def remove_minor_cc(vol_data, rej_ratio, rename_map):
"""Remove small connected components refer to rejection ratio"""
"""Usage
# rename_map = [0, 205, 420, 500, 550, 600, 820, 850]
# nii_path = '/home/xinyang/project_xy/mmwhs2017/dataset/ct_output/test/test_4.nii'
# vol_file = nib.load(nii_path)
# vol_data = vol_file.get_data().copy()
# ref_affine = vol_file.affine
# rem_vol = remove_minor_cc(vol_data, rej_ratio=0.2, class_n=8, rename_map=rename_map)
# # save
# rem_path = 'rem_cc.nii'
# rem_vol_file = nib.Nifti1Image(rem_vol, ref_affine)
# nib.save(rem_vol_file, rem_path)
#===# possible be parallel in future
"""
rem_vol = copy.deepcopy(vol_data)
class_n = len(rename_map)
# retrieve all classes
for c in range(1, class_n):
print 'processing class %d...' % c
class_idx = (vol_data==rename_map[c])*1
class_vol = np.sum(class_idx)
labeled_cc, num_cc = measurements.label(class_idx)
# retrieve all connected components in this class
for cc in range(1, num_cc+1):
single_cc = ((labeled_cc==cc)*1)
single_vol = np.sum(single_cc)
# remove if too small
if single_vol / (class_vol*1.0) < rej_ratio:
rem_vol[labeled_cc==cc] = 0
return rem_vol
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