def demo_eDP():
I = imread('images/barbara.png')
sigma = 25.0 / 255.0
PRNG = np.random.RandomState(0)
y = I + sigma * PRNG.randn(I.shape[0], I.shape[1])
gridModel = DPGridModel('models/DP')
x, PSNR = gridModel.denoise(y, sigma, I)
imwrite(x, 'eDP_results.png')
def demo_inpainting():
inFileName = 'images/new_original.png'
y = imread(inFileName, outputFormat='YCbCr')
maskFileName = 'images/new_mask.png'
mask = np.array(imread(maskFileName), dtype=bool)
gridModel = HDPGridModel('models/HDP')
x = gridModel.inpaint(y, mask)
imwrite(x, 'HDP_inpainting_results.png')
def detect_with_network(network, imgs, masks, threshold=0.5, fold=-1):
#imgs = np.array([[imgs[0]]])
length = len(imgs)
outs = network.network.predict(imgs)
print('Prob map output {}'.format(outs.shape))
util.imwrite('data/probmap_{}.jpg'.format(fold), outs[0, 0, :, :])
side = outs[0][0].shape[0]
scale_factor = int(512 / side)
min_distance = int(side / 71.68)
print 'img size {}, prob size {}, min_distance {}, scale_factor {}'.format(
512, side, min_distance, scale_factor)
blob_set = []
prob_set = []
for i in range(length):
prob_map = outs[i][0]
coords = peak_local_max(prob_map, min_distance)
blobs = []
for coord in coords:
blobs.append(
[coord[0] * scale_factor, coord[1] * scale_factor, 25])
blobs = filter_by_margin(
filter_by_size(filter_by_masks(blobs, masks[i])), masks[i])
print '# coords {}'.format(len(coords))
print '# before blobs {}'.format(len(blobs))
threshold = 0
for blob in blobs:
threshold += prob_map[blob[0] / scale_factor,
blob[1] / scale_factor]
threshold /= len(coords)
tmp = []
for blob in blobs:
if prob_map[blob[0] / scale_factor,
blob[1] / scale_factor] > threshold:
tmp.append(blob)
blobs = np.array(tmp)
print 'after # blobs {}'.format(len(blobs))
if len(blobs) == 0:
raise Exception("No blobs founds at {}".format(i))
blob_set.append(blobs)
prob_set.append([])
for blob in blobs:
prob_set[-1].append(prob_map[blob[0] / scale_factor,
blob[1] / scale_factor])
prob_set[-1] = np.array(prob_set[-1])
return np.array(blob_set), np.array(prob_set)
def test_canvas(model_name, image_name, weight, prob_thresh=0.2, nms_thresh=0.4, mode=1,use_gpu=True):
print('load weight')
model = load_model(model_name, weight, mode,use_gpu)
if use_gpu:
model.to(gpudevice)
print("detecting")
image = cv2.imread(image_name)
img = prep_image(image, inp_size)
im_dim = image.shape[1], image.shape[0] # w,h
im_dim = np.array(im_dim)
output = []
if use_gpu:
# im_dim = im_dim.cuda()
img = img.to(gpudevice)
with torch.no_grad():
pred = model(img)
if use_gpu:
pred = pred.cpu()
probs = np.zeros((side * side * num, classes))
boxes = np.zeros((side * side * num, 4))
get_detection_boxes(pred, prob_thresh, nms_thresh, boxes, probs)
# im_dim = torch.FloatTensor(im_dim).repeat(1, 2).numpy()
scaling_factor = np.min(inp_size / im_dim)
for i in range(probs.shape[0]):
cls = np.argmax(probs[i])
prob = probs[i][cls]
if prob > 0:
out = np.zeros(6)
out[:4] = correct_box(boxes[i],inp_size,inp_size)
out[[0,2]] -= (inp_size-scaling_factor*im_dim[0])/2
out[[1,3]] -= (inp_size-scaling_factor*im_dim[1])/2
out[:4] = out[:4]/scaling_factor
out[[0,2]] = np.clip(out[[0,2]],0.0,im_dim[0])
out[[1,3]] = np.clip(out[[1,3]],0.0,im_dim[1])
