refactor: share the colour-norm helper; fix inversion log10 floor

[Jammy2211]

Overview

Building the matplotlib colour norm from use_log10 / vmin / vmax is written
out three times — autoarray/plot/array.py, autoarray/plot/inversion.py, and
autogalaxy/util/plot_utils.py::norm_from (added by PyAutoGalaxy#586). The copies
have already diverged, and one divergence is a live behaviour bug: inversion.py
hardcodes the 1e-4 log floor and never consults autonerves config, so a user
who changes visualize.general.general.log10_min_value gets it honoured on array
plots and silently ignored on inversion plots.

Deduplicating is how the divergence stops recurring; fixing the config floor is
the point. Split out of aplt-output-drift-remaining-repos (PyAutoGalaxy#585).

Plan

• Add one colour-norm helper to autoarray/plot/utils.py — the lowest repo that
  owns this logic, alongside auto_mask_edge and the other shared plot helpers.
• Decide each of the three divergences deliberately rather than assuming
  array.py wins on all of them, and write the decision into the helper's
  docstring.
• Call the helper from array.py and inversion.py.
• Make autogalaxy.util.plot_utils.norm_from delegate to it rather than
  reimplement it, keeping the autogalaxy-facing name so the Clicker /
  Scribbler callers added by PyAutoGalaxy#586 keep working.
• Cover the config-floor path (both call sites), explicit limits, derived vmax
  and the degenerate vmax <= vmin case with tests in PyAutoArray.

The three divergence decisions

#	Divergence	Decision
1	array.py reads log10_min_value from config and clips; inversion.py hardcodes 1e-4 and does not clip	array.py wins. The helper always reads the configured floor (fallback 1e-4) and clips. This is the behaviour fix — inversion plots change when the configured floor is not 1e-4.
2	array.py derives vmax from the clipped array; inversion.py from pixel_values, falling back to vmin * 10 when there are none	Neither wins — it is not a divergence. The two call sites colour different data. The helper's array argument means "the values being coloured"; inversion.py passes pixel_values. array=None collapses into the same fallback, so inversion's separate else branch disappears with no behaviour change.
3	array.py widens a degenerate vmax <= vmin even when explicitly passed; inversion.py only inside its elif pixel_values branch	array.py wins. LogNorm(vmin=10, vmax=1) is unusable whoever supplied the numbers. Inversion plots change when a caller passes vmax <= vmin explicitly.

Detailed implementation plan

Work Classification

Library — both repos are libraries. Library-first: PyAutoArray merges before
PyAutoGalaxy.

Affected Repositories

• PyAutoArray (primary)
• PyAutoGalaxy

Branch Survey

Repository	Current Branch	Dirty?
PyAutoArray	main	clean
PyAutoGalaxy	main	clean
PyAutoMind	claude/autoarray-shared-log-norm-c12ges	prompt file only

Branch: claude/autoarray-shared-log-norm-c12ges (remote web-github
session; no local worktree — the session clones are the working trees).

Implementation Steps

1. PyAutoArray — autoarray/plot/utils.py: add norm_from(array=None, use_log10=False, vmin=None, vmax=None). Lazy matplotlib import, as
   everywhere else in this module. Body: read log10_min_value from
   autonerves config inside try/except (fallback 1.0e-4); clip; derive
   vmin_log/vmax_log; widen unconditionally when vmax_log <= vmin_log or
   non-finite; return LogNorm. Non-log path returns Normalize when either
   limit is given, else None. Docstring records the table above.
2. PyAutoArray — autoarray/plot/array.py: replace the inline block (the
   # --- colour normalisation --- stanza) with a call to the helper.
3. PyAutoArray — autoarray/plot/inversion.py: same, passing
   array=pixel_values. Drop the now-unused inline LogNorm/Normalize use.
4. PyAutoGalaxy — autogalaxy/util/plot_utils.py: norm_from becomes a
   delegate to autoarray.plot.utils.norm_from, keeping its signature and
   docstring intent. autogalaxy may import autoarray; the reverse is not true.
5. Tests — test_autoarray/plot/test_utils.py: new class covering the
   config floor with log10_min_value monkeypatched away from 1e-4, asserting
   both call sites honour it; explicit limits; derived vmax; degenerate
   vmax <= vmin; all-NaN input.

Key Files

• autoarray/plot/utils.py — new shared helper (the reference implementation)
• autoarray/plot/array.py — call site 1 (was the reference)
• autoarray/plot/inversion.py — call site 2 (carried the bug)
• autogalaxy/util/plot_utils.py — norm_from becomes a delegate
• test_autoarray/plot/test_utils.py — new tests
• test_autogalaxy/gui/test_plot_norm.py — must stay green (pins #586 behaviour)

Constraints

• Behaviour-preserving except where a divergence is deliberately fixed; each
  such fix is named in the PR body. Thin test coverage on this path means an
  unnoticed change ships silently.
• The vitals faculty could not be consulted in this session (pyauto-heart is
  not on PATH in a web-github run) — the Heart gate still applies at ship.

