def get_data(self, image_lst, loc_lst, visualize=False):
"""
prepare data for training phase
"""
data = []
labels = []
result = []
for image, locs in zip(image_lst, loc_lst):
demo_img = self.imread(image, 1)
processed_img = self.preprocess(demo_img)
segments = self.segment(processed_img)
segments =[self.preprocess_segment(s) for s in segments]
locations = list(loc_lst)
# draw all counted objects in the image
# visualize true cells
# check if each segment is close to one true cell
for seg in segments:
data.append(seg.get_region(demo_img))
result.append(seg)
self.eval_segments(segments, locs)
labels.extend([1 if s.detected else 0 for s in segments])
if visualize:
com.visualize_segments(demo_img, segments, locations)
com.debug_im(processed_img)
com.debug_im(demo_img, True)
return data, labels, result
def test(self, image, loc_lst, viz=False):
""" test an image """
demo = self.imread(image)
assert demo is not None
correct = 0
locations = list(loc_lst)
data, labels, segments = self.get_data([image], [loc_lst])
total_segments = len(data)
testing_data = [self._extraction.compute(im) for im in data]
hist_data, hog_data = zip(*testing_data)
print "total of segments: ", total_segments
hist_data = np.array(hist_data, dtype=np.float32)
hog_data = np.array(hog_data, dtype=np.float32)
############################
# Normalize the histogram feature
hist_data = normalize(hist_data, axis=1)
##############################
# RandomizedPCA for the hog feature
hog_data = self._pca.transform(hog_data)
##############################
# Fusion of classifiers
y_proba_lbp = self.clf_lbp.predict_proba(hog_data)
y_proba_hist = self.clf_hist.predict_proba(hist_data)
y_proba = None
if self.op == "sum":
y_proba = (y_proba_hist + y_proba_lbp)
elif self.op == "max":
y_proba = np.maximum(y_proba_hist, y_proba_lbp)
elif self.op == "min":
y_proba = np.minimum(y_proba_hist, y_proba_lbp)
elif self.op == "mul":
y_proba = np.multiply(y_proba_hist, y_proba_lbp)
# print "y proba:", y_proba
result = np.argmax(y_proba, axis=1)
# score = accuracy_score(labels_test, predicted)
# visualization
for predicted, expected, s in zip(result, labels, segments):
if predicted == expected:
correct += 1
s.detected = True
if viz:
com.visualize_segments(demo, segments, locations)
com.debug_im(demo)
return total_segments, correct
def test(self, image, loc_lst, viz=False):
""" test an image """
demo = self.imread(image)
correct = 0
locations = list(loc_lst)
data, labels, segments = self.get_data([image], [loc_lst])
total_segments = len(data)
testing_data = [self._extraction.compute(im)[0] for im in data]
testing_data = np.vstack(testing_data)
result = self._classifier.predict(testing_data)
for predicted, expected, s in zip(result, labels, segments):
if predicted == expected:
correct += 1
s.detected = True
if viz:
com.visualize_segments(demo, segments, locations)
com.debug_im(demo)
return correct, total_segments
def test(self, image, loc_lst, viz=False):
""" test an image """
demo = self.imread(image)
locations = loc_lst
data, l, segments = self.get_data([image], [loc_lst])
num_samples = len(data)
labels = []
features = []
for idx, im in enumerate(data):
f = self._extraction.compute(im, self._extraction.detect(im))[1]
if f is not None:
features.append(f)
labels.append(l[idx])
testing_data = []
for feature in features:
coeffs = sparse.encode(feature, self.dictionary, self.alpha)
vector = pooling.max_pooling(coeffs)
testing_data.append(vector)
testing_data = np.vstack(testing_data)
testing_data = np.float32(testing_data)
labels = np.float32(labels)
result = self._classifier.predict(testing_data)
for predicted, expected, s in zip(result, labels, segments):
if predicted == expected:
s.detected = True
correct = len(filter(lambda x: x.detected, segments))
if viz:
com.visualize_segments(demo, segments, locations)
com.debug_im(demo)
return correct, num_samples