feat: Expand functionality of clip*-utilities

[uermel]

Add Tomogram Boundary Reference and Invert Flag to clip* Commands

Summary

• Add --ref-tomogram / -rt option to use tomogram volume boundaries as a reference surface for distance-based filtering
• Add --invert / --no-invert flag to all clip commands to control filtering direction
• Apply to all three clip commands: clippicks, clipseg, clipmesh

Motivation

Picks, segmentations, and meshes near tomogram edges are often unreliable due to:

• Missing wedge artifacts
• Edge effects from reconstruction
• Incomplete data at volume boundaries

This feature enables filtering out data within a specified distance from any tomogram boundary, improving data quality for downstream analysis.

New Options

--ref-tomogram / -rt

• Uses tomogram volume boundaries (6 faces of the bounding box) as the reference surface
• URI format: tomo_type@voxel_spacing (e.g., wbp@10.0)
• Mutually exclusive with --ref-mesh and --ref-seg

--invert / --no-invert

• Controls filtering direction for ALL reference types (mesh, segmentation, and tomogram)
• Default (--no-invert): Keep data within max_distance of reference
• With --invert: Keep data beyond max_distance of reference

Usage Examples

# Keep picks within 50Å of mesh reference (default behavior)
copick logical clippicks -i "ribosome:user1/all-001" \
  -rm "membrane:user1/boundary-001" \
  -o "ribosome:clippicks/near-001" \
  --max-distance 50.0

# Remove picks within 50Å of tomogram boundary (common use case for edge filtering)
copick logical clippicks -i "ribosome:user1/all-001" \
  -rt "wbp@10.0" \
  -o "ribosome:clippicks/interior-001" \
  --max-distance 50.0 --invert

# Keep only edge picks (within 50Å of tomogram boundary)
copick logical clippicks -i "ribosome:user1/all-001" \
  -rt "wbp@10.0" \
  -o "ribosome:clippicks/edge-001" \
  --max-distance 50.0

# Same patterns work for clipseg and clipmesh
copick logical clipseg -i "membrane:user1/full-001@10.0" \
  -rt "wbp@10.0" \
  -o "membrane:clipseg/interior-001@10.0" \
  --max-distance 50.0 --invert