Autonomy

Launched /start_dev … --auto. Prompt header Autonomy: supervised; refactor
work-type cap is safe; effective level supervised. Per the autonomy
contract that means: the plan is written here rather than presented and waited
on, work proceeds, and the run parks at ship sign-off with a question on this
issue.

Original Prompt

Click to expand starting prompt

One shared colour-norm helper — the three copies have already diverged

Type: refactor
Target: autoarray
Repos:

• PyAutoArray
• PyAutoGalaxy
  Difficulty: small
  Autonomy: supervised
  Priority: normal
  Status: formalised
  Filed: 2026-08-24

Split out of aplt-output-drift-remaining-repos (PyAutoGalaxy#585, 2026-08-24),
which added the third copy rather than widen that task into a third repo.

The duplication

Building the matplotlib colour norm from use_log10 / vmin / vmax is written
out three times:

Where	Notes
autoarray/plot/array.py:164-188	the reference implementation
autoarray/plot/inversion.py:92-107	already divergent — see below
autogalaxy/util/plot_utils.py::norm_from	added by PyAutoGalaxy#586, faithful to array.py

This is not a tidiness task — the copies disagree

array.py reads the configured floor:

log10_min = _conf.instance["visualize"]["general"]["general"]["log10_min_value"]   # fallback 1.0e-4
clipped = np.clip(array, log10_min, None)

inversion.py hardcodes 1e-4 and never consults autonerves config, and
does not clip. So a user who changes log10_min_value gets it honoured on array
plots and silently ignored on inversion plots. That is a live behaviour bug, not
a style issue, and it is the thing to fix first — the deduplication is how you
stop it recurring.

They differ in a second way worth preserving deliberately rather than by
accident: array.py derives vmax from the clipped array, inversion.py from
pixel_values and falls back to vmin_log * 10.0 when there are none. And
inversion.py's vmax_log <= vmin_log guard sits inside its elif pixel_values
branch, so an explicitly-passed degenerate vmax is not widened there but is
in array.py.

Decide which behaviour is correct for each difference before merging them —
do not assume array.py wins on all three. Write the decision into the helper's
docstring.

Shape of the fix

1. Add one helper in PyAutoArray — the lowest repo that owns this logic;
   autoarray/plot/utils.py sits alongside auto_mask_edge and the other
   shared plot helpers. Give it the array/use_log10/vmin/vmax signature
   plus whatever parameter reconciles the pixel_values difference.
2. Call it from array.py and inversion.py.
3. Make autogalaxy.util.plot_utils.norm_from delegate to it rather than
   reimplement — autogalaxy may import autoarray (dependency direction is fine;
   the reverse is not). Keep norm_from as the autogalaxy-facing name so the
   Clicker/Scribbler callers added in PyAutoGalaxy#586 keep working.

Constraints

• Behaviour-preserving except where you deliberately fix a divergence, and
  each such fix is named in the PR body. This is a plotting path with thin test
  coverage, so an unnoticed change ships silently.
• Library-first: PyAutoArray merges before PyAutoGalaxy.
• test_autogalaxy/gui/test_plot_norm.py (added by #586) already pins the
  autogalaxy behaviour — it must stay green, or its change must be justified.

Verification

Add tests in PyAutoArray covering the config-floor path (log10_min_value set to
something other than 1e-4, asserting both call sites honour it), the
explicit-limits path, the derived-vmax path, and the degenerate vmax <= vmin
case. Then the full suites in both repos, on 3.12 and 3.13.

[Jammy2211]

Implemented and pushed — parked at ship sign-off

Effective autonomy is supervised (prompt header supervised, refactor cap safe), so per the autonomy contract the run stops here: the code is written, tested and pushed, but the PRs are not opened until you sign off. Two questions below.

What was done

Branch claude/autoarray-shared-log-norm-c12ges in both repos.

• PyAutoArray (accc253) — norm_from added to autoarray/plot/utils.py, called from plot/array.py and plot/inversion.py. The config read lands as _conf_log10_min_value alongside the other _conf_* readers. The three divergence decisions are in the helper's docstring.
• PyAutoGalaxy (00a0499) — util/plot_utils.py::norm_from is now a thin delegate; the autogalaxy-facing name and signature are unchanged, so the Clicker / Scribbler callers are untouched.

The deliberate behaviour changes

Both land on plot_inversion_reconstruction only; plot_array and the autogalaxy GUI path are unchanged.

1. The configured log floor is now honoured. It hardcoded 1e-4 and never read visualize.general.general.log10_min_value. Inversion plots change when the configured floor is not 1e-4 — this is the fix the task exists for.
2. A degenerate vmax <= vmin is now widened even when passed explicitly. Its guard sat inside the elif pixel_values branch, so an explicit degenerate pair reached matplotlib unmodified.

