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align merge history - #116

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MaCuinea merged 149 commits into
matrix_transducer_feature_updatedfrom
development
Mar 31, 2026
Merged

align merge history#116
MaCuinea merged 149 commits into
matrix_transducer_feature_updatedfrom
development

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@MaCuinea MaCuinea commented Mar 31, 2026

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jkosciessa added 30 commits March 3, 2026 16:17
@jkosciessa
[param, calibration] separate focal distance from exit and bowl
cbb1987 
additional adjustments:
@jkosciessa
[distance] fix geometric focal distance estimation
63d0a73 
does not rely on T1, needs to be informed by grid size, not dimensions of planning image
@jkosciessa
[distance] attempt to calculate transducer distance during load
0528053
@jkosciessa
[calibration] update settings and naming
92e2c67
@jkosciessa
[calibration] introduce optional parameter for upper verlocity
1224bff
@jkosciessa
[calibration] optimize functions
c855b69
@jkosciessa
Merge branch 'development' of github.com:Donders-Institute/PRESTUS in…
6098fea 
…to development
@jkosciessa
[doc] create mkdocs file
78ab26d
@jkosciessa
[docs] automate pages
22dd02a
@jkosciessa
[docs] automate pages
5193cf4
@jkosciessa
[doc] minor
faa1d4e
@jkosciessa
[doc] workflow
da53daa
@jkosciessa
[doc] mkdocs deployment
17fde94
@jkosciessa
[doc] update outputs
0ff68d0
@jkosciessa
[doc] update output
1120090
@jkosciessa
[doc] update outputs
d76a82d
@jkosciessa
[doc] fix syntax
52221eb
@jkosciessa
[doc] fix links
b17498c
@jkosciessa
[doc] update
d5f497e
@jkosciessa
[doc] gh action
78c36dd
@jkosciessa
[doc] format outputs
1fd43cd
@jkosciessa
[doc] include readme
e0f0ac5
@jkosciessa
[doc] include readme
0ab229c
@jkosciessa
[doc] include readme
e9875fc
@jkosciessa
[doc] update requirements
63b3bf7
@jkosciessa
[doc] add requirements
cae3ff7
@jkosciessa
[doc] remove index
161a12a
@jkosciessa
[doc] relink root files
b399537
@jkosciessa
[doc] relink root files
4d1ad49
@jkosciessa
[doc] duplicate content where necessary
a40b5ad
sirmrmarty and others added 29 commits March 13, 2026 22:08
@sirmrmarty
[fix] variable img wasn't passed between tp_plot and transducer_posit…
eb03105 
…ioning.m
@sirmrmarty
[fix] the unoptimized parameters were passed on for recomputing Oneil
936b4c1
@sirmrmarty
[fix] nii_image wasnt available for cpu as it was still a gpuArray
d53067a
@sirmrmarty
[fix] nii_image wasnt available for cpu as it was still a gpuArray, a…
207567d 
…djusted in other instances as well
@jkosciessa
Merge pull request #109 from sirmrmarty/development
512bbab 
[fix & enhancement] localite_path fallback, slurm submission formate error, padding makeBowl, transducer position plot error, wrong parameter passing to recompute Oneil and nii_image gpuArray/cpuArray issue
@jkosciessa
[heuristic placement] add and document additional criteria, convert t…
cf5931a 
…o RAS mm, reformat txt
@jkosciessa
[doc] add example localite output table
7c29003
@jkosciessa
[doc] reformat table
4aa2eb4
@jkosciessa
[doc] refactor neuronav placement and coordinates
b8bb150
@jkosciessa
[pct] regularize kplan skull sound speed mapping to 1500
e9cdc3c
@jkosciessa
[pct doc] add comment on kPlan densities
ce2b7b0
@jkosciessa
[calibration] ensure transducer distances are present
732c39a
@jkosciessa
[hpc] hotfix cpu/gpu choice
359ac7c
@jkosciessa
[segmentation] fix log directory to segmentation folder
4e23050
@jkosciessa
[hotfix] unify hpc_wait_for_job
76cdeef
@jkosciessa
[hpc] hotfix: wait for job
fd8486b
@jkosciessa
[hpc] fix job formatting
4ea73f1
@jkosciessa
[pct] kplan: regularize min. skull density to water
1682866
@jkosciessa
[parameter] refactor parameters
cc447e1
@jkosciessa
[parameters] segmentation_only mode
69f45a8
@jkosciessa
[parameters] hotfixes, further parameter rename
ed2e7fd
@jkosciessa
[test] add initial tests
22d87b2
@jkosciessa
[reporting] add MI transcranial
2562651
@jkosciessa
[output] standardize intensity and pressure names
f90bc2f
@jkosciessa
[doc] fix formatting
4cb295a
@jkosciessa
[doc] fix formatting
28db2ff
@jkosciessa
[doc] refer to external article
2c908aa
@MaCuinea
Squashed commit of the following:
5511162 
commit 6b4f8c1
Author: Margely Cornelissen <134381864+MaCuinea@users.noreply.github.com>
Date:   Tue Mar 31 19:13:57 2026 +0200

