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sarthakpati avatar sarthakpati commented on August 25, 2024 1

Can you try by disabling resizing?

Update: instead of [3,128,128], use [128,128]. The reason behind this is that ITK reads multi-channel images as vector pixel types, and the vector dimension is not needed for processing (it is automatically handled via ITK's processing routines).

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sarthakpati avatar sarthakpati commented on August 25, 2024

Hey @orhunguley,

This is a great report, and allowed me to recreate the issue perfectly. I am hoping that I can solve it quickly and put in a PR.

Cheers!

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sarthakpati avatar sarthakpati commented on August 25, 2024

Can you try pulling from https://github.com/sarthakpati/GaNDLF/tree/100_rgb_fix to see if this fixes your problem?

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orhunguley avatar orhunguley commented on August 25, 2024

Hi Sarthak,
I got the following error with  100_rgb_fix branch:

Traceback (most recent call last):
  File "gandlf_run", line 157, in <module>
    main()
  File "gandlf_run", line 143, in main
    reset_prev=reset_prev,
  File "/home/orhunguley/Git/GanDLF_forked/GaNDLF/GANDLF/training_manager.py", line 242, in TrainingManager
    testing_data=testingData,
  File "/home/orhunguley/Git/GanDLF_forked/GaNDLF/GANDLF/training_loop.py", line 654, in training_loop
    training_data_for_torch = ImagesFromDataFrame(training_data, params, train=True)
  File "/home/orhunguley/Git/GanDLF_forked/GaNDLF/GANDLF/data/ImagesFromDataFrame.py", line 271, in ImagesFromDataFrame
    img_resized = apply_resize(img, preprocessing_params=preprocessing)
  File "/home/orhunguley/Git/GanDLF_forked/GaNDLF/GANDLF/preprocessing.py", line 87, in apply_resize
    resize_image_resolution(input, preprocessing_params["resize"]),
  File "/home/orhunguley/Git/GanDLF_forked/GaNDLF/GANDLF/preprocessing.py", line 77, in resize_image_resolution
    outputSpacing[i] = outputSpacing[i] * (inputSize[i] / output_size[i])
IndexError: index 2 is out of bounds for axis 0 with size 2

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orhunguley avatar orhunguley commented on August 25, 2024

Hi @sarthakpati,
Thanks, with setting [128, 128] the issue is solved now!

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