cleaning bash scripts|

bash_helper_scripts/get_hard_data_for_playground.sh

+# remove all the files in the source folder
+SOURCE_FOLDER=/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground
+rm -rf $SOURCE_FOLDER/*
+
+cp /home/nibio/mutable-outside-world/data/raw_for_pipeline_test/Plot69_2022-06-15_09-08-53_9pct_time.las \
+/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground
+
+# change name of the file to first.laz 
+mv /home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/Plot69_2022-06-15_09-08-53_9pct_time.las \
+/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/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
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bash_helper_scripts/get_simple_data_for_playground.sh

+# remove all the files in the source folder
+SOURCE_FOLDER=/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground
+rm -rf $SOURCE_FOLDER/*
+
+cp /home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/playground_data/* \
+/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground
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bash_helper_scripts/get_small_data_for_playground.sh

+SOURCE_FOLDER=/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground
+rm -rf $SOURCE_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
+
+# 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
+
+# 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
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bash_helper_scripts/get_strange_data_for_playground.sh

+# remove all the files in the source folder
+SOURCE_FOLDER=/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground
+rm -rf $SOURCE_FOLDER/*
+
+cp /home/nibio/mutable-outside-world/data/strange_shape_cloud_for_pipeline_test/2022-08-05_11-03-31_9pct_time_scan.laz \
+/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground
+
+# change name of the file to first.laz 
+mv /home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/2022-08-05_11-03-31_9pct_time_scan.laz \
+/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/first.laz
+
+# # copy first.laz to second.laz
+cp /home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/first.laz \
+/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/second.laz
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bash_helper_scripts/run_all.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
+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
+############################# end of parameters declaration ############################
+
+
+# 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" != "$CONDA_ENV" ]; then
+    echo "The activated conda environment is not the same as the one specified in the parameters."
+    echo "Please activate the correct conda environment and run the script again."
+    exit 1
+fi
+
+# check if conda is activated if not activate it
+# if [ -z "$CONDA_DEFAULT_ENV" ]; then
+#     echo "Conda is not activated. Activating it"
+#     conda activate pdal-env-1
+# else
+#     echo "Conda is activated"
+# fi
+
+# read input folder as a command line argument
+# show a message to provide the input folder
+data_folder=$1
+
+# if no input folder is provided, case a message and exit
+if [ -z "$data_folder" ]
+then
+    echo "No input folder provided, please provide the input folder as a command line argument"
+    exit 1
+fi
+
+# check there are las files in the input folder
+count=`ls -1 $data_folder/*.las 2>/dev/null | wc -l`
+
+if [ $count != 0 ]; then
+    echo "$count las files found in the input folder"
+else
+    echo "No las files found in the input folder. All files in the input folder should have .las extension."
+    exit 1
+fi 
+
+#TODO: do the point cloud filtering using nibio_preprocessing/filter_point_cloud.py
+echo "Doing the point cloud filtering to density of 150 points per cubic meter"
+python nibio_preprocessing/point_cloud_filter.py --dir $data_folder --density 150 --verbose --in_place
+
+# covert all the files to ply format using nibio_preprocessing/convert_files_in_folder.py
+echo "Converting all the files to ply format"
+python nibio_preprocessing/convert_files_in_folder.py --input_folder $data_folder --output_folder $data_folder --out_file_type ply
+
+# 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 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
+fi
+
+# # iterate over all files in the input folder and do sematic segmentation
+echo  "Starting semantic segmentation"
+for file in $data_folder/*.ply; do
+    # python fsct/run.py --point-cloud $file --batch_size 5 --odir $data_folder --model ./fsct/model/model.pth
+    python fsct/run.py --point-cloud $file --batch_size 5 --odir $data_folder --verbose
+done
+
+# 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 '*.segmented.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
+
+# create folder for the output of the second step
+
+mkdir -p $data_folder/instance_segmented_point_clouds
+
+# 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
+    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 '*.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 $instance_segmented_point_cloud)
+    # get the name of the instance segmented point cloud without the extension
+    instance_segmented_point_cloud_name_no_ext="${instance_segmented_point_cloud_name%.*}"
+    # 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.scale_x=0.01 \
+    --writers.las.scale_y=0.01 \
+    --writers.las.scale_z=0.01 \
+    --writers.las.extra_dims=all
+done
+
+echo "Done"
+echo "Results are in $data_folder/results"
+
+
+
+

bash_helper_scripts/run_chamfer.sh

+#!/bin/bash
+pdal chamfer sample_playground/results/input_data/output/0.las sample_playground/results/instance_segmented_point_clouds_with_ground/output/3.las
+

bash_helper_scripts/run_metrics.sh

+#!/bin/bash
+
+python nibio_postprocessing/get_instances_side_by_side.py \
+--input_folder /home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/results/instance_segmented_point_clouds/ \
+--output_folder /home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/results/instance_segmented_point_clouds/output \
+--instance_label 'instance_nr' \
+--verbose \
+# --merge
+
+python nibio_postprocessing/get_instances_side_by_side.py \
+--input_folder /home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/results/instance_segmented_point_clouds_with_ground/ \
+--output_folder /home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/results/instance_segmented_point_clouds_with_ground/output \
+--instance_label 'instance_nr' \
+--verbose \
+# --merge
+
+python nibio_postprocessing/get_instances_side_by_side.py \
+--input_folder /home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/results/input_data/ \
+--output_folder /home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/results/input_data/output \
+--instance_label 'treeID' \
+--verbose \
+# --merge
+

bash_helper_scripts/run_sample.sh

+#!/bin/sh
+# This is a sample run file for the "hello" example.
+# It is used to run the example from the main folder of the repository.
+
+#### The first step of the pipeline: Do semantic segmentation on the whole point cloud (has to be .ply file) ####
+# if the file is not .ply, convert it to .ply first using the follwing command:
+# pdal translate sample_data/sample_point_cloud.laz sample_data/sample_point_cloud_mapped.ply
+
+python fsct/run.py --point-cloud sample_data/sample_point_cloud.ply --batch_size 5 --odir sample_data
+
+#### The second step of the pipeline: do the tiling and tile index generation ####
+# move the output of the first step to the input folder of the second step
+
+mkdir -p sample_data/segmented_point_clouds
+mv sample_data/*.segmented.ply sample_data/segmented_point_clouds
+
+python nibio_preprocessing/tiling.py -i sample_data/segmented_point_clouds/ -o sample_data/segmented_point_clouds/tiled
+
+# This is the third step of the protol pipeline
+# python3 fsct/points2trees.py -t  Plot82_2022-06-13_10-35-41_9pct_time_CLIPPED.segmented.ply --tindex /home/nibio/mutable-outside-world/data/raw_data/tiled_data/Plot82_2022-06-13_10-35-41_9pct_time_CLIPPED/tile_index.dat -o ../output_dir_our/ --n-tiles 5 --slice-thickness .5 --find-stems-height 2 --find-stems-thickness .5 --pandarallel --verbose --add-leaves --add-leaves-voxel-length .5 --graph-maximum-cumulative-gap 3 --save-diameter-class --ignore-missing-tiles
+
+# python3 fsct/points2trees.py -t  /home/nibio/mutable-outside-world/data/raw_data/tiled_data/Plot82_2022-06-13_10-35-41_9pct_time_CLIPPED/000.ply --tindex /home/nibio/mutable-outside-world/data/raw_data/tiled_data/Plot82_2022-06-13_10-35-41_9pct_time_CLIPPED/tile_index.dat -o ../output_dir_our/ --n-tiles 5 --slice-thickness .5 --find-stems-height 2 --find-stems-thickness .5 --pandarallel --verbose --add-leaves --add-leaves-voxel-length .5 --graph-maximum-cumulative-gap 3 --save-diameter-class --ignore-missing-tiles
+
+# python3 fsct/points2trees.py \
+# -t /home/nibio/mutable-outside-world/data/segmented_data_conda/tiled_data/Plot82_2022-06-13_10-35-41_9pct_time_CLIPPED.segmented/000.ply \
+# --tindex /home/nibio/mutable-outside-world/data/segmented_data_conda/tiled_data/Plot82_2022-06-13_10-35-41_9pct_time_CLIPPED.segmented/tile_index.dat \
+# -o ../output_dir_our/ --n-tiles 3 --slice-thickness .5 --find-stems-height 2 --find-stems-thickness .5 --pandarallel --verbose --add-leaves --add-leaves-voxel-length .5 --graph-maximum-cumulative-gap 3 --save-diameter-class --ignore-missing-tiles
+
+mkdir -p sample_data/instance_segmented_point_clouds
+
+python3 fsct/points2trees.py \
+-t sample_data/segmented_point_clouds/tiled/sample_point_cloud.segmented/000.ply \
+--tindex sample_data/segmented_point_clouds/tiled/sample_point_cloud.segmented/tile_index.dat \
+-o sample_data/instance_segmented_point_clouds/ \
+--n-tiles 3 \
+--slice-thickness .5 \
+--find-stems-height 2 \
+--find-stems-thickness .5 \
+--pandarallel --verbose \
+--add-leaves \
+--add-leaves-voxel-length .5 \
+--graph-maximum-cumulative-gap 3 \
+--save-diameter-class \
+--ignore-missing-tiles 
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