out[4] = prob
out[5] = cls
output.append(out)
for item in output:
# item = output[i]
cls = int(item[-1])
prob = float(item[-2])
box = item[:4]
image = imwrite(image, box, voc_class_names[cls], cls, prob)
cv2.imshow("{}".format(image_name), image)
cv2.waitKey(0)
cv2.destroyAllWindows()
def save_rois(args):
imgs_tr, blobs_tr = lidc.load(pts=False)
pred_blobs_tr = detect.read_blobs('data/sbf-aam-lidc-pred-blobs.pkl')
masks_tr = np.load('data/aam-lidc-pred-masks.npy')
imgs_te, blobs_te = jsrt.load(set_name='jsrt140p')
pred_blobs_te = detect.read_blobs('data/sbf-aam-jsrt140p-pred-blobs.pkl')
masks_te = np.load('data/aam-jsrt140p-pred-masks.npy')
rois_tr = create_rois(imgs_tr,
masks_tr,
pred_blobs_tr,
args,
real_blobs=blobs_tr)
rois_te = create_rois(imgs_te,
masks_te,
pred_blobs_te,
args,
real_blobs=blobs_te)
X_tr, Y_tr, X_te, Y_te = neural.create_train_test_sets(
blobs_tr, pred_blobs_tr, rois_tr, blobs_te, pred_blobs_te, rois_te)
X_tr, Y_tr = util.split_data_pos_neg(X_tr, Y_tr)
X_te, Y_te = util.split_data_pos_neg(X_te, Y_te)
X_pos = X_tr[0]
idx = np.random.randint(0, len(X_tr[1]), len(X_pos))
X_neg = X_tr[1][idx]
print len(X_pos), len(X_neg)
for i in range(len(X_pos)):
util.imwrite('data/lidc/roi{}p.jpg'.format(i), X_pos[i][0])
np.save('data/lidc/roi{}p.npy'.format(i), X_pos[i])
util.imwrite('data/lidc/roi{}n.jpg'.format(i), X_neg[i][0])
np.save('data/lidc/roi{}n.npy'.format(i), X_neg[i])
X_pos = X_te[0]
idx = np.random.randint(0, len(X_te[1]), len(X_pos))
X_neg = X_te[1][idx]
print len(X_pos), len(X_neg)
for i in range(len(X_pos)):
util.imwrite('data/jsrt140/roi{}p.jpg'.format(i), X_pos[i][0])
np.save('data/jsrt140/roi{}p.npy'.format(i), X_pos[i])
util.imwrite('data/jsrt140/roi{}n.jpg'.format(i), X_neg[i][0])
np.save('data/jsrt140/roi{}n.npy'.format(i), X_neg[i])
def test(model_name, image_name, weight, prob_thresh=0.2, nms_thresh=0.4, mode=1, use_gpu=True):
result = get_test_result(model_name, image_name, weight, prob_thresh, nms_thresh, mode, use_gpu)
image = cv2.imread(image_name)
print('get result:%d'%len(result))
for item in result:
if len(item) == 6:
box = item[:4]
prob = float(item[4])
cls_ind = int(item[5])
cls_names = voc_class_names[cls_ind]
elif len(item) == 3:
box = item[0]
prob = item[1]
cls_ind = item[2]
cls_names = [voc_class_names[i] for i in cls_ind]
prob = [p for p in prob]
cls_ind = cls_ind[0]
image = imwrite(image, box, cls_names, cls_ind, prob)
# cv2.imshow("{}".format(image_name), image)
# cv2.waitKey(0)
cv2.imwrite('bbox_%s.png' % image_name.split('/')[-1].split('.')[0], image)
os.mkdir('local')
vout.open('./local/output.avi', fourcc, fps, sz, True)
frames = 0
start = time.time()
while cap.isOpened():
ret, frame = cap.read()
if ret:
output = predictv1(frame, model, CUDA=CUDA,nms_thresh=nms_thresh,prob_thresh=confidence)
for item in output:
# item = output[i]
cls = int(item[-1])
prob = float(item[-2])
box = item[:4]
frame = imwrite(frame, box, class_names[cls], cls)
frames += 1
fps = frames / (time.time()-start)
label='fps:{:.3f}'.format(fps)
# t_size = cv2.getTextSize(label, cv2.FONT_HERSHEY_PLAIN, 1, 1)[0]
if dv:
vout.write(frame)
cv2.putText(frame, label, (1, 10), cv2.FONT_HERSHEY_PLAIN, 1, [0, 255, 255], 1)
cv2.imshow("frame", frame)
key = cv2.waitKey(1)
if key & 0xFF == ord('q'):
break
print(time.time()-start)
sample = voc_dataset.get_item(idx)
# except Exception as e:
# print(e, idx)
# continue
image = sample["image"]
boxes = sample["bbox"]
classes = sample["classes"]
h, w, _ = image.shape
dir = 'gt'
if not os.path.exists(dir):
os.mkdir(dir)
for j in range(len(boxes)):
cls_ind = classes[j].item()
# print(cls_ind)
image = imwrite(image, convert_box(boxes[j], h, w, 1),
voc_class_names[cls_ind], cls_ind)
#plt.figure()
# plt.title("pic{}".format(i+1))
# plt.imshow(image)
# cv2.imwrite("data/temp/pic{}.jpg".format(i+1),image)
# plt.pause(1)
cv2.imshow('pic', image)
key = cv2.waitKey(0)
if key & 0xFF == ord('q'):
cv2.destroyWindow('pic')
break
elif key & 0xFF == ord('s'):
cv2.imwrite('{}/pic_gt{}.png'.format(dir, idx), image)
time.sleep(1)
idx = np.array(range(len(Y_aug)))
np.random.shuffle(idx)
return X_aug[idx], Y_aug[idx]
# Test
if __name__ == '__main__':
fname = 'grid2.jpg'
import cv2
img = cv2.imread(fname)
print img.shape
img = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
img = np.array([img])
util.imwrite('or_{}'.format(fname), img[0])
augment_params = {
'output_shape':
(img.shape[1] * (1.0 / factor), img.shape[1] * (1.0 / factor)),
'ratio':
1,
'batch_size':
32,
'rotation_range': (-18, 18),
'translation_range': (-0.12, 0.12),
'flip':
True,
'intensity_shift_std':
0.2,
'mode':
'balance_batch',
def evaluate(real, predicted, data=None, sample=False, criteria='25mm'):
assert len(real) == len(predicted)
num_imgs = len(real)
sensitivity = 0
fppi = []
iou = []
iou_pos = []
tp = 0
p = 0
MAX_DIST = 35.7142 # 25 mm
for i in range(num_imgs):
if sample:
img, mask = data.get(i)
sampled, lce, norm = preprocess(img, mask)
img = lce
found = False
found_blob_idx = -1
overlap = -1e10
for j in range(len(real[i])):
if real[i][j][0] == -1:
continue
p += 1
for k in range(len(predicted[i])):
#overlap = _iou_circle(real[i][j], predicted[i][k])
dist = _dist(real[i][j], predicted[i][k])
iou.append(dist)
if dist < MAX_DIST * MAX_DIST:
iou_pos.append(overlap)
found = True
found_blob_idx = k
break
if found:
break
#print "real blob {}".format(real[i][0])
# Assuming that we just have one true object per image at most
if found:
fppi.append(len(predicted[i]) - 1)
tp += 1
if sample:
for k in range(len(predicted[i])):
if k != found_blob_idx:
util.save_blob(
'data/fp/{}_{}_{}.jpg'.format(
i, k, data.img_paths[i].split('/')[-1]), img,
predicted[i][k])
_, masks = segment(img, [predicted[i][k]])
rmask = cv2.resize(masks[0], (128, 128),
interpolation=cv2.INTER_CUBIC)
util.imwrite(
'data/fp/{}_{}_{}_mask.jpg'.format(
i, k, data.img_paths[i].split('/')[-1]), rmask)
else:
print 'real, predicted ->', real[i][0], predicted[i][k]
util.save_blob(
'data/tp/real_{}_{}.jpg'.format(
i, data.img_paths[i].split('/')[-1]), img,
real[i][0])
util.save_blob(
'data/tp/{}_{}_{}.jpg'.format(
i, k, data.img_paths[i].split('/')[-1]), img,
predicted[i][k])
else:
fppi.append(len(predicted[i]))
if sample:
if real[i][0][0] != -1:
util.save_blob(
'data/fn/{}_{}.jpg'.format(
i, data.img_paths[i].split('/')[-1]), img,
real[i][0])
for k in range(len(predicted[i])):
util.save_blob(
