feat: CTI resurrection Phase 1 — Plotter to matplotlib viz migration

[Jammy2211]

Overview

Phase 1 of the CTI resurrection epic (Phase 0: #82 / PR #83, merged). PyAutoCTI's visualization layer still targets the autoarray Plotter/MatPlot/Visuals/Include object API that was removed from the stack, and is currently quarantined (autocti.plot detached, visualizers no-op with a logged warning, plot tests skipped). This phase rewrites it on the matplotlib function API used by PyAutoGalaxy/PyAutoLens and removes the quarantine.

Plan

• Delete the Plotter object stack: autocti/plot/abstract_plotters.py, autocti/plot/get_visuals/, 5 Plotter classes, 3 PlotterInterface classes.
• Add per-domain function modules mirroring autogalaxy/imaging/plot/fit_imaging_plots.py: dataset_1d/plot/{dataset_1d_plots,fit_plots}.py (1D line figures/subplots) and charge_injection/plot/{imaging_ci_plots,fit_ci_plots}.py (2D figures/subplots + 1D binned FPR/EPER region plots).
• CTI region overlays (parallel/serial overscan, serial prescan, FPR/EPER extracts — formerly autoarray wrap objects) become CTI-local matplotlib helpers in autocti/util/plot_utils.py.
• Rebuild autocti/plot/__init__.py as the function namespace (aplt.subplot_*); restore from . import plot in autocti/__init__.py.
• Rewire both model/visualizer.py classes onto the new functions per config/visualize/plots.yaml (drop the Phase-0 try/except quarantine); align plots.yaml schema with current ag where keys overlap.
• Replace the quarantined plot tests with tests of the new functions + visualizers; remove collect_ignore from test_autocti/conftest.py.

Out of scope: aggregator factor-graph port (Phase 2), CI/ecosystem plumbing (Phase 3), workspace update (Phase 4).

Detailed implementation plan

Affected Repositories

• PyAutoCTI (primary)

Branch Survey

Repository	Current Branch	Dirty?
./PyAutoCTI	main (post-#83 merge, clean)	clean

Suggested branch: feature/cti-resurrection-phase1

Implementation Steps

1. Inventory the figure surface from the old classes before deleting (Dataset1DPlotter.figures_1d/subplot_dataset, FitDataset1DPlotter, ImagingCIPlotter.figures_2d/figures_1d(region=…)/subplot_dataset, FitImagingCIPlotter, the three PlotterInterfaces' plots.yaml-driven orchestration).
2. Write autocti/util/plot_utils.py: 1D line/subplot helpers, 2D array helpers delegating to autoarray.structures.plot.structure_plots (plot_array_2d, plot_yx_1d) + autoarray.plot.utils (subplots, save/output helpers), and the CTI region-overlay helpers.
3. Write the four per-domain *_plots.py function modules (subplot + individual figures + fits output where the old stack had them).
4. Rebuild autocti/plot/__init__.py; restore the package import; delete the dead files.
5. Rewire dataset_1d/model/visualizer.py + charge_injection/model/visualizer.py to call the new functions, honoring config/visualize/plots.yaml; sync yaml keys.
6. New tests per module (plot_patch/output assertions, matching current ag test style); remove conftest quarantine; full suite green.

Key Files

• autocti/plot/ — namespace rebuild; object stack deleted
• autocti/{dataset_1d,charge_injection}/plot/* — new function modules
• autocti/{dataset_1d,charge_injection}/model/visualizer.py — rewire
• autocti/util/plot_utils.py — new helpers (region overlays)
• autocti/config/visualize/plots.yaml — schema sync
• test_autocti/conftest.py — remove collect_ignore

Original Prompt

PyAutoMind prompt: draft/feature/autocti/cti_resurrection_phase1_viz_migration.md (epic origin verbatim in #82).

[Jammy2211]

Phase 1 complete — PR #85 merged (0aad137). Visualization runs end-to-end on the matplotlib function API; quarantine removed; 266 tests passed / 5 skipped. Record: PyAutoMind/complete/2026/07/cti-resurrection-phase1.md. Next: Phase 2 (autofit sync — aggregator AnalysisFactor/FactorGraphModel port).