From b59516a4ecb03daf92800a5c6440d5756f4deed3 Mon Sep 17 00:00:00 2001 From: Sooyoung Cheong <64125280+c-sooyoung@users.noreply.github.com> Date: Tue, 18 Aug 2026 10:44:00 +0900 Subject: [PATCH] added example configs for silicon FIB lamella reconstructions --- config.yaml | 2 +- examples/silicon-fib/config-2V.yaml | 61 +++++++++++++++++++++++++++ examples/silicon-fib/config-30V.yaml | 62 ++++++++++++++++++++++++++++ examples/silicon-fib/config-5V.yaml | 62 ++++++++++++++++++++++++++++ examples/silicon-fib/config-8V.yaml | 62 ++++++++++++++++++++++++++++ 5 files changed, 248 insertions(+), 1 deletion(-) create mode 100644 examples/silicon-fib/config-2V.yaml create mode 100644 examples/silicon-fib/config-30V.yaml create mode 100644 examples/silicon-fib/config-5V.yaml create mode 100644 examples/silicon-fib/config-8V.yaml diff --git a/config.yaml b/config.yaml index 68bb129..6a0768d 100644 --- a/config.yaml +++ b/config.yaml @@ -5,7 +5,7 @@ job: io: input_data_path: '/home/swim/shared/Si_project/data/Si2V1_2.mat' - result_dir: '/home/swim/bo-ptycho/results/Si2V1_2/260817' + result_dir: '/home/swim/bo-ptycho/results/test' verbosity: 1 ptycho: diff --git a/examples/silicon-fib/config-2V.yaml b/examples/silicon-fib/config-2V.yaml new file mode 100644 index 0000000..68bb129 --- /dev/null +++ b/examples/silicon-fib/config-2V.yaml @@ -0,0 +1,61 @@ +job: + type: 'random+sobo' + random_iters: 16 + sobo_iters: 128 + +io: + input_data_path: '/home/swim/shared/Si_project/data/Si2V1_2.mat' + result_dir: '/home/swim/bo-ptycho/results/Si2V1_2/260817' + verbosity: 1 + +ptycho: + engine: 'fold_slice' + path: '/home/swim/fold_slice-park' + params: + voltage: 200 + alpha_max: 30 + defocus: -250 + rot_ang: 0.3 + Nlayers: 20 + thickness: 250 + rbf: 37 + tilt_x: 2 + tilt_y: 0 + scan_step_size: 0.36 + + Niter: 100 + Niter_save_results: 100 + + CBED_size: 192 + ADU: 1 + Nprobe: 1 + N_scan_x: 64 + N_scan_y: 64 + extra_print_info: 'FIB' + scan_number: 1 + gpu_id: 1 + roi_label: '0_Ndp64' + diff_pattern_blur: 1 + probe_change_start: 1 + object_change_start: 1 + grouping: 64 + probe_position_search: 1 + regularize_layers: 0.2 + variable_probe: false + + +bo: + batch: 4 + acquisition: 'ucb' + beta: 0.1 + metric: 'log_fourier' + params: + defocus: + radius: 100 + Nlayers: + radius: 5 + type: int + thickness: + radius: 150 + train_x: + train_y: diff --git a/examples/silicon-fib/config-30V.yaml b/examples/silicon-fib/config-30V.yaml new file mode 100644 index 0000000..66d315d --- /dev/null +++ b/examples/silicon-fib/config-30V.yaml @@ -0,0 +1,62 @@ +job: + type: "random+sobo" + random_iters: 16 + sobo_iters: 512 + +io: + input_data_path: '/home/swim/shared/Si_project/data/Si30V3_2.mat' + result_dir: '/home/swim/bo-ptycho/results/Si30V3_2/260816' + verbosity: 1 + +ptycho: + engine: 'fold_slice' + path: '/home/swim/fold_slice-park' + params: + voltage: 200 + alpha_max: 30 + defocus: 200 + rot_ang: 0.1 + Nlayers: 30 + thickness: 650 + rbf: 38 + tilt_x: 5 + tilt_y: 3 + scan_step_size: 0.35 + + Niter: 100 + Niter_save_results: 100 + + CBED_size: 192 + ADU: 1 + Nprobe: 1 + N_scan_x: 64 + N_scan_y: 64 + extra_print_info: 'FIB' + scan_number: 1 + gpu_id: 1 + roi_label: '0_Ndp64' + diff_pattern_blur: 1 + probe_change_start: 1 + object_change_start: 1 + grouping: 64 + probe_position_search: 1 + regularize_layers: 0.2 + variable_probe: false + +bo: + batch: 4 + acquisition: 'ucb' + beta: 0.1 + metric: 'log_fourier' + params: + alpha_max: + defocus: + radius: 100 + rot_ang: + Nlayers: + radius: 5 + type: int + thickness: + radius: 150 + train_x: + train_y: diff --git a/examples/silicon-fib/config-5V.yaml b/examples/silicon-fib/config-5V.yaml new file mode 100644 index 0000000..5f11977 --- /dev/null +++ b/examples/silicon-fib/config-5V.yaml @@ -0,0 +1,62 @@ +job: + type: "random+sobo" + random_iters: 16 + sobo_iters: 128 + +io: + input_data_path: '/home/swim/shared/Si_project/data/Si5V1_2.mat' + result_dir: '/home/swim/bo-ptycho/results/Si5V1_2/260815' + verbosity: 1 + +ptycho: + engine: 'fold_slice' + path: '/home/swim/fold_slice-park' + params: + voltage: 200 + alpha_max: 30 + defocus: -200 + rot_ang: 1 + Nlayers: 20 + thickness: 250 + rbf: 37 + tilt_x: 3 + tilt_y: -1 + scan_step_size: 0.36 + + Niter: 100 + Niter_save_results: 100 + + CBED_size: 192 + ADU: 1 + Nprobe: 1 + N_scan_x: 64 + N_scan_y: 64 + extra_print_info: 'FIB' + scan_number: 1 + gpu_id: 1 + roi_label: '0_Ndp64' + diff_pattern_blur: 1 + probe_change_start: 1 + object_change_start: 1 + grouping: 64 + probe_position_search: 1 + regularize_layers: 0.2 + variable_probe: false + +bo: + batch: 4 + acquisition: 'ucb' + beta: 0.1 + metric: 'log_fourier' + params: + alpha_max: + defocus: + radius: 100 + rot_ang: + Nlayers: + radius: 5 + type: int + thickness: + radius: 150 + train_x: + train_y: diff --git a/examples/silicon-fib/config-8V.yaml b/examples/silicon-fib/config-8V.yaml new file mode 100644 index 0000000..4f911ef --- /dev/null +++ b/examples/silicon-fib/config-8V.yaml @@ -0,0 +1,62 @@ +job: + type: "random+sobo" + random_iters: 16 + sobo_iters: 128 + +io: + input_data_path: '/home/swim/shared/Si_project/data/Si8V2_2.mat' + result_dir: '/home/swim/bo-ptycho/results/Si8V2_2/260815' + verbosity: 1 + +ptycho: + engine: 'fold_slice' + path: '/home/swim/fold_slice-park' + params: + voltage: 200 + alpha_max: 30 + defocus: -200 + rot_ang: 1.3 + Nlayers: 25 + thickness: 350 + rbf: 37 + tilt_x: 4 + tilt_y: 0 + scan_step_size: 0.36 + + Niter: 100 + Niter_save_results: 100 + + CBED_size: 192 + ADU: 1 + Nprobe: 1 + N_scan_x: 64 + N_scan_y: 64 + extra_print_info: 'FIB' + scan_number: 1 + gpu_id: 1 + roi_label: '0_Ndp64' + diff_pattern_blur: 1 + probe_change_start: 1 + object_change_start: 1 + grouping: 64 + probe_position_search: 1 + regularize_layers: 0.2 + variable_probe: false + +bo: + batch: 4 + acquisition: 'ucb' + beta: 0.1 + metric: 'log_fourier' + params: + alpha_max: + defocus: + radius: 100 + rot_ang: + Nlayers: + radius: 5 + type: int + thickness: + radius: 150 + train_x: + train_y: