From 4e52517bec801d9deaba31479113bd2242c984c3 Mon Sep 17 00:00:00 2001 From: Pierre-antoine Comby <pierre-antoine.comby@crans.org> Date: Fri, 9 Feb 2024 08:51:22 +0100 Subject: [PATCH] feat: add scenario3 --- src/conf/scenario2.yaml | 2 +- src/conf/scenario3.yaml | 72 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 73 insertions(+), 1 deletion(-) create mode 100644 src/conf/scenario3.yaml diff --git a/src/conf/scenario2.yaml b/src/conf/scenario2.yaml index 49e33a7..49d4289 100644 --- a/src/conf/scenario2.yaml +++ b/src/conf/scenario2.yaml @@ -35,7 +35,7 @@ handlers: n_samples: 25000 constant: false directionz: center-out - backend: cufinufft + backend: stacked-cufinufft n_jobs: 2 reconstructors: diff --git a/src/conf/scenario3.yaml b/src/conf/scenario3.yaml new file mode 100644 index 0000000..6be64da --- /dev/null +++ b/src/conf/scenario3.yaml @@ -0,0 +1,72 @@ +# This files contains the configuration to reproduce the scenario 3 of the Simfmri paper. +# it requires a SPARKLING trajectory. + +force_sim: false +cache_dir: ${oc.env:PWD}/cache +result_dir: ${oc.env:PWD}/results +ignore_patterns: + - "n_jobs" + +sim_params: + sim_tr: 0.1 + sim_time: 300 + shape: [-1,-1,-1] # shape will be determined with the bbox and the brainweb phantom. + fov: [-1,-1,-1] + n_coils: 32 + rng: 19980408 + lazy: true +handlers: + phantom-brainweb: + subject_id: 5 + bbox: [0.225,-0.07, 0.06, -0.055, null, null] + brainweb_folder: ${cache_dir}/brainweb + res: [1.0, 1.0, 0.943] + activation-block: + event_name: block_on + block_on: 20 + block_off: 20 + duration: 300 + bold_strength: 0.02 + noise-gaussian: + snr: 100 + acquisition-generic-noncartesian: + shot_time_ms: 20 + n_jobs: 4 + traj_files: ${oc.env:PWD}/cache/trajectory/sparkling3d-48-2688x5.bin + smaps: true + backend: "cufinufft" + +reconstructors: + sequential: + nufft_kwargs: + backend_name: cufinufft + density: cell_count + optimizer: pogm + wavelet: sym4 + threshold: sure + max_iter_per_frame: 40 +stats: + contrast_name: block_on + + +hydra: + job: + chdir: true + + run: + dir: ${result_dir}/outputs/scenario2/${now:%Y-%m-%d_%H-%M-%S} + sweep: + dir: ${result_dir}/multirun/scenario2/${now:%Y-%m-%d_%H-%M-%S} + subdir: ${hydra.job.num} + + callbacks: + gather_files: + _target_: hydra_callbacks.MultiRunGatherer + aggregator: + _partial_: true + _target_: snkf.cli.utils.aggregate_results + + latest_run: + _target_: hydra_callbacks.LatestRunLink + run_base_dir: ${result_dir}/outputs + multirun_base_dir: ${result_dir}/multirun