bash script for running sean

optimization_pipeline/sem_seg.sh

@@ -11,7 +11,7 @@ data_folder="" # path to the folder containing the data
 ############################# end of parameters declaration ############################
 
 # extract tiling parameters as command line arguments with the same default values
-while getopts "d:n:s:h:t:g:l:m:o:p:" opt; do
+while getopts "d:" opt; do
   case $opt in
     d) data_folder="$OPTARG"
     ;;

optimization_pipeline/sem_seg_sean.sh

+#!/bin/bash
+
+############################ 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
+
+# Tiling parameters
+data_folder="" # path to the folder containing the data
+
+############################# end of parameters declaration ############################
+
+# extract tiling parameters as command line arguments with the same default values
+while getopts "d:" opt; do
+  case $opt in
+    d) data_folder="$OPTARG"
+    ;;
+    \?) echo "Invalid option -$OPTARG" >&2
+    ;;
+  esac
+done
+
+# print the letters to choose from in getopts
+echo "      The list of letters for the parameters:"
+echo "d: data_folder"
+
+# print values of the parameters 
+echo "      The values of the parameters:"
+echo "data_folder: $data_folder"
+
+# Do the environment setup
+# check if PYTHONPATH is set to the current directory
+if [ -z "$PYTHONPATH" ]; then
+    echo "PYTHONPATH is not set. Setting it to the current directory"
+    export PYTHONPATH=$PWD
+else
+    echo "PYTHONPATH is set to '$PYTHONPATH'"
+fi
+
+# conda activate pdal-env-1
+
+# check if activated conda environment is the same as the one specified in the parameters
+if [ "$CONDA_DEFAULT_ENV" != "$CONDA_ENV" ]; then
+    echo "The activated conda environment is not the same as the one specified in the parameters."
+    echo "Please activate the correct conda environment and run the script again."
+    exit 1
+fi
+
+# if no input folder is provided, case a message and exit
+if [ -z "$data_folder" ]
+then
+    echo " "
+    echo "No input folder provided, please provide the input folder as a command line argument"
+    exit 1
+fi
+
+# clear input folder if CLEAR_INPUT_FOLDER is set to 1
+if [ $CLEAR_INPUT_FOLDER -eq 1 ]
+then
+    # delete all the files and folders except the ply, las and laz files in the input folder
+    echo "Clearing input folder"
+    find $data_folder/ -type f ! -name '*.ply' ! -name '*.las' ! -name '*.laz' -delete # delete all the files except the ply and las files
+    find $data_folder/* -type d -exec rm -rf {} + # delete all the folders in the input folder
+    echo "Removed all the files and folders except the ply and las files in the input folder"
+fi
+
+# check if there are las and laz files in the input folder
+count_las=`ls -1 $data_folder/*.las 2>/dev/null | wc -l`
+count_laz=`ls -1 $data_folder/*.laz 2>/dev/null | wc -l`
+
+count=$(($count_las + $count_laz))
+
+if [ $count != 0 ]; then
+    echo "$count las files found in the input folder good to go with!"
+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
+
+# 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
+
+# do the conversion to ply
+python nibio_preprocessing/convert_files_in_folder.py --input_folder $data_folder --output_folder $data_folder --out_file_type ply --verbose
+
+# clear input folder if CLEAR_INPUT_FOLDER is set to 1
+if [ $CLEAR_INPUT_FOLDER -eq 1 ]
+then
+    # delete all the files and folders except the ply and las files in the input folder
+    echo "Clearing input folder"
+    find $data_folder/ -type f ! -name '*.ply' ! -name '*.las' -delete # delete all the files except the ply and las files
+    find $data_folder/* -type d -exec rm -rf {} + # delete all the folders in the input folder
+    echo "Removed all the files and folders except the ply and las files in the input folder"
+fi
+
+# move the output of the first step to the input folder of the second step
+mkdir -p $data_folder/segmented_point_clouds
+
+# move all .segmented.ply files to the segmented_point_clouds folder if they are in the input folder
+find $data_folder/ -type f -name '*.ply' -exec mv {} $data_folder/segmented_point_clouds/ \;
+
+# do the tiling and tile index generation
+echo "Tiling and tile index generation"
+python nibio_preprocessing/tiling.py \
+-i $data_folder/segmented_point_clouds/ \
+-o $data_folder/segmented_point_clouds/tiled \
+--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
+
+# iterate over all the directories in the tiled folder
+for d in $data_folder/segmented_point_clouds/tiled/*/; do
+    for f in $d/*.ply; do
+        echo "Processing $f file..."
+        python sean_sem_seg/run_single_file.py \
+        --model /home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/fsct/model/model.pth \
+        --point-cloud $f \
+        --batch_size 10 \
+        --odir $d \
+        --verbose \
+        # --tile-index $d/tile_index.dat \
+        # --buffer 2
+    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
+# delete all the folders in the tiled subfolders
+find $data_folder/segmented_point_clouds/tiled/*/* -type d -exec rm -rf {} +
+
+# # merge the segmented point clouds
+echo "Merging the segmented point clouds"
+# iterate over all the directories in the tiled folder
+for d in $data_folder/segmented_point_clouds/tiled/*/; do
+    # get a base name of the directory
+    base_name=$(basename $d)
+    # create a name for the merged file
+    merged_file_name=$data_folder/segmented_point_clouds/$base_name.segmented.ply
+    python nibio_preprocessing/merging_and_labeling.py \
+    --data_folder $d \
+    --output_file $merged_file_name \
+    --only_merging
+done
+
+# rename all the segmented.ply files to .ply in the tiled subfolders
+for file in $data_folder/segmented_point_clouds/tiled/*/*; do
+    # skip if the file is not a ply file
+    if [[ $file != *.ply ]]; then
+        continue
+    fi
+    mv -- "$file" "${file%.segmented.ply}.ply"
+done
+
+# rename all the folder in the tiled subfolders to .segmented suffix
+for d in $data_folder/segmented_point_clouds/tiled/*; do
+    echo "Renaming $d to ${d%.segmented}"
+    # mv "$d" "${d%.segmented}"
+    mv $d{,.segmented}
+done
+
+
+# create folder for the output of the second step
+
+mkdir -p $data_folder/instance_segmented_point_clouds