Open adkrishnan opened 1 month ago
Hi @adkrishnan thanks for reporting this issue!
Legacy GUI is now not the main focus, but is still very useful. When it launches, it checks this template file and it's configs: https://github.com/kreshuklab/plant-seg/blob/aece266541317858ba3e793308a752f188302a38/plantseg/resources/config_gui_template.yaml#L84
unless there is already a config file before the installation of PlantSeg in ~/.plantseg_models/configs/
(because you had previous versions of PlantSeg). So if you try to delete the files there, the KeyError
may be fixed.
This has been documented before but I know the docs are hard to find when you actually need it:
Hey @adkrishnan Athul says you tried deleting the folder but still has KeyError
, in this case I recommend you to try and see what does this give:
(plant-seg) [qyu@kreshuk configs]$ python
Python 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:36:13) [GCC 12.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from plantseg import PATH_CONFIGS
>>> PATH_CONFIGS
PosixPath('/home/qyu/.plantseg_models/configs')
So basically you need to remove everything inside the PATH_CONFIGS
to update to the latest config.
I deleted everything and installed bioimageio.core using mamba install -c conda-forge bioimageio.core
separately along with PlantSeg
Its working now
Thankyou very much
For the missing package it is very strange because I did include it in the config: https://github.com/kreshuklab/plant-seg/blob/aece266541317858ba3e793308a752f188302a38/conda-recipe/meta.yaml#L34
But since PlantSeg works for you know I'll leave this issue open and come back later to see if anything is wrong with the environment.
Thanks again for reporting!
I get the same issue on my machine
I get the same issue on my machine
Do you know what conda uses for checking the requirements? I have bioimageio.core all three configs:
Only meta.yaml
counts. It is strange that the deps are not built into the package dependencies by Conda, but I have seen it in the past. As a short-term solution, let's add it to the installation instructions.
Only
meta.yaml
counts. It is strange that the deps are not built into the package dependencies by Conda, but I have seen it in the past.
Ohhh I never imagined Conda would do that because it feels like a major bug of it.
As a short-term solution, let's add it to the installation instructions.
Do you have time for the docs? Otherwise I can add it after our meeting.
Hello, Facing an issue while trying to open the GUI for the latest version of PlantSeg 1.8.1 after an install in a fresh environment
ModuleNotFoundError: No module named 'bioimage.io'
(same error even on trying to open Napari GUI)Even on installing bioimage.core separately displays an error in the legacy_gui/gui_widgets.py
KeyError: 'is_segmentation'