    updated docs & fix steering bug

commit bc7cb33
Author: Margely Cornelissen <134381864+MaCuinea@users.noreply.github.com>
Date:   Mon Mar 30 10:10:23 2026 +0200

    merge bug fixes

commit 61d0464
Author: Margely Cornelissen <134381864+MaCuinea@users.noreply.github.com>
Date:   Fri Mar 27 10:00:23 2026 +0100

    merge bugfixes

commit 949232c
Author: Margely Cornelissen <134381864+MaCuinea@users.noreply.github.com>
Date:   Thu Mar 26 17:39:22 2026 +0100

    update slurm and snellius compatibility

commit efc9861
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Thu Mar 26 10:25:13 2026 +0100

    [doc] refer to external article

commit 945d792
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 25 19:01:25 2026 +0100

    [doc] fix formatting

commit 0772f85
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 25 18:53:53 2026 +0100

    [doc] fix formatting

commit 57c8798
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 25 18:47:24 2026 +0100

    [output] standardize intensity and pressure names

commit edb3e7f
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 25 17:23:09 2026 +0100

    [reporting] add MI transcranial

commit 3b6821a
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 25 16:58:20 2026 +0100

    [test] add initial tests

commit 30aec4e
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Sat Mar 21 17:50:48 2026 +0100

    [parameters] hotfixes, further parameter rename

commit 5eb5730
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Thu Mar 19 23:46:15 2026 +0100

    [parameters] segmentation_only mode

commit d312257
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Thu Mar 19 23:31:34 2026 +0100

    [parameter] refactor parameters

commit 556daa2
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 17 13:14:16 2026 +0100

    [pct] kplan: regularize min. skull density to water

commit aa1d59a
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 17 12:07:26 2026 +0100

    [hpc] fix job formatting

commit f11624b
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 17 11:33:36 2026 +0100

    [hpc] hotfix: wait for job

commit 9826dcf
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Mon Mar 16 16:38:04 2026 +0100

    [hotfix] unify hpc_wait_for_job

commit d1a7fc1
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Mon Mar 16 15:30:02 2026 +0100

    [segmentation] fix log directory to segmentation folder

commit 08fd90a
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Mon Mar 16 15:28:54 2026 +0100

    [hpc] hotfix cpu/gpu choice

commit 1cb5aee
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Mon Mar 16 14:57:03 2026 +0100

    [calibration] ensure transducer distances are present

commit 2e9eadc
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Sat Mar 14 19:15:29 2026 +0100

    [pct doc] add comment on kPlan densities

commit 130e572
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Sat Mar 14 19:12:16 2026 +0100

    [pct] regularize kplan skull sound speed mapping to 1500

commit 97b9c92
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Sat Mar 14 18:36:55 2026 +0100

