Removed saving .mat files; takes up too much space

TODO.md

@@ -1,8 +1,13 @@
-- tag publish version for Si reconstruction
+TODO:
+
 - Clean up BO states
+    - unify `BOEngine.__init__()`
 - BO train_x/y transfer between engines for single job
 - multi-GPU dispatcher
 - template job sequences / yamls
+    - mobo
 - metric() function(s) for each ptycho engine
+    - FRC score
 - fold_slice: load diffractions / hdf5 files; change only param per job
-    - Possibly restructure PtychoEngine.__init__() to load data but not params
+    - restructure `FoldSlicePtychoEngine.__init__()` to load data but not params
+        - write new `prepare_data.m`

pipelines/sobo.py

@@ -39,9 +39,9 @@ def sobo_pipeline(config):
         print(f"SOBO sampling; iteration {RANDOM_ITERS + j}")
         job_config = sobo.ask()
         ptycho_engine = PTYCHOENGINE(job_config)
-        ptycho_engine.run(run_id=f"bo-{j:03d}")
+        ptycho_engine.run(run_id=f"bo-{RANDOM_ITERS + j:03d}")
         y_value = ptycho_engine.metric(METRIC)
         sobo.tell(job_config, y_value)
         with open(bo_txt, "a") as f:
             p = [f'{job_config['ptycho']['params'][key]:.2f}' for key in sobo.params]
-            f.write(f"{j: 8d}\t{y_value:.4f}\t{"\t".join(p)}\n")
+            f.write(f"{RANDOM_ITERS + j: 8d}\t{y_value:.4f}\t{"\t".join(p)}\n")

ptycho/fold_slice.py

@@ -81,9 +81,9 @@ class FoldSlicePtychoEngine(PtychoEngine):
         self._output = loadmat(mat_path)
 
         log_fourier_error = self._log_fourier_metric()
-        os.makedirs(os.path.join(self.config['io']['result_dir'], "mat"), exist_ok=True)
+        # os.makedirs(os.path.join(self.config['io']['result_dir'], "mat"), exist_ok=True)
         os.makedirs(os.path.join(self.config['io']['result_dir'], "tiff"), exist_ok=True)
-        shutil.copy(mat_path, os.path.join(self.config['io']['result_dir'], "mat", f"{log_fourier_error:.4f}_{run_id}.mat"))
+        # shutil.copy(mat_path, os.path.join(self.config['io']['result_dir'], "mat", f"{log_fourier_error:.4f}_{run_id}.mat")) # saving .mat files takes a lot of space (expect 20+ GB for 64*64 scan size, 300 iterations)
         shutil.copy(image_path, os.path.join(self.config['io']['result_dir'], "tiff", f"{log_fourier_error:.4f}_{run_id}.tiff"))