Update cmos

[KriSun95]

A PR for FOXSI-4's GSE 🦊

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First and foremost, thank you so much for opening a PR for this repository. Any contribution is greatly appreciated.

Note

To make this process as easy as possible to follow when looking over and discussing the PR, please respond to each field below.

The fields below should inform the reader of the purpose(s) for the PR without having to infer things from the code itself.

What is reason for this PR

• Bug fix
• New feature
• Behavioural change
• Other
  • ...

Describe why the PR is needed

CMOS does not have a way to display images that are validated for flight. Ways to address this will be proposed in this PR and supporting document(s) from CMOS instrument team.

Note: This PR should offer no justification for these changes, only show how they are able to be implemented in the time available. Justification for all changes should be given in the supporting documentation where each commit is subject to approval.

Please provide a description of the changes/additions being made to the package

The changes/additions are as follows:

1. Dark frame images for dark frame subtraction is implement with dark frames suitable for flight CMOS settings.
   • See commit d44eee0 for changes in the code
   • See commit 51c8215 for moving correct flight dark frames to the correct place
2. PC data is now displayed such that values below a threshold of 15 DN are set to 0 and those above or equal to 15 DN are set to 1
   • See commit 9bd1b24
3. To avoid the large bright region in the CMOS QL images from affecting the colour scaling of the image, a QL mask is applied to set a block of pixels in this lower left corner to 0 for plotting
   • See commit f5cd6cf
4. The photon ratio values shown in the GSE were changed to consider the percentage of pixels with values (dark frame subtracted) greater than or equal to 60 DN in two masked areas. On-center area (mask 1 file below) is a small square in the centre of the PC CMOS image and Off-center (mask 2 file below) is a larger square area (with height of full image but not width) that excludes the On-centre square.
   • See commit dd552d6
   • where On-centre was previously called the "whole photon ratio" in the GSE display
   • where Off-centre was previously called the "part photon ratio" in the GSE display
   • this change was rejected and reverted with commit 507220e
5. The QL image for CMOS 1 is now plotted in a log-scale colour map and the QL image for CMOS 2 is plotted with a linear-scale colour map.
   • See commit 3479f1d
   • See supporting documentation for justification also for dynamically changing colour-map minimum and maximum
   • This change involved changing how the image is plotted using matplotlib. All images in the GSE are plotted with an RGBA array; however, log-scale cannot be applied (or at least not easily) to an RGB/RGBA array when plotting with matplotlib.pyplot.imshow, for example. Therefore, the green values in the RGBA array (the colour that actually holds the image data to plot) is isolated and plotted as "grey-scale" using a custom colour-bar that runs from black to green. This is a colour-bar in-keeping with the previous previous plots of CMOS and the other detector plots.

Are there any dangers in this change

Each commit has been tested as far as I could and it does not appear to introduce anything breaking.

Note, however, that testing was limited as no data is available from flight settings that has produced an image. Therefore, the changes were validated either by corroboration in calculations from the GSE code and the instrument team member's code using noise or sealed source data, or by just trying to ensure the code runs and acts as expected with the changes applied (i.e., checking nothing breaks from the changes).

Please refer to supporting document from the CMOS instrument team for justifications and rationale for all changes in this PR.

[r-lycopene]

Here is the documentation which shows you why these changes are needed.
[https://docs.google.com/document/d/1ewaViXh3P6FQFPyb29a00uEa7fMJ3sHQZjXy9f8Fpak]

[LinErinG]

For the QL mask part, I would like to request that the mask be applied in a way with fewer changes. Since the mask is a simple one (masking out one box), I think we can hardcode the area we want to mask out and do the masking in one or two lines. I would rather do that than read in an additional file, in order to constitute a smaller change to the code. @KriSun95

[KriSun95]

For the QL mask part, I would like to request that the mask be applied in a way with fewer changes. Since the mask is a simple one (masking out one box), I think we can hardcode the area we want to mask out and do the masking in one or two lines. I would rather do that than read in an additional file, in order to constitute a smaller change to the code. @KriSun95

Commit 7f9012d addresses this comment. The file was removed and numpy is used directly to create the mask (the same code used to produce the file in the first place). This means that the mask code is more transparent and another file does not need to be introduced into the repository. The overall code structure is kept as to only produce the mask once at the start and allow numpy to handle the quick masking for plotting.

Additionally, commit 507220e reverts the changes made in commit dd552d6 as this requested edit to the GSE was not accepted. The bullet point in the top description will be struck through.