feat: Add import/export commands and API

[uermel]

Summary

This PR adds comprehensive import/export functionality for picks, tomograms, and segmentations, enabling interoperability with common cryo-ET software packages including RELION, Dynamo, and TOM/Artiatomi toolbox.

New Features

CLI Commands

Import Commands (copick add)

• copick add picks: Import particle picks from external formats

  • Supports EM (TOM toolbox motivelist), STAR (RELION), Dynamo (.tbl), and CSV formats
  • Automatic format detection from file extension
  • Batch import with --tomolist or --index-map for mapping tomogram indices to run names
  • Coordinate and orientation conversion to copick's native format

• copick add tomogram: Import tomograms from external formats

  • Supports MRC, Zarr, TIFF, and EM formats
  • Optional multiscale pyramid generation
  • Batch import via --tomolist for Dynamo-style tomogram lists

• copick add segmentation: Import segmentations from external formats

  • Supports MRC, Zarr, TIFF, and EM formats
  • Support for both binary and multilabel segmentations

Export Commands (copick export)

• copick export picks: Export particle picks to external formats

  • Supports EM, STAR, Dynamo, and CSV formats
  • URI-based filtering (e.g., "ribosome:user1/*")
  • STAR export with optional optics group
  • Flat directory structure for multi-run exports

• copick export tomogram: Export tomograms to external formats

  • Supports MRC, TIFF, and Zarr formats
  • Configurable pyramid level selection

• copick export segmentation: Export segmentations to external formats

  • Supports MRC, TIFF, Zarr, and EM formats
  • Configurable pyramid level selection and compression

Functional API

New modules provide programmatic access to all import/export functionality:

• copick.ops.add: Functions for importing picks, tomograms, and segmentations
• copick.ops.export: Functions for exporting picks, tomograms, and segmentations
• copick.util.formats: Format-specific I/O utilities and coordinate transformations
• copick.util.handlers: Format handlers with capability detection for extensible format support

Supported Format Conventions

Format	Euler Convention	Coordinate System
EM/TOM (Artiatomi)	ZXZ intrinsic	1-indexed, corner-origin
Dynamo	ZXZ intrinsic with inversion	1-indexed, corner-origin
STAR/RELION	ZYZ with inversion	Pixels (Angstrom via voxel size)
CSV (copick native)	Full 4x4 matrix	Angstrom, corner-origin

Batch Import Features

• Tomolist support: Import particles grouped by tomogram index using Dynamo-style tomolist files
• Index map support: Custom CSV/TSV mapping from tomogram indices to run names
• Run name extraction: Automatic run name derivation from filenames with regex support

[codecov-commenter]

Codecov Report

❌ Patch coverage is 60.69215% with 761 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/copick/ops/add.py	19.50%	208 Missing and 19 partials ⚠️
src/copick/util/formats.py	54.22%	189 Missing and 33 partials ⚠️
src/copick/ops/export.py	55.89%	104 Missing and 27 partials ⚠️
tests/test_import_export.py	90.86%	30 Missing and 6 partials ⚠️
src/copick/util/handlers/registry.py	56.06%	26 Missing and 3 partials ⚠️
tests/conftest.py	8.33%	22 Missing ⚠️
src/copick/util/handlers/picks/star.py	70.31%	13 Missing and 6 partials ⚠️
src/copick/util/handlers/volume/zarr.py	51.28%	15 Missing and 4 partials ⚠️
src/copick/util/handlers/picks/dynamo.py	53.84%	12 Missing ⚠️
src/copick/util/handlers/picks/em.py	53.84%	12 Missing ⚠️
... and 6 more

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