Closed mcblache closed 1 month ago
Hello,
When FULL_IMG
is enable BiaPy will try to feed the entire image into the GPU, that's why it's crashing. Disable it to predict the image patch by patch (I'd recommend to increase TEST.PADDING
too, e.g. (100,100)
to have more smoother output), and if it finishes without errors the images should be in a folder called "per_image" (please check the section in our semantic segmentation doc to see the folders that are created on that workflow).
Did you try it again with my recommendations?
Hello,
Thank you very much for your answer. Sorry, I expressed myself incorrectly. In the "per image" folder, the image is not complete. For example, the initial image of size 17879 X 28292 pixels has a prediction image of size 17879 X 17879 pixels. Maybe, am I making another configuration mistake?
Thank you
Yes I tried and there are no errors when using your settings. Thank you.
The prediction should be the same size as the input image. Can you please pull the last version of the code and infer again?
I used the BIAPY GUI with the version v3.3.12 - GUI V1.0.6 in this configuration the prediction image is not complete.
When I used a notebook with a new environment conda (biapy version 3.4.2) the prediction is OK.
Thank you very much for your answer
We need to update the GUI to the new version 3.4.3 of BiaPy, where some bugs are already fixed. If you can use for the moment the notebook (recently updated all to 3.4.3) that's great. I will write you though the #4 issue so you can check the new version of the GUI when we finish it. I'm closing this.
Hello,
I used the Biapy GUI to train an UNET (Semantic Segmentation template) on 2D with RGB images (slide scanner image). I would like to predict a large image (1.5GB). However, Biapy do a memory error:
Note that the process 62791 is biapy himself.
I don't understand. This image is smaller than the training images.
I do patches 512X512. When I put FULL-IMG = False it works but I do not have the prediction of all the images. Can you help me please?
Thanks
Marie-Claire
PS: Here are my settings :