removed old examples

examples/260805-Si/Si_02V1_2.sub

@@ -1,25 +0,0 @@
-#!/bin/bash
-#SBATCH --job-name=Si2V
-#SBATCH --nodes=1
-#SBATCH --ntasks=1
-#SBATCH --cpus-per-task=1
-#SBATCH --gres=gpu:rtx-6000ada:1
-#SBATCH --time=100:00:00
-#SBATCH --output=/home/swim/slurm-logs/job_%j.log
-
-echo "2V"
-pwd
-hostname
-date
-
-export PATH=/home/shared/MATLAB/R2021a/bin:$PATH
-export PATH=/usr/local/cuda-11.4/bin:$PATH
-export LD_LIBRARY_PATH=/usr/local/cuda-11.4/lib64:$LD_LIBRARY_PATH
-
-source /home/swim/bo-ptycho/venv/bin/activate
-
-cat examples/260805-Si/Si_02V1_2.yaml
-python -u main.py examples/260805-Si/Si_02V1_2.yaml
-
-date
-echo "SLURM JOB FINISHED"

examples/260805-Si/Si_02V1_2.yaml

@@ -1,59 +0,0 @@
-job:
-  type: "random+sobo"
-  random_iters: 30
-  sobo_iters: 300
-
-io:
-  input_data_path: '/home/swim/Si_project/data/Si2V1_2.mat'
-  result_dir: '/home/swim/bo-ptycho/results/260805-si/Si2V1_2'
-  verbosity: 1
-
-ptycho:
-  engine: 'fold_slice'
-  path: '/home/swim/fold_slice'
-  params:
-    voltage: 200
-    alpha_max: 30
-    defocus: -250
-    rot_ang: 0.3
-    Nlayers: 20
-    thickness: 250
-    rbf: 37
-    Nprobe: 1
-    N_scan_x: 64
-    N_scan_y: 64
-    tilt_x: 2
-    tilt_y: 0 
-    scan_step_size: 0.36
-    Niter: 100
-    Niter_save_results: 100
-    CBED_size: 192
-    ADU: 1
-    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_posiiton_search: 1
-    regularize_layers: 0.2
-    variable_probe: false
-
-bo:
-  mode: 'sobo'
-  acquisition: 'ucb'
-  metric: 'log_fourier'
-  params:
-    alpha_max:
-    defocus:
-      radius: 100
-    rot_ang:
-    Nlayers:
-      radius: 5
-      type: int
-    thickness:
-      radius: 100
-  train_x:
-  train_y:

examples/260805-Si/Si_05V1_2.sub

@@ -1,25 +0,0 @@
-#!/bin/bash
-#SBATCH --job-name=Si5V
-#SBATCH --nodes=1
-#SBATCH --ntasks=1
-#SBATCH --cpus-per-task=1
-#SBATCH --gres=gpu:rtx-6000ada:1
-#SBATCH --time=100:00:00
-#SBATCH --output=/home/swim/slurm-logs/job_%j.log
-
-echo "5V"
-pwd
-hostname
-date
-
-export PATH=/home/shared/MATLAB/R2021a/bin:$PATH
-export PATH=/usr/local/cuda-11.4/bin:$PATH
-export LD_LIBRARY_PATH=/usr/local/cuda-11.4/lib64:$LD_LIBRARY_PATH
-
-source /home/swim/bo-ptycho/venv/bin/activate
-
-cat examples/260805-Si/Si_05V1_2.yaml
-python -u main.py examples/260805-Si/Si_05V1_2.yaml
-
-date
-echo "SLURM JOB FINISHED"

examples/260805-Si/Si_05V1_2.yaml

@@ -1,59 +0,0 @@
-job:
-  type: "random+sobo"
-  random_iters: 30
-  sobo_iters: 300
-
-io:
-  input_data_path: '/home/swim/Si_project/data/Si5V1_2.mat'
-  result_dir: '/home/swim/bo-ptycho/results/260805-si/Si5V1_2'
-  verbosity: 1
-
-ptycho:
-  engine: 'fold_slice'
-  path: '/home/swim/fold_slice'
-  params:
-    voltage: 200
-    alpha_max: 30
-    defocus: -200
-    rot_ang: 1
-    Nlayers: 20
-    thickness: 250
-    rbf: 37
-    Nprobe: 1
-    N_scan_x: 64
-    N_scan_y: 64
-    tilt_x: 3
-    tilt_y: -1 
-    scan_step_size: 0.36
-    Niter: 100
-    Niter_save_results: 100
-    CBED_size: 192
-    ADU: 1
-    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_posiiton_search: 1
-    regularize_layers: 0.2
-    variable_probe: false
-
-bo:
-  mode: 'sobo'
-  acquisition: 'ucb'
-  metric: 'log_fourier'
-  params:
-    alpha_max:
-    defocus:
-      radius: 100
-    rot_ang:
-    Nlayers:
-      radius: 5
-      type: int
-    thickness:
-      radius: 150
-  train_x:
-  train_y:

examples/260805-Si/Si_08V1_2.sub

@@ -1,25 +0,0 @@
-#!/bin/bash
-#SBATCH --job-name=Si8V
-#SBATCH --nodes=1
-#SBATCH --ntasks=1
-#SBATCH --cpus-per-task=1
-#SBATCH --gres=gpu:rtx-6000ada:1
-#SBATCH --time=100:00:00
-#SBATCH --output=/home/swim/slurm-logs/job_%j.log
-
-echo "8V"
-pwd
-hostname
-date
-
-export PATH=/home/shared/MATLAB/R2021a/bin:$PATH
-export PATH=/usr/local/cuda-11.4/bin:$PATH
-export LD_LIBRARY_PATH=/usr/local/cuda-11.4/lib64:$LD_LIBRARY_PATH
-
-source /home/swim/bo-ptycho/venv/bin/activate
-
-cat examples/260805-Si/Si_08V1_2.yaml
-python -u main.py examples/260805-Si/Si_08V1_2.yaml
-
-date
-echo "SLURM JOB FINISHED"

examples/260805-Si/Si_08V1_2.yaml

@@ -1,59 +0,0 @@
-job:
-  type: "random+sobo"
-  random_iters: 30
-  sobo_iters: 300
-
-io:
-  input_data_path: '/home/swim/Si_project/data/Si8V1_2.mat'
-  result_dir: '/home/swim/bo-ptycho/results/260805-si/Si8V1_2'
-  verbosity: 1
-
-ptycho:
-  engine: 'fold_slice'
-  path: '/home/swim/fold_slice'
-  params:
-    voltage: 200
-    alpha_max: 30
-    defocus: -200
-    rot_ang: 1.3
-    Nlayers: 25
-    thickness: 350
-    rbf: 37
-    Nprobe: 1
-    N_scan_x: 64
-    N_scan_y: 64
-    tilt_x: 4
-    tilt_y: 0 
-    scan_step_size: 0.36
-    Niter: 100
-    Niter_save_results: 100
-    CBED_size: 192
-    ADU: 1
-    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_posiiton_search: 1
-    regularize_layers: 0.2
-    variable_probe: false
-
-bo:
-  mode: 'sobo'
-  acquisition: 'ucb'
-  metric: 'log_fourier'
-  params:
-    alpha_max:
-    defocus:
-      radius: 100
-    rot_ang:
-    Nlayers:
-      radius: 5
-      type: int
-    thickness:
-      radius: 150
-  train_x:
-  train_y:

examples/260805-Si/Si_30V3_2.sub

@@ -1,25 +0,0 @@
-#!/bin/bash
-#SBATCH --job-name=Si30V
-#SBATCH --nodes=1
-#SBATCH --ntasks=1
-#SBATCH --cpus-per-task=1
-#SBATCH --gres=gpu:rtx-6000ada:1
-#SBATCH --time=100:00:00
-#SBATCH --output=/home/swim/slurm-logs/job_%j.log
-
-echo "2V"
-pwd
-hostname
-date
-
-export PATH=/home/shared/MATLAB/R2021a/bin:$PATH
-export PATH=/usr/local/cuda-11.4/bin:$PATH
-export LD_LIBRARY_PATH=/usr/local/cuda-11.4/lib64:$LD_LIBRARY_PATH
-
-source /home/swim/bo-ptycho/venv/bin/activate
-
-cat examples/260805-Si/Si_30V3_2.yaml
-python -u main.py examples/260805-Si/Si_30V3_2.yaml
-
-date
-echo "SLURM JOB FINISHED"

examples/260805-Si/Si_30V3_2.yaml

@@ -1,59 +0,0 @@
-job:
-  type: "random+sobo"
-  random_iters: 30
-  sobo_iters: 300
-
-io:
-  input_data_path: '/home/swim/Si_project/data/Si30V3_2.mat'
-  result_dir: '/home/swim/bo-ptycho/results/260805-si/Si30V3_2'
-  verbosity: 1
-
-ptycho:
-  engine: 'fold_slice'
-  path: '/home/swim/fold_slice'
-  params:
-    voltage: 200
-    alpha_max: 30
-    defocus: 200
-    rot_ang: 0.1
-    Nlayers: 30
-    thickness: 650
-    rbf: 37
-    Nprobe: 1
-    N_scan_x: 64
-    N_scan_y: 64
-    tilt_x: 5
-    tilt_y: 3 
-    scan_step_size: 0.35
-    Niter: 100
-    Niter_save_results: 100
-    CBED_size: 192
-    ADU: 1
-    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_posiiton_search: 1
-    regularize_layers: 0.2
-    variable_probe: false
-
-bo:
-  mode: 'sobo'
-  acquisition: 'ucb'
-  metric: 'log_fourier'
-  params:
-    alpha_max:
-    defocus:
-      radius: 100
-    rot_ang:
-    Nlayers:
-      radius: 5
-      type: int
-    thickness:
-      radius: 150
-  train_x:
-  train_y:

examples/260809-Si/Si_02V1_2.sub

@@ -1,26 +0,0 @@
-#!/bin/bash
-#SBATCH --job-name=Si2V
-#SBATCH --nodes=1
-#SBATCH --ntasks=1
-#SBATCH --cpus-per-task=1
-#SBATCH --gres=gpu:rtx-6000ada:1
-#SBATCH --time=100:00:00
-#SBATCH --output=/home/swim/slurm-logs/job_%j.log
-
-echo "2V"
-pwd
-hostname
-date
-
-export PATH=/home/shared/MATLAB/R2021a/bin:$PATH
-export PATH=/usr/local/cuda-11.4/bin:$PATH
-export LD_LIBRARY_PATH=/usr/local/cuda-11.4/lib64:$LD_LIBRARY_PATH
-
-source /home/swim/bo-ptycho/venv/bin/activate
-
-YAML=examples/260809-Si/Si_02V1_2.yaml
-cat $YAML
-python -u main.py $YAML
-
-date
-echo "SLURM JOB FINISHED"

examples/260809-Si/Si_02V1_2.yaml

@@ -1,59 +0,0 @@
-job:
-  type: "random+sobo"
-  random_iters: 100
-  sobo_iters: 1000
-
-io:
-  input_data_path: '/home/swim/shared/Si_project/data/Si2V1_2.mat'
-  result_dir: '/home/swim/bo-ptycho/results/260809-Si/Si2V1_2'
-  verbosity: 1
-
-ptycho:
-  engine: 'fold_slice'
-  path: '/home/swim/fold_slice-stable'
-  params:
-    voltage: 200
-    alpha_max: 30
-    defocus: -250
-    rot_ang: 0.3
-    Nlayers: 20
-    thickness: 250
-    rbf: 37
-    Nprobe: 1
-    N_scan_x: 64
-    N_scan_y: 64
-    tilt_x: 2
-    tilt_y: 0 
-    scan_step_size: 0.36
-    Niter: 100
-    Niter_save_results: 100
-    CBED_size: 192
-    ADU: 1
-    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_posiiton_search: 1
-    regularize_layers: 0.2
-    variable_probe: false
-
-bo:
-  mode: 'sobo'
-  acquisition: 'ucb'
-  metric: 'log_fourier'
-  params:
-    alpha_max:
-    defocus:
-      radius: 100
-    rot_ang:
-    Nlayers:
-      radius: 5
-      type: int
-    thickness:
-      radius: 100
-  train_x:
-  train_y:

examples/260809-Si/Si_05V1_2.sub

@@ -1,26 +0,0 @@
-#!/bin/bash
-#SBATCH --job-name=Si5V
-#SBATCH --nodes=1
-#SBATCH --ntasks=1
-#SBATCH --cpus-per-task=1
-#SBATCH --gres=gpu:rtx-6000ada:1
-#SBATCH --time=100:00:00
-#SBATCH --output=/home/swim/slurm-logs/job_%j.log
-
-echo "5V"
-pwd
-hostname
-date
-
-export PATH=/home/shared/MATLAB/R2021a/bin:$PATH
-export PATH=/usr/local/cuda-11.4/bin:$PATH
-export LD_LIBRARY_PATH=/usr/local/cuda-11.4/lib64:$LD_LIBRARY_PATH
-
-source /home/swim/bo-ptycho/venv/bin/activate
-
-YAML=examples/260809-Si/Si_05V1_2.yaml
-cat $YAML
-python -u main.py $YAML
-
-date
-echo "SLURM JOB FINISHED"

examples/260809-Si/Si_05V1_2.yaml

@@ -1,59 +0,0 @@
-job:
-  type: "random+sobo"
-  random_iters: 100
-  sobo_iters: 1000
-
-io:
-  input_data_path: '/home/swim/shared/Si_project/data/Si5V1_2.mat'
-  result_dir: '/home/swim/bo-ptycho/results/260809-Si/Si5V1_2'
-  verbosity: 1
-
-ptycho:
-  engine: 'fold_slice'
-  path: '/home/swim/fold_slice-stable'
-  params:
-    voltage: 200
-    alpha_max: 30
-    defocus: -200
-    rot_ang: 1
-    Nlayers: 20
-    thickness: 250
-    rbf: 37
-    Nprobe: 1
-    N_scan_x: 64
-    N_scan_y: 64
-    tilt_x: 3
-    tilt_y: -1 
-    scan_step_size: 0.36
-    Niter: 100
-    Niter_save_results: 100
-    CBED_size: 192
-    ADU: 1
-    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_posiiton_search: 1
-    regularize_layers: 0.2
-    variable_probe: false
-
-bo:
-  mode: 'sobo'
-  acquisition: 'ucb'
-  metric: 'log_fourier'
-  params:
-    alpha_max:
-    defocus:
-      radius: 100
-    rot_ang:
-    Nlayers:
-      radius: 5
-      type: int
-    thickness:
-      radius: 150
-  train_x:
-  train_y:

examples/260809-Si/Si_08V1_2.sub

@@ -1,26 +0,0 @@
-#!/bin/bash
-#SBATCH --job-name=Si8V
-#SBATCH --nodes=1
-#SBATCH --ntasks=1
-#SBATCH --cpus-per-task=1
-#SBATCH --gres=gpu:rtx-6000ada:1
-#SBATCH --time=100:00:00
-#SBATCH --output=/home/swim/slurm-logs/job_%j.log
-
-echo "8V"
-pwd
-hostname
-date
-
-export PATH=/home/shared/MATLAB/R2021a/bin:$PATH
-export PATH=/usr/local/cuda-11.4/bin:$PATH
-export LD_LIBRARY_PATH=/usr/local/cuda-11.4/lib64:$LD_LIBRARY_PATH
-
-source /home/swim/bo-ptycho/venv/bin/activate
-
-YAML=examples/260809-Si/Si_08V1_2.yaml
-cat $YAML
-python -u main.py $YAML
-
-date
-echo "SLURM JOB FINISHED"

examples/260809-Si/Si_08V1_2.yaml

@@ -1,59 +0,0 @@
-job:
-  type: "random+sobo"
-  random_iters: 100
-  sobo_iters: 1000
-
-io:
-  input_data_path: '/home/swim/shared/Si_project/data/Si8V1_2.mat'
-  result_dir: '/home/swim/bo-ptycho/results/260809-Si/Si8V1_2'
-  verbosity: 1
-
-ptycho:
-  engine: 'fold_slice'
-  path: '/home/swim/fold_slice-stable'
-  params:
-    voltage: 200
-    alpha_max: 30
-    defocus: -200
-    rot_ang: 1.3
-    Nlayers: 25
-    thickness: 350
-    rbf: 37
-    Nprobe: 1
-    N_scan_x: 64
-    N_scan_y: 64
-    tilt_x: 4
-    tilt_y: 0 
-    scan_step_size: 0.36
-    Niter: 100
-    Niter_save_results: 100
-    CBED_size: 192
-    ADU: 1
-    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_posiiton_search: 1
-    regularize_layers: 0.2
-    variable_probe: false
-
-bo:
-  mode: 'sobo'
-  acquisition: 'ucb'
-  metric: 'log_fourier'
-  params:
-    alpha_max:
-    defocus:
-      radius: 100
-    rot_ang:
-    Nlayers:
-      radius: 5
-      type: int
-    thickness:
-      radius: 150
-  train_x:
-  train_y:

