Code

Add basic curvature#974

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Merged

SylviaWhittle merged 84 commits intomainAFM-SPM/TopoStats:mainfrom SylviaWhittle/curvatureAFM-SPM/TopoStats:SylviaWhittle/curvatureCopy head branch name to clipboardNov 21, 2024

+1,196-38

Commits

Commits on Oct 17, 2024

• Add beginnings of curvature file

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  9be0604

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• Add angle_diff_signed

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• Add test_angle_diff_signed

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• Add discrete_angle_difference_per_nm_circular

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• Fix normalisation and flipped subtractions in first and last index

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• Add test for discrete_angle_difference_per_nm_circular

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• Add find_curvature_defects_simple_threshold

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• Add test for find_curvature_defects_simple_threshold

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• Add calculate_trace_distances_to_last_points_circular

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• Add calculate_distances_between_distances_circular

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• Add test_trace_distances_to_last_points_circular

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• Add test_calculate_distances_between_defects_circular

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• Add calculate_number_of_defects

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• add test_caclculate_number_of_defects

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• Add calculate_curvature_stats_single_grain_circular

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• Add calculate_curvature_stats_image

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• Add plot_curvatures

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• Add plot_curvatures_individual_grains

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• Add test_plot_curvature

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• Add run_curvature_stats

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Commits on Oct 20, 2024

• Fix test_angle_diff_signed

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• Add test_calculate_curvature_stats_image

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• Disable defects functions and add linear version of angles_per_nm

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• Fix plotting for updated curvature functions and remove defects functionality

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  a70a773

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• Disable plotting test

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  01f0fce

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• Integrate curvature stats into processing.py

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  ec0dabd

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• Add curvature config option: run

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  cfb9cf6

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• Add 'pad_width' to disordered tracing output for later grain alignment

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• Fix disordered tracing test given addition of 'pad_width'

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  8775c6e

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• Add curvature config to tests

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  311a6c0

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• Fix curvature tests and disable all relating to defects

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  cfb9074

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• Fix processing tests

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• [pre-commit.ci] Fixing issues with pre-commit

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Commits on Oct 22, 2024

• Make curvature plotting functions part of the Images class

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  016782a

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• Add whole image curvature plot and individual grain curvature plots for all set

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• Add plots and config to validation

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Commits on Oct 23, 2024

• Add test for plot_curvatures

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  7ab8c91

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Commits on Nov 7, 2024

• Add beginnings of curvature file

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  d72d053

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• Add angle_diff_signed

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  a963492

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• Add test_angle_diff_signed

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  90e8722

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• Add discrete_angle_difference_per_nm_circular

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  9b15cb8

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• Fix normalisation and flipped subtractions in first and last index

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  e702aea

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• Add test for discrete_angle_difference_per_nm_circular

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  307a89b

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• Add find_curvature_defects_simple_threshold

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• Add test for find_curvature_defects_simple_threshold

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• Add calculate_trace_distances_to_last_points_circular

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• Add calculate_distances_between_distances_circular

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• Add test_trace_distances_to_last_points_circular

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• Add test_calculate_distances_between_defects_circular

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• Add calculate_number_of_defects

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• add test_caclculate_number_of_defects

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  ccf0acd

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• Add calculate_curvature_stats_single_grain_circular

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• Add calculate_curvature_stats_image

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• Add plot_curvatures

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  ef895c5

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• Add plot_curvatures_individual_grains

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  f1fef84

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• Add test_plot_curvature

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  5b6bb88

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• Add run_curvature_stats

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  378ca58

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• Fix test_angle_diff_signed

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  7f5f389

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• Add test_calculate_curvature_stats_image

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  0b1f0e1

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• Disable defects functions and add linear version of angles_per_nm

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  da3fff4

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• Fix plotting for updated curvature functions and remove defects functionality

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  7757dbd

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• Disable plotting test

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  a9a647e

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• Integrate curvature stats into processing.py

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  25e6847

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• Add curvature config option: run

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  d4dc4c1

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• Add 'pad_width' to disordered tracing output for later grain alignment

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  b982bde

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• Fix disordered tracing test given addition of 'pad_width'

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  767ee71

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• Add curvature config to tests

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  f44992f

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• Fix curvature tests and disable all relating to defects

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  8b9e2b2

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• [pre-commit.ci] Fixing issues with pre-commit

  

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• Make curvature plotting functions part of the Images class

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  3873a65

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• Add whole image curvature plot and individual grain curvature plots for all set

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• Add plots and config to validation

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  4d683aa

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• Add test for plot_curvatures

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  84acd11

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• Fix: Formatting from rebase

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• Fix tests: after rebase

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• Merge remote-tracking branch 'origin/SylviaWhittle/curvature' into SylviaWhittle/curvature

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• [pre-commit.ci] Fixing issues with pre-commit

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Commits on Nov 18, 2024

• Merge main into curvature

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• Remove: Add defect code

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Commits on Nov 19, 2024

• Fix: test_process_scan_both: topostats file needed updating to contain curvature stats.

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• Fix: test_calculate_curvature_stats_image: use absolute curvature values

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• Merge main into curvature

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• Fix: test_process_scan_both: Merge conflict

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Commits on Nov 20, 2024

• Add: test_process_scan_stages parametrisation for when curvature stats is disabled and all preceding steps are enabled

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