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v2.0.0 release - #48
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- Modified commands/analyse/analyse.py to use membrane thickness from config file for component processing. - Modified commands/analyse/cli.py to add a CLI option for membrane thickness. - Modified commands/analyse/utils/io.py to update printed summary to use outer diameters label. - Modified commands/analyse/utils/measurement.py to derive outer diameter via shell-volume-inversion formula instead of as solid sphere. - Modified config.toml to add a default membrane thickness to analyse section. - Modified utils/config.py to add a membrane thickness field to analyse's configuration schema. - Modified docs/analyse.md to include documentation on membrane thickness option. - Modified tests/integration/analyse_integration_test.py to tighten equivalent diameter range check. - Modified tests/unit/analyse_unit_test.py to update sphere diameter test with shell inversion tests.
- Modified commands/analyse/utils/geometry.py to derive relative semi-axis lengths from inertia eigenvalues using updated ellipsoid relation. - Modified tests/unit/analyse_unit_test.py to update axis derivation unit tests to use new relation formula and add a test to check for the previous inverse square root's ceiling.
- Modified commands/analyse/utils/geometry.py to return NaN for degenerate components. - Modified docs/analyse.md to update footnote on major/minor axes and relationship with equivalent diameter. - Modified tests/integration/analyse_integration_test.py to tighten the aspect ratio check for synthetic spheres. - Modified tests/unit/analyse_unit_test.py to add unit tests for axis ratio recovery and degenerate components.
- Modified commands/analyse/analyse.py to measure lumen volume using the gap-bridged mask. - Modified commands/analyse/utils/filtering.py to pad components before dilation so growth isn't asymmetrically clipped at the bounding box. - Modified docs/analyse.md to update footnote explaining lumen volume uses gap-bridged mask. - Modified tests/unit/analyse_unit_test.py to define unit tests for components at the volume boundary.
- Added .github/workflows/main_version-update-check.yaml to check that a pull request raised against main has a version number greater that then current.
- Added .github/workflows/main_publish-release.yaml to publish a GitHub release on commits to main branch.
Merge pull request #40 from holsam/gh-workflows
Merge pull request #41 from holsam/analysis-improvements
- Modified commands/label/label.py to remap component IDs to a sequential range instead of relabelling by adjacency. - Modified tests/integration/label_integration_test.py to add a unit test to check a split vesicle is written to one label. - Modified tests/unit/label_unit_test.py to make the separate vesicles closer to the merge tolerance boundary.
- Modified commands/label/label.py to counts excluded components at each filter stage and to log & write a per-file tally file beside labelled output.
- Modified commands/model/model.py to use the max workers config value from model section instead of label section.
- Modified commands/model/utils/least_squares_fit.py to read latitude span and beam-axis angle from the beam (z) column instead of the x column. - Modified tests/unit/model_unit_test.py to rebuild point cloud helpers in z, y, x order and adds tests for the beam-axis and missing-wedge guards.
- Modified commands/model/utils/least_squares_fit.py to document BIC comparison limitations and add a size-limited flag to the reliability assessment.
Merge pull request #42 from holsam/label-improvements
Merge pull request #43 from holsam/model-improvements
- Modified utils/mrc.py to read voxel sizes from MRC file header and log a warning when y or z differs from x. - Modified tests/unit/mrc_unit_test.py to add unit tests covering anisotropic header warnings.
- Modified commands/analyse/analyse.py to identify components touching the z-boundary and to flag this. - Modified commands/analyse/utils/measurement.py to add a z-boundary check and QC flag. - Modified tests/unit/analyse_unit_test.py to add unit tests for z-boundary check and QC flag.
- Modified commands/analyse/utils/measurement.py to add per-file membrane thickness estimation. - Modified commands/analyse/analyse.py to resolve membrane thickness per file and record this in results. - Modified commands/analyse/cli.py to update option help text. - Modified config.toml to set analyse thickness to "auto" and label thickness to 2.6nm. - Modified utils/config.py to update analyse's thickness key to accept 'auto'. - Modified docs/config.md to document updated defaults. - Modified docs/analyse.md to document auto mode, added output columns and update the equivalent diameter footnote. - Modified tests/unit/analyse_unit_test.py to add unit test for membrane thickness estimation. - Modified tests/integration/analyse_integration_test.py to update tests.
- Modified commands/label/label.py to identify components too small to reach the coverage threshold from components with incomplete coverage. - Modified commands/label/utils/geometric_proxies.py to expose arc-coverage grid size as a shared constant. - Modified tests/integration/label_integration_test.py to add test for exclusion tally reporting size-floor breakdown.
- Modified commands/model/model.py to log warning when input file has only one non-zero label and could be a binary segmentation. - Modified tests/integration/model_integration_test.py to add a test for warning produced when given a binary mask.
- Modified commands/analyse/analyse.py to log warning and skip MRC files carrying an EValuator marker. - Modified commands/model/model.py to write EValuator marker into the header of model output. - Modified utils/mrc.py to add EValuator marker constant, update writer utility to include optional header, and add a label reader utility. - Modified tests/integration/analyse_integration_test.py to add a test for skipped MRC files. - Modified tests/unit/mrc_unit_test.py to add tests for the header labels.
Merge pull request #44 from holsam/misc-improvements
- Modified commands/tools/benchmark_missing_wedge/benchmark_missing_wedge.py to use the degraded shell volume during convex hull processing to match other methods.
- Modified commands/tools/utils/synthetic.py to record volume-equivalent diameter as ground truth diameter and keep nominal diameter alongside.
- Modified commands/tools/benchmark_missing_wedge/benchmark_missing_wedge.py to use membrane thickness when generating shells and converting shell voxels to a diameter. - Modified commands/tools/benchmark_missing_wedge/defaults.py to add default membrane thickness for benchmarks. - Modified commands/tools/benchmark_missing_wedge/methods.py to derive outer diameter from shell voxel count.
- Modified commands/tools/benchmark_geometric_proxy/benchmark_geometric_proxy.py to record timing and error for independent diagonal baseline alongside existing methods. - Modified commands/tools/benchmark_geometric_proxy/defaults.py to registers diagonal baseline as a benchmarked method. - Modified commands/tools/benchmark_geometric_proxy/methods.py to add independent naive diagonal radius method. - Modified commands/tools/benchmark_geometric_proxy/summaries.py to assign a plot colour to diagonal baseline results. - Modified docs/tools.md to document diagonal baseline.
- Added utils/figures/theme.py to provide streamlit-free theme constants and a static theme resolver. - Moved commands/viewer/utils/plots.py to utils/figures/plots.py so figure builders no longer import streamlit. - Moved commands/viewer/utils/format.py to utils/figures/format.py so column label formatting used by the builders is not tied to viewer specifically. - Modified commands/viewer/utils/theme.py to import theme constants from new figures utility. - Modified commands/viewer/app/pages/tomogram.py to import builders and formatter from new figures utility. - Modified tests/unit/viewer_unit_test.py to import builders and formatter from new figures utility. - Added tests/unit/figures_unit_test.py to check figure builders import without streamlit.
- Added commands/plot/utils/data.py to load analyse/model results, filter debris, log any drop reasons then joins the two datasets. - Modified tests/unit/plot_unit_test.py to add adds unit tests for the data preprocessing utilities.
- Added commands/plot/utils/export.py to export plotly figures as SVG files and summary tables as XLSX files. - Modified pyproject.toml & uv.lock to add new plot optional dependency group. - Modified tests/unit/plot_unit_test.py to define unit tests for exporting.
- Modified utils/figures/plots.py to add plot-specific builder functions. - Added commands/plot/sections.py to define functions for creating figures per section. - Modified commands/plot/plot.py to use Python sections rather than R scripts. - Modified commands/plot/cli.py to replace --rscript option with --include-flagged option. - Modified commands/plot/utils/input.py to update runnable sections. - Modified utils/config.py to update plot configuration keys and section names. - Modified config.toml to update plot config table to contain defaults. - Modified pyproject.toml to remove packaged R scripts. - Removed commands/plot/r/*, utils/r/*, and commands/plot/utils/dispatch.py. - Modified tests/unit/plot_unit_test.py to replace R dispatch tests. - Modified tests/integration/plot_integration_test.py to add tests for Python section orchestration.
- Modified commands/plot/cli.py to add --agreement option. - Modified commands/plot/plot.py to run the agreement section when pairs provided. - Modified commands/plot/sections.py to add function for generating the agreement section. - Modified commands/plot/utils/input.py to parse agreement pairs. - Modified tests/unit/plot_unit_test.py to add agreement parsing and gating tests. - Modified tests/integration/plot_integration_test.py to add test for agreement.
Merge pull request #45 from holsam/figure-improvements
Merge pull request #46 from holsam/tools-improvements
- Modified commands/label/utils/merge.py to update merge logic to check if components are concentric (similar centroid, different radii) and to avoid merging these. - Modified commands/utils/config.py to add new configuration keys for concentric merge radius and centre thresholds. - Modified commands/label/label.py to pass new config keys through to merge utilities. - Modified docs/config.md to add new configuration keys to reference. - Modified docs/label.md to explain how concentric components are determined. - Modified config.toml to add defaults for new configuration keys. - Modified tests/unit/label_unit_test.py to define unit tests for concentric merge logic.
- Modified config.toml to update merge_centre_tol_factor to 0.573 (from 1.5). - Modified utils/config.py to update default value for merge_centre_tol_factor to 0.573. - Modified tests/unit/config_unit_test.py to check the merge_centre_tol_factor value in config.toml matches the schema in utils/config.py. - Modified tests/unit/label_unit_test.py to check the default merge_centre_tol_factor does not merge neighbours. - Modified docs/config.md to update default merge_centre_tol_factor value in reference.
- Modified commands/analyse/utils/measurement.py to remove touches Z boundary from QC flags. - Modified commands/analyse/analyse.py to add touches Z boundary check to output CSV. - Modified tests/unit/analyse_unit_test.py to remove tests checking Z boundary is in QC flags. - Modified tests/unit/plot_unit_test.py to update tests to not use Z boundary check. - Modified docs/analyse.md to include Z boundary check in output.
- Modified commands/analyse/utils/measurement.py to add functions for calculating outer diamter from largest xy slice. - Modified commands/analyse/analyse.py to add xy diameter as additional reported measurement. - Modified tests/units/analyse_unit_test.py to add tests for xy diameter calculation. - Modified docs/analyse.md to add xy diameter to reported measurements.
- Modified commands/plot/utils/data.py to add populations based on filtered QC and Z clipping. - Modified commands/plot/sections.py to run sections over populations for comparison. - Modified tests/unit/plot_unit_test.py to add tests for population splits.
- Modified commands/plot/utils/data.py to join fitted diameters to analyse frames. - Modified commands/plot/sections.py to load fitted diamters and use model output for comparisons. - Modified tests/unit/plot_unit_test.py to add tests attaching fitted diameters.
- Modified commands/plot/utils/data.py to add functions to aggregate tomogram data. - Modified commands/plot/sections.py to use per-tomogram rather than per-EV values. - Modified tests/unit/plot_unit_test.py to add tests for tomogram aggregation.
- Modified commands/plot/sections.py to plot scatter and correlation stats at tomogram-level instead of EV-level. - Modified test/unit/plot_unit_test.py to add tests for tomogram-level stats.
- Modified tests/cli/cli_test.py to fix test using previous R dispatch code so it uses current section runner. - Modified tests/integration/plot_integration_test.py to use three tomograms for comparison test and PCA.
- Modified tests/integration/analyse_integration_test.py to include added columns to expected CSV columns.
- Modified tests/unit/config_unit_test.py to update expected default plot sections.
Merge pull request #47 from holsam/gen-improvements
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Pull Request (PR) description
analyse(Implement improvements toanalyselogic #41),label(Implement improvements tolabellogic #42),model(Implement improvements tomodellogic #43) andtool(Implementtoolcommand improvements #46) commands.plotandviewerfor consistency (Refactor figure generation #45)Issues resolved
Resolves #17