examples/260809-Si/Si_30V3_2.sub

@@ -1,26 +0,0 @@
-#!/bin/bash
-#SBATCH --job-name=Si30V
-#SBATCH --nodes=1
-#SBATCH --ntasks=1
-#SBATCH --cpus-per-task=1
-#SBATCH --gres=gpu:rtx-6000ada:1
-#SBATCH --time=100:00:00
-#SBATCH --output=/home/swim/slurm-logs/job_%j.log
-
-echo "30V"
-pwd
-hostname
-date
-
-export PATH=/home/shared/MATLAB/R2021a/bin:$PATH
-export PATH=/usr/local/cuda-11.4/bin:$PATH
-export LD_LIBRARY_PATH=/usr/local/cuda-11.4/lib64:$LD_LIBRARY_PATH
-
-source /home/swim/bo-ptycho/venv/bin/activate
-
-YAML=examples/260809-Si/Si_30V3_2.yaml
-cat $YAML
-python -u main.py $YAML
-
-date
-echo "SLURM JOB FINISHED"

examples/260809-Si/Si_30V3_2.yaml

@@ -1,59 +0,0 @@
-job:
-  type: "random+sobo"
-  random_iters: 100
-  sobo_iters: 1000
-
-io:
-  input_data_path: '/home/swim/shared/Si_project/data/Si30V3_2.mat'
-  result_dir: '/home/swim/bo-ptycho/results/260809-Si/Si30V3_2'
-  verbosity: 1
-
-ptycho:
-  engine: 'fold_slice'
-  path: '/home/swim/fold_slice-stable'
-  params:
-    voltage: 200
-    alpha_max: 30
-    defocus: 175
-    rot_ang: 0.1
-    Nlayers: 30
-    thickness: 680
-    rbf: 37
-    Nprobe: 1
-    N_scan_x: 64
-    N_scan_y: 64
-    tilt_x: 5
-    tilt_y: 3 
-    scan_step_size: 0.35
-    Niter: 100
-    Niter_save_results: 100
-    CBED_size: 192
-    ADU: 1
-    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_posiiton_search: 1
-    regularize_layers: 0.2
-    variable_probe: false
-
-bo:
-  mode: 'sobo'
-  acquisition: 'ucb'
-  metric: 'log_fourier'
-  params:
-    alpha_max:
-    defocus:
-      radius: 50
-    rot_ang:
-    Nlayers:
-      radius: 5
-      type: int
-    thickness:
-      radius: 100
-  train_x:
-  train_y:

examples/260812-Si/2V.yaml

@@ -1,60 +0,0 @@
-job:
-  type: "random+sobo"
-  random_iters: 8
-  sobo_iters: 128
-
-io:
-  input_data_path: '/home/swim/shared/Si_project/data/Si2V1_2.mat'
-  result_dir: '/home/swim/bo-ptycho/results/260812-Si/Si2V1_2'
-  verbosity: 1
-
-ptycho:
-  engine: 'fold_slice'
-  path: '/home/swim/fold_slice-stable'
-  params:
-    voltage: 200
-    alpha_max: 30
-    defocus: -250
-    rot_ang: 0.3
-    Nlayers: 20
-    thickness: 250
-    rbf: 37
-    Nprobe: 1
-    N_scan_x: 64
-    N_scan_y: 64
-    tilt_x: 2
-    tilt_y: 0 
-    scan_step_size: 0.36
-    Niter: 100
-    Niter_save_results: 100
-    CBED_size: 192
-    ADU: 1
-    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: 512
-    probe_posiiton_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: 100
-  train_x:
-  train_y:

examples/260812-Si/job.sub

@@ -1,26 +0,0 @@
-#!/bin/bash
-#SBATCH --job-name=Si2V
-#SBATCH --nodes=1
-#SBATCH --ntasks=1
-#SBATCH --cpus-per-task=1
-#SBATCH --gres=gpu:rtx-6000ada:4
-#SBATCH --time=100:00:00
-#SBATCH --output=/home/swim/slurm-logs/job_%j.log
-
-echo "2V"
-pwd
-hostname
-date
-
-export PATH=/home/shared/MATLAB/R2021a/bin:$PATH
-export PATH=/usr/local/cuda-11.4/bin:$PATH
-export LD_LIBRARY_PATH=/usr/local/cuda-11.4/lib64:$LD_LIBRARY_PATH
-
-source /home/swim/bo-ptycho/venv/bin/activate
-
-YAML=examples/260812-Si/2V.yaml
-cat $YAML
-python -u main.py $YAML
-
-date
-echo "SLURM JOB FINISHED"