update for hyper params search

bash_helper_scripts/get_val_corrected_after_sem_seg_selected_files.sh

+#!/bin/bash
+
+TARGET_FOLDER=/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground
+# clean the folder
+rm -rf $TARGET_FOLDER/*
+
+mkdir $TARGET_FOLDER/segmented_point_clouds
+mkdir $TARGET_FOLDER/instance_segmented_point_clouds
+
+cp -r /home/nibio/mutable-outside-world/data/corrected/validation_after_seg/burum2_tile_-100_0.las $TARGET_FOLDER
+cp -r /home/nibio/mutable-outside-world/data/corrected/validation_after_seg/Plot89_tile_-25_0.las $TARGET_FOLDER
+cp -r /home/nibio/mutable-outside-world/data/corrected/validation_after_seg/plot82_tile_-25_0.las $TARGET_FOLDER
+cp -r /home/nibio/mutable-outside-world/data/corrected/validation_after_seg/Plot104_tile_-25_0.las $TARGET_FOLDER
+
+cp -r /home/nibio/mutable-outside-world/data/corrected/validation_after_seg/segmented_point_clouds/burum2_tile_-100_0.segmented.ply $TARGET_FOLDER/segmented_point_clouds
+cp -r /home/nibio/mutable-outside-world/data/corrected/validation_after_seg/segmented_point_clouds/Plot89_tile_-25_0.segmented.ply $TARGET_FOLDER/segmented_point_clouds
+cp -r /home/nibio/mutable-outside-world/data/corrected/validation_after_seg/segmented_point_clouds/plot82_tile_-25_0.segmented.ply $TARGET_FOLDER/segmented_point_clouds
+cp -r /home/nibio/mutable-outside-world/data/corrected/validation_after_seg/segmented_point_clouds/Plot104_tile_-25_0.segmented.ply $TARGET_FOLDER/segmented_point_clouds
+
+cp -r /home/nibio/mutable-outside-world/data/corrected/validation_after_seg/segmented_point_clouds/tiled/burum2_tile_-100_0.segmented $TARGET_FOLDER/segmented_point_clouds/tiled
+cp -r /home/nibio/mutable-outside-world/data/corrected/validation_after_seg/segmented_point_clouds/tiled/Plot89_tile_-25_0.segmented $TARGET_FOLDER/segmented_point_clouds/tiled
+cp -r /home/nibio/mutable-outside-world/data/corrected/validation_after_seg/segmented_point_clouds/tiled/plot82_tile_-25_0.segmented $TARGET_FOLDER/segmented_point_clouds/tiled
+cp -r /home/nibio/mutable-outside-world/data/corrected/validation_after_seg/segmented_point_clouds/tiled/Plot104_tile_-25_0.segmented $TARGET_FOLDER/segmented_point_clouds/tiled
+
+
+

bayes_opt_run.py

@@ -44,6 +44,20 @@ pbounds = {
     'add_leaves_edge_length': (0.2, 1.5)
 }
 
+# partially fixed params for faster optimization
+
+# pbounds = {
+#     'n_tiles': (3, 3),
+#     'slice_thickness': (0.25, 0.75), # important
+#     'find_stems_height': (1.6, 1.6), # 1.6
+#     'find_stems_thickness': (0.1, 1.0), # important
+#     'graph_maximum_cumulative_gap': (12.9, 12.9), # 12.9
+#     'add_leaves_voxel_length': (0.25, 0.25), # 0.25
+#     'find_stems_min_points': (50, 500), # important
+#     'graph_edge_length': (0.92, 0.92), # 0.92
+#     'add_leaves_edge_length': (0.85, 0.85) # 0.85
+# }
+
 optimizer = BayesianOptimization(
     f=bayes_opt_main,
     pbounds=pbounds,
@@ -52,12 +66,12 @@ optimizer = BayesianOptimization(
 )
 
 # load the logs
-load_logs(optimizer, logs=["./bayes_opt_run_logs.json"])
+# load_logs(optimizer, logs=["./our_model_opt.json"])
 
-logger = JSONLogger(path="./bayes_opt_run_logs_1.json")
+logger = JSONLogger(path="./our_model_non_cut_trees_4_files.json")
 optimizer.subscribe(Events.OPTIMIZATION_STEP, logger)
 
 optimizer.maximize(
-    init_points=1,
-    n_iter=100
+    init_points=5,
+    n_iter=200
 )

nibio_preprocessing/convert_files_in_folder.py

 import os
 import argparse
+from joblib import Parallel, delayed
 from matplotlib import use
 from tqdm import tqdm
 
@@ -78,8 +79,12 @@ class ConvertFilesInFolder(object):
             logging.info("Found {} files that can be converted.".format(len(file_paths)))
 
         # iterate over all files and convert them
-        for file_path in tqdm(file_paths):
-            self.convert_file(file_path)
+
+        # for file_path in tqdm(file_paths):
+        #     self.convert_file(file_path)
+
+        # use joblib to speed up the process
+        Parallel(n_jobs=-1)(delayed(self.convert_file)(file_path) for file_path in tqdm(file_paths))
         
         # print out the progress
         if self.verbose: