added example configs for silicon FIB lamella reconstructions

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:

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:

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:

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:

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: