new job

config.yaml

@@ -1,18 +1,18 @@
 io:
-  input_data_path: '/home/swim/data/BTO_01_crop.mat'
-  result_dir: '/home/swim/Si_project/wrapper/results'
+  input_data_path: '/home/swim/Si_project/data/Si2V1_1.mat'
+  result_dir: '/home/swim/Si_project/wrapper/results260721'
   verbosity: 1
 
 ptycho:
   engine: 'fold_slice'
   path: '/home/swim/Si_project/lemon-ptychography/fold_slice'
   params:
+    voltage: 200
     alpha_max: 30
     defocus: -200
-    rot_ang: 1
+    rot_ang: 0.3
     Nlayers: 20
     thickness: 250
-    voltage: 200
     rbf: 37
     Nprobe: 1
     N_scan_x: 64
@@ -21,23 +21,23 @@ ptycho:
     tilt_y: 0 
     scan_step_size: 0.36
     Niter: 100
-    Niter_save_results: 100
+    Niter_save_results: 50
     CBED_size: 192
     ADU: 1
-    extra_print_info: 'test'
+    extra_print_info: 'swim Si2V1_1.mat'
     scan_number: 1
     gpu_id: 1
     roi_label: '0_Ndp64'
     diff_pattern_blur: 1
     probe_change_start: 1
     object_change_start: 1
-    grouping: 128
+    grouping: 64
     probe_posiiton_search: 1
-    regularize_layers: 0.1
+    regularize_layers: 0.2
     variable_probe: 'false'
 
 bo:
-  parallel_jobs: 4
+  parallel_jobs: 1
   max_iterations: 64
   mode: 'sobo'
   acquisition: 'ucb'
@@ -47,10 +47,10 @@ bo:
       radius: 100
     rot_ang:
     Nlayers:
-      radius: 10
+      radius: 5
       type: int
     thickness:
       radius: 100
-  train_x: '/home/swim/Si_project/wrapper/results/train_x.npy'
-  train_y: '/home/swim/Si_project/wrapper/results/train_y.npy'
+  train_x:
+  train_y:
   

job.sub

@@ -19,6 +19,6 @@ export LD_LIBRARY_PATH=/usr/local/cuda-11.4/lib64:$LD_LIBRARY_PATH
 source /home/swim/Si_project/wrapper/venv/bin/activate
 
 cat config.yaml
-python -u bo-ptycho.py config.yaml
+python -u main.py config.yaml
 
 echo "SLURM JOB FINISHED"

main.py

@@ -1,22 +1,24 @@
 import os
 import sys
 import yaml
+import numpy as np
 
 import bo
 import ptycho
 
 def main(config):
 
-    randombo = bo.RandomBOEngine(config)
+    result_dir = config['io']['result_dir']
+    os.makedirs(result_dir, exist_ok=True)
 
-    max_iterations = config['bo']['max_iterations']
+    randombo = bo.RandomBOEngine(config)
 
     for j in range(10):
         job_config = randombo.ask()
 
         ptycho_engine = ptycho.FoldSlicePtychoEngine(job_config)
         ptycho_engine.run()
-        y_value = ptycho_engine.metric()
+        y_value = -np.log(ptycho_engine.metric())
 
         randombo.tell(job_config, y_value)
 
@@ -25,13 +27,15 @@ def main(config):
 
 
     sobo = bo.SingleObjectiveBOEngine(config)
+    sobo.train_x = randombo.state['train_x']
+    sobo.train_y = randombo.state['train_y']
 
-    for j in range(max_iterations):
+    for j in range(config['bo']['max_iterations']):
         job_config = sobo.ask()
 
         ptycho_engine = ptycho.FoldSlicePtychoEngine(job_config)
         ptycho_engine.run()
-        y_value = ptycho_engine.metric()
+        y_value = -np.log(ptycho_engine.metric())
 
         sobo.tell(job_config, y_value)