diff --git a/bash_helper_scripts/get_val_corrected_after_sem_seg_selected_files.sh b/bash_helper_scripts/get_val_corrected_after_sem_seg_selected_files.sh new file mode 100755 index 0000000000000000000000000000000000000000..ec5973e9fe02ad0e60cc1f87017c67a2d8925e9a --- /dev/null +++ b/bash_helper_scripts/get_val_corrected_after_sem_seg_selected_files.sh @@ -0,0 +1,26 @@ +#!/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 + + + diff --git a/bayes_opt_run.py b/bayes_opt_run.py index 2296cb5972c395b0eb50e34114135102b5e9b116..b357369d2e39959e4c0caadc914abf7000a688d4 100644 --- a/bayes_opt_run.py +++ b/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 ) diff --git a/nibio_preprocessing/convert_files_in_folder.py b/nibio_preprocessing/convert_files_in_folder.py index 8eb804024a1811bcd793ae1da5f026ca10070492..d811aa8dff4167ebccb921f9435208c414cda88b 100644 --- a/nibio_preprocessing/convert_files_in_folder.py +++ b/nibio_preprocessing/convert_files_in_folder.py @@ -1,5 +1,6 @@ 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: