plant-seg
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Possible issues in 1.8.1
Good afternoon,
I am running the 1.8.1 version of plantseg on a linux Mint 22 machine. Everything works as intended but in some case I get the following error:
2024-10-01 17:44:23,683 [MainThread] INFO PlantSeg - Computing segmentation with dtWS...
Traceback (most recent call last):
File "/home/pcasanova/anaconda3/envs/plant-seg/bin/plantseg", line 10, in <module>
sys.exit(main())
^^^^^^
File "/home/pcasanova/anaconda3/envs/plant-seg/lib/python3.12/site-packages/plantseg/run_plantseg.py", line 83, in main
process_config(args.config)
File "/home/pcasanova/anaconda3/envs/plant-seg/lib/python3.12/site-packages/plantseg/run_plantseg.py", line 64, in process_config
raw2seg(config)
File "/home/pcasanova/anaconda3/envs/plant-seg/lib/python3.12/site-packages/plantseg/pipeline/raw2seg.py", line 149, in raw2seg
output_paths = pipeline_step()
^^^^^^^^^^^^^^^
File "/home/pcasanova/anaconda3/envs/plant-seg/lib/python3.12/site-packages/plantseg/pipeline/steps.py", line 70, in __call__
return [self.read_process_write(input_path) for input_path in self.input_paths]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/pcasanova/anaconda3/envs/plant-seg/lib/python3.12/site-packages/plantseg/pipeline/steps.py", line 88, in read_process_write
output_data = self.process(input_data)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/pcasanova/anaconda3/envs/plant-seg/lib/python3.12/site-packages/plantseg/segmentation/gasp.py", line 84, in process
ws = self.dt_watershed(pmaps)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/pcasanova/anaconda3/envs/plant-seg/lib/python3.12/site-packages/plantseg/segmentation/functional/segmentation.py", line 73, in dt_watershed
segmentation, _ = distance_transform_watershed(boundary_pmaps, **ws_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/pcasanova/anaconda3/envs/plant-seg/lib/python3.12/site-packages/elf/segmentation/watershed.py", line 138, in distance_transform_watershed
seeds = compute_maxima(dt, marker=np.nan, allowAtBorder=True, allowPlateaus=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
RuntimeError:
Invariant violation!
connected components: Need more labels than can be represented in the destination type.
(/home/conda/feedstock_root/build_artifacts/libvigra_1725360696982/work/include/vigra/union_find.hxx:283)
I have no idea if its an issue from my side but I was wondering if somebody else had this issue before
And not related but also a bit bothersome is that in regular monitors (1920x1080) the gui screem does not work because the run button does not fit. I run it with the config files so it does not affet me but I thought that it was worth mentioning.