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Fix edge refinement #49

Merged
merged 136 commits into from
Nov 5, 2024
Merged

Fix edge refinement #49

merged 136 commits into from
Nov 5, 2024

Commits on Jul 10, 2024

  1. make edge names to be refined clearer

    @j-zimmermann
    j-zimmermann committed Jul 10, 2024
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Commits on Jul 16, 2024

  1. idea for edge markers

    @j-zimmermann
    j-zimmermann committed Jul 16, 2024
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Commits on Jul 17, 2024

  1. refine directed contacts, add tests scripts for mesh

    @j-zimmermann
    j-zimmermann committed Jul 17, 2024
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Commits on Jul 23, 2024

  1. update mesh example

    JPPayonk committed Jul 23, 2024
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Commits on Jul 24, 2024

  1. change refinement of directed contacts (abbott_stjude & medtronic)

    @kenichi-maeda
    kenichi-maeda committed Jul 24, 2024
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Commits on Jul 25, 2024

  1. only label outer edges

    JPPayonk committed Jul 25, 2024
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  2. clean edge refinement

    JPPayonk committed Jul 25, 2024
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Commits on Jul 30, 2024

  1. unoriented base contact

    @kenichi-maeda
    kenichi-maeda committed Jul 30, 2024
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Commits on Aug 7, 2024

  1. work on directed contacts

    @j-zimmermann
    j-zimmermann committed Aug 7, 2024
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Commits on Aug 8, 2024

  1. comments on rotation

    @j-zimmermann
    j-zimmermann committed Aug 8, 2024
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  2. reproduce bug

    @kenichi-maeda
    kenichi-maeda committed Aug 8, 2024
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  3. remove one rotation

    @j-zimmermann
    j-zimmermann committed Aug 8, 2024
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Commits on Aug 12, 2024

  1. adjust rotation of electrode

    @j-zimmermann
    j-zimmermann committed Aug 12, 2024
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  2. use non-standard direction in example

    @j-zimmermann
    j-zimmermann committed Aug 12, 2024
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  3. updated version of rotation in comment, agrees without?

    @j-zimmermann
    j-zimmermann committed Aug 12, 2024
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  4. add default in comments

    @j-zimmermann
    j-zimmermann committed Aug 12, 2024
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Commits on Aug 13, 2024

  1. WIP: angle not correct

    @j-zimmermann
    j-zimmermann committed Aug 13, 2024
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  2. fix rotation / spin issue

    @j-zimmermann
    j-zimmermann committed Aug 13, 2024
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Commits on Aug 14, 2024

  1. test examples that don't work

    @j-zimmermann
    j-zimmermann committed Aug 14, 2024
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  2. a better check for the orientation

    @j-zimmermann
    j-zimmermann committed Aug 14, 2024
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  3. enable log to file

    @j-zimmermann
    j-zimmermann committed Aug 14, 2024
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Commits on Aug 18, 2024

  1. example with custom electrode

    @j-zimmermann
    j-zimmermann committed Aug 18, 2024
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Commits on Aug 19, 2024

  1. more flexibility in interface

    @j-zimmermann
    j-zimmermann committed Aug 19, 2024
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  2. set default output path

    @j-zimmermann
    j-zimmermann committed Aug 19, 2024
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  3. write StimSets mesh to results directory (no cleanup yet)

    @j-zimmermann
    j-zimmermann committed Aug 19, 2024
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Commits on Aug 21, 2024

  1. merge updated tests

    @j-zimmermann
    j-zimmermann committed Aug 21, 2024
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  2. update output

    @j-zimmermann
    j-zimmermann committed Aug 21, 2024
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Commits on Aug 22, 2024

  1. GMRES did not converge properly

    @j-zimmermann
    j-zimmermann committed Aug 22, 2024
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  2. new benchmark

    @j-zimmermann
    j-zimmermann committed Aug 22, 2024
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Commits on Aug 25, 2024

  1. fix geometry issue

    @j-zimmermann
    j-zimmermann committed Aug 25, 2024
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  2. new test for electrode edges

    @j-zimmermann
    j-zimmermann committed Aug 25, 2024
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  3. test for multiple electrodes

    @j-zimmermann
    j-zimmermann committed Aug 25, 2024
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  4. scripts to debug meshes / geo issues

