Fix bugs#33
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Move numpy.empty array allocation outside the per-object loop in compute_texture. It was being reset on every iteration, discarding all previous objects' Haralick values and leaving only the last object intact. All prior objects received uninitialized memory from numpy.empty. Adds test_texture_values_correct_per_object: independently computes expected Haralick values per object with mahotas and asserts the pipeline output matches, catching any regression where the array is reset inside the loop. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…-zero bug get_outline used find_boundaries with the default mode='thick', which returns both inner (object-side) and outer (background-side) boundary pixels. Because the image is zeroed outside the cell before get_outline is called, outer boundary pixels always have intensity 0, so numpy.min(edge pixels) always returned 0 regardless of actual edge intensity. Switching to mode='inner' restricts the edge mask to pixels inside the object boundary, so all edge pixels have real cell intensities. Adds test_min_intensity_edge_not_zero_for_bright_cell: a cell with uniform intensity 100 must have MinIntensityEdge=100, not 0. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Port all fixes from the NF1_3D audit to the equivalent ZedProfiler modules: - colocalization: initialize combined_thresh before try block (Bug 2), add numpy.any guard on overlap section, fix Accurate/Fast dispatch inversion (Bug 3), remove dead pre-loop pearsonr initialization (Bug 4), and fix compute_colocalization hard-coding fast_costes='Accurate' ignoring the caller's argument (Bug B) - granularity: guard per-axis scale factor against division-by-zero when a dimension has size 1, in both _upsample_3d and the background upsampling block (Bug 7) - neighbors: replace bbox-crop adjacency detection with 1-voxel morphological dilation so face-touching objects are detected correctly (Bug 5) - intensity: rename bbox variables to avoid collision with max_intensity_* names (Bug 9), add index=1 to scipy.ndimage.sum so it sums only the target object's voxels (Bug 10) Add regression tests in each test file covering all fixed bugs. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Adds "Fast" as a distinct third mode (linear with adaptive skipping) matching CellProfiler's Accurate/Fast/Faster nomenclature. Previously "Fast" routed to bisection -- it now routes to linear_costes with fast_costes="Fast", and "Faster" routes to bisection. Fixes bisection_costes_threshold_calculation returning thresholds normalised to [0,1] (mid/scale_max) instead of raw pixel units. The outer dispatch's `image > thr` comparison requires raw values, so this was silently bypassing Costes thresholding in "Faster" mode. CellProfiler's library has the same bug; this is an intentional divergence, documented in a comment. Also updates both docstrings to describe all three modes, and adds value-based tests: convergence across all three modes, low threshold for correlated images, high threshold for anti-correlated images (linear only), and a documented test for bisection's degenerate anti-correlated edge case. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Switch README badge from a hardcoded shields.io percentage to a live Codecov badge that updates automatically on every push - Add coverage XML upload to the run_tests matrix job via codecov/codecov-action@v5 (no token needed for public repos) - Remove the coverage_and_badge job and the stale-badge check entirely One-time setup: activate the repo at codecov.io/gh/WayScience/ZedProfiler. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Running coverage on the full matrix (8 combinations) was redundant. Coverage is now measured once on ubuntu-24.04 + Python 3.13 in a separate job, and the matrix run_tests job is back to plain pytest. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Welcome to Codecov 🎉Once you merge this PR into your default branch, you're all set! Codecov will compare coverage reports and display results in all future pull requests. Thanks for integrating Codecov - We've got you covered ☂️ |
Both are obsolete now that the README uses a dynamic Codecov badge. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
MikeLippincott
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Most of the code was reviewed in the NF1_3D repo first, so not many comments here
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Description
Fixing bugs identified and fixed in WayScience/NF1_3D_organoid_profiling_pipeline#147
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