def main():
parser = argparse.ArgumentParser()
parser.add_argument('--debug', default=False, type=strtobool)
parser.add_argument('--dir_dataset', type=Path, default='../../dataset')
parser.add_argument('--batch_size', type=int, default=8)
parser.add_argument('--epochs', type=int, default=1)
parser.add_argument('--alpha', type=float, default=-1)
parser.add_argument('--seed', type=int, default=1048)
params = parser.parse_args()
if params.debug:
logger = init_logger('_log/debug.log', level=10)
else:
logger = init_logger('_log/main.log', level=20)
logger.info(vars(params))
try:
run(**vars(params))
except Exception:
logger.info(traceback.format_exc())
def main():
if params.debug:
logger = init_logger('_log/train_debug.log', level=10)
else:
logger = init_logger(f'_log/train_{params.model_name}.log', level=20)
logger.info(f'torch version {torch.__version__}')
logger.info(f'numpy version {np.__version__}')
logger.info(f'pandas version {pd.__version__}')
logger.info(vars(params))
train(**vars(params))
# from lib import dl
# dl.trace_start("trace.html",interval=5,auto=True)
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('command', metavar='COMMAND', help='command: init, tests')
parser.add_argument('-c', '--config', metavar='CONFIG', help='config file')
args = parser.parse_args()
if args.command == 'tests':
suite = TestLoader().discover('tests', pattern='*.py')
result = TextTestRunner(verbosity=2).run(suite)
result = 0 if result.wasSuccessful() else 1
exit(result)
cfg = read_config(args.config)
logger = init_logger()
renderer = DistributedRenderer()
qualifier = DistributedQualifier()
base_image_path = cfg['main']['populationPath'] + basename(cfg['main']['baseImage'])
fitnessMachine = MeshFitnessMachine(base_image_path, renderer, qualifier)
population = Population(MeshGenome, fitnessMachine)
population.generation = int(db.get('generation', default=0))
accuracy.register(population)
monitor.register(population)
if args.command == 'reset' or not population.generation:
population.initialize()
else:
population.load()
def main():
tic = time.time()
if params.debug:
logger = init_logger('_log/03_make_sub_debug.log', level=10)
else:
logger = init_logger('_log/03_make_sub.log', level=20)
level5data = LyftDataset(data_path='../../dataset/test',
json_path='../../dataset/test/data/',
verbose=True)
sub_pre = pd.read_csv(params.path_sub_pre)
print(sub_pre.head())
sample = pd.read_csv('../../dataset/sample_submission.csv')
print(sample.head())
target_tokens = sample['Id']
if params.debug:
target_tokens = target_tokens[:20]
list_subs = list()
img_size = 2048
lidar_range = 100
for i, target_token in enumerate(tqdm(target_tokens)):
target_subs = sub_pre.query('token==@target_token')
list_sub_token = list()
for _, target_sub in target_subs.iterrows():
x = target_sub['x']
y = target_sub['y']
z = target_sub['z']
length = target_sub['length']
width = target_sub['width']
height = target_sub['height']
rotate = target_sub['rotate']
width = width * (lidar_range * 2) / (img_size - 1)
length = length * (lidar_range * 2) / (img_size - 1)
height = height * (lidar_range * 2) / (img_size - 1)
x = x * (lidar_range * 2) / (img_size - 1) - lidar_range
y = y * (lidar_range * 2) / (img_size - 1) - lidar_range
z = z * (lidar_range * 2) / (img_size - 1) - lidar_range
rotate = -rotate
quat = Quaternion(math.cos(rotate / 2), 0, 0, math.sin(rotate / 2))
print(quat.yaw_pitch_roll)
pred_box = Box([x, y, z], [width, length, height], quat)
my_sample = level5data.get('sample', target_token)
rev_token = level5data.get('sample_data',
my_sample['data']['LIDAR_TOP'])['token']
rev_box = reverse_box(pred_box, level5data, rev_token)
sub_i = '{:.9f} '.format(target_sub['confidence']) + \
' '.join(['{:.3f}'.format(v) for v in rev_box.center]) + \
' ' + ' '.join(['{:.3f}'.format(v) for v in rev_box.wlh]) + \
' {:.3f}'.format(rev_box.orientation.yaw_pitch_roll[0]) + ' {}'.format(target_sub['name'])
logger.debug('sub_i')
logger.debug(sub_i)
list_sub_token.append(sub_i)
if len(list_sub_token) == 0:
sub_token = ''
else:
sub_token = ' '.join(list_sub_token)
logger.info('submit token !')
logger.info(sub_token)
list_subs.append(sub_token)
submission = pd.DataFrame()
submission['Id'] = target_tokens
submission['PredictionString'] = list_subs
dir_sub = Path('_submission')
dir_sub.mkdir(exist_ok=True)
submission.to_csv(dir_sub / params.path_sub_pre.name, index=False)
logger.info('elapsed time: {:.1f} [min]'.format(
(time.time() - tic) / 60.0))
def main():
random.seed(params.seed)
np.random.seed(params.seed)
tic = time.time()
logger = init_logger('_log/log_b{:d}_l{:d}_nd{:d}_seed{:d}'.format(
params.batch_size, params.num_layer, params.node_dim, params.seed))
logger.info('parameters')
logger.info(vars(params))
train, valid, test, train_moles, valid_moles = load_dataset(params.seed)
train_moles = sorted(train_moles)
valid_moles = sorted(valid_moles)
valid.sort_values('molecule_name', inplace=True)
logger.info('train moles: {} ...'.format(train_moles[:5]))
logger.info('valid moles: {} ...'.format(valid_moles[:5]))
test_moles = sorted(list(set(test['molecule_name'])))
test.sort_values('molecule_name', inplace=True)
logger.info('train data: {}'.format(train.shape))
logger.info('valid data: {}'.format(valid.shape))
logger.info('test data: {}'.format(test.shape))
structures = pd.read_csv('../../input/structures.csv')
structures_groups = structures.groupby('molecule_name')
bonds = pd.read_csv('../../input/bonds.csv')
bonds_gp = bonds.groupby('molecule_name')
train_charges = pd.read_csv('../../input/train_ob_charges.csv')
train_charges_gp = train_charges.groupby('molecule_name')
test_charges = pd.read_csv('../../input/test_ob_charges.csv')
test_charges_gp = test_charges.groupby('molecule_name')
train_targets = train.groupby('molecule_name')
valid_targets = valid.groupby('molecule_name')
test_targets = test.groupby('molecule_name')
if params.debug:
random.shuffle(train_moles)
train_moles = train_moles[:5000]
test_moles = test_moles[:1000]
valid.sort_values('id', inplace=True)
test.sort_values('id', inplace=True)
list_atoms = list(set(structures['atom']))
train_graphs = dict()
for mole in tqdm(train_moles):
train_graphs[mole] = Graph(structures_groups.get_group(mole),
bonds_gp.get_group(mole), list_atoms,
train_charges_gp.get_group(mole))
valid_graphs = dict()
for mole in tqdm(valid_moles):
valid_graphs[mole] = Graph(structures_groups.get_group(mole),
bonds_gp.get_group(mole), list_atoms,
train_charges_gp.get_group(mole))
test_graphs = dict()
for mole in tqdm(test_moles):
test_graphs[mole] = Graph(structures_groups.get_group(mole),
bonds_gp.get_group(mole), list_atoms,
test_charges_gp.get_group(mole))
model = EdgeUpdateNet(num_layer=params.num_layer,
node_dim=params.node_dim,
edge_dim=params.edge_dim,
gpu=params.gpu)
if params.gpu >= 0:
logger.info('transfer model to GPU {}'.format(params.gpu))
model.to_gpu(params.gpu)
optimizer = optimizers.Adam(alpha=5e-4)
optimizer.setup(model)
model.cleargrads()
epoch = 2 if params.debug else params.epoch
for ep in range(epoch):
logger.info('')
logger.info('')
logger.info('start epoch {}'.format(ep))
logger.info('')
# -------------------------
logger.info('')
logger.info('training')
loss_value = 0
random.shuffle(train_moles)
train_batches_moles = generate_batches(structures_groups, train_moles,
params.batch_size)
random.shuffle(train_batches_moles)
for batch_moles in tqdm(train_batches_moles):
list_train_X = list()
list_train_y = list()
for target_mol in batch_moles:
list_train_X.append(train_graphs[target_mol])
list_train_y.append(train_targets.get_group(target_mol))
with chainer.using_config('train', ep == 0):
loss = model(list_train_X, list_train_y)
model.cleargrads()
loss.backward()
optimizer.update()
loss_value += cuda.to_cpu(loss.data)
logger.info('train loss: {:.3f}'.format(
float(loss_value) / len(train_moles)))
# -------------------------
logger.info('')
logger.info('validation')
valid_df = predicts(structures_groups, valid_moles, valid_graphs,
valid_targets, model, params.batch_size)
valid_pred = valid_df[['fc', 'sd', 'pso', 'dso']]
valid_score = calc_score(valid, valid_pred.values)
logger.info('valid score: {:.3f}'.format(valid_score))
# -------------------------
optimizer.alpha = optimizer.alpha * 0.95
logger.info('change learning rate: {:.6f}'.format(optimizer.alpha))
if (ep + 1) % 20 == 0:
# -------------------------
# save model
dir_model = Path('_model')
logger.info('save model')
dir_model.mkdir(exist_ok=True)
serializers.save_npz(
dir_model / 'model_ep{}_seed{}.npz'.format(ep, params.seed),
model)
# -------------------------
# make submission
logger.info('')
logger.info('test')
test_df = predicts(structures_groups, test_moles, test_graphs,
test_targets, model, params.batch_size)
make_submission(test_df,
ep,
valid_score,
params.seed,
dir_sub=Path('_submission'))
make_submission(valid_df,
ep,
valid_score,
params.seed,
dir_sub=Path('_valid'))
toc = time.time() - tic
logger.info('Elapsed time {:.1f} [min]'.format(toc / 60))
def main():
if params.debug:
logger = init_logger('_log/01_train_debug.log', level=10)
else:
logger = init_logger('_log/01_train.log', level=20)
tic = time.time()
logger.info('parameters')
logger.info(vars(params))
num_iter = 100 if params.debug else params.num_iter
num_epoch = 2 if params.debug else params.num_epoch
list_train_img_all = os.listdir(f'../../input/{params.dataset}/train')
random.shuffle(list_train_img_all)
coords = pd.read_csv(f'../../input/{params.dataset}/coordinates.csv')
target_classes = params.target_classes.split(',')
logger.info(f'target_classes: {target_classes}')
coords = coords.query('name in @target_classes')
target_imgs = [f'{s}.png' for s in coords['token']]
list_train_img_all = list(set(list_train_img_all) & set(target_imgs))
rate_valid = 0.1
list_train_img = list_train_img_all[:-int(
len(list_train_img_all) * rate_valid)]
list_valid_img = list_train_img_all[
-int(len(list_train_img_all) * rate_valid):]
if params.debug:
list_train_img = list(list_train_img[:16])
list_valid_img = list(list_train_img)
else:
assert len(set(list_train_img) & set(list_valid_img)) == 0
logger.info('number of train images: {}'.format(len(list_train_img)))
logger.info('number of valid images: {}'.format(len(list_valid_img)))
# build model
model = build_model()
# optimizer
optimizer = optim.Adam(filter(lambda p: p.requires_grad,
model.parameters()),
lr=1e-4)
dir_model = Path('_models')
dir_model.mkdir(exist_ok=True)
# train for each epoch
for ep in range(num_epoch):
logger.info('')
logger.info('==> start epoch {}'.format(ep))
# train
model = train_main(model, params.dataset, optimizer, list_train_img,
target_classes, num_iter, ep,
params.distance_upper_bound)
# validate
validate(model,
params.dataset,
list_valid_img,
target_classes,
epoch=ep)
# change learning rate
for param_group in optimizer.param_groups:
param_group['lr'] *= 0.95
logger.info('change learning rate into: {:.6f}'.format(
param_group['lr']))
# save model
torch.save(model, dir_model / 'model_ep{}.pt'.format(ep))
# save model
torch.save(model, dir_model / 'model.pt')
# show elapsed time
toc = time.time() - tic
logger.info('Elapsed time: {:.1f} [min]'.format(toc / 60.0))
def predict_main(model_name, dataset_name, threshold, threshold2, overlap):
list_sample_submission = pd.read_csv('../../dataset/sample_submission.csv')
list_test_img = list_sample_submission['Id'].tolist()
if params.debug:
logger = init_logger('_log/02_detect_debug.log', level=10)
logger.info('debug mode !')
list_test_img = list_test_img[:100] # use only 100 images for dry-run
else:
logger = init_logger('_log/02_detect.log', level=20)
logger.info('parameters')
logger.info(vars(params))
tic = time.time()
# load model
dir_model = Path('_models')
model = torch.load(dir_model / model_name)
cpu_count = multiprocessing.cpu_count()
logger.info('num_cpu: {}'.format(cpu_count))
model.eval()
list_subs = list()
dataset = SampleDataset(
dir_img=f'../../input/{dataset_name}/test',
coord_path=f'../../input/{dataset_name}/coordinates.csv',
crop_type=0
)
dir_save = Path('./_test')
dir_save.mkdir(exist_ok=True)
step = 64
predict_one_wrap = partial(predict_one,
dir_save=dir_save,
threshold=threshold,
threshold2=threshold2,
overlap=overlap)
for j in tqdm(range(0, len(list_test_img), step), desc='batch loop'):
list_inputs = list()
# for i, target_name in enumerate(tqdm(list_test_img)):
for i in tqdm(range(j, min(j+step, len(list_test_img))), desc='gpu loop'):
target_name = list_test_img[i]
img_input, _, original = dataset[f'{target_name}.png']
input_tensor = torch.unsqueeze(img_input, 0)
# input_tensor = augment_input(img_input)
with torch.no_grad():
net_out = model.forward(input_tensor.cuda())
net_out_numpy = [tensor.cpu().data.numpy() for tensor in net_out]
net_out_numpy_batch = [tensor[0, :, :, :] for tensor in net_out_numpy]
list_inputs.append((i, target_name, net_out_numpy_batch))
if i < 50:
original.save(dir_save / '{}_original_{}.png'.format(i, target_name[:12]))
# list_subs_batch = [predict_one_wrap(ip) for ip in tqdm(list_inputs)]
with Pool(cpu_count) as p:
list_subs_batch = list(tqdm(p.imap_unordered(predict_one_wrap, list_inputs),
total=len(list_inputs), desc='nmp loop'))
list_subs.extend(list_subs_batch)
submission = pd.concat(list_subs, axis=0)
# save submission
dir_submission = Path('_submission_pre')
dir_submission.mkdir(exist_ok=True)
submission.to_csv(dir_submission / 'submit_{}_th{}_gth{}_ov{}.csv'.format(
params.model.stem, params.threshold, params.threshold2, params.overlap),
index=False, float_format='%.9f')
logger.info('elapsed time: {:.1f} [min]'.format((time.time() - tic) / 60.0))
