Add multi-source image metadata to IjImage info#192
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JAVA8_HOME was only for ad-hoc Java 8 downgrade checks and is not needed to build: the core targets Java 8 bytecode via the JDK 21 compiler's --release flag, and the dev mvn exec:exec fork cannot run on Java 8 anyway (--add-opens is Java 9+). Remove pkgs.jdk8 from both devShells and the justfile note.
- vite ^6.4.3 -> ^8.0.12 (resolves to 8.0.16; now Rolldown + Oxc + Lightning CSS) - @tailwindcss/vite ^4.2.1 -> ^4.2.2 (required: Vite 8 support landed in 4.2.2) - tailwindcss ^4.2.1 -> ^4.2.2 (lockstep with the vite plugin) - @vitejs/plugin-vue ^5.2.4 -> ^6.0.7 (current major; 5.x also declares vite ^8) No vite.config.ts / tsconfig / Node changes needed (Node already >=22.12 in the nix shell, CI, and Dockerfile). vue-tsc, vite build, and prettier all pass.
Bumps [pypdf](https://github.com/py-pdf/pypdf) from 6.12.2 to 6.13.3. - [Release notes](https://github.com/py-pdf/pypdf/releases) - [Changelog](https://github.com/py-pdf/pypdf/blob/main/CHANGELOG.md) - [Commits](py-pdf/pypdf@6.12.2...6.13.3) --- updated-dependencies: - dependency-name: pypdf dependency-version: 6.13.3 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com>
fiji/fiji 'master' (the Fiji-Stable line) currently parents to pom-scijava 40.0.0, so this keeps the plugin aligned with the stable distribution while staying on Java 8 (no nix/CI toolchain change). Moves off 38.0.1: imglib2 6.3.0 -> 7.1.5, imagej2 2.15.0 -> 2.17.0, jackson 2.16.1 -> 2.18.0. Supersedes Dependabot #115 (38.0.1 -> 44.0.0), which would raise the build's Java floor from 8 to 11.
syntax_error_counter in LeaderDriven.run() was never reset, so it tracked cumulative ReAct syntax errors across a whole dialog and could abort a task after 3 scattered, fully-recovered errors. Reset it to 0 at the recovery send_correction (the single choke point where the agent_resp-is-None branch routes), matching the existing tool_retry_counter reset idiom. A model that is genuinely stuck still aborts after max_syntax_errors consecutive errors. Adds a regression test (test_leader_syntax_reset.py) covering both the cumulative-with-recovery case (now completes) and the 3-consecutive case (still aborts). Assisted-by: Claude-Code:GLM-5.2
- BooleanParameterSchema.validate() now returns null on success to match its siblings, and the Javadoc on ParameterSchema.validate() is corrected to match the implementation (null = valid). - StringParameterSchema enum constructor rejects null entries while still accepting blank strings, which are legitimate AWT Choice/List item labels passed by ChoiceNode/ListNode.getActions(). Assisted-by: Claude-Code:GLM-5.2
nodeToSimpleMap printed every combined word to stdout, polluting output during JSON tree serialization. Drop the stray debug statement. Assisted-by: Claude-Code:GLM-5.2
Add JUnit 5 unit tests (83 tests, all passing) for the six pure-logic classes with no ImageJ/runtime coupling: Trie, JsonBase64ImageTruncator, FromTo, BoundedLog, FlexibleLocalDateTimeDeserializer, and the Action/ParameterSchema hierarchy. JaCoCo coverage runs through the existing pom-scijava setup. Build wiring: - plugin/pom.xml: junit-jupiter test dependency (version via the inherited junit-jupiter.version property). - justfile: test-plugin and test-cov-plugin targets. - .github/workflows/test.yaml: java-test CI job (JDK 21). Assisted-by: Claude-Code:GLM-5.2
Introduces an info field on IjImage (Java + Python), populated from the image's metadata, tracked in equals and the snapshot Difference so metadata changes surface in diffs, and rendered as a filtered Metadata block in perception output. Java: buildImageMetadata assembles the "Info" property, every other String-valued property, and FileInfo.description into one deduped block (LinkedHashSet, whole-string equality), capped at 4000 chars. info is part of IjImage.equals and of the IjImage.Difference FromTo. Python: IjImage gains info, IjImageDifference gains the matching FromTo field, and _describe appends a Metadata block after the structured fields, dropping OME keys that duplicate them (SizeX/SizeY/SizeZ/SizeC/SizeT, PhysicalSize* and units, BitsPerSample/BitsPerPixel/SignificantBits, PixelType). The raw info is preserved on the model. Assisted-by: Claude-Code:GLM-5.2
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I suggest if you detect the ImageDescription: {"shape": [60, 2, 256, 256]}, should block stack size: 120 (1 channels, 120 slices, 1 frames); |
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@00JackLu I completely understand your concerns, but there is one issue here: this image actually has 120 frames. It is not In general, this PR is intended to fill in the missing information. We did not perform any specific checks on the image data to reconcile it with the description. It may be worth adding an extra commit with more context to help the LLM understand why these two pieces of information appear to be different or even contradictory. |
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Introduces an info field on IjImage (Java + Python), populated from the image's metadata, tracked in equals and the snapshot Difference so metadata changes surface in diffs, and rendered as a filtered Metadata block in perception output.
Java: buildImageMetadata assembles the "Info" property, every other String-valued property, and FileInfo.description into one deduped block (LinkedHashSet, whole-string equality), capped at 4000 chars. info is part of IjImage.equals and of the IjImage.Difference FromTo.
Python: IjImage gains info, IjImageDifference gains the matching FromTo field, and _describe appends a Metadata block after the structured fields, dropping OME keys that duplicate them (SizeX/SizeY/SizeZ/SizeC/SizeT, PhysicalSize* and units, BitsPerSample/BitsPerPixel/SignificantBits, PixelType). The raw info is preserved on the model.
Assisted-by: Claude-Code:GLM-5.2