feat: 3D bandpass filtering and lazy loading

[jtschwar]

Pull Request Overview

This PR adds 3D bandpass filtering functionality to the copick-torch package and refactors the code structure for better organization. The main changes include:

• Added a new bandpass filter implementation with cosine low-pass and high-pass filtering capabilities
• Refactored downsampling functionality to include GPU memory fallback handling
• Removed the old CLI structure in favor of entry points-based command registration
• Reorganized code by moving worker functions into appropriate modules

Reviewed Changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
pyproject.toml	Adds entry point for the new bandpass command
copick_torch/filters/downsample.py	Adds GPU memory fallback handling and extracts run_downsampler function from entry point module
copick_torch/filters/bandpass.py	New file implementing 3D cosine bandpass filtering with low-pass and high-pass capabilities
copick_torch/entry_points/run_membrane_seg.py	Refactors to separate command handler from execution logic
copick_torch/entry_points/run_filter3d.py	New entry point for bandpass filtering command
copick_torch/entry_points/run_downsample.py	Refactored to call downsample.run_downsampler and adds docstrings
copick_torch/cli.py	Removed old CLI structure (file deleted)

[Copilot]

Pull Request Overview

This PR adds 3D bandpass filtering functionality to the copick-torch package and refactors the code structure for better organization. The main changes include:

• Added a new bandpass filter implementation with cosine low-pass and high-pass filtering capabilities
• Refactored downsampling functionality to include GPU memory fallback handling
• Removed the old CLI structure in favor of entry points-based command registration
• Reorganized code by moving worker functions into appropriate modules

Reviewed Changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
pyproject.toml	Adds entry point for the new bandpass command
copick_torch/filters/downsample.py	Adds GPU memory fallback handling and extracts run_downsampler function from entry point module
copick_torch/filters/bandpass.py	New file implementing 3D cosine bandpass filtering with low-pass and high-pass capabilities
copick_torch/entry_points/run_membrane_seg.py	Refactors to separate command handler from execution logic
copick_torch/entry_points/run_filter3d.py	New entry point for bandpass filtering command
copick_torch/entry_points/run_downsample.py	Refactored to call downsample.run_downsampler and adds docstrings
copick_torch/cli.py	Removed old CLI structure (file deleted)

Comments suppressed due to low confidence (1)

copick_torch/entry_points/run_filter3d.py:186

• Mixing implicit and explicit returns may indicate an error, as implicit returns always return None.

def get_tomo_shape(root, run_ids, tomo_alg, voxel_size):

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