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cabouman / mbircone

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Background offset #130

Closed dyang37 closed 1 year ago

dyang37 commented 1 year ago

This is a pull request to merge background offset correction into master.

Compared to the previous PR, this PR makes the following changes:

  1. Use the median sinogram view instead of the mean sinogram view.

  2. Modified the script test_background_offset.py to include the following test results: a. Display the sinogram view before and after the offset correction. The purpose is to visually inspect that the background value after the correction is closer to 0. b. Plot the sinogram view with negative pixels marked in red. The purpose is to show that the area containing the object of interest has no negative pixels after the correction. c. Added a print message to show the number of negative pixels before and after the background correction.

  3. Added a new test script test_background_offset_with_recon.py. The purpose is to perform thorough test of the background offset correction by comparing the recon results before & after the correction. Results are shown below:

Recon with original sinogram: recon_orig_sino_axial210

Recon with corrected sinogram: recon_corrected_sino_axial210

The nubs on the top and bottom are better reconstructed with the corrected sinogram data.

cabouman commented 1 year ago

I ran both test scripts to completion. The images look very nice. I also looked at the scripts, and they looked good too. I'll accept the PR, but we need to make sure that the readthedocs paper is OK after this is merged into the main branch.

dyang37 commented 1 year ago

Thanks Dr. Bouman. I do see that the calc_background_offset() function is in the online readthedocs page: https://mbircone.readthedocs.io/en/latest/preprocess.html

From: Charles A Bouman @.> Sent: Monday, May 22, 2023 12:10 PM To: cabouman/mbircone @.> Cc: Yang, Diyu @.>; Author @.> Subject: Re: [cabouman/mbircone] Background offset (PR #130)

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Merged #130https://github.com/cabouman/mbircone/pull/130 into master.

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