    [doc] refactor neuronav placement and coordinates

commit b0a6acd
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Sat Mar 14 18:04:36 2026 +0100

    [doc] reformat table

commit f113dc1
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Sat Mar 14 18:00:48 2026 +0100

    [doc] add example localite output table

commit 5949d3b
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Sat Mar 14 17:48:54 2026 +0100

    [heuristic placement] add and document additional criteria, convert to RAS mm, reformat txt

commit 5ed4b79
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Sat Mar 14 15:01:22 2026 +0100

    Merge pull request #109 from sirmrmarty/development

    [fix & enhancement] localite_path fallback, slurm submission formate error, padding makeBowl, transducer position plot error, wrong parameter passing to recompute Oneil and nii_image gpuArray/cpuArray issue

commit 11e3d0b
Author: sirmrmarty <martinwimmers@gmail.com>
Date:   Sat Mar 14 13:44:35 2026 +0100

    [fix] nii_image wasnt available for cpu as it was still a gpuArray, adjusted in other instances as well

commit 55c9cdb
Author: sirmrmarty <martinwimmers@gmail.com>
Date:   Sat Mar 14 08:35:46 2026 +0100

    [fix] nii_image wasnt available for cpu as it was still a gpuArray

commit db9b219
Author: sirmrmarty <martinwimmers@gmail.com>
Date:   Sat Mar 14 07:25:47 2026 +0100

    [fix] the unoptimized parameters were passed on for recomputing Oneil

commit 5b45e88
Author: sirmrmarty <martinwimmers@gmail.com>
Date:   Fri Mar 13 22:08:56 2026 +0100

    [fix] variable img wasn't passed between tp_plot and transducer_positioning.m

commit 75725e0
Author: sirmrmarty <martinwimmers@gmail.com>
Date:   Fri Mar 13 21:00:42 2026 +0100

    [fix] if localite_path isn't defined the fallback should be the output_dir

commit cdcfda4
Author: sirmrmarty <martinwimmers@gmail.com>
Date:   Fri Mar 13 20:50:44 2026 +0100

    [fix] the slurm submission error due to sbatch format error

commit fd688fd
Author: sirmrmarty <martinwimmers@gmail.com>
Date:   Fri Mar 13 16:11:21 2026 +0100

    adding padding when makeBowl is used and transducer is out of bounds

commit 7f39d3c
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Fri Mar 13 14:43:02 2026 +0100

    Merge remote-tracking branch 'sirmrmarty/development' into development

commit c2043d9
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Fri Mar 13 14:33:46 2026 +0100

    [doc] draft documentation for heuristic transducer placement

commit 034d4b3
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Fri Mar 13 14:05:36 2026 +0100

    [heuristic feature, refactor, doc] added ear removal to heuristic, localite T1 output

commit 610c000
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Fri Mar 13 12:12:56 2026 +0100

    [tp] further refactoring, add ear exclusion

commit 27c59a5
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Thu Mar 12 17:42:48 2026 +0100

    [tp] reorder steps, idenitfy missing plot inputs

commit 0a698cd
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Thu Mar 12 17:03:21 2026 +0100

    [hotfix] fix PRESTUS path loading

commit 41eac0c
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Thu Mar 12 16:50:08 2026 +0100

    [tp-hpc, default] fix tp hpc submission, fix check for expected sim path

commit 3de52c4
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Thu Mar 12 16:29:03 2026 +0100

    [transducer placement] continue refactoring

commit bb9964c
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Thu Mar 12 14:02:27 2026 +0100

    [map] central function for coordinate mapping

commit 053771f
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Thu Mar 12 10:57:43 2026 +0100

    [transducer positioning] draft refactoring, hpc integration

commit 8d6546e
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 11 21:50:17 2026 +0100

    [beauty] simplify variable passing

commit 7bc831a
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 11 21:28:11 2026 +0100

    [hotfix]

commit 0b42972
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 11 20:55:53 2026 +0100

