Update matrix_transducer branch with dev - #112

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MaCuinea wants to merge 147 commits into

matrix_transducer_feature_updatedfrom

Commits on Mar 3, 2026

Commits on Mar 4, 2026

[calibration] optimize functions
jkosciessa
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c855b69
Merge branch 'development' of github.com:Donders-Institute/PRESTUS into development
jkosciessa
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6098fea
[doc] create mkdocs file
jkosciessa
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78ab26d
[docs] automate pages
jkosciessa
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22dd02a
[docs] automate pages
jkosciessa
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5193cf4
[doc] minor
jkosciessa
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faa1d4e
[doc] workflow
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da53daa
[doc] mkdocs deployment
jkosciessa
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17fde94
[doc] update outputs
jkosciessa
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0ff68d0
[doc] update output
jkosciessa
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1120090
[doc] update outputs
jkosciessa
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d76a82d
[doc] fix syntax
jkosciessa
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52221eb
[doc] fix links
jkosciessa
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b17498c
[doc] update
jkosciessa
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d5f497e
[doc] gh action
jkosciessa
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78c36dd
[doc] format outputs
jkosciessa
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1fd43cd
[doc] include readme
jkosciessa
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e0f0ac5
[doc] include readme
jkosciessa
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0ab229c
[doc] include readme
jkosciessa
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e9875fc
[doc] update requirements
jkosciessa
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63b3bf7
[doc] add requirements
jkosciessa
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cae3ff7
[doc] remove index
jkosciessa
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161a12a
[doc] relink root files
jkosciessa
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b399537
[doc] relink root files
jkosciessa
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4d1ad49
[doc] duplicate content where necessary
jkosciessa
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a40b5ad
[doc] install reorder
jkosciessa
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d810fb2
[doc] update readmes
jkosciessa
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fcb2924
[doc] image integration
jkosciessa
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013a6b6
[doc] update documentation pages
jkosciessa
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a02cc42
[doc] hotfixes
jkosciessa
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4e7ad86
[doc] beauty update
jkosciessa
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e17dd01
[pct] add example creation script
jkosciessa
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c583c59
[doc] update documentation pages
jkosciessa
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ab9cc50
[doc] include examples
jkosciessa
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aea5acd
[doc] attempt to link html
jkosciessa
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6679702
[doc] attempt to link html
jkosciessa
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c966712
[doc] update documentation, starting guide
jkosciessa
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0fdb774
[doc] update pages
jkosciessa
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7f7eb56
[doc] reorder start guide
jkosciessa
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e4a6024
[doc] add pct image
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01869f6
[doc] add links
jkosciessa
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525f50c

Commits on Mar 5, 2026

added dynamic pressure display in the html report and remove CEM and temperature from water stimulation report
sirmrmarty
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59155af
change the pressure units for the safety dashboard as well
sirmrmarty
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83ee019
change the pressure units for the acoustic section as well
sirmrmarty
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2dba8ec
Merge pull request #108 from sirmrmarty/development
jkosciessa
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2b99ce8
[doc] update contributions
jkosciessa
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ac27843
Merge branch 'development' of github.com:Donders-Institute/PRESTUS into development
jkosciessa
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9f8c49e
[doc] add changelog
jkosciessa
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f1e0035
[doc] update formatting
jkosciessa
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450864b
[calibration] refactor, facilitate structure passing
jkosciessa
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ae62bae
[hotfix] uncomment calibration
jkosciessa
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23b3e64
[calibration] hotfixes + outsource force overwrite
jkosciessa
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7889769
[calibration] hotfix
jkosciessa
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1b3aaf3

Commits on Mar 6, 2026

[calibration] hotfixes
jkosciessa
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24e2461
[calibration] hotfixes, documentation
jkosciessa
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e2d91ed
[doc] fix formatting
jkosciessa
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f036139
[doc] formula formatting
jkosciessa
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3fd5b93
[calibration, doc] document calibration config
jkosciessa
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874c322
[doc] separate transducer and calibration doc
jkosciessa
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d2af40b
[bug] fix exit plane visualization, fix bowl distance param readin
jkosciessa
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b67d51c
[doc] update simnibs installation guide
jkosciessa
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da99bba
[seg] hotfix
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471d449
[log] track SimNIBS version used for segmentation
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dfaf6f6

