def test_submitAllUnsubmitted_unsubmittedSubmission_isSubmitted(self):
unsubmitted = create_submission(submitted=None)
self.submitter.dataAccess.save(unsubmitted)
self.submitter.submit_all_unsubmitted()
assert self.submitter.reddit.submit.called
def test_submitAllUnsubmitted_submittedSubmission_isNotSubmitted(self):
submitted = create_submission()
self.submitter.dataAccess.save(submitted)
self.submitter.submit_all_unsubmitted()
assert not self.submitter.reddit.submit.called
def _predict(pipeline_name, dev_mode):
logger.info('reading data in')
if dev_mode:
meta_test = pd.read_csv(params.test_filepath, nrows=cfg.DEV_SAMPLE_SIZE)
else:
meta_test = pd.read_csv(params.test_filepath)
data = {'input': {'X': meta_test,
'y': None,
},
}
pipeline = PIPELINES[pipeline_name]['inference'](cfg.SOLUTION_CONFIG)
pipeline.clean_cache()
output = pipeline.transform(data)
pipeline.clean_cache()
y_pred = output['clipped_prediction']
logger.info('creating submission...')
submission = create_submission(meta_test, y_pred)
logger.info('verifying submittion')
sample_submission = pd.read_csv(params.sample_submission_filepath)
verify_submission(submission, sample_submission)
if dev_mode:
logger.info('submittion can\'t be saved in dev mode')
else:
submission_filepath = os.path.join(params.experiment_dir, 'submission.csv')
submission.to_csv(submission_filepath, index=None, encoding='utf-8')
logger.info('submission saved to {}'.format(submission_filepath))
logger.info('submission head \n\n{}'.format(submission.head()))
def infer_fold_TTA(self, fold_index, mode = 'max_map', Cycle = None):
print(mode)
val_loader = get_foldloader(self.image_size, self.batch_size/2, fold_index, mode='val')
_, max_map, thres = self.val_TTA(fold_index, val_loader, is_load = True, mode = mode, Cycle = Cycle)
if fold_index<0:
return
infer = self.get_infer_TTA(fold_index, thres)
if Cycle is None:
name_tmp = 'fold_{}_TTA_{}{:.3f}at{:.3f}.csv'.format(fold_index,mode,max_map,thres)
else:
name_tmp = 'fold_{}_Cycle_{}_TTA_{}{:.3f}at{:.3f}.csv'.format(fold_index, Cycle, mode, max_map, thres)
output_name = os.path.join(self.model_save_path, 'fold_' + str(fold_index),name_tmp)
submission = create_submission(infer)
submission.to_csv(output_name, index=None)
def _predict(pipeline_name, dev_mode):
logger.info('reading data in')
if dev_mode:
TEST_DAYS_HOURS = cfg.DEV_TEST_DAYS_HOURS
else:
TEST_DAYS_HOURS = eval(params.test_days_hours)
meta_test_suplement = read_csv_time_chunks(params.test_chunks_dir,
prefix='test',
days_hours=TEST_DAYS_HOURS,
usecols=cfg.FEATURE_COLUMNS + cfg.ID_COLUMN,
dtype=cfg.COLUMN_TYPES['inference'],
logger=logger)
meta_test = pd.read_csv(params.test_filepath,
usecols=cfg.FEATURE_COLUMNS + cfg.ID_COLUMN,
dtype=cfg.COLUMN_TYPES['inference'])
meta_test_full = pd.concat([meta_test_suplement, meta_test], axis=0).reset_index(drop=True)
meta_test_full.drop_duplicates(subset=cfg.ID_COLUMN, keep='last', inplace=True)
meta_test_full['click_time'] = pd.to_datetime(meta_test_full['click_time'], format='%Y-%m-%d %H:%M:%S')
data_hash_channel_send(ctx, 'Test Data Hash', meta_test_full)
if dev_mode:
meta_test_full = meta_test_full.sample(cfg.DEV_SAMPLE_TEST_SIZE, replace=False)
data = {'input': {'X': meta_test_full[cfg.FEATURE_COLUMNS],
'y': None,
},
}
pipeline = PIPELINES[pipeline_name]['inference'](cfg.SOLUTION_CONFIG)
pipeline.clean_cache()
output = pipeline.transform(data)
pipeline.clean_cache()
y_pred = output['y_pred']
logger.info('creating submission full test')
full_submission = create_submission(meta_test_full, y_pred)
full_submission_filepath = os.path.join(params.experiment_dir, 'full_submission.csv')
full_submission.to_csv(full_submission_filepath, index=None, encoding='utf-8')
logger.info('subsetting submission')
submission = pd.merge(full_submission, meta_test[cfg.ID_COLUMN], on=cfg.ID_COLUMN, how='inner')
submission_filepath = os.path.join(params.experiment_dir, 'submission.csv')
submission.to_csv(submission_filepath, index=None, encoding='utf-8')
logger.info('submission saved to {}'.format(submission_filepath))
logger.info('submission head \n\n{}'.format(submission.head()))
def ensemble_np(args, np_files, save_np=None):
preds = []
for np_file in np_files:
pred = np.load(np_file)
print(np_file, pred.shape)
preds.append(pred)
y_pred_test = generate_preds(np.mean(preds, 0),
(settings.ORIG_H, settings.ORIG_W),
args.pad_mode)
if save_np is not None:
np.save(save_np, np.mean(preds, 0))
meta = get_test_loader(args.batch_size,
index=0,
dev_mode=False,
pad_mode=args.pad_mode).meta
submission = create_submission(meta, y_pred_test)
submission.to_csv(args.sub_file, index=None, encoding='utf-8')
def infer_5fold(self):
self.G.eval()
test_dir = r'/data/shentao/Airbus/AirbusShipDetectionChallenge_384/test'
test_loader = get_5foldloader(self.image_size, 1, 0, mode='test')
predict_dict = {}
for fold_index in range(5):
self.load_pretrained_model(fold_index)
for i, (id) in enumerate(test_loader):
image_path = os.path.join(test_dir, id[0])
output_mat = self.infer_one_img_from_path_8(image_path)
output_mat = output_mat.reshape(
[self.image_size, self.image_size])
output_mat[output_mat > 1.0] = 1.0
output_mat[output_mat < 0.0] = 0.0
if id[0] not in predict_dict:
predict_dict[id[0]] = output_mat
else:
predict_dict[id[0]] += output_mat
if i % 1000 == 0 and i > 0:
print(self.model_name + ' fold index: ' + str(fold_index) +
' ' + str(i))
out = []
for id in predict_dict:
output_mat = predict_dict[id] / 5.0
output_mat[output_mat > 0.5] = 1
output_mat[output_mat <= 0.5] = 0
output_mat = output_mat.astype(np.uint8)
out.append([id, output_mat])
submission = create_submission(out, 768, 768)
submission.to_csv(self.model_name + '_' + str(self.pretrained_model) +
'_5fold.csv',
index=None)
def _predict(pipeline_name, dev_mode):
logger.info('PREDICTION')
logger.info('reading data...')
if dev_mode:
logger.info('running in "dev-mode". Sample size is: {}'.format(cfg.DEV_SAMPLE_SIZE))
application_test = pd.read_csv(params.test_filepath, nrows=cfg.DEV_SAMPLE_SIZE)
else:
application_test = pd.read_csv(params.test_filepath)
data = {'input': {'X': application_test,
'y': None,
},
}
pipeline = PIPELINES[pipeline_name]['inference'](cfg.SOLUTION_CONFIG)
pipeline.clean_cache()
logger.info('Start pipeline transform')
output = pipeline.transform(data)
pipeline.clean_cache()
y_pred = output['clipped_prediction']
if not dev_mode:
logger.info('creating submission file...')
submission = create_submission(application_test, y_pred)
logger.info('verifying submission...')
sample_submission = pd.read_csv(params.sample_submission_filepath)
verify_submission(submission, sample_submission)
submission_filepath = os.path.join(params.experiment_directory, 'submission.csv')
submission.to_csv(submission_filepath, index=None, encoding='utf-8')
logger.info('submission persisted to {}'.format(submission_filepath))
logger.info('submission head \n\n{}'.format(submission.head()))
if params.kaggle_api:
logger.info('making Kaggle submit...')
os.system('kaggle competitions submit -c home-credit-default-risk -f {} -m {}'
.format(submission_filepath, params.kaggle_message))
def _predict(pipeline_name, dev_mode):
logger.info('reading data in')
if dev_mode:
meta_test = pd.read_csv(params.test_filepath,
usecols=cfg.FEATURE_COLUMNS + cfg.ID_COLUMN,
dtype=cfg.COLUMN_TYPES['inference'],
nrows=cfg.DEV_SAMPLE_TEST_SIZE)
else:
meta_test = pd.read_csv(params.test_filepath,
usecols=cfg.FEATURE_COLUMNS + cfg.ID_COLUMN,
dtype=cfg.COLUMN_TYPES['inference'])
meta_test['click_time'] = pd.to_datetime(meta_test['click_time'],
format='%Y-%m-%d %H:%M:%S')
data_hash_channel_send(ctx, 'Test Data Hash', meta_test)
data = {
'input': {
'X': meta_test[cfg.FEATURE_COLUMNS],
'y': None,
},
}
pipeline = PIPELINES[pipeline_name]['inference'](cfg.SOLUTION_CONFIG)
pipeline.clean_cache()
output = pipeline.transform(data)
pipeline.clean_cache()
y_pred = output['y_pred']
logger.info('creating submission')
submission = create_submission(meta_test, y_pred)
submission_filepath = os.path.join(params.experiment_dir, 'submission.csv')
submission.to_csv(submission_filepath, index=None, encoding='utf-8')
logger.info('submission saved to {}'.format(submission_filepath))
logger.info('submission head \n\n{}'.format(submission.head()))
def _predict(pipeline_name, dev_mode):
logger.info('reading data in')
if dev_mode:
meta_test = pd.read_csv(params.test_filepath, nrows=cfg.DEV_SAMPLE_SIZE)
else:
meta_test = pd.read_csv(params.test_filepath)
data = {'input': {'X': meta_test,
'y': None,
},
}
pipeline = PIPELINES[pipeline_name]['inference'](cfg.SOLUTION_CONFIG)
pipeline.clean_cache()
output = pipeline.transform(data)
pipeline.clean_cache()
y_pred = output['clipped_prediction']
logger.info('creating submission test')
submission = create_submission(meta_test, y_pred)
submission_filepath = os.path.join(params.experiment_dir, 'submission.csv')
submission.to_csv(submission_filepath, index=None, encoding='utf-8')
logger.info('submission saved to {}'.format(submission_filepath))
logger.info('submission head \n\n{}'.format(submission.head()))
def _predict_in_chunks(pipeline_name, submit_predictions, dev_mode, chunk_size):
meta = pd.read_csv(os.path.join(params.meta_dir, 'stage{}_metadata.csv'.format(params.competition_stage)))
meta_test = meta[meta['is_test'] == 1]
if dev_mode:
meta_test = meta_test.sample(9, random_state=1234)
logger.info('processing metadata of shape {}'.format(meta_test.shape))
submission_chunks = []
for meta_chunk in generate_data_frame_chunks(meta_test, chunk_size):
data = {'input': {'meta': meta_chunk,
'meta_valid': None,
'train_mode': False,
'target_sizes': [(300, 300)] * len(meta_chunk)
},
}
pipeline = PIPELINES[pipeline_name]['inference'](SOLUTION_CONFIG)
pipeline.clean_cache()
output = pipeline.transform(data)
pipeline.clean_cache()
y_pred = output['y_pred']
submission_chunk = create_submission(meta_chunk, y_pred, logger, CATEGORY_IDS)
submission_chunks.extend(submission_chunk)
submission_filepath = os.path.join(params.experiment_dir, 'submission.json')
submission = submission_chunks
with open(submission_filepath, "w") as fp:
fp.write(json.dumps(submission))
logger.info('submission saved to {}'.format(submission_filepath))
logger.info('submission head \n\n{}'.format(submission[0]))
if submit_predictions:
_make_submission(submission_filepath)
def main():
#%% Reading data
train = pd.read_csv('./data/cs-training.csv', index_col=0)
X = train.drop('SeriousDlqin2yrs', axis=1)
y = train.SeriousDlqin2yrs
#Feature Engineering
print(f'Starting shape: {X.shape}')
X = (X.pipe(utils.replace_w_sensible_values).pipe(utils.replace_na).pipe(
utils.log_transform_df).pipe(utils.add_AgeDecade).
pipe(utils.add_boolean_DebtRatio_33).pipe(
utils.add_boolean_DebtRatio_43).pipe(
utils.add_features_per_dependent).pipe(
utils.add_features_per_creditline).pipe(
utils.add_features_per_estate).pipe(
utils.add_features_distance_from_mean).pipe(
utils.add_features_distance_from_median).pipe(
utils.add_features_distance_from_std))
print(f'Post feature engineering shape:{X.shape}')
# %% Train Test Split
X_train, X_test, y_train, y_test = train_test_split(
X, y, random_state=RANDOM_STATE, stratify=y)
# %% LightGBM Classifier
lgb_model = lgb.LGBMClassifier(
silent=False,
random_state=RANDOM_STATE,
objective='binary',
metrics='auc',
boosting='gbdt',
scale_pos_weight=13.960106382978724 #T/P-1
)
# %% Stratified Kfold parameters
skf = StratifiedKFold(n_splits=5, random_state=RANDOM_STATE)
# %% Tuning Parameters for RandomSearch
tuning_params = {
'num_leaves': [5, 10, 15, 31, 40, 50],
'scale_pos_weight': [1, 10, 14, 16], # T/P-1 = 13.96
'n_estimators': [100, 250, 500, 750, 1000],
'learning_rate': [0.025, 0.01, 0.05, 0.1],
'max_depth': [3, 5, 7],
'min_child_weight': range(3, 6, 1),
'subsample': [i / 10.0 for i in range(6, 10)],
'colsample_bytree': [i / 10.0 for i in range(6, 10)],
'reg_alpha': [1e-5, 1e-2, 0.1, 1, 100]
}
gs = RandomizedSearchCV(estimator=lgb_model,
param_distributions=tuning_params,
n_iter=50,
scoring='roc_auc',
cv=skf,
refit=True,
verbose=True)
gs.fit(X_train, y_train)
# %% Extraction and selection of final features
impt_features = utils.get_feature_importance(gs, X_train)
impt_features.to_csv(f'output/{RANDOM_PREFIX}_impt_features.csv',
index=False)
final_features = impt_features[
impt_features['importance'] > 0].feature.values
X_train = X_train.loc[:, final_features]
X_test = X_test.loc[:, final_features]
# %% Final Model
best_lgb = lgb.LGBMClassifier().set_params(**gs.best_params_)
best_lgb.fit(X_train, y_train)
# %% Calculating model performance, plotting AUC and PRC curves
utils.calculate_model_performance(best_lgb, X_train, X_test, y_train,
y_test, RANDOM_PREFIX)
# %% Create Submission for Kaggle
utils.create_submission(best_lgb, final_features, RANDOM_PREFIX)
def main(args):
# 1. Prepare data & models
# individual transformations for validation and test data did not give not reduce MSE-loss
train_transforms = transforms.Compose([
ScaleMinSideToSize((SCALE_SIZE, SCALE_SIZE)),
CropCenter(CROP_SIZE),
TransformByKeys(transforms.ToPILImage(), ("image", )),
TransformByKeys(transforms.Grayscale(3),
("image", )), # grayscale image for best score
TransformByKeys(transforms.ColorJitter(brightness=[0.8, 1.2]),
("image", )), # random choose brightness in range
TransformByKeys(transforms.ToTensor(), ("image", )),
TransformByKeys(
transforms.Normalize(mean=[0.5, 0.5, 0.5], std=[0.5, 0.5, 0.5]),
("image", )),
])
print('----------------------------------------------------------')
print('Script for Kaggle competition "Thousand Facial Landmarks"')
print('----------------------------------------------------------')
print('Reading data...')
train_dataset = ThousandLandmarksDataset(os.path.join(args.data, 'train'),
train_transforms,
split="train")
train_dataloader = data.DataLoader(train_dataset,
batch_size=args.batch_size,
num_workers=0,
pin_memory=True,
shuffle=True,
drop_last=True)
val_dataset = ThousandLandmarksDataset(os.path.join(args.data, 'train'),
train_transforms,
split="val")
val_dataloader = data.DataLoader(val_dataset,
batch_size=args.batch_size,
num_workers=0,
pin_memory=True,
shuffle=False,
drop_last=False)
print("Creating model...")
device = torch.device(
"cuda: 0"
) # default GPU device, because train this net on CPU is eternity :)
# this network was selected through experimentation from the list: resnet18, resnet34, resnext50, resnext101, alexnet, InceptionV3, InceptionV4 etc
model = models.resnext50_32x4d(pretrained=True)
# adding new layers with regularization (dropout or batchnorm) did not give effect
model.fc = nn.Linear(model.fc.in_features, 2 * NUM_PTS, bias=True)
model.to(device)
optimizer = optim.Adam(model.parameters(),
lr=args.learning_rate,
amsgrad=True)
loss_fn = fnn.mse_loss
# 2. Train & validate
print("Ready for training...")
best_val_loss = np.inf
for epoch in range(args.epochs):
train_loss = train(model,
train_dataloader,
loss_fn,
optimizer,
device=device)
val_loss = validate(model, val_dataloader, loss_fn, device=device)
print("Epoch #{:2}:\ttrain loss: {:5.2}\tval loss: {:5.2}".format(
epoch, train_loss, val_loss))
if val_loss < best_val_loss:
best_val_loss = val_loss
with open(f"{args.name}_best.pth", "wb") as fp:
torch.save(model.state_dict(), fp)
# 3. Predict
test_dataset = ThousandLandmarksDataset(os.path.join(args.data, 'test'),
train_transforms,
split="test")
test_dataloader = data.DataLoader(test_dataset,
batch_size=args.batch_size,
num_workers=0,
pin_memory=True,
shuffle=False,
drop_last=False)
with open(f"{args.name}_best.pth", "rb") as fp:
best_state_dict = torch.load(fp, map_location="cpu")
model.load_state_dict(best_state_dict)
test_predictions = predict(model, test_dataloader, device)
with open(f"{args.name}_test_predictions.pkl", "wb") as fp:
pickle.dump(
{
"image_names": test_dataset.image_names,
"landmarks": test_predictions
}, fp)
create_submission(args.data, test_predictions, f"{args.name}_submit.csv")
dtrain=x_train,
num_boost_round=132,
#early_stopping_rounds=4,
verbose_eval=1)
by_test = bst.predict(x_test)
# C
cx_train, cy_train, cx_test, c_idxs = get_data('c')
x_train = xgb.DMatrix(cx_train, label=cy_train)
x_test = xgb.DMatrix(cx_test)
neg_pos_rate = np.sum(cy_train == 0) / np.sum(cy_train == 1)
params = {
'max_depth': 2,
'eta': 0.1, # learning rate
# 'scale_pos_weight': neg_pos_rate, # Balance classes ?
'silent': 1,
'objective': 'binary:logistic',
'nthread': 4,
'eval_metric': ['logloss']
}
bst = xgb.train(
params=params,
dtrain=x_train,
num_boost_round=142,
#early_stopping_rounds=10,
verbose_eval=1)
cy_test = bst.predict(x_test)
# Create submission
create_submission(ay_test, by_test, cy_test, a_idxs, b_idxs, c_idxs)
import models, utils, datasets, predict
import logging, sys
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)
scales = {'Chicago': (0.78, 0.88, 1),
'Chicago RAC': (0.6, 0.8, 0.1),
'New Haven': (0.89, 1, 0.68),
'New Haven RAC': (1, 1, 1),
'Oakland': (0.84, 1, 0.51),
'Oakland RAC': (1, 0.94, 0.23),
'Richmond': (0.64, 1, 1),
'Richmond RAC': (1, 1, 1)}
if __name__=='__main__':
if len(sys.argv) == 1:
print "No model name was given! Run again using format: \n\t",
print "python test.py modelname"
else:
modelname = sys.argv[1]
pred = models.test_model(modelname)
categories = datasets.load_dataset('Categories')
n_pred = pred.shape[0]
pred = predict.apply_scales(pred, categories[-n_pred:], scales)
name = modelname + ".csv"
utils.create_submission(name, pred)
print "Saved submission with name %s" %(name)
def main(args):
os.makedirs("runs", exist_ok=True)
# 1. prepare data & models
train_transforms = transforms.Compose([
ScaleMinSideToSize((CROP_SIZE, CROP_SIZE)),
CropCenter(CROP_SIZE),
TransformByKeys(transforms.ToPILImage(), ("image", )),
TransformByKeys(transforms.ToTensor(), ("image", )),
TransformByKeys(
transforms.Normalize(mean=[0.5, 0.5, 0.5], std=[0.25, 0.25, 0.25]),
("image", )),
])
print("Reading data...")
train_dataset = ThousandLandmarksDataset(os.path.join(args.data, "train"),
train_transforms,
split="train")
train_dataloader = DataLoader(train_dataset,
batch_size=args.batch_size,
num_workers=4,
pin_memory=True,
shuffle=True,
drop_last=True)
val_dataset = ThousandLandmarksDataset(os.path.join(args.data, "train"),
train_transforms,
split="val")
val_dataloader = DataLoader(val_dataset,
batch_size=args.batch_size,
num_workers=4,
pin_memory=True,
shuffle=False,
drop_last=False)
device = torch.device(
"cuda:0"
) # if args.gpu and torch.cuda.is_available() else torch.device("cpu")
print("Creating model...")
model = models.resnet18(pretrained=True)
model.requires_grad_(False)
model.fc = nn.Linear(model.fc.in_features, 2 * NUM_PTS, bias=True)
model.fc.requires_grad_(True)
model.to(device)
optimizer = optim.Adam(model.parameters(),
lr=args.learning_rate,
amsgrad=True)
loss_fn = fnn.mse_loss
time.sleep(60)
# 2. train & validate
print("Ready for training...")
best_val_loss = np.inf
for epoch in range(args.epochs):
train_loss = train(model,
train_dataloader,
loss_fn,
optimizer,
device=device)
val_loss = validate(model, val_dataloader, loss_fn, device=device)
print("Epoch #{:2}:\ttrain loss: {:5.2}\tval loss: {:5.2}".format(
epoch, train_loss, val_loss))
if val_loss < best_val_loss:
best_val_loss = val_loss
with open(os.path.join("runs", f"{args.name}_best.pth"),
"wb") as fp:
torch.save(model.state_dict(), fp)
# 3. predict
test_dataset = ThousandLandmarksDataset(os.path.join(args.data, "test"),
train_transforms,
split="test")
test_dataloader = DataLoader(test_dataset,
batch_size=args.batch_size,
num_workers=4,
pin_memory=True,
shuffle=False,
drop_last=False)
with open(os.path.join("runs", f"{args.name}_best.pth"), "rb") as fp:
best_state_dict = torch.load(fp, map_location="cpu")
model.load_state_dict(best_state_dict)
test_predictions = predict(model, test_dataloader, device)
with open(os.path.join("runs", f"{args.name}_test_predictions.pkl"),
"wb") as fp:
pickle.dump(
{
"image_names": test_dataset.image_names,
"landmarks": test_predictions
}, fp)
create_submission(args.data, test_predictions,
os.path.join("runs", f"{args.name}_submit.csv"))
# oof_prediction[val_] = la.predict(val_X)
oof_prediction[val_] = light_gbm.transform(val_X)['prediction']
oof_prediction[oof_prediction < 0] = 0
# _preds = la.predict(test_X)
_preds = light_gbm.transform(test_X)['prediction']
_preds[_preds < 0 ] = 0
sub_prediction += np.expm1(_preds) / len(folds)
oof_scores.append(mean_squared_error(TARGET[val_], oof_prediction[val_])**0.5)
print('Fold %d RMSE : %.5f' % (fold_ + 1, oof_scores[-1]))
gc.collect()
# Lasso
la = linear_model.Lasso()
TARGET = pd.DataFrame(TARGET)
for fold_, (trn_, val_) in enumerate(folds):
trn_X, trn_y = train_X.iloc[trn_], TARGET.iloc[trn_]
val_X, val_y = train_X.iloc[val_], TARGET.iloc[val_]
la.fit(trn_X, trn_y)
oof_prediction[val_] = la.predict(val_X)
oof_prediction[oof_prediction < 0] = 0
_preds = la.predict(test_X)
_preds[_preds < 0 ] = 0
sub_prediction += np.expm1(_preds) / len(folds)
oof_scores.append(mean_squared_error(TARGET.iloc[val_], oof_prediction[val_])**0.5)
print('Fold %d RMSE : %.5f' % (fold_ + 1, oof_scores[-1]))
gc.collect()
submission = utils.create_submission(sub_prediction, test)
submission.to_csv("first_trial.csv", index=False)
prediction_2 = predict2(image_fps_val, min_conf=0.92, augment=False)
def merge_predictions(prediction, prediction_2):
prediction_3 = copy.deepcopy(prediction)
for patient_id in list(prediction_2.keys()):
if len(prediction_2[patient_id])>0:
prediction_3[patient_id] = []
return prediction_3
prediction_3 = merge_predictions(prediction, prediction_2)
iou_all_mean,tp,fp,tn,fn = iou(truth, prediction_3)
print(iou_all_mean,tp,fp,tn,fn) # 0.21805178140096618 248 235 948 69
# Prepare prediction set on test data
if True:
image_fps_test = get_image_fps(TEST_DIR)
image_fps_test.sort()
prediction_test = predict(image_fps_test, min_conf=0.96, augment=True)
prediction_test_2 = predict2(image_fps_test, min_conf=0.92, augment=False)
prediction_test_3 = merge_predictions(prediction_test, prediction_test_2)
create_submission(prediction_test_3)
submission = pd.read_csv('prediction.csv')
def main(args):
# 1. prepare data & models
train_transforms = transforms.Compose([
ScaleMinSideToSize((CROP_SIZE, CROP_SIZE)),
CropCenter(CROP_SIZE),
TransformByKeys(transforms.ToPILImage(), ("image", )),
TransformByKeys(transforms.ToTensor(), ("image", )),
TransformByKeys(
transforms.Normalize(mean=[0.485, 0.456, 0.406],
std=[0.229, 0.224, 0.225]),
("image", ),
),
])
print("Reading data...")
train_dataset = ThousandLandmarksDataset(
os.path.join(args.data, "train"),
train_transforms,
split="train",
debug=args.debug,
)
train_dataloader = data.DataLoader(
train_dataset,
batch_size=args.batch_size,
num_workers=4,
pin_memory=True,
shuffle=True,
drop_last=True,
)
val_dataset = ThousandLandmarksDataset(
os.path.join(args.data, "train"),
train_transforms,
split="val",
debug=args.debug,
)
val_dataloader = data.DataLoader(
val_dataset,
batch_size=args.batch_size,
num_workers=4,
pin_memory=True,
shuffle=False,
drop_last=False,
)
print("Creating model...")
device = torch.device("cuda: 0") if args.gpu else torch.device("cpu")
model = models.resnet50(pretrained=True)
model.fc = nn.Linear(model.fc.in_features, 2 * NUM_PTS, bias=True)
model.to(device)
for name, child in model.named_children():
if name in ["fc"]:
for param in child.parameters():
param.requires_grad = True
else:
for param in child.parameters():
param.requires_grad = False
optimizer = optim.SGD(
filter(lambda p: p.requires_grad, model.parameters()),
lr=args.learning_rate,
momentum=0.9,
weight_decay=1e-04,
)
scheduler = optim.lr_scheduler.OneCycleLR(
optimizer,
max_lr=0.1,
steps_per_epoch=len(train_dataloader),
epochs=args.epochs)
loss = L.WingLoss(width=10, curvature=2, reduction="mean")
# 2. train & validate
print("Ready for training...")
for epoch in range(args.epochs):
train_loss = train(model,
train_dataloader,
loss,
optimizer,
device=device,
scheduler=scheduler)
val_loss = validate(model, val_dataloader, loss, device=device)
print("Epoch #{:2}:\ttrain loss: {:6.3}\tval loss: {:6.3}".format(
epoch, train_loss, val_loss))
# 2.1. train continued
for p in model.parameters():
p.requires_grad = True
optimizer = optim.AdamW(
[
{
"params": model.conv1.parameters(),
"lr": 1e-6
},
{
"params": model.bn1.parameters(),
"lr": 1e-6
},
{
"params": model.relu.parameters(),
"lr": 1e-5
},
{
"params": model.maxpool.parameters(),
"lr": 1e-5
},
{
"params": model.layer1.parameters(),
"lr": 1e-4
},
{
"params": model.layer2.parameters(),
"lr": 1e-4
},
{
"params": model.layer3.parameters(),
"lr": 1e-3
},
{
"params": model.layer4.parameters(),
"lr": 1e-3
},
{
"params": model.avgpool.parameters(),
"lr": 1e-2
},
{
"params": model.fc.parameters(),
"lr": 1e-2
},
],
lr=args.learning_rate,
weight_decay=1e-06,
amsgrad=True,
)
scheduler = optim.lr_scheduler.CosineAnnealingWarmRestarts(optimizer,
T_0=10,
T_mult=2)
print("Ready for training again...")
best_val_loss = np.inf
for epoch in range(args.epochs):
train_loss = train(model,
train_dataloader,
loss,
optimizer,
device=device,
scheduler=scheduler)
val_loss = validate(model, val_dataloader, loss, device=device)
print("Epoch #{:2}:\ttrain loss: {:6.3}\tval loss: {:6.3}".format(
epoch, train_loss, val_loss))
if val_loss < best_val_loss:
best_val_loss = val_loss
with open(f"{args.name}_best.pth", "wb") as fp:
torch.save(model.state_dict(), fp)
# 3. predict
if not args.debug:
test_dataset = ThousandLandmarksDataset(
os.path.join(args.data, "test"),
train_transforms,
split="test",
debug=args.debug,
)
test_dataloader = data.DataLoader(
test_dataset,
batch_size=args.batch_size,
num_workers=4,
pin_memory=True,
shuffle=False,
drop_last=False,
)
with open(f"submit/{args.name}_best.pth", "rb") as fp:
best_state_dict = torch.load(fp, map_location="cpu")
model.load_state_dict(best_state_dict)
test_predictions = predict(model, test_dataloader, device)
with open(f"submit/{args.name}_test_predictions.pkl", "wb") as fp:
pickle.dump(
{
"image_names": test_dataset.image_names,
"landmarks": test_predictions,
},
fp,
)
create_submission(args.data, test_predictions,
f"submit/{args.name}_submit.csv")
print('Dropping Id columns in data...', end='')
Xtrain = Xtrain.drop(['Id'], axis=1)
Ytrain = Ytrain.drop(Ytrain.columns[0], axis=1)
Xtest_id = Xtest['Id'] #To save in sumission file
Xtest = Xtest.drop(['Id'], axis=1)
print('Done')
# print('Xtrain', Xtrain)
# print('ytrain', Ytrain.values.ravel())
# print('Xtest', Xtest)
log = {}
print('Training with gradient_boosting_tree_model...', end='')
Ytest, gbt_log = gradient_boosting_tree_model(Xtrain, Ytrain, Xtest)
log['gbt_log'] = gbt_log
create_submission(Xtest_id, Ytest, 'gradient_boosting_tree_model')
print('Done')
print('Training with random_forest_model...', end='')
Ytest, rf_log = random_forest_model(Xtrain, Ytrain, Xtest)
log['rf_log'] = rf_log
create_submission(Xtest_id, Ytest, 'random_forest_model')
print('Done')
print('Training with extra_trees_model...', end='')
Ytest, et_log = extra_trees_model(Xtrain, Ytrain, Xtest)
log['et_log'] = et_log
create_submission(Xtest_id, Ytest, 'extra_trees_model')
print('Done')
print('Training with xgboost_model...', end='')
def main(args):
os.makedirs("runs", exist_ok=True)
# 1. prepare data & models
# train_transforms = transforms.Compose([
# ScaleMinSideToSize((CROP_SIZE, CROP_SIZE)),
# CropCenter(CROP_SIZE),
# TransformByKeys(transforms.ToPILImage(), ("image",)),
# TransformByKeys(transforms.ToTensor(), ("image",)),
# TransformByKeys(transforms.Normalize(mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225]), ("image",)), # (0.485, 0.456, 0.406), (0.229, 0.224, 0.225)
# ])
crop_size = (224, 224)
train_transforms = transforms.Compose([
CropFrame(9),
ScaleMinSideToSize((CROP_SIZE, CROP_SIZE)),
CropCenter(CROP_SIZE),
FlipHorizontal(),
Rotator(30),
# CropRectangle(crop_size),
ChangeBrightnessContrast(alpha_std=0.05, beta_std=10),
TransformByKeys(transforms.ToPILImage(), ("image", )),
TransformByKeys(transforms.ToTensor(), ("image", )),
TransformByKeys(
transforms.Normalize(mean=[0.485, 0.456, 0.406],
std=[0.229, 0.224, 0.225]), ("image", )),
])
valid_transforms = transforms.Compose([
CropFrame(9),
ScaleMinSideToSize((CROP_SIZE, CROP_SIZE)),
CropCenter(CROP_SIZE),
# CropRectangle(crop_size),
TransformByKeys(transforms.ToPILImage(), ("image", )),
TransformByKeys(transforms.ToTensor(), ("image", )),
TransformByKeys(
transforms.Normalize(mean=[0.485, 0.456, 0.406],
std=[0.229, 0.224, 0.225]), ("image", )),
])
print("Reading data...")
train_dataset = ThousandLandmarksDataset(os.path.join(args.data, "train"),
train_transforms,
split="train")
train_dataloader = DataLoader(train_dataset,
batch_size=args.batch_size,
num_workers=4,
pin_memory=True,
shuffle=True,
drop_last=True)
val_dataset = ThousandLandmarksDataset(os.path.join(args.data, "train"),
valid_transforms,
split="val")
val_dataloader = DataLoader(val_dataset,
batch_size=args.batch_size,
num_workers=4,
pin_memory=True,
shuffle=False,
drop_last=False)
device = torch.device("cuda:0") if args.gpu and torch.cuda.is_available(
) else torch.device("cpu")
print("Creating model...")
# model = models.resnext50_32x4d(pretrained=True)
# model.fc = nn.Linear(model.fc.in_features, 2 * NUM_PTS, bias=True)
# checkpoint = torch.load("./runs/baseline_full3_best.pth", map_location='cpu')
# model.load_state_dict(checkpoint, strict=True)
model = RESNEXT_steroid()
model.to(device)
for p in model.base_net.parameters():
p.requires_grad = False
# model.base_net[8].requires_grad = True
for p in model.fc.parameters():
p.requires_grad = True
for p in model.linear7.parameters():
p.requires_grad = True
for p in model.attention.parameters():
p.requires_grad = True
for p in model.linear1.parameters():
p.requires_grad = True
# model.to(device)
optimizer = optim.Adam(model.parameters(),
lr=args.learning_rate,
amsgrad=True)
# criterion = AdaptiveWingLoss()
# criterion = torch.nn.MSELoss(size_average=True)
# loss_fn = fnn.mse_loss
criterion = fnn.l1_loss
lr_scheduler = optim.lr_scheduler.ReduceLROnPlateau(optimizer,
mode='min',
factor=1 / np.sqrt(10),
patience=4,
verbose=True,
threshold=0.01,
threshold_mode='abs',
cooldown=0,
min_lr=1e-6,
eps=1e-08)
# 2. train & validate
print("Ready for training...")
best_val_loss = np.inf
for epoch in range(args.epochs):
train_loss = train(model,
train_dataloader,
criterion,
optimizer,
device=device)
val_loss, mse_loss = validate(model,
val_dataloader,
criterion,
device=device)
lr_scheduler.step(val_loss)
print(
"Epoch #{:2}:\ttrain loss: {:5.2}\tval loss: {:5.2}\tmse loss: {:5.2}"
.format(epoch, train_loss, val_loss, mse_loss))
if val_loss < best_val_loss:
best_val_loss = val_loss
with open(os.path.join("runs", f"{args.name}_best.pth"),
"wb") as fp:
torch.save(model.state_dict(), fp)
# 3. predict
test_dataset = ThousandLandmarksDataset(os.path.join(args.data, "test"),
train_transforms,
split="test")
test_dataloader = DataLoader(test_dataset,
batch_size=args.batch_size,
num_workers=4,
pin_memory=True,
shuffle=False,
drop_last=False)
with open(os.path.join("runs", f"{args.name}_best.pth"), "rb") as fp:
best_state_dict = torch.load(fp, map_location="cpu")
model.load_state_dict(best_state_dict)
test_predictions = predict(model, test_dataloader, device)
with open(os.path.join("runs", f"{args.name}_test_predictions.pkl"),
"wb") as fp:
pickle.dump(
{
"image_names": test_dataset.image_names,
"landmarks": test_predictions
}, fp)
create_submission(args.data, test_predictions,
os.path.join("runs", f"{args.name}_submit.csv"))
import models, utils, datasets, predict
import logging, sys
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)
scales = {
'Chicago': (0.78, 0.88, 1),
'Chicago RAC': (0.6, 0.8, 0.1),
'New Haven': (0.89, 1, 0.68),
'New Haven RAC': (1, 1, 1),
'Oakland': (0.84, 1, 0.51),
'Oakland RAC': (1, 0.94, 0.23),
'Richmond': (0.64, 1, 1),
'Richmond RAC': (1, 1, 1)
}
if __name__ == '__main__':
if len(sys.argv) == 1:
print "No model name was given! Run again using format: \n\t",
print "python test.py modelname"
else:
modelname = sys.argv[1]
pred = models.test_model(modelname)
categories = datasets.load_dataset('Categories')
n_pred = pred.shape[0]
pred = predict.apply_scales(pred, categories[-n_pred:], scales)
name = modelname + ".csv"
utils.create_submission(name, pred)
print "Saved submission with name %s" % (name)
datetime.utcnow().strftime('%Y-%m-%d_%H%M%S')
logr.info('writing fit {} pipeline to disk as {}'.format(job, model_name))
try:
joblib.dump(pipeline, os.path.join('saved_models', model_name) + '.pkl', compress=3)
except OverflowError, e:
# this is annoying; look into it later
logr.warn('joblib write failed with error={}'.format(e))
logr.info('proceeding with predictions without writing model to disk')
# do something useful with the fit model
if args.submission:
# make predictions for a leaderboard submission
logr.info('writing predictions to formatted submission file')
utils.create_submission(predictions,
pipeline_detail['name'],
comment=pipeline_detail['note'])
else:
# if we already did CV through the gridsearch, then just take
# the best score and make predictions
if hasattr(pipeline, 'best_params_'):
logr.info('predicting test values with best-choice gridsearch params')
predictions = pipeline.predict(X_test)
# fake an array of CV scores to play nice with plot formatting later
scores = np.array([pipeline.best_score_])
# otherwise, do some cross validation
else:
# otherwise, run a cross-validation for test accuracy
cv = 3
logr.info('cross validating model predictions with cv={}'.format(cv))
predictions = cross_val_predict(pipeline, X_test, y_test, cv=cv)
def _predict(pipeline_name, dev_mode):
logger.info('reading data in')
if dev_mode:
TEST_DAYS_HOURS = cfg.DEV_TEST_DAYS_HOURS
else:
TEST_DAYS_HOURS = eval(params.test_days_hours)
meta_test_suplement = read_csv_time_chunks(
params.test_chunks_dir,
prefix='test',
days_hours=TEST_DAYS_HOURS,
usecols=cfg.FEATURE_COLUMNS + cfg.ID_COLUMN,
dtype=cfg.COLUMN_TYPES['inference'],
logger=logger)
meta_test = pd.read_csv(params.test_filepath,
usecols=cfg.FEATURE_COLUMNS + cfg.ID_COLUMN,
dtype=cfg.COLUMN_TYPES['inference'])
meta_test_full = pd.concat([meta_test_suplement, meta_test],
axis=0).reset_index(drop=True)
meta_test_full.drop_duplicates(subset=cfg.ID_COLUMN,
keep='last',
inplace=True)
meta_test_full['click_time'] = pd.to_datetime(meta_test_full['click_time'],
format='%Y-%m-%d %H:%M:%S')
data_hash_channel_send(ctx, 'Test Data Hash', meta_test_full)
if dev_mode:
meta_test_full = meta_test_full.sample(cfg.DEV_SAMPLE_TEST_SIZE,
replace=False)
data = {
'input': {
'X': meta_test_full[cfg.FEATURE_COLUMNS],
'y': None,
},
}
pipeline = PIPELINES[pipeline_name]['inference'](cfg.SOLUTION_CONFIG)
pipeline.clean_cache()
output = pipeline.transform(data)
pipeline.clean_cache()
y_pred = output['y_pred']
logger.info('creating submission full test')
full_submission = create_submission(meta_test_full, y_pred)
full_submission_filepath = os.path.join(params.experiment_dir,
'full_submission.csv')
full_submission.to_csv(full_submission_filepath,
index=None,
encoding='utf-8')
logger.info('subsetting submission')
submission = pd.merge(full_submission,
meta_test[cfg.ID_COLUMN],
on=cfg.ID_COLUMN,
how='inner')
submission_filepath = os.path.join(params.experiment_dir, 'submission.csv')
submission.to_csv(submission_filepath, index=None, encoding='utf-8')
logger.info('submission saved to {}'.format(submission_filepath))
logger.info('submission head \n\n{}'.format(submission.head()))
def run(args):
task = args['model']
submit = args['submission']
# 1.)Load data for training model
X_train_full, y_train_full = utils.load_train_data(task)
if submit:
# making a submission; train on all given data
print('fitting models to entire training set')
X_train, y_train = X_train_full, y_train_full
X_test = utils.load_test_data(task)
else:
# running an experiment - cross validate with train/test split
test_size = args['test_size']
print('fitting models to cv train/test split with train% = {}'.format(1-test_size))
X_train, X_val, y_train, y_val = train_test_split(X_train_full,y_train_full, test_size=test_size, random_state=args['random_state'])
# 2.) Get pipeline
if task == 'Visit':
pipeline_detail = visit[args['expt']]
X_train, y_train = utils.sample_negatives(X_train, y_train, 2)
if not submit:
X_val, y_val = utils.sample_negatives(X_val, y_val, 1)
else:
pipeline_detail = rating[args['expt']]
pipeline = pipeline_detail['pl']
# Fit model to training data
print('fitting model to array sizes (xtrain, ytrain)={}'.format([i.shape for i in [X_train, y_train]]))
print('fitting experiment pipeline with signature={}'.format(pipeline))
pipeline.fit(X_train, y_train)
# 3.) For non-submission experiments, get the best parameters from grid search
if submit:
fname_spec = '_submission_'
else:
# log all results + call out the winner
if hasattr(pipeline, 'best_params_'):
print('best gridsearch score={}'.format(pipeline.best_score_))
print('best set of pipeline params={}'.format(pipeline.best_params_))
print('now displaying all pipeline param scores...')
cv_results = pipeline.cv_results_
for params, mean_score, scores in list(zip(cv_results['params'], cv_results['mean_test_score'], cv_results['std_test_score'])):
print("{:0.3f} (+/-{:0.03f}) for {}".format(mean_score, scores.std() * 2, params))
fname_spec = '_expt_'
model_name = utils.short_name(pipeline) + fname_spec + datetime.utcnow().strftime('%Y-%m-%d_%H%M%S')
# 4.) Prepare submission
if submit:
print('writing predictions to formatted submission file')
predictions = pipeline.predict(X_test)
if hasattr(pipeline, 'best_params_'):
print('predicting test values with best-choice gridsearch params')
utils.create_submission(predictions, pipeline_detail['name'], X_test)
else:
cv = args['k-fold']
print('cross validating model predictions with cv={}'.format(cv))
predictions = cross_val_predict(pipeline, X_val, y_val, cv=cv)
# print("cross val prediction", accuracy_score(y_val, predictions))
print("cross val prediction", mean_squared_error(y_val, predictions))
predictions_train = pipeline.predict(X_train)
predictions_test = pipeline.predict(X_val)
if task == 'Visit':
print('obtained train accuracy = {:.2f}, test accuracy = {:.2f} pipeline={} '.format(
accuracy_score(y_train, predictions_train),
accuracy_score(y_val, predictions_test),
pipeline))
print('calculating confusion matrix')
try:
cf = confusion_matrix(y_val, predictions)
print("confusion matrix: ", cf)
sb.heatmap(cf)
except RuntimeError as e:
print('plotting error. matplotlib backend may need to be changed (see readme). error={}'.format(e))
print('plot may still have been saved, and model has already been saved to disk.')
else:
print('obtained train mse = {:.2f} test mse={}, pipeline={} '.format(
mean_squared_error(y_train, predictions_train),
mean_squared_error(y_val, predictions_test),
pipeline))
if args['cross_val_score']:
# this gives a better idea of uncertainty, but it adds 'cv' more
print('cross validating model accuracy with cv={}'.format(cv))
scores = cross_val_score(pipeline, X_val, y_val, cv=cv)
print('obtained accuracy={:0.2f}% +/- {:0.2f} with cv={}, \
pipeline={} '.format(scores.mean() * 100,
scores.std() * 100 * 2,
cv,
pipeline))
print('completed with pipeline {}'.format(pipeline_detail['name']))