def process(self):
import gzip
try:
os.makedirs(os.path.join(self.root,self.raw_folder))
os.makedirs(os.path.join(self.root,self.processed_folder))
except:
pass
files=os.listdir(self.raw_folder)
for file in files:
print('Processing %s' % file)
file_path=os.path.join(self.root,self.raw_folder,file)
with open(file_path.replace('.gz',''),'wb') as out_f, \
gzip.GzipFile(file_path) as zip_f:
out_f.write(zip_f.read())
training_set = (
read_image_file(os.path.join(self.root, self.raw_folder, 'train-images-idx3-ubyte')),
read_label_file(os.path.join(self.root, self.raw_folder, 'train-labels-idx1-ubyte'))
)
test_set = (
read_image_file(os.path.join(self.root, self.raw_folder, 't10k-images-idx3-ubyte')),
read_label_file(os.path.join(self.root, self.raw_folder, 't10k-labels-idx1-ubyte'))
)
with open(os.path.join(self.root, self.processed_folder, self.training_file), 'wb') as f:
torch.save(training_set, f)
with open(os.path.join(self.root, self.processed_folder, self.test_file), 'wb') as f:
torch.save(test_set, f)
print('Done!')
def gen():
engine = BasicEngine(model)
labels = read_label_file(label)
cap = get_cap()
# a = engine.get_num_of_output_tensors()
# b = engine.total_output_array_size()
# c = engine.get_output_tensor_size(0)
# d = engine.required_input_array_size()
# print(a, b, c, d)
while True:
_, frame = cap.read()
input_val = cv2.resize(frame, (432, 368))
input_val = input_val.flatten()
ans = engine.RunInference(input_val)
heat_map = ans[1].reshape([54, 46, 57])
prop = heat_map[1, :, :]
prop = np.multiply(prop, 255)
# prop = cv2.resize(prop, (460, 640))
_, buffer = cv2.imencode(".jpg", prop)
yield (b'--frame\r\n'
b'Content-Type: image/jpeg\r\n\r\n' +
io.BytesIO(buffer).read() + b'\r\n')
def reorg_cifar10_data(data_dir, label_file, train_dir, test_dir, input_dir,
valid_ratio):
# Reorganize train & test data prevent overfit
n_train_per_label, idx_label = utils.read_label_file(
data_dir, label_file, train_dir, valid_ratio)
utils.reorg_train_valid(data_dir, train_dir, input_dir, n_train_per_label,
idx_label)
utils.reorg_test(data_dir, test_dir, input_dir)
def _GetDataset():
_ITEMS_TO_DESCRIPTIONS = {
'image': 'A [W x H x Channel] image',
'label': 'A single integer'
}
keys_to_features = {
'image/encoded':
tf.FixedLenFeature((), tf.string, default_value=''),
'image/format':
tf.FixedLenFeature((), tf.string, default_value='jpg'),
'image/class/label':
tf.FixedLenFeature([],
tf.int64,
default_value=tf.zeros([], dtype=tf.int64)),
}
shape = [cfg.IMAGE_SIZE, cfg.IMAGE_SIZE, cfg.IMAGE_CHANNEL]
items_to_handlers = {
'image':
slim.tfexample_decoder.Image(image_key='image/encoded',
format_key='image/format',
shape=shape,
channels=cfg.IMAGE_CHANNEL),
'label':
slim.tfexample_decoder.Tensor('image/class/label'),
}
decoder = slim.tfexample_decoder.TFExampleDecoder(keys_to_features,
items_to_handlers)
return slim.dataset.Dataset(data_sources=cfg.PATH_RECORD,
reader=tf.TFRecordReader,
decoder=decoder,
num_samples=cfg.NUM_EXAMPLES,
num_classes=cfg.NUM_CLASSES,
items_to_descriptions=_ITEMS_TO_DESCRIPTIONS,
labels_to_names=utils.read_label_file(
cfg.PATH_LABELS))
def predict(image_fps,
config,
min_conf,
submission_file=None,
label_file=None,
eval_dir=None):
labels = None
if label_file:
labels = read_label_file(label_file)
submit_dict = None
if submission_file:
submit_dict = {'patientId': [], 'PredictionString': []}
for image_id in tqdm(image_fps):
ds = pydicom.read_file(image_id)
original_image = ds.pixel_array
resize_factor = original_image.shape[0] / config.IMAGE_MIN_DIM
# Convert to RGB for consistency.
original_image = np.stack((original_image, ) * 3, -1)
image, _, _, _, _ = utils.resize_image(
original_image,
min_dim=config.IMAGE_MIN_DIM,
min_scale=config.IMAGE_MIN_SCALE,
max_dim=config.IMAGE_MAX_DIM,
mode=config.IMAGE_RESIZE_MODE)
patient_id = os.path.splitext(os.path.basename(image_id))[0]
results = model.detect([image])
r = results[0]
assert (len(r['rois']) == len(r['class_ids']) == len(r['scores']))
if submit_dict:
submit_dict['patientId'].append(patient_id)
boxes = []
for i in range(len(r['rois'])):
if r['scores'][i] > min_conf:
x1 = r['rois'][i][1]
y1 = r['rois'][i][0]
width = (r['rois'][i][3] - x1)
height = (r['rois'][i][2] - y1)
boxes.append('{0} {1} {2} {3} {4}'.format(
r['scores'][i], x1 * resize_factor, y1 * resize_factor,
width * resize_factor, height * resize_factor))
if submit_dict:
submit_dict['PredictionString'].append(' '.join(boxes))
# draw predicted boxes
if len(r['rois']) != 0:
visutil.visualize_boxes_and_labels_on_image_array(
original_image,
np.array(r['rois']) * resize_factor,
r['class_ids'],
r['scores'],
{1: {
'id': 1,
'name': 'pneumonia'
}},
use_normalized_coordinates=False,
max_boxes_to_draw=3,
min_score_thresh=min_conf,
)
# draw ground truth boxes
if labels:
visutil.visualize_boxes_and_labels_on_image_array(
original_image,
labels[patient_id]['boxes'],
[labels[patient_id]['label']] *
len(labels[patient_id]['boxes']),
None,
{1: {
'id': 1,
'name': 'pneumonia'
}},
use_normalized_coordinates=False,
)
im = Image.fromarray(original_image)
im.save(os.path.join(eval_dir, patient_id + '.jpg'))
if submit_dict:
pd.DataFrame(submit_dict).to_csv(submission_file, index=False)
parser.add_argument('weight_file')
parser.add_argument('data_file')
parser.add_argument('test_images_file')
parser.add_argument('submission_file')
parser.add_argument('images_out_dir')
parser.add_argument('--label-file')
parser.add_argument('-g', '--gpu-index', type=int, default=0)
parser.add_argument('-t', '--threshold', type=float, default=0.2)
args = parser.parse_args()
if not os.path.exists(args.images_out_dir):
os.mkdir(args.images_out_dir)
labels = None
if args.label_file:
labels = read_label_file(args.label_file)
net = load_net(args.config_file.encode(), args.weight_file.encode(),
args.gpu_index)
meta = load_meta(args.data_file.encode())
submit_dict = {'patientId': [], 'PredictionString': []}
with open(args.test_images_file, 'r') as test_images_file:
for line in tqdm(test_images_file):
patient_id = os.path.split(line.strip())[1].split('.')[0]
# read the image
im = np.array(Image.open(line.strip()))
infer_result = detect(net,