new yaml schema, new TODO

LICENSE

@@ -0,0 +1,19 @@
+Copyright (c) 2026 Sooyoung Cheong
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the "Software"),
+to deal in the Software without restriction, including without limitation the
+rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+sell copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

TODO.md

@@ -1,5 +1,4 @@
 # TODO:
-
 - fold_slice:
     - load diffractions / hdf5 files; change only param per job
     - restructure `FoldSlicePtychoEngine.__init__()` to load data but not params
@@ -17,10 +16,9 @@
 - change job.sub to job.sh
     - dynamic jobname
     - pre-check result directory
-- clean up examples for Si-FIB paper version
 
 # TODAY:
-- rename `BOEngine` to `Sampler`
+- change yaml schema, use stages in config-new.yaml
 - separation of available GPUs and parallel sample batches
 - prepare next batch for efficient GPU use
 

config-new.yaml

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+io:
+  input_data_path: '/home/swim/shared/Si_project/data/Si2V1_2.mat'
+  result_dir: '/home/swim/bo-ptycho/results/test'
+  verbosity: 1
+
+ptycho:
+  engine: 'fake'
+  # 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: 10
+    Niter_save_results: 10
+
+    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
+
+search:
+  metric: log_fourier
+  
+  params:
+    defocus:
+      radius: 100
+    Nlayers:
+      radius: 5
+      type: int
+    thickness:
+      radius: 150
+  
+  train_x:
+  train_y:
+
+  stages:
+    # - sampler: fixed
+    
+    # - sampler: grid
+    #   defocus: 7
+    #   Nlayers: 11
+    #   thickness: 7
+
+    - sampler: random
+      samples: 16
+
+    - sampler: sobo
+      samples: 256
+      batch: 4
+      acquisition: 'ucb'
+      beta: 0.1

readme.md

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+# bo-ptycho
+
+This code is a (re)implementation of Bayesian Optimized ptychography in python for use at LEMON lab, used for
+
+- Optimization-based Thickness Estimation and FIB-induced Damage Characterization of TEM Sample via Multislice Electron Ptychography (manuscript)
+
+
+
+## Code usage
+
+Prerequisites:
+1. Create a python virtual environment with [requirements.txt](./requirements.txt)
+2. Download [fold_slice](#)
+2. Download [experimental data](#)
+
+Reconstruction and parameter optimization:
+1. Edit [config.yaml](./config.yaml)
+    - Example configurations can be found under `examples/silicon-fib/`
+    - Set io.input_data_path and io.result_dir as needed (WARNING: the result directory will be completely removed)
+    - Set ptycho.path to your fold_slice path
+2. Edit [job.sub](./job.sub)
+    - Set the SBATCH configurations as needed (especially `gres` and `output`)
+    - The number of GPUs should match bo.batch in config.yaml
+    - Set the virtual environment path
+    - Set the config.yaml path
+3. Submit the job via SLURM