def cut_out_non_lungs_z (images3, pmasks3, images3_seg, uid, dim):
HU_LUNGS_MIN = -900 # the algo is sensitive to this value -- keep it 900 unless retested
HU_LUNGS_MAX = -400
pix_lungs_min = hu_to_pix(HU_LUNGS_MIN)
pix_lungs_max = hu_to_pix(HU_LUNGS_MAX)
mid = dim // 2
ymin = int(0.4 * images3.shape[3]) ## BUG was 4
ymax = int(0.6 * images3.shape[3]) ## # waut it failed for tne one following 4b351d0c19be183cc880f5af3fe5abee ( index 240 is out of bounds for axis 3 with size 240)
zmin_new = images3.shape[0] // 2
zmax_new = images3.shape[0] // 2
j = ymin
for j in range(ymin, ymax+1):
img_cut = images3[:,0,mid, j]
img_cut_lungs = (img_cut > pix_lungs_min) & (img_cut < pix_lungs_max)
lungs_across = np.sum(img_cut_lungs, axis = 1)
noise_bottom_some = np.mean(lungs_across[0:10]) # increase by 2
noise = np.max([3*np.min(lungs_across), 0.05 * np.max(lungs_across), noise_bottom_some]) # experimanetal -- could fail is scan has only central part of lungs and no borders at all -- CHECK
zmin, zmax = find_lungs_range(lungs_across, noise)
if zmin < zmin_new:
zmin_new = zmin
if zmax > zmax_new:
#print ("j, zmax: ", j, zmax)
zmax_new = zmax
### do not cut it to fine (add few pixels on each side ...)
zmin_new = np.max([0, zmin_new-mid])
zmax_new = np.min([images3.shape[0], zmax_new+mid])
print("cut_out_non_lungs_z from to:", images3.shape[0], zmin_new, zmax_new, uid )
if ((zmax_new-zmin_new)/images3.shape[0] < 0.5):
print ("SUSPICSIOUS large cut of > 50%, NOT executing ...")
else:
images3 = images3[zmin_new:zmax_new]
pmasks3 = pmasks3[zmin_new:zmax_new]
images3_seg = images3_seg[zmin_new:zmax_new]
return images3, pmasks3, images3_seg
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