Segment identical trees

[pentadotddot]

Hi!

Great tool!

After segmenting the tree stems, is it possible to cluster the trees one-by-one? So like add an ID or a unique color to the trees, creating identical segmentations, to measure single tree properties.

Thank you in advance!

Also I get a strange error while its evaluating one of my pointclouds:

Loading file... /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/working_point_cloud.las
Choosing most confident labels...
Saving file: /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/segmented.las
Saved.
Semantic segmentation took 31.120779752731323 s
Semantic segmentation done
Loading segmented point cloud...
Loading file... /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/segmented.las
Making DTM...
    DTM Done
Saving file: /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/DTM.las
Saved.
Plot area is approximately 0.041975 ha
Getting heights above DTM...
Saving file: /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/terrain_points.las
Saved.
Saving file: /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/stem_points.las
Saved.
Saving file: /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/vegetation_points.las
Saved.
Saving file: /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/cwd_points.las
Saved.
Saving file: /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/segmented_cleaned.las
Saved.
Post-processing took 4.3995654582977295 seconds
Post processing done.
Loading file... /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/stem_points.las
stempoints ['x', 'y', 'z', 'red', 'green', 'blue', 'label', 'height_above_DTM']
Loading file... /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/DTM.las
Loading file... /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/terrain_points.las
Loading file... /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/vegetation_points.las
/home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/ground_veg.las is empty...
Loading file... /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/cwd_points.las
Canopy Cover Fraction: 0.4922597696809515
Understory Veg Fraction: 0.0
Coarse Woody Debris Fraction: 0.019444968850292618
Making and clustering slices...
 24 / 24
Done

Clustering skeleton...
Saving skeleton and cluster array...
Saving file: /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/skeleton_cluster_visualisation.las
Saved.
Making kdtree...
Making initial branch/stem section clusters...
 12 / 12
Done

Starting multithreaded cylinder fitting... This can take a while.
 12 / 12
Done

Deleting cyls with CCI less than: 0.3
Saving cylinder array...
Saving file: /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/full_cyl_array.las
Saved.
Making full_cyl visualisation...
 44 / 44
Done


Saving cylinder visualisation...
Saving file: /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/initial_cyl_vis.las
Saved.
Sorting Cylinders...
 0.01.000

Correcting Cylinder assignments...
Tree ID 10 / 19
/home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/sorted_full_cyl_array.las is empty...
Cylinder interpolation...
Getting heights above DTM...
/home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/interpolated_full_cyl_array.las is empty...
(0, 14)
Cylinder Outlier Removal...
Saving file: /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/tree_aware_cropped_point_cloud.las
Saved.
Measuring plot took 206.86684823036194 s
Measuring plot done.
Loading file... /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/DTM.las
Loading file... /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/cwd_points.las
Loading file... /home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/ground_veg.las
/home/mobilrouter/FSCT/data/train/NeRF_F_I_smaller_FSCT_output/ground_veg.las not found.
Traceback (most recent call last):
  File "/home/mobilrouter/FSCT/./scripts/run.py", line 54, in <module>
    FSCT(
  File "/home/mobilrouter/FSCT/scripts/run_tools.py", line 49, in FSCT
    report_writer.make_report()
  File "/home/mobilrouter/FSCT/scripts/report_writer.py", line 50, in make_report
    self.plot_outputs()
  File "/home/mobilrouter/FSCT/scripts/report_writer.py", line 161, in plot_outputs
    self.ground_veg_map[self.ground_veg[:, self.veg_dict["height_above_dtm"]] >= 0.5, 2] = 1
IndexError: index 7 is out of bounds for axis 1 with size 3