    @j-zimmermann
    j-zimmermann committed Aug 25, 2024
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  5. ignore more files

    @j-zimmermann
    j-zimmermann committed Aug 25, 2024
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Commits on Aug 26, 2024

  1. handle output path correctly

    @j-zimmermann
    j-zimmermann committed Aug 26, 2024
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  2. permit free choice of ground contact

    @j-zimmermann
    j-zimmermann committed Aug 26, 2024
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Commits on Aug 27, 2024

  1. update ci to only use ruff

    @j-zimmermann
    j-zimmermann committed Aug 27, 2024
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  2. export field too if needed

    @j-zimmermann
    j-zimmermann committed Aug 27, 2024
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Commits on Aug 28, 2024

  1. FIX: active grounding check and VTA threshold

    @Kinway25
    Kinway25 committed Aug 28, 2024
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  2. export vtk from input

    @j-zimmermann
    j-zimmermann committed Aug 28, 2024
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  3. adjust spin angle of all directed electrodes

    @j-zimmermann
    j-zimmermann committed Aug 28, 2024
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  4. adjust spin angle of cartesia electrodes, needs to be checked

    @j-zimmermann
    j-zimmermann committed Aug 28, 2024
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  5. remove superfluous rotations

    @j-zimmermann
    j-zimmermann committed Aug 28, 2024
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Commits on Aug 29, 2024

  1. add tests for spin direction of directed electrodes

    @j-zimmermann
    j-zimmermann committed Aug 29, 2024
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  2. export also electrode mesh

    @j-zimmermann
    j-zimmermann committed Aug 29, 2024
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Commits on Aug 30, 2024

  1. fix face naming for microelectrode

    JPPayonk committed Aug 30, 2024
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  2. Merge branch 'main' into fix_edge_refinement

    @j-zimmermann
    j-zimmermann committed Aug 30, 2024
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  3. expose voxel size

    @j-zimmermann
    j-zimmermann committed Aug 30, 2024
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  4. all electrode contacts need to be in brain

    @j-zimmermann
    j-zimmermann committed Aug 30, 2024
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Commits on Aug 31, 2024

  1. update OOC results

    @j-zimmermann
    j-zimmermann committed Aug 31, 2024
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  2. add informative output to AMR

    @j-zimmermann
    j-zimmermann committed Aug 31, 2024
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Commits on Sep 2, 2024

  1. fix medtronic contacts

    @j-zimmermann
    j-zimmermann committed Sep 2, 2024
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  2. fix abbott electrode

    @j-zimmermann
    j-zimmermann committed Sep 2, 2024
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  3. fix vercise electrode

    @j-zimmermann
    j-zimmermann committed Sep 2, 2024
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  4. update dixi electrodes

    @j-zimmermann
    j-zimmermann committed Sep 2, 2024
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  5. fix neuropace

    @j-zimmermann
    j-zimmermann committed Sep 2, 2024
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  6. fixed pins medical

    @j-zimmermann
    j-zimmermann committed Sep 2, 2024
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  7. define lead diameter for all electrodes, make export more robust

    @j-zimmermann
    j-zimmermann committed Sep 2, 2024
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  8. clearer error message for wrong input parameter

    @j-zimmermann
    j-zimmermann committed Sep 2, 2024
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  9. catch zero-thickness of encap layer better

    @j-zimmermann
    j-zimmermann committed Sep 2, 2024
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  10. fix MicroProbes

    @j-zimmermann
    j-zimmermann committed Sep 2, 2024
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  11. update tests

    @j-zimmermann
    j-zimmermann committed Sep 2, 2024
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  12. fix microelectrode

    @j-zimmermann
    j-zimmermann committed Sep 2, 2024
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Commits on Sep 5, 2024

  1. UPD: higher precision for grounded current 

    Needed for optimized stim. protocols
    @Kinway25
    Kinway25 authored Sep 5, 2024
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Commits on Sep 6, 2024

  1. add utilities for VTA

    @j-zimmermann
    j-zimmermann committed Sep 6, 2024
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Commits on Sep 7, 2024

  1. update output message

    @j-zimmermann
    j-zimmermann committed Sep 7, 2024
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  2. base setting for convergence study

    @j-zimmermann
    j-zimmermann committed Sep 7, 2024
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  3. rename activation threshold to make unit clear