The third difference — array.py deriving vmax from the image, inversion.py from pixel_values — was not merged into one behaviour. The helper's array argument means "the values being coloured"; the two call sites genuinely colour different data. array=None takes the same fallback as an all-NaN array, which is exactly what inversion's separate else branch did, so no behaviour changed there.

Verification

Suite	Result
test_autoarray/plot	17 passed (11 new)
test_autoarray (full)	1157 passed, 55 skipped
test_autogalaxy/gui/test_plot_norm.py (pins #586)	9 passed, file untouched
test_autogalaxy (full, against this PyAutoArray branch)	1119 passed, 1 skipped

Two caveats, stated plainly:

• The 8 inversion/inversion/test_{abstract,factory}.py sparse-operator failures in this environment are present on unmodified main (verified by stashing) and are unrelated to plotting. CI is the real check.
• Ran on Python 3.12 only — this session has no 3.13 environment. The prompt asks for both; CI covers 3.13.

The new tests were checked for teeth, not just green: reverting plot_inversion_reconstruction to the hardcoded floor makes test__plot_inversion_reconstruction fail with assert 0.0001 == 0.003.

Question 1 — ship sign-off (blocking)

Open the two PRs, PyAutoArray first (library-first: PyAutoArray#488 merges before the PyAutoGalaxy one)?

• Yes → the PRs go up with the two behaviour changes named in the bodies, and the task moves to ready-to-ship in the Mind registry. Merge stays yours either way.
• No / changes wanted → say which of the two behaviour changes you want reverted to the old inversion behaviour and I will re-work before opening anything.

One thing the ship gate could not do here: pyauto-heart is not on PATH in this web-github session, so the vitals faculty was never consulted. The Heart verdict is unknown, not green. If you would rather the gate ran properly, this needs a session that can reach Heart.

Question 2 — an orphaned prompt file (non-blocking)

The prompt this task started from did not exist on PyAutoMind/main. It was only ever committed to claude/aplt-output-drift-repos-33n81z (dd7501f1, "file the three aplt-output-drift follow-ups + queue them"), and **no PR was ever opened for that branch** — so all three follow-ups filed that day, plus the queue.mdentries, are invisible tomain`, the dashboard and the Brain router.

I recovered this one file onto the task branch and advanced it draft/ → active/. The other two are still stranded:

• draft/workspaces/euclid_crlf_line_endings.md
• the queue.md additions from that commit

Want me to open a PR for that PyAutoMind branch, or recover the remaining files the same way? Either works; doing nothing loses them quietly, which is why it is worth a look. This is not blocking the ship decision.

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Generated by Claude Code

[Jammy2211]

Shipped

Repo	PR	Merge commit	CI
PyAutoArray	#489	b690c3e	3/3 green — 3.12, 3.13, nojax
PyAutoGalaxy	#587	0c7bc62	4/4 green — 3.12, 3.13, nojax, docs-build
PyAutoMind	#313	d7132c9	no checks configured on PRs (registry state only)

Library-first order honoured: PyAutoArray merged first, PyAutoGalaxy after. Every leg on every run was completed + success before either merge; both branches verified merged into main afterwards (rev-list origin/main..branch = 0).

What landed

autoarray.plot.utils.norm_from is now the single colour-norm implementation, called by plot/array.py, plot/inversion.py, and by delegation from autogalaxy.util.plot_utils.norm_from. The config read lands once as _conf_log10_min_value.

Two deliberate behaviour changes, both on plot_inversion_reconstruction only — plot_array and the autogalaxy GUI path are untouched:

1. The configured log10_min_value is honoured. It hardcoded 1e-4. This is the bug the task existed for.
2. A degenerate vmax <= vmin is widened however it arose, not only in the derived branch.

The third difference was deliberately not reconciled: array means "the values being coloured", so array.py passing the image and inversion.py passing pixel_values is correct rather than divergent. All three decisions are in the helper's docstring, as the prompt required.

Notes worth keeping

• The Heart gate could not give a real verdict. pyauto-heart readiness returned stale, score 35 — every reason status unknown (no report.json, install verification not run, five repos unknown). That is Heart with an empty sensor bank in a fresh web-github container, not a health signal. The merge decision rested on real CI instead, which is the sensor Heart was missing. Flagging it because a stale Heart on a green-CI change is a gate that did not actually gate.
• The prompt file was not on main when the task started. It lived only on the unmerged filing branch claude/aplt-output-drift-repos-33n81z, so /start_dev on the given path found nothing until it was recovered from that branch. PR PyAutoMind#311 landed that branch mid-task, which is why the Mind close-out hit a merge conflict — main was adding the prompt to draft/ as this branch folded it into complete/. Resolved by dropping the draft copy and marking its queue.md line # DONE. Nothing warns about a filing branch with no PR.

Completion record: complete/2026/08/shared-log-norm-helper.md. Both merged PRs remain in the pending-release queue; no release was performed.

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Generated by Claude Code