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Baseline indexer part1#25

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jbeilstenedmands wants to merge 75 commits intoDiamondLightSource:mainDiamondLightSource/fast-feedback-service:mainfrom jbeilstenedmands:baseline_indexer_part1jbeilstenedmands/fast-feedback-service:baseline_indexer_part1Copy head branch name to clipboard

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Commits on Dec 10, 2024

• Add start of an indexer program

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• Add xyz_to_rlp function as a first step working example

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• Add fft3d with pocketfft

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• Tidying, comment out parser for now

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• Add last bit of indexing part 1 - getting candidate vecs

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• Try extracting some metadata from the h5 file through the reader.

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• Add reading of scan start and osc width

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• Add a more formal beam model

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• Add initialization from json data

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• Add json serialization, add dx2 scan class

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• Add gonio dx2 model

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• Include eigen, move models dir

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• Use dx2 repo

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• Add command line parsing, remove reader, update to dx2 detector

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• Add pocketfft as dependency

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• Use new panel model from dx2

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• Start basis vector combination code

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• Add basis vector combinations and index assignment

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• Update and tidying

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• Tidy up, add some extra arguments, output a simple experiment list

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• Add some prediction and calculating reflection properties

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• Add better results output for candidates

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• Template array reading, add candidate vecs output json

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• Move into baseline_indexer folder, just to candidate vecs for now

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• Output tidying

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• Use standard argparse for baseline indexer

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• Updates

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• Add these back in

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• Remove code now in dx2

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• Revert changes to h5read.c

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• Remove unneeded struct and import

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• Newlines

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• Revert changes to h5read.h

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Commits on Jan 10, 2025

• Output an example experiment list, add a test as an example of how to run

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Commits on Jan 13, 2025

• Allow setting of number of fft grid points

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Commits on Jan 17, 2025

• Add more comments into code, function docstrings.

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• Merge branch 'main' into baseline_indexer_part1

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Commits on Jan 20, 2025

• Apply suggestions from code review - small changes/one-liners

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• Add more suggestions from code review.

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• More suggested changes.

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• Some tidying

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• Add dx2 as a dependency

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• Use the new experiment class

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• Add autodiscovery and settable nthreads for fft

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• Merge branch 'DiamondLightSource:main' into baseline_indexer_part1

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• Use spdlog to log to console and file with suitable log levels

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• Use parser.is_used for nthreads parameter

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• Remove CUDA requirements from CMakelists and fix cmake warnings

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• Add a dev flag for cmake to switch between dx2 as a subdirectory or the git repo.

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• Pin to the merged dx2 commit.

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Commits on Jan 21, 2025

• Update file paths in test, tidying

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Commits on Jan 22, 2025

• Update dx2 source discovery

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• Update CMakeLists.txt

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• Use an unordered map rather than array

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• Update test due to sign changes

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Commits on Jan 23, 2025

• Merge branch 'main' into baseline_indexer_part1

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• Use common logger

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Commits on Jan 29, 2025

• Add unit test for xyz_to_rlp

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Commits on Feb 3, 2025

• Add test for fft3d file

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Commits on Feb 4, 2025

• Add flood-fill test, move to tests subdirectory

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• Update test to test the rmsd cutoff filter

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Commits on Feb 6, 2025

• Rename sites_to_vecs to peaks_to_rlvs, add test

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