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Documentation, pCT, HCP updates #59

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Documentation, pCT, HCP updates #59

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jkosciessa
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Added documentation on pCT + HPC usage. Slightly edited pCT-to-tissue conversion and added k-plan variant.

jkosciessa and others added 30 commits September 30, 2024 13:45
@jkosciessa
clean up documentation
9e902f8 
add pulsed example, different setups need to be verified
@jkosciessa
document submodule versions
5ac113f 
References #55
@jkosciessa
[cleanup] remove outdated function
0546670
@jkosciessa
[pCT] offer k-Plan setup
8e26e2d 
References #56
@jkosciessa
[pCT] correct incorrect field from prior commit
155a107
@jkosciessa
[doc] include different pseudoCT variants
e1aa3bb 
References #43
@jkosciessa
[doc] document pCT creation, add more verbose comments
88dcc9c 
References #43
@jkosciessa
[doc] document HPC use cases
b7073a0
@jkosciessa
[pCT] make create function more verbose
9ccf5cd
@jkosciessa
[doc] protocol MATLAB version support (HPC-GPU)
a91d514 
References #50
@jkosciessa
[hcp] update min. req for qsub to be CUDA 8
f62243b
@jkosciessa
[doc, pCT] include pCT forumlas
b9327b0 
References #43
@jkosciessa
[pCT] change carpino regularization, save debug plot
c61a3e4 
References #43
@jkosciessa
[doc] minor update to pCT doc
3978145
@jkosciessa
[pCT] throw error when unsupported setup is specified
c02f3c6
@jkosciessa
[bug pCT] correct debug plot output
03dcacc
@MaCuinea
#61 Run simnibs segmentation code doesn't support SLURM
db0535a
@MaCuinea
Revert "#61 Run simnibs segmentation code doesn't support SLURM"
94ea3d7 
This reverts commit db0535a.
@MaCuinea
initial setup automated acoustic profiling
3710179
@MaCuinea
Feature to use default foci
c9ca060
@jkosciessa
[cleanup] change script location for saving debug images
98abbb2
@jkosciessa
Merge remote-tracking branch 'origin/master' into development
0d54e8a
@jkosciessa
merge acoustic_profiling
08a20bb
@jkosciessa
Merge branch 'development' of github.com:Donders-Institute/PRESTUS in…
34070dc 
…to development
@jkosciessa
[bug] fix file name
ca16b85
@jkosciessa
[beauty] make code slightly more accessible
ae3214f
@jkosciessa
add transducer calibration function
501ca12
@MaCuinea
initial sim based on real phases + yaml output
2115bca 
- increased job polling
- add phase tables for initial simulation
- describe focus either wrt exit plane or wrt mid bowl
- add Kenneth's Imasonic data to config
- save new transducer info in yaml file for easy plugin
@MaCuinea
Merge branch 'acoustic_profiling' into development
3a24937
@MaCuinea
Merge pull request #69 from Donders-Institute/development
8fc779d 
Prepare acoustic_profiling for merge
KTZ228 and others added 16 commits January 9, 2025 16:51
@KTZ228
Added note to default config regarding ld_library_path in slurm
f18cae6
@MaCuinea
Refactored and commented acoustic profiling
4bbd13b
@MaCuinea
Merge pull request #71 from Donders-Institute/acoustic_profiling
4246df3 
Semi-automated acoustic profiling
@MaCuinea
increase default grid dims to capture deep focus of Imasonics
1b5a2cc
@MaCuinea
revert transducer to original in tutorial_config
56f6911
@MaCuinea
fix bugs in tutorial
6190914 
- if and else statement for use cpu and use donders hpc
- no hardcoded n-elements
@MaCuinea
tutorial - fixed additional hardcoded n_elements
03f1b32
@MaCuinea
simple example of a main
8817c48
@MaCuinea
Merge pull request #70 from KTZ228/development
78b299a 
Added note to default config regarding ld_library_path in slurm
@jkosciessa
[feature] SLURM GPU specification
c925b58
@jkosciessa
[feature] SLURM GPU specification
92c77d5
@jkosciessa
[feature] harmonize variable names, improve RAM, add option to not sa…
679c509 
…ve mat
@jkosciessa
[pCT] resolve merge conflict
df3a2ee
@jkosciessa
add DOI, REF
1c1443c
@jkosciessa
Merge remote-tracking branch 'origin/master' into development
1f0e3eb
@jkosciessa
Merge remote-tracking branch 'origin/master' into development
367aff1
@jkosciessa
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Now also includes some variable renaming and intermediate cleanup to reduce RAM load (679c509). GPU setup can be more specifically requested.

Includes all prior branch updates (e.g., acoustic profiling).

@jkosciessa jkosciessa requested a review from MaCuinea March 27, 2025 13:09
@jkosciessa
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I think given the number of different changes, this would warrant a new (sub-)version number.

@jkosciessa jkosciessa changed the title Documentation + pCT updates Updates: Doc, pCT, HCP Mar 27, 2025
@jkosciessa jkosciessa changed the title Updates: Doc, pCT, HCP Iterative documentation, pCT, HCP updates Mar 27, 2025
@jkosciessa jkosciessa changed the title Iterative documentation, pCT, HCP updates Documentation, pCT, HCP updates Mar 27, 2025
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3 participants
@jkosciessa @MaCuinea @KTZ228