    [platform] rename submit medium to platform, remove special case for calibration

commit fd55568
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 11 20:31:43 2026 +0100

    [refactor] pipeline renamed, hpc submission refactored

commit b480266
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 11 17:25:33 2026 +0100

    [hotfix]

commit 14676a5
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 11 17:19:14 2026 +0100

    [pipeline] allow to turn off individual modules, comment on run_acoustic

commit a1017f1
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 11 17:18:36 2026 +0100

    [pct] add header to html

commit a1418c7
Author: sirmrmarty <martinwimmers@gmail.com>
Date:   Wed Mar 11 16:36:51 2026 +0100

    [fix] adjust the velocity to match the max_isppa

commit b63eef9
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 11 16:35:53 2026 +0100

    [pct, param] allow to turn off nifti creation, include pCT in html if used

commit 2b10558
Author: sirmrmarty <martinwimmers@gmail.com>
Date:   Wed Mar 11 16:02:04 2026 +0100

    [feature] fitting velocity exactly to desired intensity

commit 6b09def
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 11 13:33:18 2026 +0100

    [hcp] refactor slurm submission, relabel temp files

commit e99d9b7
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 11 12:11:44 2026 +0100

    [smooth, param] smoothing changed to FWHM mm, parameter name changed

commit e145f96
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 11 11:32:26 2026 +0100

    [bug] skull expansion labels could mismatch when removing layers

commit ad85700
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 10 19:17:19 2026 +0100

    [hotfix] correctly grab labels from medium not layers

    bug notable when dropping requested layers

commit 40d251d
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 10 18:31:07 2026 +0100

    [pct] hotfix

commit d70e8b0
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 10 18:21:44 2026 +0100

    [neuronav] update localite readin for GUM files

commit 69bebb6
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 10 15:53:19 2026 +0100

    [pct] hotfix for debug plot

commit b60db29
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 10 15:20:31 2026 +0100

    [pct] hotfix: uncomment key script parts

commit 78500ad
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 10 15:11:40 2026 +0100

    [doc] update quick start guide

commit bf45458
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 10 14:55:14 2026 +0100

    [doc] update link to (outdated) tutorial

commit 00da4df
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 10 14:50:02 2026 +0100

    remove outdated examples

commit 745153f
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 10 12:35:22 2026 +0100

    [cpp] prevent string error for variable passing

commit 76a9d66
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 10 12:34:37 2026 +0100

    [calibration] example: force create output folder

commit 2f84e92
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 10 12:10:17 2026 +0100

    [segmentation] add option to call segementation within matlab

commit 4dec417
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 10 11:34:09 2026 +0100

    [calibration] fix distance encoding for opt oneil

commit 4420015
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 10 11:24:43 2026 +0100

    [FD] throw warning not error if focal distance is missing (e.g., to allow only segmentation run)

commit 41edd26
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 10 11:08:59 2026 +0100

    [calibration] encourage use of project-specific config folder

    Provide option to specify a config folder in example, if not provided this will default back to the PRESTUS config folder, but it is not recommended to edit files there.

commit c5497ed
Author: sirmrmarty <martinwimmers@gmail.com>
Date:   Tue Mar 10 10:15:55 2026 +0100

    fix the axial_profile issue in plot_sim as well

commit 5cc9d4f
Author: sirmrmarty <martinwimmers@gmail.com>
Date:   Tue Mar 10 09:33:36 2026 +0100

    [fix] use profile_target.axial_distance_bowl as x-axis in compute_oneil_solution and recompute_oneil_solution.
    Fixes size mismatch error when plotting the desired profile: axial_position
    (from simulation grid) and profile_target.axial_intensity can have different lengths.

commit 40a01e6
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Mon Mar 9 19:16:16 2026 +0100

    [feature] implement smoothing of acoustic property maps, redefine smoothing kernels

commit 3ccec9f
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Mon Mar 9 17:54:12 2026 +0100

