I am using the new version of PlantSeg (v1.6.0) with napari viewer.
Data-Processing, Prediction with CUDA, and 2D Watershed run fine,
but I am having trouble with napari shutting down when I run Clustering with GASP.
$ plantseg --napari
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
WARNING: QMainWindowLayout::count: ?
WARNING: QMainWindowLayout::count: ?
WARNING: QMainWindowLayout::count: ?
WARNING: QMainWindowLayout::count: ?
WARNING: QMainWindowLayout::count: ?
INFO: PlantSeg Napari info - 19:05:18 22.09.2023 - Main: Plantseg is ready!
INFO: PlantSeg Napari info - 19:05:56 22.09.2023 - Open file: 2019.02.01_ClearSee 53_late stage.lif_F_z000_ch00_compresses Correctly imported, voxel_size: [0.3, 0.07700000053201803, 0.07700000053201803] um
INFO: PlantSeg Napari info - 19:06:01 22.09.2023 - Gaussian Smoothing: Widget Gaussian Smoothing computation started
INFO: PlantSeg Napari info - 19:07:07 22.09.2023 - Gaussian Smoothing: Widget Gaussian Smoothing computation complete in 65.77s
INFO: PlantSeg Napari info - 19:07:15 22.09.2023 - Rescaling: Widget Rescaling computation started
INFO: PlantSeg Napari info - 19:08:24 22.09.2023 - Rescaling: Widget Rescaling computation complete in 68.78s
INFO: PlantSeg Napari info - 19:08:44 22.09.2023 - UNet Predictions: Widget UNet Predictions computation started
2023-09-22 19:08:44,627 [Dummy-2] INFO PlantSeg - Using batch size of 1 for prediction
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2023/2023 [05:59<00:00, 5.62it/s]
INFO: PlantSeg Napari info - 19:14:50 22.09.2023 - UNet Predictions: Widget UNet Predictions computation complete in 365.95s
INFO: PlantSeg Napari info - 19:15:15 22.09.2023 - Watershed Segmentation: Widget Watershed Segmentation computation started
INFO: PlantSeg Napari info - 19:17:38 22.09.2023 - Watershed Segmentation: Widget Watershed Segmentation computation complete in 142.95s
INFO: PlantSeg Napari info - 19:45:14 22.09.2023 - GASP Clustering: Widget GASP Clustering computation started
Killed
The parameters are as follows, using mostly default values.
Data
Arabidopsis thaliana ovules dataset
Hi!
I am using the new version of PlantSeg (v1.6.0) with napari viewer. Data-Processing, Prediction with CUDA, and 2D Watershed run fine, but I am having trouble with napari shutting down when I run Clustering with GASP.
The parameters are as follows, using mostly default values. Data Arabidopsis thaliana ovules dataset
Prediction model: generic_confocal_3D_unet Device: cuda Watershed Stacked:2D Threshold: 0.50 Min-size: 100 Clustering Aggl.Mode: GASP Segmentation factor: 0.60 Min-size: 100
The napari window suddenly closed and the terminal displayed "Killed", but no other error messages were displayed. Please give me some advice.