Comments (5)
This snippet should do it for you. :)
cc_labels = cc3d.connected_components(img)
cc_segids, pxct = np.unique(cc_labels, return_counts=True)
mask_ids = [ sid for sid, ct in zip(cc_segids, pxct) if ct < dust_threshold and sid != 0 ]
cc_labels[ np.in(cc_labels, mask_ids) ] = 0
If you're willing to download another dependency I also write a package called fastremap
that can do it like so, which may be slightly faster or less memory intensive:
cc_labels = cc3d.connected_components(img)
cc_segids, pxct = np.unique(cc_labels, return_counts=True)
mask_ids = [ sid for sid, ct in zip(cc_segids, pxct) if ct < dust_threshold and sid != 0 ]
cc_labels = fastremap.mask(cc_labels, mask_ids)
from connected-components-3d.
Thanks william-silversmith.
from connected-components-3d.
You're welcome!
from connected-components-3d.
from this above code:
cc_labels = cc3d.connected_components(img)
cc_segids, pxct = np.unique(cc_labels, return_counts=True)
mask_ids = [ sid for sid, ct in zip(cc_segids, pxct) if ct < dust_threshold and sid != 0 ]
cc_labels[ np.in(cc_labels, mask_ids) ] = 0
when i use volume image to this above code, nothing 3d small object removed ? so how to remove small 3d volume object? i set dust_threshold= 50, but its not working[ small object cannot removed] ?
@william-silversmith
from connected-components-3d.
For anyone reading this thread these days, cc3d.dust
is available as of 3.7.0 which will remove components smaller than a specified number of voxels. If you want to do something fancy like "as a fraction of the size of the largest shape" you can do a pass with cc3d.statistics
to compute it.
from connected-components-3d.
Related Issues (20)
- Applying Dust and largest_k dtype output option HOT 2
- dust sugnature HOT 1
- Massive memory Leak HOT 7
- 1D Array of 4 Elements Incorrect HOT 5
- Cannot find reference 'dust' in 'cc3d.py' HOT 2
- Question on comparing individual lesions between two masks based on the cc3d.statistics output. HOT 1
- Additional metrics support HOT 2
- Does cc3d also work with memmory-mapped numpy arrays and array-like data? HOT 14
- cc3d.statistics["bounding_boxes"] are wrong HOT 1
- largest_k fails for transposed arrays HOT 6
- About the lastest_k function HOT 4
- Statistics output HOT 7
- Question on the output of contacts HOT 9
- Periodic Boundary Conditions HOT 4
- Is the output label of largest_k ordered? HOT 2
- Add a better error for type support. HOT 4
- cc3d.statistics['bounding_boxes'] is contains floats instead of int as slice positions HOT 2
- voxel_connectivity_graph and contacts can not be applied in 2D label HOT 5
- Build Equivalence Table Two Z Slices at a Time
- cc3d.dust fails HOT 3
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