'data/fp/{}_{}_{}.jpg'.format(
i, k, data.img_paths[i].split('/')[-1]), img,
predicted[i][k])
_, masks = segment(img, [predicted[i][k]])
rmask = cv2.resize(masks[0], (128, 128),
interpolation=cv2.INTER_CUBIC)
util.imwrite(
'data/fp/{}_{}_{}_mask.jpg'.format(
i, k, data.img_paths[i].split('/')[-1]), rmask)
#print "found {}, overlap {}".format(found, overlap)
#if paths != None:
# util.show_blobs_real_predicted(paths[i], [real[i]], predicted[i])
fppi = np.array(fppi)
iou = np.array(iou)
iou_pos = np.array(iou_pos)
sensitivity = tp * 1.0 / p
#return sensitivity, np.mean(fppi), np.std(fppi), np.mean(iou), np.std(iou), np.mean(iou_pos), np.std(iou_pos)
return sensitivity, np.mean(fppi), np.std(fppi)
def save_result(self, img, path):
fn = join(self.results_dir, path)
directory = os.path.dirname(fn)
if not os.path.exists(directory):
os.mkdir(directory)
util.imwrite(img, fn)
def test_many(model_name,test_file,weight, prob_thresh=0.1, nms_thresh=0.5, mode=1,pd=True,use_gpu=True):
print('load weight')
model = load_model(model_name, weight, mode, use_gpu)
if use_gpu:
model.to(gpudevice)
print("detecting")
images = []
try:
images = [os.path.join(test_file, img) for img in os.listdir(test_file) if img.endswith('.jpg') or img.endswith('.png')]
except NotADirectoryError:
try:
with open(test_file) as f:
for l in f:
images.append(l.strip())
except Exception as e:
print(e)
sys.exit(1)
except FileNotFoundError:
print("No file or directory with the name {}".format(images))
sys.exit(1)
if not os.path.exists('det'):
os.mkdir('det')
random.shuffle(images)
since = time.time()
for imp in images:
print(imp)
image = cv2.imread(imp)
h, w, _ = image.shape
pred = get_pred(image,model,use_gpu)
probs = np.zeros((side * side * num, classes))
boxes = np.zeros((side * side * num, 4))
get_detection_boxes(pred, prob_thresh, nms_thresh, boxes, probs)
maxclsind = np.argmax(probs, 1)
maxprob = np.max(probs, 1)
mask = maxprob > 0
if np.sum(mask) == 0:
continue
maskbox = boxes[mask]
maskprob = maxprob[mask]
maskind = maxclsind[mask]
if pd:
output = postdeal(maskbox,maskprob,maskind,h,w)
for it in output:
box = it[0]
prob = it[1]
cls_ind = it[2]
cls_names = [voc_class_names[i] for i in cls_ind]
prob = [p for p in prob]
cls_ind = cls_ind[0]
image = imwrite(image, box, cls_names, cls_ind, prob)
else:
maskbox = correct_boxes(maskbox, h, w)
for i in range(maskbox.shape[0]):
image = imwrite(image, maskbox[i], voc_class_names[maskind[i]], maskind[i], maskprob[i])
# boxes, probs, cls_indices = get_detection_boxes_1(pred, prob_thresh, nms_thresh, True)
# for i, box in enumerate(boxes):
# if probs[i] == 0:
# continue
# box = convert_box(box,h,w)
# cls_index = int(cls_indices[i])
# # print(cls_index)
# prob = float(probs[i])
# image = imwrite(image, box, voc_class_names[cls_index], cls_index, prob)
cv2.imshow("img", image)
key = cv2.waitKey(0)
if key & 0xFF == ord('q'):
cv2.destroyAllWindows()
break
elif key & 0xFF == ord('s'):
cv2.imwrite('det/bbox_%s.png' % imp.split('/')[-1].split('.')[0], image)
# time.sleep(2)
print('{:.3f}s per image'.format((time.time()-since)/len(images)))
def save_frames(filepattern, video):
for i in range(video.shape[-1]):
util.imwrite(video[...,i], filepattern % i)
