Add opt-in keep_largest_component to CropForeground/CropForegroundd - #9126
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CropForeground computes its bounding box over ALL foreground pixels selected by select_fn, so disconnected regions (e.g. laterality labels/scanner text annotations in mammograms, separate from the breast tissue) get pulled into the crop alongside the intended anatomy. Add an opt-in keep_largest_component flag (default False, preserves existing behavior) to generate_spatial_bounding_box, CropForeground and CropForegroundd. When set, it applies MONAI's own get_largest_connected_component_mask to the select_fn mask before computing the bounding box, keeping only the largest connected region. Opt-in rather than default because select_fn can legitimately select multiple disjoint structures (e.g. several organs in one volume) that should all remain in the box. Fixes Project-MONAI#8988 Signed-off-by: MDSALMANSHAMS <salmanshams67@gmail.com>
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Included review availability: Your plan provides up to 8 included reviews per hour; 7 remain after this review. 📝 WalkthroughWalkthroughAdds Estimated code review effort: 2 (Simple) | ~10 minutes Merge Risk: ⚪ Minimal · up to The opt-in option selects the largest foreground component through both crop transforms while preserving existing default behavior. No concrete merge-blocking risk was identified. 🚥 Pre-merge checks | ✅ 5✅ Passed checks (5 passed)
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In `@monai/transforms/croppad/array.py`:
- Line 826: Move keep_largest_component to the end of the existing explicit
parameters in both CropForeground and CropForegroundd constructors, immediately
before **pad_kwargs, so prior positional argument bindings remain unchanged. Add
regression tests covering the previous positional constructor order for both
classes.
In `@monai/transforms/croppad/dictionary.py`:
- Around line 905-911: Add a focused CropForegroundd regression case to the
dictionary transform test cases, using disconnected foreground components with
keep_largest_component=True and asserting the output retains only the largest
component’s crop. Ensure the case exercises forwarding of this flag through the
dictionary wrapper.
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monai/transforms/croppad/array.pymonai/transforms/croppad/dictionary.pymonai/transforms/utils.pytests/transforms/test_crop_foreground.pytests/transforms/test_generate_spatial_bounding_box.py
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agourakis82
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Nice, this matches what we discussed on #8988 — opt-in flag, default False (no behavior change), and it reuses get_largest_connected_component_mask from monai/transforms/utils.py rather than reimplementing connected-component logic. I checked monai/transforms/utils.py and confirmed keep_largest_component is applied to the select_fn(data).any(0) mask before the bounding-box loop, which is the right place (matches how get_largest_connected_component_mask expects a (spatial_dim1[, spatial_dim2, ...]) array with no channel dim). The keep_largest_component=False/no-foreground path also degrades safely — get_largest_connected_component_mask returns an all-False mask via its num_features <= num_components branch, so no crash there.
Two things worth fixing before merge though:
-
Parameter insertion breaks positional-arg callers — in
monai/transforms/croppad/array.py::CropForeground.__init__(and the dict version incroppad/dictionary.py::CropForegroundd.__init__),keep_largest_componentis inserted betweenallow_smallerandreturn_coords/k_divisiblerather than appended at the end of the signature. Since all the params before**pad_kwargsare positional-or-keyword, any caller that constructsCropForeground(...)/CropForegroundd(...)with positional args pastallow_smaller(e.g. passingreturn_coords,k_divisible,mode,start_coord_key, etc. positionally) will silently get the wrong values bound to the wrong parameters — this is exactly the risk CodeRabbit's automated review flagged. I didn't find any positional call sites in-tree (monai/auto3dseg/utils.pyand the dictionary.py internal call both use kwargs), but it's still a public API break for downstream users. Suggest movingkeep_largest_componentto the end of the parameter list (right beforek_divisible/mode/lazy/**pad_kwargs, after all pre-existing params) so no existing positional binding shifts. -
No
CropForegrounddtest forkeep_largest_component—tests/transforms/test_crop_foreground.pyandtests/transforms/test_generate_spatial_bounding_box.pyboth got the two-component-blob-plus-isolated-pixel test case (flag True vs False), buttests/transforms/test_crop_foregroundd.pyhas no equivalent case, so the dict transform's forwarding ofkeep_largest_componentthroughCropForegroundd.__init__->CropForeground.__init__is untested end-to-end. Given the PR description explicitly calls outCropForegrounddas in scope, worth adding oneTESTS.append(...)entry there mirroring the array test.
Move keep_largest_component to the end of the parameter list in both CropForeground.__init__ and CropForegroundd.__init__ (right before **pad_kwargs) instead of inserting it mid-signature. The mid-signature insertion shifted return_coords/k_divisible/mode/lazy (array) and k_divisible/mode/start_coord_key/end_coord_key/allow_missing_keys/lazy (dict) for any caller constructing these transforms with positional arguments past allow_smaller -- a public API break for downstream users even though no in-tree call site used positional args. Also add a CropForegroundd regression case for keep_largest_component (disconnected-component crop), mirroring the existing CropForeground and generate_spatial_bounding_box tests -- the dict wrapper's forwarding of this flag was previously untested end-to-end. Signed-off-by: MDSALMANSHAMS <salmanshams67@gmail.com>
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Thanks for the review, @agourakis82 — both points fixed in 1a8e059:
Ran the full local suite ( |
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Fixes #8988
Description
CropForeground/CropForegrounddcompute the bounding box over all foreground pixels selected byselect_fn. When the foreground mask has disconnected regions — e.g. a laterality label or scanner annotation sitting away from the breast tissue in a mammogram — the box stretches out to cover them too, instead of tightly cropping just the anatomy of interest.This adds an opt-in
keep_largest_component: bool = Falseparameter togenerate_spatial_bounding_box,CropForeground, andCropForegroundd. When set, it reuses MONAI's ownget_largest_connected_component_mask(already used byKeepLargestConnectedComponent) on theselect_fnmask before computing the bounding box, keeping only the largest connected region.Default is
False(no behavior change) becauseselect_fncan legitimately select multiple disjoint structures that should all stay in the box (e.g. several organs in one volume) — this can't be the default without silently changing existing pipelines, same reasoning asallow_smaller's own default change in v1.5.0.Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests --disttests.make htmlcommand in thedocs/folder.Ran the specific test files locally (
test_generate_spatial_bounding_box.py,test_crop_foreground.py,test_crop_foregroundd.py) — 147 passed.black/isort/ruffall clean on the changed files.