tls.sh

#!/bin/bash

############################ parameters #################################################
# General parameters
CLEAR_INPUT_FOLDER=1  # 1: clear input folder, 0: not clear input folder
CONDA_ENV="pdal-env" # conda environment for running the pipeline

# Tiling parameters
data_folder="" # path to the folder containing the data
N_TILES=3
SLICE_THICKNESS=0.5
FIND_STEMS_HEIGHT=1.5
FIND_STEMS_THICKNESS=0.5
GRAPH_MAXIMUM_CUMULATIVE_GAP=3
ADD_LEAVES_VOXEL_LENGTH=0.5
FIND_STEMS_MIN_POINTS=50
GRAPH_EDGE_LENGTH=1.0
ADD_LEAVES_EDGE_LENGTH=1.0

############################# 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
  case $opt in
    d) data_folder="$OPTARG"
    ;;
    n) N_TILES="$OPTARG"
    ;;
    s) SLICE_THICKNESS="$OPTARG"
    ;;
    h) FIND_STEMS_HEIGHT="$OPTARG"
    ;;
    t) FIND_STEMS_THICKNESS="$OPTARG"
    ;;
    g) GRAPH_MAXIMUM_CUMULATIVE_GAP="$OPTARG"
    ;;
    l) ADD_LEAVES_VOXEL_LENGTH="$OPTARG"
    ;;
    m) FIND_STEMS_MIN_POINTS="$OPTARG"
    ;;
    o) GRAPH_EDGE_LENGTH="$OPTARG"
    ;;
    p) ADD_LEAVES_EDGE_LENGTH="$OPTARG"
    ;;
    \?) echo "Invalid option -$OPTARG" >&2
    ;;
  esac
done

# print the letters to choose from in getopts
echo "      The list of letters for the parameters:"
echo "d: data_folder"
echo "n: N_TILES"
echo "s: SLICE_THICKNESS"
echo "h: FIND_STEMS_HEIGHT"
echo "t: FIND_STEMS_THICKNESS"
echo "g: GRAPH_MAXIMUM_CUMULATIVE_GAP"
echo "l: ADD_LEAVES_VOXEL_LENGTH"
echo "m: FIND_STEMS_MIN_POINTS"
echo "o: GRAPH_EDGE_LENGTH"
echo "p: ADD_LEAVES_EDGE_LENGTH"

echo " "
# print values of the parameters 
echo "      The values of the parameters:"
echo "data_folder: $data_folder"
echo "N_TILES: $N_TILES"
echo "SLICE_THICKNESS: $SLICE_THICKNESS"
echo "FIND_STEMS_HEIGHT: $FIND_STEMS_HEIGHT"
echo "FIND_STEMS_THICKNESS: $FIND_STEMS_THICKNESS"
echo "GRAPH_MAXIMUM_CUMULATIVE_GAP: $GRAPH_MAXIMUM_CUMULATIVE_GAP"
echo "ADD_LEAVES_VOXEL_LENGTH: $ADD_LEAVES_VOXEL_LENGTH"
echo "FIND_STEMS_MIN_POINTS: $FIND_STEMS_MIN_POINTS"
echo "GRAPH_EDGE_LENGTH: $GRAPH_EDGE_LENGTH"
echo "ADD_LEAVES_EDGE_LENGTH: $ADD_LEAVES_EDGE_LENGTH"

# exit 0

# 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

# Do the instances and iterate over all the segmented point clouds
for segmented_point_cloud in $data_folder/segmented_point_clouds/*.segmented.ply; do
    # get the name of the segmented point cloud
    segmented_point_cloud_name=$(basename $segmented_point_cloud)
    # get the name of the segmented point cloud without the extension
    segmented_point_cloud_name_no_ext="${segmented_point_cloud_name%.*}"
    # create a directory for the instance segmented point clouds
    mkdir -p $data_folder/instance_segmented_point_clouds/$segmented_point_cloud_name_no_ext
    # iterate over all the tiles of the segmented point cloud
    for tile in $data_folder/segmented_point_clouds/tiled/$segmented_point_cloud_name_no_ext/*.ply; do
        # get the name of the tile
        tile_name=$(basename $tile)
        # get the name of the tile without the extension
        tile_name_no_ext="${tile_name%.*}"
        echo "Processing $tile"
        # show the output folder
        echo "Output folder: $data_folder/instance_segmented_point_clouds/$segmented_point_cloud_name_no_ext/$tile_name_no_ext"
        python3 fsct/points2trees.py \
        -t $tile \
        --tindex $data_folder/segmented_point_clouds/tiled/$segmented_point_cloud_name_no_ext/tile_index.dat \
        -o $data_folder/instance_segmented_point_clouds/$segmented_point_cloud_name_no_ext/$tile_name_no_ext \
        --n-tiles $N_TILES \
        --slice-thickness $SLICE_THICKNESS \
        --find-stems-height $FIND_STEMS_HEIGHT \
        --find-stems-thickness $FIND_STEMS_THICKNESS \
        --pandarallel --verbose \
        --add-leaves \
        --add-leaves-voxel-length $ADD_LEAVES_VOXEL_LENGTH \
        --graph-maximum-cumulative-gap $GRAPH_MAXIMUM_CUMULATIVE_GAP \
        --save-diameter-class \
        --ignore-missing-tiles \
        --find-stems-min-points $FIND_STEMS_MIN_POINTS \
        --graph-edge-length $GRAPH_EDGE_LENGTH \
        --add-leaves-edge-length $ADD_LEAVES_EDGE_LENGTH 
    done
done

