(old) Move from 2d to 3d array operations

[PinkShnack]

About

We should allow stacks of 2D arrays as inputs. This will likely speed up processing of large datasets, and certainly will when we add Cupy as an FFTFilter (#10). Several things to note:

• Allowed formats e.g. RGB, 2d, 3d (see below)
• What should be returned to the user: currently, a 3d array with the shape (z, y, x), with z being the number of images in the stack.
  • We can provide convenience functions for users to convert between formats. I think we should limit this as a "per image" basis. In other words, the functions should handle image input, not qpretrieve classes.

To do

• FFTFilter Base class work with 3D arrays
• run_pipeline steps for OAH and QLSI should also work with 3D arrays.
• Benchmark single 2d array prcessed n times against stack of n images all processed at once. Put in docs.
• Image formats. The following formats should continue to work.
  • 2D images (y, x) should be converted internally to (z, y, x)
  • 3D images (image stacks) (z, y, x) will work with above
  • 2D RGB images (y, x, 3) or RGBA (y, x, 4). The data will be assumed to be greyscale, and each channel equal. The first channel will be taken and converted as in the 2D images case above.
    • A warning should be passed to the user.
  • The shape of the returned field will be 3D, and we will provide convenience functions for conversion back to the original format.
• docs
  • compare old (3d input -> 3d output) and new versions (2d input -> 3d output)
  • show image format conversion
  • show benchmark for 2d vs 3d.
• tests:
  • data input type examples taken from real examples
  • hologram fixture not inputting size argument
  • compare 2d and 3d FFT algorithms, ensure consistency
• cicd passed
• update changelog

[PinkShnack]

This will be removed

[PinkShnack]

Hey @paulmueller, I know you are picky with the commit history. This PR is just branched off from #8, and therefore has old commits where I worked with the Cupy code. So the history isn't perfectly "clean". I've cleaned this up, but if you really want me to create a fresh branch from main, let me know.

[paulmueller]

Hey @paulmueller, I know you are picky with the commit history. This PR is just branched off from #8, and therefore has old commits where I worked with the Cupy code. So the history isn't perfectly "clean". I've cleaned this up, but if you really want me to create a fresh branch from main, let me know.

Yes, please create a fresh branch. It should be fairly simple though (create new branch and copy paste all files with override to the new working directory).

[PinkShnack]

This is being continued in #12