You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
(plant-seg) acom0007@MU00158125X ~ % plantseg --config /Users/acom0007/Downloads/config_pred_wide_applicability.yaml
You are using the latest version of PlantSeg: 1.8.1.
/Users/acom0007/micromamba/envs/plant-seg/lib/python3.11/site-packages/plantseg/models/zoo.py:286: UserWarning: Model generic_plant_nuclei_3D not found in the models zoo configuration.
warn(f"Model {model_name} not found in the models zoo configuration.")
Traceback (most recent call last):
File "/Users/acom0007/micromamba/envs/plant-seg/bin/plantseg", line 10, in <module>
sys.exit(main())
^^^^^^
File "/Users/acom0007/micromamba/envs/plant-seg/lib/python3.11/site-packages/plantseg/run_plantseg.py", line 83, in main
process_config(args.config)
File "/Users/acom0007/micromamba/envs/plant-seg/lib/python3.11/site-packages/plantseg/run_plantseg.py", line 64, in process_config
raw2seg(config)
File "/Users/acom0007/micromamba/envs/plant-seg/lib/python3.11/site-packages/plantseg/pipeline/raw2seg.py", line 117, in raw2seg
config = config_validation(config)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/acom0007/micromamba/envs/plant-seg/lib/python3.11/site-packages/plantseg/pipeline/config_validation.py", line 263, in config_validation
config = recursive_config_check(config, template)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/acom0007/micromamba/envs/plant-seg/lib/python3.11/site-packages/plantseg/pipeline/config_validation.py", line 191, in recursive_config_check
config[key] = recursive_config_check(config[key], template[key])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/acom0007/micromamba/envs/plant-seg/lib/python3.11/site-packages/plantseg/pipeline/config_validation.py", line 187, in recursive_config_check
config[key] = value(key, config[key])
^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/acom0007/micromamba/envs/plant-seg/lib/python3.11/site-packages/plantseg/pipeline/config_validation.py", line 146, in __call__
out = check(key, out, self.fallback)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/acom0007/micromamba/envs/plant-seg/lib/python3.11/site-packages/plantseg/pipeline/config_validation.py", line 100, in model_exist
_error_message(f"value must be one of {_list_models}", key, value, fallback)
File "/Users/acom0007/micromamba/envs/plant-seg/lib/python3.11/site-packages/plantseg/pipeline/config_validation.py", line 29, in _error_messageraiseRuntimeError(_error)
RuntimeError: key: model_name has got value: generic_plant_nuclei_3D, but value must be one of ['generic_confocal_3D_unet', 'generic_light_sheet_3D_unet', 'confocal_3D_unet_ovules_ds1x', 'confocal_3D_unet_ovules_ds2x', 'confocal_3D_unet_ovules_ds3x', 'confocal_2D_unet_ovules_ds2x', 'lightsheet_3D_unet_root_ds1x', 'lightsheet_3D_unet_root_ds2x', 'lightsheet_3D_unet_root_ds3x', 'lightsheet_2D_unet_root_ds1x', 'lightsheet_3D_unet_root_nuclei_ds1x', 'lightsheet_2D_unet_root_nuclei_ds1x', 'confocal_2D_unet_sa_meristem_cells', 'confocal_3D_unet_sa_meristem_cells', 'lightsheet_3D_unet_mouse_embryo_cells', 'confocal_3D_unet_mouse_embryo_nuclei', 'PlantSeg_3Dnuc_platinum']
We're not sure if this is a typo in the demo config file, or a placeholder that wasn't meant to be used, or a missing update to plantseg...?
At any rate, the README instructions only specify to change the path, so we would super appreciate more guidance on how to use the models correctly! 🙏
The text was updated successfully, but these errors were encountered:
I just tried to run the generic plantseg segmentation with a collaborator using the sample config file, which uses this model:
go-nuclear/plantseg/configs/config_pred_wide_applicability.yaml
Line 40 in 12caacb
but we ran into this error:
We're not sure if this is a typo in the demo config file, or a placeholder that wasn't meant to be used, or a missing update to plantseg...?
At any rate, the README instructions only specify to change the
path
, so we would super appreciate more guidance on how to use the models correctly! 🙏The text was updated successfully, but these errors were encountered: