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…les (PolusAI#327) Make theEnvironment.singleROI the single source of truth for wholeslide mode across all entry points and scan sites. - dirs_and_files.cpp: set singleROI=true when wholeslide detected from directory structure, so downstream scan sites see the flag - new_bindings_py.cpp: fill labelFiles with empty strings when single_roi=True; fix validation to allow empty seg list in that case; only check seg file existence when path is non-empty - nyxus.py: allow mask_files=None when single_roi=True; pass [] instead of None to the C++ binding - slideprops.cpp, phase1.cpp, phase2.cpp: replace independent spL==nullptr / fname_seg.empty() checks with theEnvironment.singleROI (3 sites in phase2.cpp) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Five pytest cases covering the fixed single_roi=True path in featurize_files: - no mask files → succeeds, one row per image with label=1 - mask files supplied but single_roi=True → mask is ignored, results identical to no-mask case - single_roi=False (segmented) → multiple rows per image (unchanged behavior) - single_roi=False, no mask → raises IOError (unchanged behavior) - single_roi=True results consistent with featurize_directory when no seg dir given Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
The polus version of read_2D_dataset() has no Environment parameter, so theEnvironment is undeclared there. The callers (featurize_directory_imp et al.) already set env.singleROI before calling read_2D_dataset, making this assignment redundant anyway. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…nisotropic This function has no Environment& parameter, so env.singleROI would fail to compile. The variable was also never used — the function is wholeslide- only by definition and feeds pixels unconditionally. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
gatherRoisMetrics_2_slideprops_2D and _3D have no Environment parameter so env.singleROI doesn't compile there. p.fname_seg.empty() is the correct local signal: in the wholeslide path labelFiles are empty strings, so fname_seg is empty iff singleROI is true. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…anisotropic__OLD Same issue as scan_trivial_wholeslide_anisotropic in phase2_2d.cpp: no Environment parameter so env.singleROI doesn't compile, and the variable was never used anyway — this is a wholevolume-only function. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Use ROI_label instead of label (polus column name) - featurize_directory wholeslide: pass int_dir as label_dir (same-dir detection) instead of '' which polus rejects with OSError Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…comparison intensity_image legitimately differs in format (full path vs basename) between the two code paths, so skip string columns in numeric comparison. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
… does not get it.
…yxus into fix/issue-327-single-roi-polus
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Fixes #327 |
…yxus into fix/issue-327-single-roi-polus
Merge conflict residue introduced a validation block that used labelFiles before it was declared (its declaration is inside the else branch). Remove the duplicate pre-check block; the segmented path's existing validation inside the else branch is sufficient. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…ctions On Linux, Python's memory allocator reuses freed object addresses, so id(new_nyx) can equal id(old_nyx). The pynyxus_cache returns the old Environment whose singleROI=true (left over from a prior whole-slide featurize_directory call). initialize_environment calls compile_feature_settings() with that stale value, baking SINGLEROI=true into all feature settings. When featurize_montage_imp later sets singleROI=false, the settings were never refreshed, causing ContourFeature::calculate to call buildWholeSlideContour (AABB corners) instead of buildRegularContour, producing PERIMETER=22.0 for a speckle-only mask. Fix: - Make compile_feature_settings() idempotent by clearing f_settings_ and feature2settings_ at the start. - Call compile_feature_settings() in every featurize_*_imp function right after singleROI is assigned, so SINGLEROI in feature settings always matches the current run mode. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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