Merge of PRESTUS feature updates #34
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Updated version of PRESTUS that contains new code to make a pseudoCT (make_pseudoCT folder) and run simulations with the obtained pseudoCT
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Commit f14f5e0 integrated the three parts of the pseudoCT code into a continuous function with relative paths etc. Successfully ran this with a Donders 2deg UTE image. All fixed parameters, so no dependencies (beyond software toolboxes). Added an example call script as part of the documentation. |
gpu currently tied to Donders specification
make function backwards-compatible to configs missing the usepseudoCT field
parameters.heatingvideo
originally hardcoded to elecar's paths
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@jkosciessa do you agree that I can add the .Rhistory to .gitignore bc we don't need it, right? |
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Yes, but let's first delete it, otherwise it will remain in the repo forever. Taking care of it now. |
This reverts commit 5d22507.
additional paths are expected to be specified as individual cell strings
if not a git repo it will simply show "fatal: not a git repository (or any of the parent directories): .git"
This reverts commit 85aa3fe.
The prior version did not specify how to include additional subtoolboxes. This is now specified, and results in separable cell trings that will be added at the onset of single_subject_pipeline. The assert function easily threw errors when some (usually hardcoded) specs such as paths were inconsistent. Now it throws an interactive warning instead. The MATLAB version check has been moved to the load_parameters check, and similarly throws an interactive warning instead of an error (e.g., acoustic sim seems to run fine also with R2019b).
axis function in MATLAB changed with R2022a
Now uses consistent variable naming in single_subject_pipeline that caused crashes. Mask expansion was previously not applied to pseudoCT, which led to inconsistent image dimensions.
Donders-Institute#40 Tissue parameters and transducer specifications previously mixed 250 and 500 kHz parameters.
This commit integrated smooth_and crop.m and setup_medium.m across setup variants to harmonise how tissues are labeled. All previously hardcoded tissue labels are now referring to the config. The medium mask output of pseudo-CT generation has been reindexed according to the default layered setup and the conversion to tissue mask labels is performed in smooth_and_crop.m similar to the original layered setup. Minor documentation additions. Function getidx.m has been added to rapidly grab tissue labels from the parameters structure.
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3195d93 is a big one. As specified in the commit:
I forgot a few things in there:
I do not expect any backcompat issues, but given that changes relate to the tissue mapping, it would be good to inspect the outputs in the I am currently running both |
Each time we run a simulation, the `parameter` file gets added to the output. The current naming is time-dependent to avoid overwrites, but in the case of running multiple simulations with varying parameters (e.g., intensities) in the same folder, it is not too helpful, e.g., `sub-001_parameters_11_06_2024_163206_990.mat`. Now the suffix (which usually specifies the setup) is included and timing info is sparsened.
move example calls out of function directory, dynamically code path separator
Medium properties are most informative for varied tissue types. They do not change for an individual, such that it may not require us to append a suffix that specifies targets , stimulation parameters etc.. However, they could previously get overwritten if a water simulation was run posthoc. This should ensure this does not happen.
Try to fix part of issue Donders-Institute#40 (for layered solution); save estimated attenuation coefficients as debug output
Hi all,
I have merged previous changes in the DI master branch (i.e., @KTZ228's changes) and @eleonoracarpino's open pull request into my recent version.
This includes small feature updates:
I have also merged @eleonoracarpino's pseudoCT branch. Despite rebasing that branch, this turned out messier than I hoped, so I had to manually redo some recent changes.
I am currently testing this full merge, and will also try out the pseudoCT implementation. If I run into hiccups, I will update this pull request.
It would be great if someone else can also validate this version prior to a merge.