cleaning before production v0

.gitignore

@@ -15,4 +15,5 @@ wandb/
 sample_data/segmented_point_clouds/*
 *.dat
 *.json
-*.png
+*.png
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+*.txt
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bash_helper_scripts/are_files_identical.sh

+
+
+./bash_helper_scripts/get_austrian_sample_instance_p2.sh
+pdal translate maciek/p2_instance.las maciek/p2_instance.ply
+python fsct/run.py --model /home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/fsct/model/model.pth --point-cloud maciek/p2_instance.ply --batch_size 10 --odir maciek/ --verbose --keep-npy
+
+python helpers/compare_files_in_folders.py --folder1 maciek/p2_instance.tmp --folder2 old_maciek/p2_instance.tmp --verbose
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run_all_fine_grained.sh → bash_helper_scripts/run_all_fine_grained.sh

@@ -111,7 +111,7 @@ 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 \
+        --model /home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/fsct/model/model.pth \
         --point-cloud $f \
         --batch_size 5 \
         --odir $d \

config/config.yaml

-files_formats:
+general:
+  input_folder: 'some_path'
+  output_folder: 'some_path'
+  run_sematic_segmentation: true
+  run_instance_segmentation: false
+label_formats:
   label_for_instances_in_gt: 'treeID'
-  label_for_instances_in_predicted:  
+  label_for_instances_in_predicted: 'instance_nr'
+semantic_segmentation_params:
+  first: 'some'

test_run.sh

-#!/bin/bash
-
-# run run_all_command_lines.sh with the following arguments:
-
-data_folder="/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground" 
-N_TILES=3
-
-SLICE_THICKNESS=0.382368454442735
-FIND_STEMS_HEIGHT=1.8948172056774
-FIND_STEMS_THICKNESS=0.9980435744231868
-GRAPH_MAXIMUM_CUMULATIVE_GAP=13.841583930676254
-ADD_LEAVES_VOXEL_LENGTH=0.19332721135500391
-FIND_STEMS_MIN_POINTS=495
-GRAPH_EDGE_LENGTH=0.5652008887940575
-ADD_LEAVES_EDGE_LENGTH=0.5622733957401558
-
-# get test data from the following link:
-bash ./bash_helper_scripts/get_terrestial_sem_seg_test.sh
-
-# run run_all_command_lines.sh with the following arguments:
-./run_all_command_line.sh -d $data_folder \
--n $N_TILES \
--s $SLICE_THICKNESS \
--h $FIND_STEMS_HEIGHT \
--t $FIND_STEMS_THICKNESS \
--g $GRAPH_MAXIMUM_CUMULATIVE_GAP \
--l $ADD_LEAVES_VOXEL_LENGTH \
--m $FIND_STEMS_MIN_POINTS \
--o $GRAPH_EDGE_LENGTH \
--p $ADD_LEAVES_EDGE_LENGTH
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