Support custom axis names in GEFF node property I/O - #7
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If we try to open a GEFF file, e.g. generated with pycellin, the position props names are not neceaarily x, y, z, t. The names are defined in the 'axes' properties, which we need to read. - Add getAxisNameByType() and getAxisNamesByType() methods to GeffMetadata - Modify GeffNode.readFromN5() to read coordinates from dynamic axis paths - Modify GeffNode.writeToN5() to write coordinates to dynamic axis paths - Add test for custom axis names (frame, cell_x, cell_y instead of t, x, y, z) - Maintain backward compatibility with standard axis names Fixes issue where GEFF files with non-standard axis names (e.g., 'frame' instead of 't', 'cell_x' instead of 'x') could not be read. Did this in part with Claude
Document that node property paths for time and spatial coordinates are
resolved from the axis names declared in GeffMetadata rather than being
hardcoded to "t", "x", "y", "z".
- Add "Custom axis names" feature bullet explaining the fallback behaviour
- Update GeffNode description to mention axis-aware I/O
- Add getAxisNameByType() / getAxisNamesByType() to GeffMetadata description
- Annotate the Data Format file-tree to show paths as <t>/<x>/<y>/<z>
with a note that names come from the axes array in metadata
- Add usage example showing round-trip with custom axis names
("frame", "cell_x", "cell_y")
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Summary
t,x,y,z) arenow resolved from the axis names declared in
GeffMetadatarather than beinghardcoded. A GEFF file whose axes are named
frame,cell_x,cell_ywill beread and written correctly without any special handling by the caller.
t,x,y,z) when no axes are definedin metadata, preserving full backward compatibility.
zis neither read nor written.GeffMetadata:getAxisNameByType(String type)– name of the first axis matching the given typegetAxisNamesByType(String type)– names of all axes matching the given type, in declaration orderusage example showing a round-trip with non-standard axis names.
Tests completed
mvn test), including a new round-trip test(
testCustomAxisNames) covering write and read with axes namedframe,cell_x,cell_y.cd cross-language-tests && uv run run_tests.py).