def detect_vessels(self, additional_mask=None):
im = self._image
mask = self._mask
# green channel & remove light reflex
im_gray = remove_light_reflex(im)
# CLAHE
clahe = cv2.createCLAHE(3, (7, 7))
im_clahe = clahe.apply(im_gray)
# Haar transform
wp = pywt.WaveletPacket2D(im_clahe,
wavelet='haar',
maxlevel=1,
mode='sym')
wp.decompose()
im_haar = wp['a'].data
im_haar = remove_light_reflex(im_haar)
mask = ImageReader.rescale_mask(im_haar, self.mask)
try:
hasAdditionalMask = additional_mask.size > 0
additional_mask = ImageReader.rescale_mask(im_haar,
additional_mask)
except AttributeError:
hasAdditionalMask = False
# compute the image mean to "invert" the image
# for the gausssian matched filter
mean_thresh, _, _, _ = cv2.mean(im_haar, mask)
if hasAdditionalMask:
im_haar[additional_mask != 0] = mean_thresh
im_haar = mean_thresh - im_haar
# Gaussian Matched and FDOG filter responses
K_MF = gaussian_matched_filter_kernel(31, 5)
K_FDOG = fdog_filter_kernel(31, 5)
kernels_mf = createMatchedFilterBank(K_MF, 12)
kernels_fdog = createMatchedFilterBank(K_FDOG, 12)
im_matched_mf = applyFilters(im_haar, kernels_mf)
im_matched_fdog = applyFilters(im_haar, kernels_fdog)
# normalize local mean of FDOG response
local_mean_fdog = cv2.blur(im_matched_fdog, (11, 11))
local_mean_fdog = cv2.normalize(local_mean_fdog,
alpha=0,
beta=1,
norm_type=cv2.NORM_MINMAX)
# set the threshold matrix
mean_thresh, _, _, _ = cv2.mean(im_matched_mf, mask)
ref_thresh = mean_thresh * self._norm_const
ref_thresh = ref_thresh * (1 + local_mean_fdog)
# show the results
if self._is_debug:
show_images([self._reader.image])
show_images([im_gray, im_haar], titles=["gray", "haar"])
show_images([im_matched_mf, im_matched_fdog],
titles=["mf", "fdog"])
im_vessels = im_matched_mf.copy()
im_vessels[im_vessels < ref_thresh] = 0
im_vessels[mask == 0] = 0
im_vessels[im_vessels != 0] = 1
im_vessels = im_vessels.astype('uint8')
if self._is_debug:
show_images([im_vessels], titles=["vessels"])
self._im_norm = mh.stretch(im_matched_mf)
return ImageReader.rescale_mask(self.image, im_vessels)