    @j-zimmermann
    j-zimmermann committed Sep 7, 2024
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  4. add VTA volume computation and export

    @j-zimmermann
    j-zimmermann committed Sep 7, 2024
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  5. update test case for new lattice resolution

    @j-zimmermann
    j-zimmermann committed Sep 7, 2024
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  6. update input file parameter name

    @j-zimmermann
    j-zimmermann committed Sep 7, 2024
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  7. catch case when no activation threshold is provided

    @j-zimmermann
    j-zimmermann committed Sep 7, 2024
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Commits on Sep 8, 2024

  1. catch points outside lattice

    @j-zimmermann
    j-zimmermann committed Sep 8, 2024
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  2. catch points outside lattice

    @j-zimmermann
    j-zimmermann committed Sep 8, 2024
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  3. update AMR impedance handling

    @j-zimmermann
    j-zimmermann committed Sep 8, 2024
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  4. add base parameters for PAM

    @j-zimmermann
    j-zimmermann committed Sep 8, 2024
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  5. expose electrode parameters

    @j-zimmermann
    j-zimmermann committed Sep 8, 2024
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Commits on Sep 9, 2024

  1. structure for convergence study

    @j-zimmermann
    j-zimmermann committed Sep 9, 2024
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  2. initialise point models when final mesh is ready

    @j-zimmermann
    j-zimmermann committed Sep 9, 2024
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  3. no large files in release

    @j-zimmermann
    j-zimmermann committed Sep 9, 2024
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  4. add material mesh refinement

    @j-zimmermann
    j-zimmermann committed Sep 9, 2024
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Commits on Sep 10, 2024

  1. update AMR routine with more output and better control

    @j-zimmermann
    j-zimmermann committed Sep 10, 2024
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  2. update file handler and convergence routine

    @j-zimmermann
    j-zimmermann committed Sep 10, 2024
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  3. catch NEURON error (WIP)

    @j-zimmermann
    j-zimmermann committed Sep 10, 2024
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Commits on Sep 11, 2024

  1. use gzipped file

    @j-zimmermann
    j-zimmermann committed Sep 11, 2024
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  2. remove line

    @j-zimmermann
    j-zimmermann committed Sep 11, 2024
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  3. change deprecated numpy function

    @j-zimmermann
    j-zimmermann committed Sep 11, 2024
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  4. overwrite impedances only when computed

    @j-zimmermann
    j-zimmermann committed Sep 11, 2024
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Commits on Sep 14, 2024

  1. add metrics for PAM

    @j-zimmermann
    j-zimmermann committed Sep 14, 2024
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  2. add VCM report

    @j-zimmermann
    j-zimmermann committed Sep 14, 2024
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  3. PAM files

    @j-zimmermann
    j-zimmermann committed Sep 14, 2024
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  4. make sure directory exists

    @j-zimmermann
    j-zimmermann committed Sep 14, 2024
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  5. full layout for convergence study

    @j-zimmermann
    j-zimmermann committed Sep 14, 2024
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  6. full layout for convergence study vercise

    @j-zimmermann
    j-zimmermann committed Sep 14, 2024
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  7. update case grounding

    @j-zimmermann
    j-zimmermann committed Sep 14, 2024
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  8. update case grounding

    @j-zimmermann
    j-zimmermann committed Sep 14, 2024
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  9. fix typo

    @j-zimmermann
    j-zimmermann committed Sep 14, 2024
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  10. add PAM layout

    @j-zimmermann
    j-zimmermann committed Sep 14, 2024
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  11. update currents

    @j-zimmermann
    j-zimmermann committed Sep 14, 2024
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  12. add PAM layout

    @j-zimmermann
    j-zimmermann committed Sep 14, 2024
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  13. adjust lattice shape

    @j-zimmermann
    j-zimmermann committed Sep 14, 2024
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  14. adjust lattice shape

    @j-zimmermann
    j-zimmermann committed Sep 14, 2024
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Commits on Sep 15, 2024

  1. updated PAM files

    @j-zimmermann
    j-zimmermann committed Sep 15, 2024
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  2. added Vercise PAM files

    @j-zimmermann
    j-zimmermann committed Sep 15, 2024
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  3. typo

    @j-zimmermann
    j-zimmermann committed Sep 15, 2024
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  4. Revert "added Vercise PAM files" 