    [clean] medium mapping

commit 6a74a0b
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Mon Mar 9 17:28:47 2026 +0100

    [doc] update

commit 159e4b8
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Mon Mar 9 17:25:31 2026 +0100

    [grid] optional grid padding to prevent transducer out-of-bounds

commit 83c23e6
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Mon Mar 9 16:45:11 2026 +0100

    [pipeline] add more parameters to turn off pipeline steps

    important: this will impact the default parameters...add new fields

commit 0f642ef
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Mon Mar 9 16:01:10 2026 +0100

    [doc] update parameters

commit 30f3c5c
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Mon Mar 9 15:57:50 2026 +0100

    [doc] update parameters

commit 78ce611
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Mon Mar 9 15:41:06 2026 +0100

    [pct, doc] make a note w.r.t. defaults

commit 64740cc
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Mon Mar 9 15:37:23 2026 +0100

    [pct] change use_pseudoCT param name, update doc

commit 53a2ded
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Mon Mar 9 15:27:07 2026 +0100

    [pct] individual media mapping flags and functions, updated doc

commit ac77229
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Fri Mar 6 22:59:35 2026 +0100

    [log] track SimNIBS version used for segmentation

commit 66b0e27
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Fri Mar 6 17:47:04 2026 +0100

    [seg] hotfix

commit bb8f3ce
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Fri Mar 6 17:04:37 2026 +0100

    [doc] update simnibs installation guide

commit fb61199
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Fri Mar 6 15:16:26 2026 +0100

    [bug] fix exit plane visualization, fix bowl distance param readin

commit fa4fe45
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Fri Mar 6 12:59:58 2026 +0100

    [doc] separate transducer and calibration doc

commit 6f27a4c
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Fri Mar 6 12:49:36 2026 +0100

    [calibration, doc] document calibration config

commit 149e239
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Fri Mar 6 12:14:37 2026 +0100

    [doc] formula formatting

commit eb41765
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Fri Mar 6 12:08:21 2026 +0100

    [doc] fix formatting

commit b7f7acf
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Fri Mar 6 12:03:33 2026 +0100

    [calibration] hotfixes, documentation

commit ac69f28
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Fri Mar 6 10:42:53 2026 +0100

    [calibration] hotfixes

commit 9a1ca4c
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Thu Mar 5 21:56:34 2026 +0100

    [calibration] hotfix

commit fa45f1b
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Thu Mar 5 21:37:18 2026 +0100

    [calibration] hotfixes + outsource force overwrite

commit 7c75bbd
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Thu Mar 5 21:21:05 2026 +0100

    [hotfix] uncomment calibration

commit 78cf1e6
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Thu Mar 5 21:19:23 2026 +0100

    [calibration] refactor, facilitate structure passing

    major refatcoring of calibration code to ease comparison between targeted, simulated, and analytical profiles, major internal variable renaming, adjustment of empirical target profile to length of simulation axis, fitting constraint to min/max depth of non-NaN intensities

commit 0c2927b
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Thu Mar 5 13:48:02 2026 +0100

    [doc] update formatting

commit 200bfc0
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Thu Mar 5 13:38:03 2026 +0100

    [doc] add changelog

commit 41f5542
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Thu Mar 5 12:48:07 2026 +0100

    Merge branch 'development' of github.com:Donders-Institute/PRESTUS into development

commit 940a0e5
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Thu Mar 5 12:47:43 2026 +0100

    [doc] update contributions

commit d276b22
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Thu Mar 5 12:21:30 2026 +0100

    Merge pull request #108 from sirmrmarty/development

    [html] proper unit to display pressure in the dashboard

commit c045c98
Author: sirmrmarty <martinwimmers@gmail.com>
Date:   Thu Mar 5 12:08:00 2026 +0100

    change the pressure units for the acoustic section as well

commit d15faf9
Author: sirmrmarty <martinwimmers@gmail.com>
Date:   Thu Mar 5 11:57:00 2026 +0100

    change the pressure units for the safety dashboard as well

commit 575f95c
Author: sirmrmarty <martinwimmers@gmail.com>
Date:   Thu Mar 5 11:42:26 2026 +0100

    added dynamic pressure display in the html report and remove CEM and temperature from water stimulation report

commit e13f284
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 19:52:38 2026 +0100

