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Xppmask#373

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hoidn wants to merge 132 commits intolcls-users:xppmasklcls-users/btx:xppmaskfrom hoidn:xppmaskhoidn/btx:xppmaskCopy head branch name to clipboard

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Commits on Mar 26, 2024

• Squashed commit

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• imports and input handling

  

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Commits on Apr 2, 2024

• update tests

  

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• update tests

  

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Commits on Apr 16, 2024

• Finished and tested first 4 stages

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• start implementing pump probe step

  

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Commits on May 7, 2024

• Update test_xppmask.py and add xpploader module

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• Fix XPP loader

  

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Commits on May 13, 2024

• cleanup; save delays and laser condition in data loading stage

  

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• add pump_probe.py

  

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Commits on May 14, 2024

• pump probe analysis task

  

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Commits on May 20, 2024

• fix imports

  

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• symlink for testing

  

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• update tests

  

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• update tests

  

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• update tests

  

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Commits on May 21, 2024

• use roi in spatial mask definition

  

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• Enhance test suite and data processing

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Commits on May 22, 2024

• cleanup

  

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• update test config dict

  

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• debug

  

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• tested pump probe analysis end to end

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• add readme on xpp pump probe workflow

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• update readme

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Commits on May 28, 2024

• remove unneeded config parameters

  

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• Merge branch 'xppmask' of github.com:hoidn/btx into xppmask

  

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• fix path

  

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• paths

  

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Commits on May 30, 2024

• Update xppmask tests and implementation

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Commits on May 31, 2024

• in pump probe curve calculation, filter by the number of frames per delay bin

  

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• cleanup

  

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Commits on Oct 10, 2024

• feat: Refactor CalculatePValues class in btx/processing/xppmask.py

  

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• fix: Add type hints to CalculatePValues class

  

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• feat: Refactor CalculatePValues class

  

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Commits on Oct 14, 2024

• feat: Add btx/processing/flatten.py

  

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• feat: Add support for including specific files in the flatten script

  

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Commits on Oct 23, 2024

• feat: Add build_pump_probe_masks.py

  

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• refactor

  

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• wip

  

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• finished individual tasks and their functional tests

  

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• pump probe task test

  

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• types

  

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• feat: Update import path for MakeHistogramInput and MakeHistogramOutput

  

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• feat: Optimize _calculate_histograms using Numba JIT and memoization

  

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• fix: Update memoization decorator to handle instance methods correctly

  

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• feat: Add btx/processing/core/adapters.py

  

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• Let's analyze the output from the added debug prints:

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• fix: Update adapter validation to expect one parameter instead of two

  

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• Based on the additional debug prints, let's analyze the output:

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• fix: Update validation logic for plot_diagnostics method

  

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• feat: Update import path for LoadDataInput and LoadDataOutput

  

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Commits on Oct 24, 2024

• fix: Improve TaskAdapter validation logic

  

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• feat: Add task.py

  

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• fix: Remove validation methods from Task base class

  

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• fix: remove validation logic from TaskAdapter

  

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• feat: Add pipeline.py

  

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• fix: Remove cross-cutting validation methods while preserving essential array shape/type checking

  

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• fix: Simplify LoadData class by removing unnecessary methods and validations

  

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• fix: Remove unnecessary config validation from LoadData class

  

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• fix: Remove unnecessary _validate_config method

  

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• refactor: Update import paths for CalculatePValuesInput and MeasureEMDInput/Output

  

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• fix: Remove validation methods while preserving essential array shape/type checking

  

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• refactor: Update import paths for btx_types

  

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• fix: Remove unnecessary config validation

  

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• feat: Add btx/processing/core/__init__.py

  

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• fix: Remove AdapterValidationError import and reference

  

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• feat: Add pipeline integration test

  

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• test: Improve assertions in pipeline integration test

  

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• Here is the one-line commit message for the provided diffs:

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• fix: Simplify task adapter and pipeline

  

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• The updated code should now work without any errors:

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• feat: simplify pipeline and task adapter components

  

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• fix: remove input/output types from task registry in integration tests

  

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• fix: Extract dimensions from input data for test_histogram_pipeline

  

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• fix: Add missing PipelineResult class and update test imports

  

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• fix: Add PipelineBuilder class to pipeline.py and update imports in test_pipeline_integration.py

  

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• fix: Add forward reference type hint for Pipeline

  

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• fix: Update Pipeline.run() to properly wrap task outputs in the correct input types

  

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• fix: wrap LoadDataOutput in MakeHistogramInput before passing to MakeHistogram task

  

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• fix: Import MakeHistogramInput in pipeline.py

  

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• fix: handle task input wrapping for all transitions

  

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Commits on Oct 25, 2024

• feat: Add detailed error diagnostics to pump-probe analysis

  

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• refactor: Handle invalid p-values in _calculate_p_values method

  

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• fix: Handle invalid p-values in pump_probe analysis

  

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• fix: Handle invalid p-values in pump_probe diagnostics plotting

  

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• fix: Handle log p-value formatting in pump_probe.py

  

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• fix: Handle infinity in p-value plotting for pump-probe analysis

  

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• feat: Remove relative error plot panel

  

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• feat: remove 'signal difference' panel and change remaining panels to vertical arrangement

  

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• finished a round of debugging; pipeline almost done

  

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• cleanup and add test of the end-to-end analysis pipeline using simulated pump probe data

  

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• fix: move energy thresholding from xpploader.py to load_data.py

  

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• fix: Configure logging to file instead of console

  

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• feat: Add energy filter to PumpProbeAnalysis task

  

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• feat: Add heatmap plots for total and energy-filtered intensity distributions

  

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• feat: Consolidate overview diagnostics and intensity maps into a single four-panel plot

  

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• feat: change energy filtering from (E0, dE) to (Emin, Emax)

  

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• feat: add Poisson background with lambda=5 to frames

  

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• feat: add EMD value distribution to null distribution histogram

  

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• add setup.py

  

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• rm builders

  

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• fix: Reduce minimum count threshold for pump-probe analysis

  

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• wip delay handling fixes

  

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• wip delay handling fixes

  

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• wip delay handling fixes

  

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• wip delay handling fixes

  

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• wip delay handling fixes

  

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• fix: enable debug prints in pump_probe analysis

  

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• chore: comment out print statements

  

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• fix: Fix indentation error in pump_probe.py

  

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• wip fixing incorrect error bar calculation

  

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• fix: remove QQ plot of differences

  

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• add working end to end pipeline for xppl1030522 analysis

  

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• Merge branch 'stable' into xppmask

  

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• add example pipeline output

  

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• add hdf5 to npz extraction script to for that run / experiment

  

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• cleanup

  

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• add readme

  

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• add readme

  

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• feat: Add process() method to MakeHistogram task

  

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• feat: Add process method to LoadData class

  

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• feat: Add process() method to MeasureEMD class

  

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• fix: Add missing import for MakeHistogramOutput

  

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• feat: Add process() method to CalculatePValues class and update script

  

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• feat: add process() method to CalculatePValues class and update script

  

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• feat: add process() method to BuildPumpProbeMasks

  

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• fix: Add missing imports to BuildPumpProbeMasks class

  

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• feat: add new process() method to PumpProbeAnalysis class

  

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• fix: Add missing imports for LoadDataOutput and BuildPumpProbeMasksOutput

  

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Commits on Oct 26, 2024

• update README

  

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• update README

  

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• update README

  

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