENH: Add more grid operators for face restictions.

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• MAINT: Move face-flux computations part of the common Wasserstein class.

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Commits on Aug 30, 2023

• ENH: Revise solver structure for Newton steps and add more monitoring.

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• MAINT: Switch to fixing zero potential at the center of the grid.

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Commits on Sep 2, 2023

• ENH: Add possibility to utilize true potential system through gauss

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• DOC Improve documentation

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• DOC: improve documentation

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• ENH: Add two variants to project cell to face data.

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• MAINT: Rename method

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• MAINT: Change signature

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Commits on Sep 3, 2023

• MAINT: Improve doc, naming

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• MAINT: Exclude for now redundant routine, and add some keywords.

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• MAINT: More precise error message

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• MAINT: Improve doc, and move code, improve efficiency.

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• MAINT: Restructure linear solver allowing for external control

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Commits on Sep 9, 2023

• MAINT: adapt bregman algorithm and use similar monitoring as for Newton

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• MAINT: add convergence criterion for Bregman split

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Commits on Sep 10, 2023

• MAINT: reorganize code

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• MAINT: Refactor shrink

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Commits on Sep 12, 2023

• BUG: Use correct mass matrix

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• MAINT: Extend signature of l1 dissipation

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• Bug: Also use a name when not storing the plots

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• MAINT: init implicit Bregman

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Commits on Sep 13, 2023

• MAINT: Add flag for switching between implicit and explicit Bregman

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• MAINT: backup of all old code snippets

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• MAINT: remove attempts to improve Bregman

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Commits on Sep 14, 2023

• ENH: Add new Bregman type split, with updated weights and shrink factor.

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• MAINT: Add missing import.

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• ENH: Add possibility to use AMG for Bregman as well.

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Commits on Sep 15, 2023

• MAINT: Remove hardcoded plotting specifications.

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• MAINT: Make Bregman convergence criterion depending on distance

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• TST: Add test for wasserstein computations.

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• TST: Enhance wasserstein test and differ between different BRegman modes

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Commits on Sep 16, 2023

• STY: black and flake8

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• MAINT/STY: Add user-access to steer bregman modes.

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• MAINT: Exclude 3d wasserstein file - soon obsolete.

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• MAINT: Add pyamg to dev requirements.

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• STY: flake8

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• STY: black

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• MAINT: Init extraction of a grid object to be used for Wasserstein distances

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Commits on Sep 17, 2023

• MAINT: Copy tensor grid setup from Wasserstein file.

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• MAINT: Provide basic FV utilities (copied from Wasserstein).

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• MAINT: Adapt Wasserstein class to extracted grid and fv management.

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• MAINT: Reorganize setup of Wasserstein distances

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• MAINT: basic maintanence

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• MAINT: Replace hardcoded slices.

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• MAINT: Reuse code

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Commits on Sep 18, 2023

• MAINT: Add fv utils to darsia.

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  548ec88

• MAINT: strip down code

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• MAINT: Reorganize setup

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• MAINT: Move FV type projections to fv file.

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• MAINT: init reorganization of solver setup

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• DOC/MAINT: Reorganize definition of L

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  3ded585

• MAINT: Reorganize linear solution - for Newton

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• MAINT: rename attribute

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• MAINT: Reorganize and bundle linear solution.

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• DOC: Add better documentation of attributes

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• TST: Extend Wasserstein test - add more solvers, prepare for 3d

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Commits on Sep 19, 2023

• MAINT: Generalize grid as preparation for extension to 3d.

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• TST: Provide test capabilities for 2d grids.

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• BUG: Fix divergence - wrong sorting.

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• ENH: Provide face volumes for grids.

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• TST: Enhance grid test, check nontrivial voxel size

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• TST: Provide test for fv divergence operator.

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• DOC: Add better descriptions of FV ojects.

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• MAINT: Generalize/adapt reconstruction of tangential fluxes on faces.

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• MAINT: Generalize/adapt vector reconstruction of fluxes on cells.

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• MAINT: Use updated tangential reconstruction in Wasserstein computations.

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• MAINT: Clean up file, rename cell index attribute

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• MAINT: Use shorter names for attributes in Grid.

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• DOC: Add more attribute descriptions.

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• MAINT: Adapt variable renaming.

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• ENH: Extend tensor grid utilities to 3d

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• TST: Add 3d grid test

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• MAINT: Apply consistent ordering of faces and cells.

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• TST: Adapt test new consistent indexing.

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• TST: Adapt divergence test for new indexing, and add 3d test

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• TST: Add test for mass matrices.

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• MAINT: adapt renaming and fix error (use concatenate)

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• BUG: Apply correct ordering in reshaping

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• TST: Add many more fv tests.

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Commits on Sep 21, 2023

• ENH: Significanlty simplify code for tangential reconstruction and add full reconstruction.

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• TST: Cover tangential and full face reconstruction.

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• MAINT: Improve error message for compatibility check of coordinate systems.

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• MAINT: Move 2d requirement from general compatibiliity check

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  6603ce4

• MAINT: Adapt use of reconstruction operator.

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• TST: Add 3d wasserstein test

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• MAINT: Remove obsolete 3d wasserstein file.

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