live-image-tracking-tools/geff - CodSpeed

live-image-tracking-tools

geff

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Performance History

Latest Results

Expose Mesh in geff_spec init

mesh-add-on

4 days ago

Deduplicate the write-rollback logic in write_arrays validate_metadata and validate_structure failures both deleted the partial geff and re-raised with the same added context. Factored into _rollback_invalid_write, shared by both call sites.

shape-property-validation

4 days ago

Add data and metadata validation for mesh properties Adds validate_mesh (shape/dtype/index-bounds/degenerate-triangle checks, with missing-row handling) alongside the existing sphere/ellipsoid/polygon validators, wired in via ValidationConfig.mesh. Adds _validate_mesh_metadata to geff_spec.utils.validate_metadata, checking that mesh.vertices/ triangles/vertex_normals/triangle_normals name real node properties and that vertex_axes names refer to valid spatial axes. Regenerates geff-schema.json for the Mesh docstrings from the prior commit.

mesh-add-on

4 days ago

Move validate_metadata into geff-spec's utils module GeffMetadata, PropMetadata, and RelatedObject are all defined in geff-spec, and other metadata-construction helpers already live in geff_spec.utils, so the cross-reference validation belongs there too rather than in a separate geff.validate.metadata module. No behavior change, just a relocation: geff/validate/data.py and geff/core_io/_base_write.py now import validate_metadata from geff_spec.utils.

shape-property-validation

4 days ago

Add data and metadata validation for mesh properties Adds validate_mesh (shape/dtype/index-bounds/degenerate-triangle checks, with missing-row handling) alongside the existing sphere/ellipsoid/polygon validators, wired in via ValidationConfig.mesh. Adds _validate_mesh_metadata to the opt-in validate_metadata() framework, checking that mesh.vertices/ triangles/vertex_normals/triangle_normals name real node properties and that vertex_axes names refer to valid spatial axes. Regenerates geff-schema.json for the Mesh docstrings from the prior commit.

mesh-add-on

4 days ago

Add data/metadata validation for sphere, ellipsoid, and polygon properties Threads a `missing` mask through validate_sphere/validate_ellipsoid so missing rows no longer trip numeric checks, adds validate_polygon with equivalent checks, and introduces an opt-in validate_metadata() that checks sphere/ellipsoid/polygon/track_node_props/related_objects property names actually exist in node_props_metadata. It's opt-in (ValidationConfig.metadata) rather than an eager pydantic validator because some writers (e.g. _ctc.py) intentionally build GeffMetadata with a placeholder node_props_metadata before patching it in from the real data. Also fixes a latent bug in _trackmate_xml.py where TRACK_ID was referenced by track_node_props but never added to node_props_metadata.

shape-property-validation

4 days ago

Add additional documentation about how to specify related object paths (#450) # Proposed Change Documents how to specify paths for related objects. Hopefully closes #448 and #430 # Types of Changes What types of changes does your code introduce? Delete those that do not apply. - Documentation update Which topics does your change affect? Delete those that do not apply. - Specification # Checklist Put an x in the boxes that apply. You can also fill these out after creating the PR. If you're unsure about any of them, don't hesitate to ask. We're here to help! This is simply a reminder of what we are going to look for before merging your code. - [x] I have read the [developer/contributing](https://github.com/live-image-tracking-tools/geff/blob/main/CONTRIBUTING) docs. - [x] I have written docstrings and checked that they render correctly by looking at the docs preview (link left as a comment on the PR). ## If you changed the specification - [x] I have updated the GeffMetadata and the json schema using `pytest --update-schema` if necessary. - [x] I have updated docs/specification.md to reflect the change.

main

4 days ago

Specify posix path

rel-obj-path

5 days ago

Latest Branches

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Support meshes as a special node property#449

4 days ago

287c0a1

mesh-add-on

0%

Validate sphere/ellipsoid/polygon data and metadata cross-references#453

4 days ago

a2054a5

shape-property-validation

0%

Add additional documentation about how to specify related object paths#450

5 days ago

ac5325a

rel-obj-path

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