    This reverts commit ceff225.
    @j-zimmermann
    j-zimmermann committed Sep 15, 2024
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  5. added Vercise PAM files

    @j-zimmermann
    j-zimmermann committed Sep 15, 2024
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Commits on Sep 16, 2024

  1. add monopolar case

    @j-zimmermann
    j-zimmermann committed Sep 16, 2024
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Commits on Sep 17, 2024

  1. add point refinement

    @j-zimmermann
    j-zimmermann committed Sep 17, 2024
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Commits on Sep 28, 2024

  1. update PAM convergence study

    @j-zimmermann
    j-zimmermann committed Sep 28, 2024
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  2. run for new PAM model

    @j-zimmermann
    j-zimmermann committed Sep 28, 2024
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Commits on Oct 7, 2024

  1. final VTA layout

    @j-zimmermann
    j-zimmermann committed Oct 7, 2024
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  2. add comparison in time domain for not-activated neurons

    @j-zimmermann
    j-zimmermann committed Oct 7, 2024
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  3. just Jacobi is more stable

    @j-zimmermann
    j-zimmermann committed Oct 7, 2024
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Commits on Oct 10, 2024

  1. update preconditioner

    @j-zimmermann
    j-zimmermann committed Oct 10, 2024
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  2. update preconditioner

    @j-zimmermann
    j-zimmermann committed Oct 10, 2024
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  3. update preconditioner

    @j-zimmermann
    j-zimmermann committed Oct 10, 2024
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  4. add new pam studies

    @j-zimmermann
    j-zimmermann committed Oct 10, 2024
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Commits on Oct 11, 2024

  1. preconditioner is set by string not set

    @j-zimmermann
    j-zimmermann committed Oct 11, 2024
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Commits on Oct 13, 2024

  1. update source code to catch bug

    @j-zimmermann
    j-zimmermann committed Oct 13, 2024
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Commits on Oct 14, 2024

  1. deprecate Python 3.8 because of EOL

    @j-zimmermann
    j-zimmermann committed Oct 14, 2024
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Commits on Oct 15, 2024

  1. truncate time-domain output vector

    @j-zimmermann
    j-zimmermann committed Oct 15, 2024
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Commits on Oct 16, 2024

  1. fix indexing error

    @j-zimmermann
    j-zimmermann committed Oct 16, 2024
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Commits on Oct 19, 2024

  1. run truncation test

    @j-zimmermann
    j-zimmermann committed Oct 19, 2024
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Commits on Oct 22, 2024

  1. split export function

    @j-zimmermann
    j-zimmermann committed Oct 22, 2024
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Commits on Oct 24, 2024

  1. FIX: correct position of the first contact

    @Kinway25
    Kinway25 authored Oct 24, 2024
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  2. Merge branch 'fix_edge_refinement' of github.com:SFB-ELAINE/OSS-DBSv2… 

    … into fix_edge_refinement
    @j-zimmermann
    j-zimmermann committed Oct 24, 2024
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  3. add mesh scripts

    @j-zimmermann
    j-zimmermann committed Oct 24, 2024
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  4. stimsets overview

    @j-zimmermann
    j-zimmermann committed Oct 24, 2024
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  5. update reference meshes

    @j-zimmermann
    j-zimmermann committed Oct 24, 2024
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Commits on Oct 29, 2024

  1. add issue template

    @j-zimmermann
    j-zimmermann committed Oct 29, 2024
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Commits on Nov 3, 2024

  1. update wire for microprobes electrode (#58) 

    * update wire for microprobes electrode

---------

Co-authored-by: JPPayonk <[email protected]>
    @JPPayonk
    JPPayonk and JPPayonk authored Nov 3, 2024
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  2. update convergence results

    @j-zimmermann
    j-zimmermann committed Nov 3, 2024
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  3. Merge branch 'fix_edge_refinement' of github.com:SFB-ELAINE/OSS-DBSv2… 

    … into fix_edge_refinement
    @j-zimmermann
    j-zimmermann committed Nov 3, 2024
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  4. update preconditioner

    @j-zimmermann
    j-zimmermann committed Nov 3, 2024
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Commits on Nov 4, 2024

  1. update default Lead-DBS

    @j-zimmermann
    j-zimmermann committed Nov 4, 2024
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