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Improve the denoise quality from hard thresholding

Zhang, Chen requested to merge local_sigma into next

This PR introduces the following changes:

  • patch in a block is now ordered based on similarity instead of the naive search order
  • the missing threshold calculator is now added back in the hard thresholding function
  • the example notebook is updated
  • the second step, re-filtering is temporarily disabled as we need more time to understand how to properly compute the sigma for wiener_hadamard filter.

Example output from notebook (assuming 2% detector gain error): bm3d_vs_bm3dornl_sino

Testing instructions

  • Create and activate the conda environment
  • Checkout the feature branch
  • Run unit test
  • Run the example notebook

EWM item: 5223

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