From f03642c4d1bb64e6d399f1819d1b4ff8daa3c497 Mon Sep 17 00:00:00 2001
From: Maciej Wielgosz <maciej.wielgosz@nibio.no>
Date: Sat, 17 Dec 2022 12:57:30 +0100
Subject: [PATCH] update sematic seg. sean with switch off flag for removal of
small tiles
---
bash_helper_scripts/get_test_corrected.sh | 8 ++++++
optimization_pipeline/sem_seg_sean.sh | 30 ++++++++++++++++-------
2 files changed, 29 insertions(+), 9 deletions(-)
create mode 100755 bash_helper_scripts/get_test_corrected.sh
diff --git a/bash_helper_scripts/get_test_corrected.sh b/bash_helper_scripts/get_test_corrected.sh
new file mode 100755
index 0000000..67adabf
--- /dev/null
+++ b/bash_helper_scripts/get_test_corrected.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/corrected/test/*.las $TARGET_FOLDER
+
diff --git a/optimization_pipeline/sem_seg_sean.sh b/optimization_pipeline/sem_seg_sean.sh
index 962c376..74b1f12 100755
--- a/optimization_pipeline/sem_seg_sean.sh
+++ b/optimization_pipeline/sem_seg_sean.sh
@@ -7,14 +7,19 @@ CONDA_ENV="pdal-env-1" # conda environment for running the pipeline
# Tiling parameters
data_folder="" # path to the folder containing the data
+remove_small_tiles=0 # 1: remove small tiles, 0: not remove small tiles
############################# end of parameters declaration ############################
# extract tiling parameters as command line arguments with the same default values
-while getopts "d:" opt; do
+
+# add remove_small_tiles parameter
+while getopts "d:z:" opt; do
case $opt in
d) data_folder="$OPTARG"
;;
+ z) remove_small_tiles="$OPTARG"
+ ;;
\?) echo "Invalid option -$OPTARG" >&2
;;
esac
@@ -27,6 +32,7 @@ echo "d: data_folder"
# print values of the parameters
echo " The values of the parameters:"
echo "data_folder: $data_folder"
+echo "remove_small_tiles: $remove_small_tiles"
# Do the environment setup
# check if PYTHONPATH is set to the current directory
@@ -108,14 +114,20 @@ python nibio_preprocessing/tiling.py \
--tile_size 10
# remove small tiles using nibio_preprocessing/remove_small_tiles.py
-for d in $data_folder/segmented_point_clouds/tiled/*; do
- echo "Removing small tiles from $d"
- python nibio_preprocessing/remove_small_tiles.py \
- --dir $d \
- --tile_index $d/tile_index.dat \
- --min_density 75 \
- --verbose
-done
+
+# make it conditional bassed remove_small_tiles parameter
+if [ $remove_small_tiles -eq 1 ]
+then
+ # iterate over all the directories in the tiled folder
+ for d in $data_folder/segmented_point_clouds/tiled/*; do
+ echo "Removing small tiles from $d"
+ python nibio_preprocessing/remove_small_tiles.py \
+ --dir $d \
+ --tile_index $d/tile_index.dat \
+ --min_density 75 \
+ --verbose
+ done
+fi
# iterate over all the directories in the tiled folder
for d in $data_folder/segmented_point_clouds/tiled/*/; do
--
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