def test(self, image, loc_lst, viz=False):
""" test an image """
demo = self.imread(image)
correct = 0
if viz:
for loc in loc_lst:
cv2.circle(demo, loc, 2, (0, 0, 255), 3)
data, labels, segments = self.get_data([image], [loc_lst])
total_segments = len(data)
testing_data = [self.preprocess_pca(im)for im in data]
testing_data = np.vstack(testing_data)
testing_data = self._pca.transform(testing_data)
result = self._classifier.predict(testing_data)
for predicted, expected, s in zip(result, labels, segments):
print "predicted: ", predicted
print "expected: ", expected
if predicted == expected:
correct += 1
if viz:
s.draw(demo, (0, 255, 0), 1)
else:
if viz:
s.draw(demo, (255, 255, 0), 1)
if viz:
com.debug_im(demo)
return total_segments, correct
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 watershed(image):
""" the watershed algorithm """
if len(image.shape) != 2:
raise TypeError("The input image must be gray-scale ")
# thresholding
_, thres = cv2.threshold(image, 0, 255,
cv2.THRESH_BINARY_INV + cv2.THRESH_OTSU)
kernel = np.ones((1, 1), np.uint8)
opening = cv2.morphologyEx(thres, cv2.MORPH_OPEN, kernel, iterations=1)
bg = cv2.dilate(opening, kernel, iterations=2)
dist_transform = cv2.distanceTransform(thres, cv2.cv.CV_DIST_L2, 3)
com.debug_im(dist_transform)
_, fg = cv2.threshold(dist_transform, 0.7*dist_transform.max(), 255, 0)
fg = np.uint8(fg)
unknown = cv2.subtract(bg, fg)
markers, _ = label(fg)
markers = markers + 1
markers[unknown == 255] = 0
image = cv2.cvtColor(image, cv2.COLOR_GRAY2RGB)
cv2.watershed(image, markers)
markers[markers == -1] = 0
markers = markers.astype(np.uint8)
contours, _ = cv2.findContours(markers,
cv2.RETR_LIST,
cv2.CHAIN_APPROX_SIMPLE)
segments = [Contour(points_lst) for points_lst in contours]
for s in segments:
s.draw(image, (255, 255, 0), 1)
com.debug_im(image)
return 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
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, gray_img = self.preprocess(demo_img)
segments = self.segment(processed_img, gray_img, demo_img)
correct = 0
# draw all counted objects in the image
if visualize:
for seg in segments:
seg.draw(demo_img, (0, 255, 0), 1)
for loc in locs:
cv2.circle(demo_img, loc, 2, (0, 255, 0), 1)
# visualize true cells
# check if each segment is close to one true cell
for seg in segments:
data.append(seg.get_region(gray_img))
result.append(seg)
if len(locs) == 0:
labels.append(-1)
continue
point, dist = com.nearest_point(seg.center, locs)
if dist <= self._db.tol:
locs.remove(point)
correct += 1
labels.append(1)
if visualize:
seg.draw(demo_img, (255, 255, 0), 1)
else:
labels.append(-1)
if visualize:
com.debug_im(gray_img)
com.debug_im(processed_img)
com.debug_im(demo_img, True)
return data, labels, result
# data_train = np.transpose(data_train)
data_test = np.array(data_test)
# data_test = np.transpose(data_test)
# Randomized PCA
n_components = 400
# pca = SparsePCA(n_components, n_jobs=-1).fit(data_train)
# pca = RandomizedPCA(n_components, whiten=True).fit(data_train)
print data_train.shape
pca = PCA(n_components=400).fit(data_train)
print "components size: ", pca.components_.shape
pca_features_train = pca.transform(data_train)
pca_features_test = pca.transform(data_test)
print pca_features_train.shape
for feature in pca_features_train:
com.debug_im(feature.reshape(20, 20))
# grid_param = {"kernel": ("rbf", "poly", "sigmoid"),
# "C": np.logspace(-5, -3, num=8, base=2),
# "gamma": np.logspace(-15, 3, num=8, base=2)}
# clf = GridSearchCV(SVC(class_weight="auto"), grid_param)
# clf = clf.fit(pca_features_train, labels_train)
# print clf.best_estimator_
# y_pred = clf.predict(pca_features_test)
# score = accuracy_score(labels_test, y_pred)
# scores.append(score)