Commits on Mar 9, 2026

[pct] individual media mapping flags and functions, updated doc
jkosciessa
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f57facc
[pct] change use_pseudoCT param name, update doc
jkosciessa
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d628038
[pct, doc] make a note w.r.t. defaults
jkosciessa
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b7f5cb2
[doc] update parameters
jkosciessa
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505276b
[doc] update parameters
jkosciessa
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359ceff
[pipeline] add more parameters to turn off pipeline steps
jkosciessa
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7027738
[grid] optional grid padding to prevent transducer out-of-bounds
jkosciessa
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9ae3215
[doc] update
jkosciessa
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b268bb1
[clean] medium mapping
jkosciessa
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36f734c
[feature] implement smoothing of acoustic property maps, redefine smoothing kernels
jkosciessa
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970449b

Commits on Mar 10, 2026

[fix] use profile_target.axial_distance_bowl as x-axis in compute_oneil_solution and recompute_oneil_solution.
sirmrmarty
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68cd43d
fix the axial_profile issue in plot_sim as well
sirmrmarty
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07d93c8
[calibration] encourage use of project-specific config folder
jkosciessa
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e388e59
[FD] throw warning not error if focal distance is missing (e.g., to allow only segmentation run)
jkosciessa
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6836dac
[calibration] fix distance encoding for opt oneil
jkosciessa
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2ef1b7e
[segmentation] add option to call segementation within matlab
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765821f
[calibration] example: force create output folder
jkosciessa
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f6dfbfa
[cpp] prevent string error for variable passing
jkosciessa
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8019263
remove outdated examples
jkosciessa
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60252e2
[doc] update link to (outdated) tutorial
jkosciessa
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679c8ba
[doc] update quick start guide
jkosciessa
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0d75ccb
[pct] hotfix: uncomment key script parts
jkosciessa
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e5aa59f
[pct] hotfix for debug plot
jkosciessa
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569c8f0
[neuronav] update localite readin for GUM files
jkosciessa
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5fd957b
[pct] hotfix
jkosciessa
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7175f4c
[hotfix] correctly grab labels from medium not layers
jkosciessa
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61a0509

Commits on Mar 11, 2026

[bug] skull expansion labels could mismatch when removing layers
jkosciessa
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f45b9a2
[smooth, param] smoothing changed to FWHM mm, parameter name changed
jkosciessa
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19c1187
[hcp] refactor slurm submission, relabel temp files
jkosciessa
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dc70a4a
[feature] fitting velocity exactly to desired intensity
sirmrmarty
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5a4506f
[pct, param] allow to turn off nifti creation, include pCT in html if used
jkosciessa
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25177ef
[fix] adjust the velocity to match the max_isppa
sirmrmarty
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2ff8725
[pct] add header to html
jkosciessa
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25b9293
[pipeline] allow to turn off individual modules, comment on run_acoustic
jkosciessa
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ea492c7
[hotfix]
jkosciessa
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8aea927
[refactor] pipeline renamed, hpc submission refactored
jkosciessa
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79f375a
[platform] rename submit medium to platform, remove special case for calibration
jkosciessa
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609bb98
[hotfix]
jkosciessa
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1215130
[beauty] simplify variable passing
jkosciessa
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3188796

Commits on Mar 12, 2026

[transducer positioning] draft refactoring, hpc integration
jkosciessa
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a7b607d
[map] central function for coordinate mapping
jkosciessa
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5559d50
[transducer placement] continue refactoring
jkosciessa
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bcc5955
[tp-hpc, default] fix tp hpc submission, fix check for expected sim path
jkosciessa
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10d34f1
[hotfix] fix PRESTUS path loading
jkosciessa
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609fbcb
[tp] reorder steps, idenitfy missing plot inputs
jkosciessa
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06847b2

Commits on Mar 13, 2026

Commits on Mar 14, 2026

Commits on Mar 16, 2026

Commits on Mar 17, 2026

[hpc] hotfix: wait for job
jkosciessa
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fd8486b
[hpc] fix job formatting
jkosciessa
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4ea73f1
[pct] kplan: regularize min. skull density to water
jkosciessa
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1682866

Commits on Mar 19, 2026

[parameter] refactor parameters
jkosciessa
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cc447e1
[parameters] segmentation_only mode
jkosciessa
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69f45a8

Commits on Mar 21, 2026

[parameters] hotfixes, further parameter rename
jkosciessa
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ed2e7fd

Commits on Mar 25, 2026

[test] add initial tests
jkosciessa
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22d87b2
[reporting] add MI transcranial
jkosciessa
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2562651
[output] standardize intensity and pressure names
jkosciessa
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f90bc2f
[doc] fix formatting
jkosciessa
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4cb295a
[doc] fix formatting
jkosciessa
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28db2ff

Commits on Mar 26, 2026

[doc] refer to external article
jkosciessa
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2c908aa