Refactor ReaDDy processing and all visualization#62

Merged

blairlyons merged 67 commits intomainfrom

debug-update-viz

Jul 29, 2024

Commits on Jun 25, 2024

update readdy module to match cytosim as much as possible
Blair Lyons
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Commits on Jun 26, 2024

script to copy readdy outputs
Blair Lyons
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Commits on Jun 27, 2024

visualize individual trajectories, leverage readdy post processing code, add pickles
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visualize combined
Blair Lyons
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Commits on Jul 1, 2024

add readdy baseline individual viz
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WIP tomography viz
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tomography visualization
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Merge branch 'main' into update-viz
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Commits on Jul 2, 2024

calculate compression metrics on tomography data for viz
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Commits on Jul 3, 2024

WIP debugging tomography visualization and analysis
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Commits on Jul 9, 2024

dim reduction viz, tomography viz in separate files
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WIP adding options to pca viz
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Commits on Jul 10, 2024

Commits on Jul 15, 2024

merged in changes from testing PCA viz with options
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update colors and camera position for combined viz
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Commits on Jul 16, 2024

PCA viz tested with all options
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Commits on Jul 17, 2024

test and tweak individual readdy viz
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test and tweak individual cytosim viz
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updated camera views for individual and PCA viz
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finish commit
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add ipdb to requirements
mogres
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Methods to calculate twist angle
mogres
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Methods to visualize twist angle
mogres
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Commits on Jul 18, 2024

Commits on Jul 19, 2024

lint
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more lint
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and more linting
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fix saving tomography 2D plots
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tweaks to dim reduction and tomography viz
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lint
Blair Lyons
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Commits on Jul 25, 2024

Update subcell_pipeline/analysis/compression_metrics/README.md

Blair Lyons
and
jessicasyu
authored
changes from review
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add h5py with pdm, remove unused imageio dep, remove broken tests
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don't run tests on build since there aren't any
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calculate total steps for readdy
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Commits on Jul 29, 2024

remove .pdm-python and add to gitignore
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Merge remote-tracking branch 'origin/feature/polymer_twist' into debug-update-viz
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more changes from review
Blair Lyons
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