1290 add abm visualization from paper to memilio plot

[xsaschako]

Changes and Information

Please briefly list the changes (main added features, changed items, or corrected bugs) made:

• add visualization for the abm runs.

If need be, add additional information and what the reviewer should look out for in particular:

Merge Request - Guideline Checklist

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Checks by code author

• Every addressed issue is linked (use the "Closes #ISSUE" keyword below)
• New code adheres to coding guidelines
• No large data files have been added (files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
• Tests are added for new functionality and a local test run was successful (with and without OpenMP)
• Appropriate documentation for new functionality has been added (Doxygen in the code and Markdown files if necessary)
• Proper attention to licenses, especially no new third-party software with conflicting license has been added
• (For ABM development) Checked benchmark results and ran and posted a local test above from before and after development to ensure performance is monitored.

Checks by code reviewer(s)

• Corresponding issue(s) is/are linked and addressed
• Code is clean of development artifacts (no deactivated or commented code lines, no debugging printouts, etc.)
• Appropriate unit tests have been added, CI passes, code coverage and performance is acceptable (did not decrease)
• No large data files added in the whole history of commits(files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
• On merge, add 2-5 lines with the changes (main added features, changed items, or corrected bugs) to the merge-commit-message. This can be taken from the briefly-list-the-changes above (best case) or the separate commit messages (worst case).

[Copilot]

Pull Request Overview

This PR adds new visualization modules to support ABM simulation output analysis for infection states and ICU/death comparisons. Key changes include:

• Introduction of plotAbmInfectionStates.py for visualizing infection states and spatial location types.
• Introduction of plotAbmICUAndDeadComp.py for comparing ICU occupancy and deaths between simulation results and real-world data.
• Addition of helper functions for file loading and axis formatting to support the new visualizations.

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
pycode/memilio-plot/memilio/plot/plotAbmInfectionStates.py	New module for plotting infection states and location types from simulation HDF5 data.
pycode/memilio-plot/memilio/plot/plotAbmICUAndDeadComp.py	New module for plotting and comparing ICU occupancy and cumulative deaths with real-world data.

Comments suppressed due to low confidence (2)

pycode/memilio-plot/memilio/plot/plotAbmICUAndDeadComp.py:71

• The variable 'age_grous_string' appears to be misspelled. Consider renaming it to 'age_groups_string' for clarity.

age_grous_string = ['Age 0-4', 'Age 5-14', 'Age 15-34', 'Age 35-59', 'Age 60-79', 'Age 80+'] # Adjust as needed

pycode/memilio-plot/memilio/plot/plotAbmICUAndDeadComp.py:30

• Consider using a context manager (e.g., 'with h5py.File(..., 'r') as f:') when opening HDF5 files to ensure they are properly closed after reading.

f_p50 = h5py.File(path+"/infection_state_per_age_group/0/p50/Results.h5", 'r')

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 97.20%. Comparing base (2d50c90) to head (ab2e0e8).

Additional details and impacted files

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##             main    #1291   +/-   ##
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  Coverage   97.20%   97.20%           
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  Files         167      167           
  Lines       14915    14915           
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  Hits        14498    14498           
  Misses        417      417           

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[mknaranja]

Thanks for bringing this close to our previous plot style from the assessment paper. @jubicker Could you have a look for the detailed review?