From 54af7cb1fe3d89b1b2667253290c50adafc6b04a Mon Sep 17 00:00:00 2001
From: Maciej Wielgosz <nibio@nibio.no>
Date: Thu, 27 Oct 2022 11:33:31 +0200
Subject: [PATCH] model path added
---
run_all_fine_grained.sh | 17 +++++++++--------
1 file changed, 9 insertions(+), 8 deletions(-)
diff --git a/run_all_fine_grained.sh b/run_all_fine_grained.sh
index 9f7c82b..67771bd 100755
--- a/run_all_fine_grained.sh
+++ b/run_all_fine_grained.sh
@@ -3,7 +3,7 @@
############################ parameters #################################################
# General parameters
CLEAR_INPUT_FOLDER=1 # 1: clear input folder, 0: not clear input folder
-CONDA_ENV="pdal-env-1" # conda environment for running the pipeline
+CONDA_ENV="pdal-env" # conda environment for running the pipeline
# Tiling parameters
N_TILES=3
@@ -65,7 +65,7 @@ else
echo "No las or laz files found in the input folder."
echo "All files in the input folder should have *.las or *.laz extension."
exit 1
-fi
+fi
# do the conversion from laz to las if there are laz files in place (this is need for metrics calculation)
python nibio_preprocessing/convert_files_in_folder.py --input_folder $data_folder --output_folder $data_folder --out_file_type las --in_place --verbose
@@ -97,7 +97,7 @@ 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
+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 \
@@ -111,14 +111,15 @@ for d in $data_folder/segmented_point_clouds/tiled/*/; do
for f in $d/*.ply; do
echo "Processing $f file..."
python fsct/run.py \
+ --model /home/nibio/mutable-outside-world/code/instance_segmentation_classic/fsct/model/model.pth
--point-cloud $f \
- --batch_size 10 \
+ --batch_size 5 \
--odir $d \
--verbose \
# --tile-index $d/tile_index.dat \
# --buffer 2
done
-done
+done
# remove all the files in the tiled subfolders except the *segmented.ply and tile_index.dat files
find $data_folder/segmented_point_clouds/tiled/*/ -type f ! -name '*segmented.ply' ! -name 'tile_index.dat' -delete # delete all the files except the segmented.ply files
@@ -140,7 +141,7 @@ for d in $data_folder/segmented_point_clouds/tiled/*/; do
done
# rename all the segmented.ply files to .ply in the tiled subfolders
-for file in $data_folder/segmented_point_clouds/tiled/*/*; do
+for file in $data_folder/segmented_point_clouds/tiled/*/*; do
# skip if the file is not a ply file
if [[ $file != *.ply ]]; then
continue
@@ -221,7 +222,7 @@ find $data_folder/segmented_point_clouds/ -maxdepth 1 -type f -name '*segmented.
# # create the instance segmented point clouds folder
mkdir -p $data_folder/results/instance_segmented_point_clouds
-# iterate over all the instance segmented point clouds
+# iterate over all the instance segmented point clouds
# move instance segmented point clouds to the instance segmented point clouds folder and rename them
for instance_segmented_point_cloud in $data_folder/instance_segmented_point_clouds/*; do
# get the name of the instance segmented point cloud
@@ -261,7 +262,7 @@ python nibio_preprocessing/add_ground_to_inst_seg_folders.py --sem_seg_folder sa
# create the instance segmented point clouds with ground folder
mkdir -p $data_folder/results/instance_segmented_point_clouds_with_ground
-
+
# to add the ground to the instance segmented point clouds
python nibio_preprocessing/add_ground_to_inst_seg_folders.py \
--sem_seg_folder $data_folder/results/segmented_point_clouds/ \
--
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