# do merging of the instance segmented point clouds
for instance_segmented_point_cloud in $data_folder/instance_segmented_point_clouds/*; do
    python nibio_preprocessing/merging_and_labeling.py \
    --data_folder $instance_segmented_point_cloud \
    --output_file $instance_segmented_point_cloud/output_instance_segmented.ply
done

# create the results folder
mkdir -p $data_folder/results

# # create the input data folder
mkdir -p $data_folder/results/input_data

# # move input data (ply and las) to the input data folder
find $data_folder/ -maxdepth 1 -type f -name '*.ply' -exec mv {} $data_folder/results/input_data/ \;
find $data_folder/ -maxdepth 1 -type f -name '*.las' -exec mv {} $data_folder/results/input_data/ \;

# # create the segmented point clouds folder
mkdir -p $data_folder/results/segmented_point_clouds

# move segmented point clouds to the segmented point clouds folder
find $data_folder/segmented_point_clouds/ -maxdepth 1 -type f -name '*segmented.ply' -exec mv {} $data_folder/results/segmented_point_clouds/ \;

# # create the instance segmented point clouds folder
mkdir -p $data_folder/results/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 $data_folder/instance_segmented_point_clouds/*; do
    # get the name of the instance segmented point cloud
    instance_segmented_point_cloud_name=$(basename $instance_segmented_point_cloud)
    # get the name of the instance segmented point cloud without the extension and add the suffix instance_segmented
    instance_segmented_point_cloud_name_no_ext="${instance_segmented_point_cloud_name%.*}.instance_segmented"
    # move the instance segmented point cloud to the instance segmented point clouds folder
    find $instance_segmented_point_cloud/ -maxdepth 1 -type f -name '*.ply' -exec mv {} $data_folder/results/instance_segmented_point_clouds/$instance_segmented_point_cloud_name_no_ext.ply \;
    # map the instance segmented point cloud to las file
    pdal translate \
    $data_folder/results/instance_segmented_point_clouds/$instance_segmented_point_cloud_name_no_ext.ply \
    $data_folder/results/instance_segmented_point_clouds/$instance_segmented_point_cloud_name_no_ext.las \
    --writers.las.dataformat_id=3 \
    --writers.las.extra_dims=all
done

 # change the names of the segmented files to *.segmented.las
for segmented_point_cloud_in_ply in $data_folder/results/segmented_point_clouds/*; do
    # get the prefix of the point clouds
    SEGMENTED_POINT_CLOUDS_PREFIX="segmented."
    # get the ending of the point clouds
    SEGMENTED_POINT_CLOUDS_EXTENSION="ply"
    # get the name of the ply point cloud
    segmented_point_cloud_in_ply_name=$(basename $segmented_point_cloud_in_ply)
    # got the name of the las file without the starting prefix and the .ply extension
    segmented_point_cloud_in_las_name_no_prefix_no_extension=${segmented_point_cloud_in_ply_name#$SEGMENTED_POINT_CLOUDS_PREFIX}
    segmented_point_cloud_in_las_name_no_extension=${segmented_point_cloud_in_las_name_no_prefix_no_extension%.$SEGMENTED_POINT_CLOUDS_EXTENSION}
    # convert it to las and move it to the segmented point clouds folder
    pdal translate \
    $segmented_point_cloud_in_ply \
    $data_folder/results/segmented_point_clouds/$segmented_point_cloud_in_las_name_no_extension.las \
    --writers.las.dataformat_id=3 \
    --writers.las.extra_dims=all
done

# 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/ \
--inst_seg_folder $data_folder/results/instance_segmented_point_clouds/ \
--output_folder $data_folder/results/instance_segmented_point_clouds_with_ground \
--verbose

echo " "
echo "Done"
# print path to the results folder and the subfolders
echo "Results can be found here: $data_folder/results"
echo "Results containing the input point clouds can be found here:  $data_folder/results/input_data"
echo "Results containing the segmented point clouds can be found here:  $data_folder/results/segmented_point_clouds"
echo "Results containing the instance segmented point clouds can be found here:  $data_folder/results/instance_segmented_point_clouds"
echo "Results containing the instance segmented point clouds with ground can be found here:  $data_folder/results/instance_segmented_point_clouds_with_ground"