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Commit 9eb2c4c3 authored by Kimberly Isobel Meechan's avatar Kimberly Isobel Meechan
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add texture features

parent b4e83b75
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1 merge request!9Morphology
......@@ -13,6 +13,8 @@ from skimage.measure import regionprops, marching_cubes_lewiner, mesh_surface_ar
from skimage.transform import resize
from skimage.util import pad
from scipy.ndimage.morphology import distance_transform_edt
from mahotas.features import haralick
from skimage.morphology import label, remove_small_objects
def log(msg):
......@@ -122,6 +124,23 @@ def intensity_row_features(raw, mask):
return mean_intensity, st_dev
def texture_row_features(raw, mask):
# errors if there are small, isolated spots (because I'm using ignore zeros as true)
# so here remove components that are < 10 pixels
labelled = label(mask)
if len(np.unique(labelled)) > 2:
labelled = remove_small_objects(labelled, min_size=10)
mask = labelled != 0
mask = mask.astype('uint8')
# set regions outside mask to zero
raw_copy = raw.copy()
raw_copy[mask == 0] = 0
hara = haralick(raw_copy, ignore_zeros=True, return_mean=True, distance=2)
return hara
# compute morphology (and intensity features) for label range
def morphology_features_for_label_range(table, ds, ds_raw,
scale_factor_seg, scale_factor_raw,
......
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