smallbaselinApp: generate maskObs.h5 & use it while plotting geometry

[yunjunz]

Description of proposed changes

• smallbaselineApp:

  • generate maskObs.h5, in addition to maskConnComp.h5 file, in reference_point step
  • use -m maskObs.h5 while plotting geometry at the end to get rid of the zero values in the incidence/azimuthAngle and lat/lon data for a more meaningful display

• modify_network: print # of acquisitions to keep

Reminders

• Pass Pre-commit check (green)
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• If modifying functionality, describe changes to function behavior and arguments in a comment below the function declaration.
• If adding new functionality, add a detailed description to the documentation and/or an example.

[sourcery-ai]

Reviewer's Guide

This PR teaches smallbaselineApp to generate a new observation mask from the geometry file and use it when plotting geometry products, and enhances modify_network to print the number of acquisitions kept, improving diagnostic output and visualization quality.

Sequence diagram for generating and using maskObs.h5 in smallbaselineApp

sequenceDiagram
    participant app as smallbaselineApp
    participant ut as ut
    participant gm as generate_mask
    participant ta as temporal_average
    participant viewer as view_command

    app->>ut: check_loaded_dataset(workDir, print_msg=False)
    ut-->>app: stack_file, geom_file

    app->>gm: main([stack_file, --nonzero, -o maskConnComp.h5, --update])
    app->>ta: main([stack_file, --dataset, phase, -o avgSpatialCoh.h5])
    app->>ta: main([stack_file, --dataset, phase, -o avgSpatialSNR.h5])

    app->>gm: main([geom_file, incidenceAngle, --nonzero, -o maskObs.h5, --update])

    app->>viewer: plot_result(print_aux=True)
    viewer->>viewer: relpath(stack_file, geom_file, maskObs.h5, maskTempCoh.h5)
    viewer->>viewer: build geometry view args [geom_file, -m, maskObs.h5]
    viewer-->>app: geometry plotted without zero valued observations

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Updated class diagram for smallbaselineApp and modify_network

classDiagram
    class smallbaselineApp {
        workDir
        generate_ifgram_aux_file()
        run_reference_point(step_name)
        plot_result(print_aux)
    }

    class modify_network {
        get_date12_to_drop(inps)
    }

    smallbaselineApp : maskConnComp_h5
    smallbaselineApp : maskObs_h5
    smallbaselineApp : avgSpatialCoh_h5
    smallbaselineApp : avgSpatialSNR_h5
    smallbaselineApp : geo_dir
    smallbaselineApp : pic_dir

    modify_network : date_to_keep
    modify_network : date_to_drop

    modify_network : print number of acquisitions to remove
    modify_network : print number of acquisitions to keep

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File-Level Changes

Change	Details	Files
Generate an observation mask (maskObs.h5) from the geometry file during auxiliary file generation and use it when plotting geometry to avoid zero-valued areas.	Update generate_ifgram_aux_file to retrieve both stack and geometry files from check_loaded_dataset Rename the existing connected-component mask variable for clarity and add a new path for maskObs.h5 Invoke generate_mask on incidenceAngle in the geometry file to create maskObs.h5 In plot_result, add maskObs.h5 path handling (including relative path conversion) and pass it via -m when plotting the geometry dataset	src/mintpy/smallbaselineApp.py
Improve modify_network diagnostics by printing the number of acquisitions retained.	After computing date_to_keep, print the count and list of acquisitions to keep alongside the already-printed removals	src/mintpy/modify_network.py

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[sourcery-ai]

Hey there - I've reviewed your changes - here's some feedback:

• In generate_ifgram_aux_file, you assume geom_file is present and contains an incidenceAngle dataset; consider guarding this block (e.g., check geom_file is not None and that incidenceAngle exists) to avoid runtime errors in workflows without geometry.
• In plot_result, maskObs.h5 is always passed as -m to the geometry view command, but it may not exist if generate_ifgram_aux_file wasn’t run or geometry is missing; consider checking for the file’s existence and falling back to plotting without -m when it’s unavailable.

Prompt for AI Agents

Please address the comments from this code review:

## Overall Comments
- In `generate_ifgram_aux_file`, you assume `geom_file` is present and contains an `incidenceAngle` dataset; consider guarding this block (e.g., check `geom_file` is not None and that `incidenceAngle` exists) to avoid runtime errors in workflows without geometry.
- In `plot_result`, `maskObs.h5` is always passed as `-m` to the geometry view command, but it may not exist if `generate_ifgram_aux_file` wasn’t run or geometry is missing; consider checking for the file’s existence and falling back to plotting without `-m` when it’s unavailable.

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