[1pt] Add lake masking to stage- and flow-based CatFIM

[EmilyDeardorff]

Previously, CatFIM would inundate areas that we know to be lakes based on our FIM data. This update masks out lakes from stage- and flow-based CatFIM inundation.

Changes

• inundation-mapping/tools/catfim/generate_categorical_fim_mapping.py: Added code to stage-based CatFIM to filter out HydroIDs that are associated with a non-null LakeID. Also uses new lake masking function to mask lakes from flow- and stage-based CatFIM right before the tifs are saved, at the end of produce_stage_based_lid_tifs(). Comments in this area were also cleaned up.
• inundation-mapping/tools/tools_shared_functions.py: Added function that uses the water bodies geopackage to mask out lakes from a tiff.

Testing

• Tested flow- and stage-based CatFIM at site auon6 (HUC 04140201)

• Additional testing detailed in Issue 1358

• Potential HUC/site combos where stage-based CatFIM intersects a lake (for additional testing):
  '07090002' 'okfi2'
  '07130008' 'kcai2'
  '07140202' 'ylow4'
  '10070001' 'brlk1'
  '11070204' 'tifm7'
  '11070208' 'olbo2'
  '11100301' 'wtnw2'
  '05020002' 'cpei3'
  '04300108' 'wlbn6'
  '04040002' 'racw3'

• Potential HUC/site combos where flow-based CatFIM intersects a lake (for additional testing):

ahps_lid	huc
hrho2	11100302
dibt2	12020002
lolt2	12030201

Deployment Plan (For developer use)

How does the changes affect the product?

• Code only?
• If applicable, has a deployment plan be created with the deployment person/team?
• Require new or adjusted data inputs? Does it have start, end and duration code (in UTC)?
• If new or updated data sets, has the FIM code been updated and tested with the new/adjusted data (subset is fine, but must be a subset of the new data)?
• Require new pre-clip set?
• Has new or updated python packages?

Issuer Checklist (For developer use)

You may update this checklist before and/or after creating the PR. If you're unsure about any of them, please ask, we're here to help! These items are what we are going to look for before merging your code.

• Informative and human-readable title, using the format: [_pt] PR: <description>
• Links are provided if this PR resolves an issue, or depends on another other PR
• If submitting a PR to the dev branch (the default branch), you have a descriptive Feature Branch name using the format: dev-<description-of-change> (e.g. dev-revise-levee-masking)
• Changes are limited to a single goal (no scope creep)
• The feature branch you're submitting as a PR is up to date (merged) with the latest dev branch
• pre-commit hooks were run locally
• Any change in functionality is tested
• New functions are documented (with a description, list of inputs, and expected output)
• Placeholder code is flagged / future todos are captured in comments
• CHANGELOG updated with template version number, e.g. 4.x.x.x
• Add yourself as an assignee in the PR as well as the FIM Technical Lead

Merge Checklist (For Technical Lead use only)

• Update CHANGELOG with latest version number and merge date
• Update the Citation.cff file to reflect the latest version number in the CHANGELOG
• If applicable, update README with major alterations

[RobHanna-NOAA]

Testing for Stage Based looks great. Carson mentioned we should add this to Flow Based as well.

[EmilyDeardorff]

Implemented this change to flow-based and it looks like it's working as expected! I just need to do a bit more testing and then we should be good to go. The lake needing to be masked out from this example is in the bottom right corner. In the example with lake masking, we can see that inundation in the lake polygon has been removed.

[RobHanna-NOAA]

looks good. Tested against:

• 11100301 - olbo2 - good for FB and SB
• 04140201 - auon6 - good for FB and SB
• 11100302 - hrho2 - good for FB, changed as expected.

However.. 11100302 - hrho2 for SB showed a likely unrelated issue
in the new version it says that it is not mapped as Gage not in HAND usgs gages records.
But it was mapped and fine in 4.5.11.1

I will make a separate card for it.