From 52264d67ecaf43fa3dd33ad2021c4a61cbccc86c Mon Sep 17 00:00:00 2001
From: Maciej Wielgosz <maciej.wielgosz@nibio.no>
Date: Wed, 9 Nov 2022 12:16:15 +0100
Subject: [PATCH] small updates in metrics and helper functions
---
.../get_small_data_for_playground.sh | 21 +++++++++++--------
.../get_terrestial_sem_seg_validation.sh | 8 +++++++
...instance_segmentation_metrics_in_folder.py | 8 -------
nibio_preprocessing/tiling.py | 4 ++--
pipeline_test.py | 2 --
python_wrapper_over_run_sh.py | 0
run_all_command_line.sh | 2 +-
7 files changed, 23 insertions(+), 22 deletions(-)
create mode 100755 bash_helper_scripts/get_terrestial_sem_seg_validation.sh
delete mode 100644 python_wrapper_over_run_sh.py
diff --git a/bash_helper_scripts/get_small_data_for_playground.sh b/bash_helper_scripts/get_small_data_for_playground.sh
index a5d4c9e..fe1fd63 100755
--- a/bash_helper_scripts/get_small_data_for_playground.sh
+++ b/bash_helper_scripts/get_small_data_for_playground.sh
@@ -1,13 +1,16 @@
-SOURCE_FOLDER=/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground
-rm -rf $SOURCE_FOLDER/*
+TARGET_FOLDER=/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/maciek
+rm -rf $TARGET_FOLDER/*
-cp /home/nibio/mutable-outside-world/data/small_file_pipeline_test/small_file_pipeline_test.las \
-/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground
+cp /home/nibio/mutable-outside-world/data/small_file_pipeline_test/small_file_pipeline_test.las $TARGET_FOLDER
# change name of the file to first.laz
-mv /home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/small_file_pipeline_test.las \
-/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/first.las
+mv $TARGET_FOLDER/small_file_pipeline_test.las $TARGET_FOLDER/first.las
-# copy first.laz to second.laz
-cp /home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/first.las \
-/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/second.las
\ No newline at end of file
+# make a copy of the file
+cp $TARGET_FOLDER/first.las $TARGET_FOLDER/second.las
+
+# # make a copy of the file
+# cp $TARGET_FOLDER/first.las $TARGET_FOLDER/third.las
+
+# # make a copy of the file
+# cp $TARGET_FOLDER/first.las $TARGET_FOLDER/fourth.las
\ No newline at end of file
diff --git a/bash_helper_scripts/get_terrestial_sem_seg_validation.sh b/bash_helper_scripts/get_terrestial_sem_seg_validation.sh
new file mode 100755
index 0000000..782d436
--- /dev/null
+++ b/bash_helper_scripts/get_terrestial_sem_seg_validation.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+TARGET_FOLDER=/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground
+# clean the folder
+rm -rf $TARGET_FOLDER/*
+
+cp /home/nibio/mutable-outside-world/data/terestial_data_for_training_sem_seg_model/validation/*.las $TARGET_FOLDER
+
diff --git a/metrics/instance_segmentation_metrics_in_folder.py b/metrics/instance_segmentation_metrics_in_folder.py
index b9e6509..23b6f4e 100644
--- a/metrics/instance_segmentation_metrics_in_folder.py
+++ b/metrics/instance_segmentation_metrics_in_folder.py
@@ -7,14 +7,10 @@ class InstanceSegmentationMetricsInFolder():
self,
gt_las_folder_path,
target_las_folder_path,
- gt_label_name='gt_label', #TODO: implement the same as in the instance_segmentation_metrics.py
- target_label_name='target_label', #TODO: implement the same as in the instance_segmentation_metrics.py
verbose=False
):
self.gt_las_folder_path = gt_las_folder_path
self.target_las_folder_path = target_las_folder_path
- self.gt_label_name = gt_label_name
- self.target_label_name = target_label_name
self.verbose = verbose
def main(self):
@@ -80,8 +76,6 @@ if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('--gt_las_folder_path', type=str, required=True)
parser.add_argument('--target_las_folder_path', type=str, required=True)
- parser.add_argument('--gt_label_name', type=str, default='gt_label')
- parser.add_argument('--target_label_name', type=str, default='target_label')
parser.add_argument('--verbose', action='store_true', help="Print information about the process")
args = parser.parse_args()
@@ -89,8 +83,6 @@ if __name__ == '__main__':
instance_segmentation_metrics_in_folder = InstanceSegmentationMetricsInFolder(
args.gt_las_folder_path,
args.target_las_folder_path,
- gt_label_name=args.gt_label_name,
- target_label_name=args.target_label_name,
verbose=args.verbose
)
diff --git a/nibio_preprocessing/tiling.py b/nibio_preprocessing/tiling.py
index f854eb6..b9186ef 100644
--- a/nibio_preprocessing/tiling.py
+++ b/nibio_preprocessing/tiling.py
@@ -1,4 +1,5 @@
import argparse
+from joblib import Parallel, delayed
import pdal
import os, glob
import json
@@ -84,8 +85,7 @@ class Tiling:
files = glob.glob(self.input_folder + "/*.ply")
# loop through all the files
- for file in tqdm(files):
- self.do_tiling_of_single_file(file)
+ Parallel(n_jobs=(os.cpu_count() - 2))(delayed(self.do_tiling_of_single_file)(file) for file in tqdm(files))
def convert_single_file_from_las_to_ply(self, file):
"""
diff --git a/pipeline_test.py b/pipeline_test.py
index e43b5a2..ec8de94 100644
--- a/pipeline_test.py
+++ b/pipeline_test.py
@@ -92,8 +92,6 @@ def main():
metric = InstanceSegmentationMetricsInFolder(
gt_las_folder_path = '/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/results/input_data',
target_las_folder_path = '/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/results/instance_segmented_point_clouds_with_ground',
- gt_label_name='treeID',
- target_label_name='treeID',
verbose=True
)
diff --git a/python_wrapper_over_run_sh.py b/python_wrapper_over_run_sh.py
deleted file mode 100644
index e69de29..0000000
diff --git a/run_all_command_line.sh b/run_all_command_line.sh
index e70a422..696c516 100755
--- a/run_all_command_line.sh
+++ b/run_all_command_line.sh
@@ -161,7 +161,7 @@ for d in $data_folder/segmented_point_clouds/tiled/*/; do
python fsct/run.py \
--model /home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/fsct/model/model.pth \
--point-cloud $f \
- --batch_size 5 \
+ --batch_size 10 \
--odir $d \
--verbose \
# --tile-index $d/tile_index.dat \
--
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