Prior inspect peaks work by mgiammar · Pull Request #124 · Lucaslab-Berkeley/Leopard-EM

mgiammar · 2026-04-24T22:42:47Z

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jdickerson95 · 2026-04-30T20:46:53Z

@mgiammar I've implemented the inspect peaks, including frc and frame correlations.
I've also updated Leopard-EM to use the new deformation field class, so the tests will definitely fail until a new version of the monorepo is released.

…uted match-template Squashed rebuild of the mdg_inspect_peaks PR (Lucaslab-Berkeley#124) on top of development_v1.3 to remove duplicated upstream history. Tree is identical to prior branch tip 84d1ce8.

mgiammar · 2026-06-08T22:03:30Z

@jdickerson95 have updated the TeamTomo dependencies to >=v0.5.2 so those aspects of CI should pass now

…lated components

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Pull request overview

This PR introduces a peak-inspection workflow that exposes full local scoring tensors (cross-correlation maps or FRC spectra) for offline inspection, and adds a per-frame inspection manager for movie frame-by-frame scoring with optional fixed whitening/normalization reuse. It also refactors parts of the refine/inspect backend setup for multi-device execution and adds random Fourier dropout support in preprocessing.

Changes:

Add PeakInspectionManager / FrameInspectionManager plus CLI examples and config templates for inspecting local score tensors and per-frame results.
Extend backend correlation codepaths to optionally skip projection normalization and to compute FRC outputs.
Refactor image filtering/normalization utilities and backend setup helpers; add tests to lock in reducer/stacking behavior.

Reviewed changes

Copilot reviewed 29 out of 29 changed files in this pull request and generated 1 comment.

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File	Description
tests/pydantic_models/test_particle_stack.py	Adds coverage for aligned-movie particle extraction and movie→image stack API behavior.
tests/pydantic_models/test_frame_inspection_manager.py	New unit tests for frame inspection reduction/stacking and CSV output behavior.
tests/backend/test_core_refine_template.py	New deterministic snapshot test for `_reduce_refine_best_zscore`.
tests/backend/test_core_match_template.py	Avoids division-by-zero in set-overlap assertions.
src/leopard_em/utils/image_processing.py	Splits normalization into a reusable `get_image_normalization_factor` and adds optional precomputed filter/normalization inputs.
src/leopard_em/utils/ctf_utils.py	Adds helper to move tensor-valued CTF kwargs onto a target device.
src/leopard_em/utils/backend_setup.py	Refactors backend input setup; adds per-frame filter setup helper and deformation-field type updates.
src/leopard_em/pydantic_models/results/match_template_result.py	Tweaks error message formatting for write-permission / overwrite checks.
src/leopard_em/pydantic_models/managers/refine_template_manager.py	Allows optional `template_tensor` override and updates deformation-field handling.
src/leopard_em/pydantic_models/managers/peak_inspection_manager.py	New manager to run inspect backend and optionally save self-describing outputs.
src/leopard_em/pydantic_models/managers/match_template_manager.py	Disables random Fourier dropout for image-side filtering during match-template setup.
src/leopard_em/pydantic_models/managers/frame_inspection_manager.py	New per-frame inspection manager (frame iteration, fixed filters, CSV summaries, optional dose-weighting).
src/leopard_em/pydantic_models/managers/init.py	Exports the new managers.
src/leopard_em/pydantic_models/data_structures/particle_stack.py	Adds per-frame particle movie extraction; updates deformation-field integration and refactors movie extraction internals.
src/leopard_em/pydantic_models/config/movie_config.py	Switches deformation field loading to `DeformationField.from_csv`.
src/leopard_em/pydantic_models/config/correlation_filters.py	Adds `RandomFourierDropoutConfig` and integrates it into combined filters.
src/leopard_em/backend/cross_correlation.py	Adds optional projection normalization toggle and implements batched FRC scoring.
src/leopard_em/backend/core_refine_template.py	Refactors multi-device tensor movement/stream handling; factors correlation batching and reducer logic.
src/leopard_em/backend/core_differentiable_refine.py	Ensures tensor-valued CTF kwargs are moved onto the active device before CTF stack construction.
src/leopard_em/analysis/inspect_peaks.py	New inspect backend entrypoint producing full local hypothesis tensors (CC or FRC), multi-device compatible.
src/leopard_em/analysis/inspect_peaks_result.py	New save/load helpers for self-describing `.npz` inspection outputs.
src/leopard_em/analysis/init.py	Re-exports inspection result save/load helpers.
pyproject.toml	Bumps required Python to 3.11 and updates TeamTomo dependency versions / adds FRC dependency.
programs/inspect_peaks/run_inspect_peaks.py	New example script for peak inspection producing a self-describing `.npz`.
programs/inspect_peaks/run_frame_inspection.py	New example script for per-frame inspection producing refine-like CSVs.
programs/inspect_peaks/inspect_peaks_example_config.yaml	New example YAML config for peak inspection.
programs/inspect_peaks/frame_inspection_example_config.yaml	New example YAML config for per-frame inspection.
.github/workflows/python-publish.yml	Updates CI python versions and bumps GitHub release action major version.
.github/workflows/pylint.yml	Updates lint workflow python versions.

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- Introduced per-frame inspection capabilities in `inspect_peaks_result.py`, allowing independent scoring of each movie frame. - Updated `InspectionResult` to include a `frame_index` for tracking frame-specific results. - Modified `save_inspection_result` to handle per-frame data, including new axes for frame-specific results. - Refactored `FrameInspectionManager` to streamline per-frame processing and result collection, including a new method for saving results to `.npz` files. - Added tests for saving and loading inspection results, ensuring correct handling of both spatial and per-frame data formats. - Adjusted `PreprocessingFilters` to conditionally apply random Fourier dropout during filter combination. - Removed unused methods related to cross-correlation peak reduction and CSV output from `FrameInspectionManager`.

* feat: inspect peaks, fourier dropout, frame correlations, and distributed match-template Squashed rebuild of the mdg_inspect_peaks PR (Lucaslab-Berkeley#124) on top of development_v1.3 to remove duplicated upstream history. Tree is identical to prior branch tip 84d1ce8. * feat: pull out mean/std normalization into z-score from refinement core * feat: implement peak inspection result saving/loading and refactor related components * refactor: streamline peak inspection methods * refactor: major restructuring of the per-frame inspect peaks manager * Enhance per-frame inspection and result handling - Introduced per-frame inspection capabilities in `inspect_peaks_result.py`, allowing independent scoring of each movie frame. - Updated `InspectionResult` to include a `frame_index` for tracking frame-specific results. - Modified `save_inspection_result` to handle per-frame data, including new axes for frame-specific results. - Refactored `FrameInspectionManager` to streamline per-frame processing and result collection, including a new method for saving results to `.npz` files. - Added tests for saving and loading inspection results, ensuring correct handling of both spatial and per-frame data formats. - Adjusted `PreprocessingFilters` to conditionally apply random Fourier dropout during filter combination. - Removed unused methods related to cross-correlation peak reduction and CSV output from `FrameInspectionManager`. * fix: filter warnings raised internally by mrcfile

* ci(dependabot): bump softprops/action-gh-release from 2 to 3 (#122) Bumps [softprops/action-gh-release](https://github.com/softprops/action-gh-release) from 2 to 3. - [Release notes](https://github.com/softprops/action-gh-release/releases) - [Changelog](https://github.com/softprops/action-gh-release/blob/master/CHANGELOG.md) - [Commits](softprops/action-gh-release@v2...v3) --- updated-dependencies: - dependency-name: softprops/action-gh-release dependency-version: '3' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bugfix to send correlation mean/var to proper devices on multi-GPU refine template (#125) * (docs) migrate to zensical as build backend * (docs) API build for zensical * (docs) update paper ref and citation to published manuscript * (CI/CD) update deployment pipeline for documentation with zensical * ci(dependabot): bump codecov/codecov-action from 6 to 7 (#128) Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 6 to 7. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v6...v7) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-version: '7' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * (fix): CI/CD disable pre-release install dependencies * Prior inspect peaks work (#124) * feat: inspect peaks, fourier dropout, frame correlations, and distributed match-template Squashed rebuild of the mdg_inspect_peaks PR (#124) on top of development_v1.3 to remove duplicated upstream history. Tree is identical to prior branch tip 84d1ce8. * feat: pull out mean/std normalization into z-score from refinement core * feat: implement peak inspection result saving/loading and refactor related components * refactor: streamline peak inspection methods * refactor: major restructuring of the per-frame inspect peaks manager * Enhance per-frame inspection and result handling - Introduced per-frame inspection capabilities in `inspect_peaks_result.py`, allowing independent scoring of each movie frame. - Updated `InspectionResult` to include a `frame_index` for tracking frame-specific results. - Modified `save_inspection_result` to handle per-frame data, including new axes for frame-specific results. - Refactored `FrameInspectionManager` to streamline per-frame processing and result collection, including a new method for saving results to `.npz` files. - Added tests for saving and loading inspection results, ensuring correct handling of both spatial and per-frame data formats. - Adjusted `PreprocessingFilters` to conditionally apply random Fourier dropout during filter combination. - Removed unused methods related to cross-correlation peak reduction and CSV output from `FrameInspectionManager`. * fix: filter warnings raised internally by mrcfile * Tracking possible detections via correlation table (and zipfft integration) (#126) * feat: only update statistics on valid correlation region Under the standard benchmark setup, this should be excluding ~25% of pixels during the conditional update based on MIP value. Benchmarking the code did not show a significant performance change, however. Statistics updates though are not consuming the majority of computation time. * feat: add correlation table to multi-GPU match template * fix: update correlation table for stability * feat: initial integration with zipFFT * test: update unit tests for zipFFT consistency * fix: minor bug fixes for zipfft match template * fix: changed to mitigate errors on feature integration * feat: integrate all stats updates together and simplify backend logic * lint: work towards passing linter * ci(dependabot): bump softprops/action-gh-release from 2 to 3 (#122) Bumps [softprops/action-gh-release](https://github.com/softprops/action-gh-release) from 2 to 3. - [Release notes](https://github.com/softprops/action-gh-release/releases) - [Changelog](https://github.com/softprops/action-gh-release/blob/master/CHANGELOG.md) - [Commits](softprops/action-gh-release@v2...v3) --- updated-dependencies: - dependency-name: softprops/action-gh-release dependency-version: '3' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bugfix to send correlation mean/var to proper devices on multi-GPU refine template (#125) * feat: add CorrelationTable model and integrate into match template results * test: add basic test coverage for correlation table * fix: add tensordict dependency and update pytest filterwarnings * fix: import errors after merge conflict resolution * feat: add hdf5-backed version of MatchTemplateResult * feat: integrate into match template manager * test: add unit tests covering new result functionality * feat: (untested) initial work on hdf5 backed result formats * fix: failing CI from old file path attributes * (fix) resolve edge-case in unit test data setup * feat: add corr table for distributed backend, address review comments * feat: add option to skip re-download of example data --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Josh Dickerson <jdickerson@mrc-lmb.cam.ac.uk> * (docs) add updates to data format sections * (docs) add information on zipFFT backend * (docs) restrict documentation dependencies * (docs) add documentation on inspect peaks/frames * (docs) remove python 3.10 as supported version * (lint) fix pylint errors towards allowing CI/CD --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Josh Dickerson <jdickerson@mrc-lmb.cam.ac.uk>

jdickerson95 marked this pull request as ready for review April 30, 2026 20:44

mgiammar added the enhancement New feature or request label May 16, 2026

feat: inspect peaks, fourier dropout, frame correlations, and distrib…

5e97fce

…uted match-template Squashed rebuild of the mdg_inspect_peaks PR (Lucaslab-Berkeley#124) on top of development_v1.3 to remove duplicated upstream history. Tree is identical to prior branch tip 84d1ce8.

mgiammar force-pushed the mdg_inspect_peaks branch from 84d1ce8 to 5e97fce Compare June 8, 2026 22:02

mgiammar commented Jun 8, 2026

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mgiammar added 4 commits June 9, 2026 11:37

feat: pull out mean/std normalization into z-score from refinement core

b710cfb

feat: implement peak inspection result saving/loading and refactor re…

61291d4

…lated components

refactor: streamline peak inspection methods

5e61241

refactor: major restructuring of the per-frame inspect peaks manager

17335e3

mgiammar requested a review from Copilot June 15, 2026 14:57

Copilot started reviewing on behalf of mgiammar June 15, 2026 14:58 View session

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Comment thread src/leopard_em/pydantic_models/managers/match_template_manager.py Outdated

mgiammar commented Jun 15, 2026

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mgiammar commented Jun 15, 2026

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Comment thread src/leopard_em/analysis/inspect_peaks_result.py

mgiammar commented Jun 15, 2026

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Comment thread src/leopard_em/analysis/inspect_peaks_result.py Outdated

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Comment thread src/leopard_em/pydantic_models/managers/peak_inspection_manager.py

mgiammar added 2 commits July 28, 2026 12:49

fix: filter warnings raised internally by mrcfile

dcf252e

mgiammar merged commit 5ff3055 into Lucaslab-Berkeley:development_v1.3 Jul 28, 2026
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Prior inspect peaks work - #124

Prior inspect peaks work#124
mgiammar merged 7 commits into
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mgiammar:mdg_inspect_peaks

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mgiammar commented Apr 24, 2026

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