Cropping image missing values after imwarp

Question

Jorge Barrasa 2023-3-1

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https://ww2.mathworks.cn/matlabcentral/answers/1921220-cropping-image-missing-values-after-imwarp

编辑： Image Analyst 2023-3-17

I'm struggling with a theoretically simple problem, but for which I've managed to find no solution.

I've a 3D image (512x512x72) on which I have applied a rigid transformation (translation and rotation) using imwarp.

imwarp adds a given value to "pixels outside the input image" (which can be controlled via the parameter 'FillValues').

I would like to crop the output image of imwarp in a way that all those filled values are completely removed and I only keep those voxels with real values. I don't think there is a way to do this via the input parameters of imwarp.

A possible way of approaching this problem is by creating a mask (after setting 'FillValues' to NaN, for example) of the voxels with real values and then trying to come up with a way of finding the largest box that fits within that mask. This sounds simple but it is really a nightmare to try to solve this in an efficient way, so I'm not sure if that's the way to go.

Any ideas would be very appreciated :)

Thanks!

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Answer 1

Divyank 2023-3-16

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Hello @Jorge Barrasa, I believe you're on the right track with the idea of creating a mask and finding the largest box that fits within it.

Here's a possible approach:

Apply the transformation using imwarp with 'FillValues' set to NaN to create the transformed image.
Create a binary mask of the transformed image, where 1 corresponds to real voxels and 0 corresponds to NaN voxels.
Use the mask to find the minimum and maximum indices of non-zero voxels along each dimension (x, y, and z) using the min and max functions in MATLAB.
Crop the transformed image using the minimum and maximum indices found in step 3 to obtain the largest box that fits within the mask.

I hope it helps!

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Image Analyst 2023-3-16

Can you upload an example of your output image?

Jorge Barrasa 2023-3-17

Hi @Image Analyst,

The size of the image is too large to attach in the message, so I've uplodaded it to this link:

https://filesender.belnet.be/?s=download&token=ab1add6d-67e1-496c-b0fd-b124851d0637

It has a variable called tmp of size 512x512x72. Imwarp has included some NaN values in the out-of-image positions. The goal is to remove all the NaNs with a minimally sized crop.

Thanks,

Jorge

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