    [doc] add links

commit ec14e7a
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 19:40:01 2026 +0100

    [doc] add pct image

commit c01ab9d
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 19:33:47 2026 +0100

    [doc] reorder start guide

commit 0e9d222
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 19:30:24 2026 +0100

    [doc] update pages

commit 788644d
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 18:52:49 2026 +0100

    [doc] update documentation, starting guide

commit 81b1097
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 18:17:44 2026 +0100

    [doc] attempt to link html

commit 2ffdaf1
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 18:09:11 2026 +0100

    [doc] attempt to link html

commit ab7507c
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 18:07:37 2026 +0100

    [doc] include examples

commit b930653
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 17:30:01 2026 +0100

    [doc] update documentation pages

commit c9d44ad
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 17:29:24 2026 +0100

    [pct] add example creation script

commit 3722539
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 17:01:11 2026 +0100

    [doc] beauty update

commit 24c14b8
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 16:59:53 2026 +0100

    [doc] hotfixes

commit 77260e6
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 16:57:12 2026 +0100

    [doc] update documentation pages

commit 182aff2
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 14:53:01 2026 +0100

    [doc] image integration

commit e250a12
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 13:46:34 2026 +0100

    [doc] update readmes

commit 9994965
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 13:32:16 2026 +0100

    [doc] install reorder

commit 8df1faf
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 13:29:22 2026 +0100

    [doc] duplicate content where necessary

commit 875951b
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 13:22:00 2026 +0100

    [doc] relink root files

commit bbc232a
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 13:20:31 2026 +0100

    [doc] relink root files

commit 0c62708
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 13:17:24 2026 +0100

    [doc] remove index

commit c0dcf17
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 13:12:56 2026 +0100

    [doc] add requirements

commit a6dabd7
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 13:08:57 2026 +0100

    [doc] update requirements

commit e2d87d3
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 13:05:04 2026 +0100

    [doc] include readme

commit 39c292f
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 13:03:51 2026 +0100

    [doc] include readme

commit c7e8f1c
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 13:03:00 2026 +0100

    [doc] include readme

commit abc9679
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 12:50:43 2026 +0100

    [doc] format outputs

commit 7f9cc94
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 12:43:31 2026 +0100

    [doc] gh action

commit ee06f3d
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 12:40:38 2026 +0100

    [doc] update

commit 4682af3
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 12:36:02 2026 +0100

    [doc] fix links

commit 12905a8
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 12:27:33 2026 +0100

    [doc] fix syntax

commit 84ba03e
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 12:25:09 2026 +0100

    [doc] update outputs

commit 38e0111
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 12:18:50 2026 +0100

    [doc] update output

commit 7df3a1e
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 12:11:42 2026 +0100

    [doc] update outputs

commit c1ddc1d
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 12:06:40 2026 +0100

    [doc] mkdocs deployment

commit b558560
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 12:00:38 2026 +0100

    [doc] workflow

commit d12d830
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 11:56:40 2026 +0100

    [doc] minor

commit e91abb0
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 11:53:42 2026 +0100

    [docs] automate pages

commit 689cbec
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 11:49:13 2026 +0100

    [docs] automate pages

commit f008edb
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 11:42:30 2026 +0100

    [doc] create mkdocs file

commit 2e617dd
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 10:45:48 2026 +0100

    Merge branch 'development' of github.com:Donders-Institute/PRESTUS into development

commit 9032519
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Wed Mar 4 10:45:23 2026 +0100

    [calibration] optimize functions

commit f468f26
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 3 18:37:57 2026 +0100

    [calibration] introduce optional parameter for upper verlocity

commit 3c15b88
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 3 18:06:14 2026 +0100

    [calibration] update settings and naming

commit 35de8b1
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 3 17:04:55 2026 +0100

    [distance] attempt to calculate transducer distance during load

commit 6efa797
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 3 16:45:01 2026 +0100

    [distance] fix geometric focal distance estimation

    does not rely on T1, needs to be informed by grid size, not dimensions of planning image

commit 67352f1
Author: Julian Kosciessa <julian.kosciessa@donders.ru.nl>
Date:   Tue Mar 3 16:17:44 2026 +0100

    [param, calibration] separate focal distance from exit and bowl

    additional adjustments:

commit 8de0a9a
Author: Margely Cornelissen <134381864+MaCuinea@users.noreply.github.com>
Date:   Thu Mar 26 16:29:40 2026 +0100

    Snellius compatibility + validation bug fixes

commit dc0bffe
Author: Margely Cornelissen <134381864+MaCuinea@users.noreply.github.com>
Date:   Tue Mar 24 17:18:08 2026 +0100

    Update default_config.yaml

commit 5ed986a
Author: Margely Cornelissen <134381864+MaCuinea@users.noreply.github.com>
Date:   Tue Mar 24 17:17:25 2026 +0100

    support HPC Snellius

commit 8d70f75
Author: Margely Cornelissen <134381864+MaCuinea@users.noreply.github.com>
Date:   Tue Mar 24 16:26:09 2026 +0100

    support matrix visualization

commit 3f3b24d
Author: Margely Cornelissen <134381864+MaCuinea@users.noreply.github.com>
Date:   Thu Mar 19 17:30:26 2026 +0100

    additional plots & add matrix visualization

commit 29d89a0
Author: Margely Cornelissen <134381864+MaCuinea@users.noreply.github.com>
Date:   Thu Mar 19 14:18:46 2026 +0100

    only plot when debug mode

commit 0704072
Author: Margely Cornelissen <134381864+MaCuinea@users.noreply.github.com>
Date:   Thu Mar 19 14:07:49 2026 +0100

    Allow 3D steering for matrix transducers only

commit c6a3a5d
Author: Margely Cornelissen <134381864+MaCuinea@users.noreply.github.com>
Date:   Thu Mar 19 13:47:30 2026 +0100

    Clover source implementation

commit ed6a469
Author: Margely Cornelissen <134381864+MaCuinea@users.noreply.github.com>
Date:   Fri Mar 13 15:59:02 2026 +0100

    source implementation

commit ef12b6a
Author: Margely Cornelissen <134381864+MaCuinea@users.noreply.github.com>
Date:   Fri Mar 13 11:51:40 2026 +0100

    updated summary load_param + load_param write back

commit be11b30
Author: Margely Cornelissen <134381864+MaCuinea@users.noreply.github.com>
Date:   Mon Mar 9 17:05:55 2026 +0100

    prepare source_create for matrix impl.

commit 9d7bdd8
Author: Margely Cornelissen <134381864+MaCuinea@users.noreply.github.com>
Date:   Mon Mar 9 12:09:10 2026 +0100

    updated load transducer param

commit 57d1a16
Author: Margely Cornelissen <134381864+MaCuinea@users.noreply.github.com>
Date:   Fri Mar 6 17:36:49 2026 +0100

    Initial updated load_parameters

commit 2c2b9c9
Author: Margely Cornelissen <134381864+MaCuinea@users.noreply.github.com>
Date:   Tue Mar 3 17:19:45 2026 +0100

    Update tutorial_config.yaml
@MaCuinea
Revert "Squashed commit of the following:"
5d512b8 
This reverts commit 5511162.
@MaCuinea
MaCuinea merged commit 80e9055 into matrix_transducer_feature_updated Mar 31, 2026
1 check passed
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3 participants

@MaCuinea @jkosciessa @sirmrmarty