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How to visualise my training dataset to confirm it is being correctly loaded? #167
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I believe there's another bug that may be missed though. I found this because my data is grayscaled so only one channel. This line in
cc @muellerdo |
Hey @emmanuel-nwogu, good spot! Thanks!! Philip (@Deathlymad) implemented the visualization and will have a look on it :) Best Regards, |
afaik this should be fixed on the dev branch @muellerdo |
Above is the file structure of my dataset where segmentation.nii.gz and imaging.nii.gz are 3D NIFTI files with multiple slices. Also, I'm using code resembling the piece below to load the dataset.
I'm especially worried about my training data loading because I had to change the
slice_axis
in theNIFTIslicer_interface
init for the sample_data size to be correct while following this tutorial.When I run
sample = data_io.sample_loader("scan_c", load_seg=True)
, I get aSample
of shape (H, W, N, C). N is my number of slices and my C = 1.I found
visualize_samples
but I think it may be bugged. At this line, it tries to convert the sample to grayscale, even though my num of channels is 1, which leads to an IndexError. Here are the code and error respectively.Error:
I may be misusing it though, I am not sure. Please, let me know. :)
As an aside but kinda related, I tried writing my own
visualize_samples
but I could not find the definition ofoverlay_segmentation
as used here.The text was updated successfully, but these errors were encountered: