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main.py
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main.py
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from functools import partial
import os
import shutil
from attrdict import AttrDict
import neptune
from neptunecontrib.api.utils import get_filepaths
import numpy as np
import pandas as pd
from sklearn.externals import joblib
from steppy.base import Step, IdentityOperation
from steppy.adapter import Adapter, E
from common_blocks import augmentation as aug
from common_blocks import metrics
from common_blocks import models
from common_blocks import loaders
from common_blocks import pipelines
from common_blocks import utils
from common_blocks import postprocessing
utils.check_env_vars()
CONFIG = utils.read_config(config_path=os.getenv('CONFIG_PATH'))
LOGGER = utils.init_logger()
neptune.init(project_qualified_name=CONFIG.project)
# ______ ______ .__ __. _______ __ _______ _______.
# / | / __ \ | \ | | | ____|| | / _____| / |
# | ,----'| | | | | \| | | |__ | | | | __ | (----`
# | | | | | | | . ` | | __| | | | | |_ | \ \
# | `----.| `--' | | |\ | | | | | | |__| | .----) |
# \______| \______/ |__| \__| |__| |__| \______| |_______/
#
EXPERIMENT_NAME = 'baseline'
EXPERIMENT_DIR = 'data/experiments/{}'.format(EXPERIMENT_NAME)
CLONE_EXPERIMENT_DIR_FROM = '' # When running eval in the cloud specify this as for example /input/SAL-14/output/experiment
OVERWRITE_EXPERIMENT_DIR = False
DEV_MODE = False
SECOND_LEVEL = False
USE_DEPTH = False
USE_AUXILIARY_DATA = False
TAGS = ['first-level', 'training']
if OVERWRITE_EXPERIMENT_DIR and os.path.isdir(EXPERIMENT_DIR):
shutil.rmtree(EXPERIMENT_DIR)
if CLONE_EXPERIMENT_DIR_FROM != '':
if os.path.exists(EXPERIMENT_DIR):
shutil.rmtree(EXPERIMENT_DIR)
shutil.copytree(CLONE_EXPERIMENT_DIR_FROM, EXPERIMENT_DIR)
PARAMS = CONFIG.parameters
MEAN = [0.485, 0.456, 0.406]
STD = [0.229, 0.224, 0.225]
SEED = 1234
ID_COLUMN = 'id'
DEPTH_COLUMN = 'z'
if SECOND_LEVEL:
X_COLUMN = 'file_path_stacked_predictions'
else:
X_COLUMN = 'file_path_image'
Y_COLUMN = 'file_path_mask'
if USE_DEPTH:
x_columns = [X_COLUMN, DEPTH_COLUMN]
else:
x_columns = [X_COLUMN]
CONFIG = AttrDict({
'execution': {'experiment_dir': EXPERIMENT_DIR,
'num_workers': PARAMS.num_workers,
},
'general': {'img_H-W': (PARAMS.image_h, PARAMS.image_w),
'loader_mode': PARAMS.loader_mode,
'num_classes': 2,
'original_size': (101, 101),
},
'xy_splitter': {
'network': {'x_columns': x_columns,
'y_columns': [Y_COLUMN],
},
},
'reader': {
'network': {'x_columns': x_columns,
'y_columns': [Y_COLUMN],
},
},
'loaders': {'stacking': {'dataset_params': {'h': PARAMS.image_h,
'w': PARAMS.image_w,
'image_source': PARAMS.image_source,
'target_format': PARAMS.target_format,
'use_depth': USE_DEPTH,
'MEAN': MEAN,
'STD': STD
},
'loader_params': {'training': {'batch_size': PARAMS.batch_size_train,
'shuffle': True,
'num_workers': PARAMS.num_workers,
'pin_memory': PARAMS.pin_memory
},
'inference': {'batch_size': PARAMS.batch_size_inference,
'shuffle': False,
'num_workers': PARAMS.num_workers,
'pin_memory': PARAMS.pin_memory
},
},
'augmentation_params': {},
},
'resize_and_pad': {'dataset_params': {'h': PARAMS.image_h,
'w': PARAMS.image_w,
'image_source': PARAMS.image_source,
'use_depth': USE_DEPTH,
'MEAN': MEAN,
'STD': STD
},
'loader_params': {'training': {'batch_size': PARAMS.batch_size_train,
'shuffle': True,
'num_workers': PARAMS.num_workers,
'pin_memory': PARAMS.pin_memory
},
'inference': {'batch_size': PARAMS.batch_size_inference,
'shuffle': False,
'num_workers': PARAMS.num_workers,
'pin_memory': PARAMS.pin_memory
},
},
'augmentation_params': {'image_augment_train': aug.intensity_seq,
'image_augment_with_target_train': aug.resize_pad_seq(
resize_target_size=PARAMS.resize_target_size,
pad_method=PARAMS.pad_method,
pad_size=PARAMS.pad_size),
'image_augment_inference': aug.pad_to_fit_net(64,
PARAMS.pad_method),
'image_augment_with_target_inference': aug.pad_to_fit_net(64,
PARAMS.pad_method)
},
},
'pad_tta': {'dataset_params': {'h': PARAMS.image_h,
'w': PARAMS.image_w,
'image_source': PARAMS.image_source,
'use_depth': USE_DEPTH,
'MEAN': MEAN,
'STD': STD
},
'loader_params': {'training': {'batch_size': PARAMS.batch_size_train,
'shuffle': True,
'num_workers': PARAMS.num_workers,
'pin_memory': PARAMS.pin_memory
},
'inference': {'batch_size': PARAMS.batch_size_inference,
'shuffle': False,
'num_workers': PARAMS.num_workers,
'pin_memory': PARAMS.pin_memory
},
},
'augmentation_params': {
'image_augment_inference': aug.pad_to_fit_net(64, PARAMS.pad_method),
'image_augment_with_target_inference': aug.pad_to_fit_net(64,
PARAMS.pad_method),
'tta_transform': aug.test_time_augmentation_transform
},
},
'resize': {'dataset_params': {'h': PARAMS.image_h,
'w': PARAMS.image_w,
'image_source': PARAMS.image_source,
'use_depth': USE_DEPTH,
'MEAN': MEAN,
'STD': STD
},
'loader_params': {'training': {'batch_size': PARAMS.batch_size_train,
'shuffle': True,
'num_workers': PARAMS.num_workers,
'pin_memory': PARAMS.pin_memory
},
'inference': {'batch_size': PARAMS.batch_size_inference,
'shuffle': False,
'num_workers': PARAMS.num_workers,
'pin_memory': PARAMS.pin_memory
},
},
'augmentation_params': {'image_augment_train': aug.intensity_seq,
'image_augment_with_target_train': aug.resize_seq(
resize_target_size=PARAMS.resize_target_size),
'image_augment_inference': aug.resize_to_fit_net(
resize_target_size=PARAMS.resize_target_size),
'image_augment_with_target_inference': aug.resize_to_fit_net(
resize_target_size=PARAMS.resize_target_size)
},
},
'resize_tta': {'dataset_params': {'h': PARAMS.image_h,
'w': PARAMS.image_w,
'image_source': PARAMS.image_source,
'use_depth': USE_DEPTH,
'MEAN': MEAN,
'STD': STD
},
'loader_params': {'training': {'batch_size': PARAMS.batch_size_train,
'shuffle': True,
'num_workers': PARAMS.num_workers,
'pin_memory': PARAMS.pin_memory
},
'inference': {'batch_size': PARAMS.batch_size_inference,
'shuffle': False,
'num_workers': PARAMS.num_workers,
'pin_memory': PARAMS.pin_memory
},
},
'augmentation_params': {
'image_augment_inference': aug.resize_to_fit_net(
resize_target_size=PARAMS.resize_target_size),
'image_augment_with_target_inference': aug.resize_to_fit_net(
resize_target_size=PARAMS.resize_target_size),
'tta_transform': aug.test_time_augmentation_transform
},
},
},
'model': {
'network': {
'architecture_config': {'model_params': {'n_filters': PARAMS.n_filters,
'conv_kernel': PARAMS.conv_kernel,
'pool_kernel': PARAMS.pool_kernel,
'pool_stride': PARAMS.pool_stride,
'repeat_blocks': PARAMS.repeat_blocks,
'batch_norm': PARAMS.use_batch_norm,
'dropout': PARAMS.dropout_conv,
'in_channels': PARAMS.image_channels,
'out_channels': PARAMS.network_output_channels,
'nr_outputs': PARAMS.nr_network_outputs,
'architecture': PARAMS.architecture,
'activation': PARAMS.network_activation,
},
'optimizer_params': {'lr': PARAMS.lr,
},
'regularizer_params': {'regularize': True,
'weight_decay_conv2d': PARAMS.l2_reg_conv,
},
'weights_init': {'function': 'xavier',
},
},
'training_config': {'epochs': PARAMS.epochs_nr,
'shuffle': True,
'batch_size': PARAMS.batch_size_train,
'fine_tuning': PARAMS.fine_tuning,
},
'callbacks_config': {'model_checkpoint': {
'filepath': os.path.join(EXPERIMENT_DIR, 'checkpoints', 'network', 'best.torch'),
'epoch_every': 1,
'metric_name': PARAMS.validation_metric_name,
'minimize': PARAMS.minimize_validation_metric},
'exponential_lr_scheduler': {'gamma': PARAMS.gamma,
'epoch_every': 1},
'reduce_lr_on_plateau_scheduler': {'metric_name': PARAMS.validation_metric_name,
'minimize': PARAMS.minimize_validation_metric,
'reduce_factor': PARAMS.reduce_factor,
'reduce_patience': PARAMS.reduce_patience,
'min_lr': PARAMS.min_lr},
'training_monitor': {'batch_every': 0,
'epoch_every': 1},
'experiment_timing': {'batch_every': 0,
'epoch_every': 1},
'validation_monitor': {'epoch_every': 1,
'data_dir': PARAMS.train_images_dir,
'loader_mode': PARAMS.loader_mode,
'use_depth': USE_DEPTH},
'neptune_monitor': {'model_name': 'network',
'image_nr': 16,
'image_resize': 1.0,
'image_every': 10,
'use_depth': USE_DEPTH},
'early_stopping': {'patience': PARAMS.patience,
'metric_name': PARAMS.validation_metric_name,
'minimize': PARAMS.minimize_validation_metric},
}
},
},
'tta_generator': {'flip_ud': False,
'flip_lr': True,
'rotation': False,
'color_shift_runs': 0},
'tta_aggregator': {'tta_inverse_transform': aug.test_time_augmentation_inverse_transform,
'method': PARAMS.tta_aggregation_method,
'nthreads': PARAMS.num_threads
},
'thresholder': {'threshold_masks': PARAMS.threshold_masks,
},
})
# .______ __ .______ _______ __ __ .__ __. _______ _______.
# | _ \ | | | _ \ | ____|| | | | | \ | | | ____| / |
# | |_) | | | | |_) | | |__ | | | | | \| | | |__ | (----`
# | ___/ | | | ___/ | __| | | | | | . ` | | __| \ \
# | | | | | | | |____ | `----.| | | |\ | | |____.----) |
# | _| |__| | _| |_______||_______||__| |__| \__| |_______|_______/
#
def stacking_preprocessing_train(config, model_name='network', suffix=''):
reader_train = Step(name='xy_train{}'.format(suffix),
transformer=loaders.XYSplit(train_mode=True, **config.xy_splitter[model_name]),
input_data=['input'],
adapter=Adapter({'meta': E('input', 'meta')}),
experiment_directory=config.execution.experiment_dir)
reader_inference = Step(name='xy_inference{}'.format(suffix),
transformer=loaders.XYSplit(train_mode=True, **config.xy_splitter[model_name]),
input_data=['callback_input'],
adapter=Adapter({'meta': E('callback_input', 'meta_valid')}),
experiment_directory=config.execution.experiment_dir)
loader = Step(name='loader{}'.format(suffix),
transformer=loaders.ImageSegmentationLoaderStacking(train_mode=True, **config.loaders.stacking),
input_steps=[reader_train, reader_inference],
adapter=Adapter({'X': E(reader_train.name, 'X'),
'y': E(reader_train.name, 'y'),
'X_valid': E(reader_inference.name, 'X'),
'y_valid': E(reader_inference.name, 'y'),
}),
experiment_directory=config.execution.experiment_dir)
return loader
def stacking_preprocessing_inference(config, model_name='network', suffix=''):
reader_inference = Step(name='xy_inference{}'.format(suffix),
transformer=loaders.XYSplit(train_mode=False, **config.xy_splitter[model_name]),
input_data=['input'],
adapter=Adapter({'meta': E('input', 'meta')}),
experiment_directory=config.execution.experiment_dir)
loader = Step(name='loader{}'.format(suffix),
transformer=loaders.ImageSegmentationLoaderStacking(train_mode=False, **config.loaders.stacking),
input_steps=[reader_inference],
adapter=Adapter({'X': E(reader_inference.name, 'X'),
'y': E(reader_inference.name, 'y'),
}),
experiment_directory=config.execution.experiment_dir,
cache_output=True)
return loader
def network(config, suffix='', train_mode=True):
if SECOND_LEVEL:
preprocessing_train = stacking_preprocessing_train
preprocessing_inference = stacking_preprocessing_inference
else:
preprocessing_train = pipelines.preprocessing_train
preprocessing_inference = pipelines.preprocessing_inference
if train_mode:
preprocessing = preprocessing_train(config, model_name='network', suffix=suffix)
else:
preprocessing = preprocessing_inference(config, suffix=suffix)
if USE_DEPTH:
Network = models.SegmentationModelWithDepth
else:
Network = models.SegmentationModel
network = utils.FineTuneStep(name='network{}'.format(suffix),
transformer=Network(**config.model['network']),
input_data=['callback_input'],
input_steps=[preprocessing],
adapter=Adapter({'datagen': E(preprocessing.name, 'datagen'),
'validation_datagen': E(preprocessing.name, 'validation_datagen'),
'meta_valid': E('callback_input', 'meta_valid'),
}),
is_trainable=True,
fine_tuning=config.model.network.training_config.fine_tuning,
experiment_directory=config.execution.experiment_dir)
if config.general.loader_mode == 'resize_and_pad':
size_adjustment_function = partial(postprocessing.crop_image, target_size=config.general.original_size)
elif config.general.loader_mode == 'resize' or config.general.loader_mode == 'stacking':
size_adjustment_function = partial(postprocessing.resize_image, target_size=config.general.original_size)
else:
raise NotImplementedError
mask_resize = Step(name='mask_resize{}'.format(suffix),
transformer=utils.make_apply_transformer(size_adjustment_function,
output_name='resized_images',
apply_on=['images']),
input_steps=[network],
adapter=Adapter({'images': E(network.name, 'mask_prediction'),
}),
experiment_directory=config.execution.experiment_dir)
return mask_resize
def network_tta(config, suffix=''):
if SECOND_LEVEL:
raise NotImplementedError('Second level does not work with TTA')
preprocessing, tta_generator = pipelines.preprocessing_inference_tta(config, model_name='network')
if USE_DEPTH:
Network = models.SegmentationModelWithDepth
else:
Network = models.SegmentationModel
network = Step(name='network{}'.format(suffix),
transformer=Network(**config.model['network']),
input_data=['callback_input'],
input_steps=[preprocessing],
is_trainable=True,
experiment_directory=config.execution.experiment_dir)
tta_aggregator = pipelines.aggregator('tta_aggregator{}'.format(suffix), network,
tta_generator=tta_generator,
experiment_directory=config.execution.experiment_dir,
config=config.tta_aggregator)
prediction_renamed = Step(name='prediction_renamed{}'.format(suffix),
transformer=IdentityOperation(),
input_steps=[tta_aggregator],
adapter=Adapter({'mask_prediction': E(tta_aggregator.name, 'aggregated_prediction')
}),
experiment_directory=config.execution.experiment_dir)
if config.general.loader_mode == 'resize_and_pad':
size_adjustment_function = partial(postprocessing.crop_image, target_size=config.general.original_size)
elif config.general.loader_mode == 'resize' or config.general.loader_mode == 'stacking':
size_adjustment_function = partial(postprocessing.resize_image, target_size=config.general.original_size)
else:
raise NotImplementedError
mask_resize = Step(name='mask_resize{}'.format(suffix),
transformer=utils.make_apply_transformer(size_adjustment_function,
output_name='resized_images',
apply_on=['images']),
input_steps=[prediction_renamed],
adapter=Adapter({'images': E(prediction_renamed.name, 'mask_prediction'),
}),
experiment_directory=config.execution.experiment_dir)
return mask_resize
# __________ ___ _______ ______ __ __ .___________. __ ______ .__ __.
# | ____\ \ / / | ____| / || | | | | || | / __ \ | \ | |
# | |__ \ V / | |__ | ,----'| | | | `---| |----`| | | | | | | \| |
# | __| > < | __| | | | | | | | | | | | | | | | . ` |
# | |____ / . \ | |____ | `----.| `--' | | | | | | `--' | | |\ |
# |_______/__/ \__\ |_______| \______| \______/ |__| |__| \______/ |__| \__|
#
def train():
meta = pd.read_csv(PARAMS.metadata_filepath)
meta_train = meta[meta['is_train'] == 1]
cv = utils.KFoldBySortedValue(n_splits=PARAMS.n_cv_splits, shuffle=PARAMS.shuffle, random_state=SEED)
for train_idx, valid_idx in cv.split(meta_train[DEPTH_COLUMN].values.reshape(-1)):
break
meta_train_split, meta_valid_split = meta_train.iloc[train_idx], meta_train.iloc[valid_idx]
if USE_AUXILIARY_DATA:
auxiliary = pd.read_csv(PARAMS.auxiliary_metadata_filepath)
train_auxiliary = auxiliary[auxiliary[ID_COLUMN].isin(meta_valid_split[ID_COLUMN].tolist())]
meta_train_split = pd.concat([meta_train_split, train_auxiliary], axis=0)
if DEV_MODE:
meta_train_split = meta_train_split.sample(PARAMS.dev_mode_size, random_state=SEED)
meta_valid_split = meta_valid_split.sample(int(PARAMS.dev_mode_size / 2), random_state=SEED)
with neptune.create_experiment(name=EXPERIMENT_NAME,
params=PARAMS,
tags=TAGS + ['train'],
upload_source_files=get_filepaths(),
properties={'experiment_dir': EXPERIMENT_DIR}):
data = {'input': {'meta': meta_train_split
},
'callback_input': {'meta_valid': meta_valid_split
}
}
pipeline_network = network(config=CONFIG, train_mode=True)
pipeline_network.clean_cache()
pipeline_network.fit_transform(data)
pipeline_network.clean_cache()
def evaluate():
meta = pd.read_csv(PARAMS.metadata_filepath)
meta_train = meta[meta['is_train'] == 1]
cv = utils.KFoldBySortedValue(n_splits=PARAMS.n_cv_splits, shuffle=PARAMS.shuffle, random_state=SEED)
for train_idx, valid_idx in cv.split(meta_train[DEPTH_COLUMN].values.reshape(-1)):
break
meta_valid_split = meta_train.iloc[valid_idx]
y_true_valid = utils.read_masks(meta_valid_split[Y_COLUMN].values)
if DEV_MODE:
meta_valid_split = meta_valid_split.sample(PARAMS.dev_mode_size, random_state=SEED)
data = {'input': {'meta': meta_valid_split,
},
'callback_input': {'meta_valid': None
}
}
with neptune.create_experiment(name=EXPERIMENT_NAME,
params=PARAMS,
tags=TAGS + ['evaluate'],
upload_source_files=get_filepaths(),
properties={'experiment_dir': EXPERIMENT_DIR}):
pipeline_network = network(config=CONFIG, train_mode=False)
pipeline_postprocessing = pipelines.mask_postprocessing(config=CONFIG)
pipeline_network.clean_cache()
output = pipeline_network.transform(data)
valid_masks = {'input_masks': output
}
output = pipeline_postprocessing.transform(valid_masks)
pipeline_network.clean_cache()
pipeline_postprocessing.clean_cache()
y_pred_valid = output['binarized_images']
LOGGER.info('Calculating IOU and IOUT Scores')
iou_score, iout_score = calculate_scores(y_true_valid, y_pred_valid)
LOGGER.info('IOU score on validation is {}'.format(iou_score))
neptune.send_metric('IOU', iou_score)
LOGGER.info('IOUT score on validation is {}'.format(iout_score))
neptune.send_metric('IOUT', iout_score)
results_filepath = os.path.join(EXPERIMENT_DIR, 'validation_results.pkl')
LOGGER.info('Saving validation results to {}'.format(results_filepath))
joblib.dump((meta_valid_split, y_true_valid, y_pred_valid), results_filepath)
def predict():
meta = pd.read_csv(PARAMS.metadata_filepath)
meta_test = meta[meta['is_train'] == 0]
if DEV_MODE:
meta_test = meta_test.sample(PARAMS.dev_mode_size, random_state=SEED)
data = {'input': {'meta': meta_test,
},
'callback_input': {'meta_valid': None
}
}
with neptune.create_experiment(name=EXPERIMENT_NAME,
params=PARAMS,
tags=TAGS + ['predict'],
upload_source_files=get_filepaths(),
properties={'experiment_dir': EXPERIMENT_DIR}):
pipeline_network = network(config=CONFIG, train_mode=False)
pipeline_postprocessing = pipelines.mask_postprocessing(config=CONFIG)
pipeline_network.clean_cache()
predicted_masks = pipeline_network.transform(data)
test_masks = {'input_masks': predicted_masks
}
output = pipeline_postprocessing.transform(test_masks)
pipeline_network.clean_cache()
pipeline_postprocessing.clean_cache()
y_pred_test = output['binarized_images']
submission = utils.create_submission(meta_test, y_pred_test)
submission_filepath = os.path.join(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 train_evaluate_cv():
meta = pd.read_csv(PARAMS.metadata_filepath)
if DEV_MODE:
meta = meta.sample(PARAMS.dev_mode_size, random_state=SEED)
meta_train = meta[meta['is_train'] == 1]
with neptune.create_experiment(name=EXPERIMENT_NAME,
params=PARAMS,
tags=TAGS + ['train', 'evaluate', 'on_cv_folds'],
upload_source_files=get_filepaths(),
properties={'experiment_dir': EXPERIMENT_DIR}):
cv = utils.KFoldBySortedValue(n_splits=PARAMS.n_cv_splits, shuffle=PARAMS.shuffle, random_state=SEED)
fold_iou, fold_iout = [], []
for fold_id, (train_idx, valid_idx) in enumerate(cv.split(meta_train[DEPTH_COLUMN].values.reshape(-1))):
train_data_split, valid_data_split = meta_train.iloc[train_idx], meta_train.iloc[valid_idx]
if USE_AUXILIARY_DATA:
auxiliary = pd.read_csv(PARAMS.auxiliary_metadata_filepath)
train_auxiliary = auxiliary[auxiliary[ID_COLUMN].isin(valid_data_split[ID_COLUMN].tolist())]
train_data_split = pd.concat([train_data_split, train_auxiliary], axis=0)
LOGGER.info('Started fold {}'.format(fold_id))
iou, iout, _ = fold_fit_evaluate_loop(train_data_split, valid_data_split, fold_id)
LOGGER.info('Fold {} IOU {}'.format(fold_id, iou))
neptune.send_metric('Fold {} IOU'.format(fold_id), iou)
LOGGER.info('Fold {} IOUT {}'.format(fold_id, iout))
neptune.send_metric('Fold {} IOUT'.format(fold_id), iout)
fold_iou.append(iou)
fold_iout.append(iout)
iou_mean, iou_std = np.mean(fold_iou), np.std(fold_iou)
iout_mean, iout_std = np.mean(fold_iout), np.std(fold_iout)
log_scores(iou_mean, iou_std, iout_mean, iout_std)
def train_evaluate_predict_cv():
meta = pd.read_csv(PARAMS.metadata_filepath)
if DEV_MODE:
meta = meta.sample(PARAMS.dev_mode_size, random_state=SEED)
meta_train = meta[meta['is_train'] == 1]
meta_test = meta[meta['is_train'] == 0]
with neptune.create_experiment(name=EXPERIMENT_NAME,
params=PARAMS,
tags=TAGS + ['train', 'evaluate', 'predict', 'on_cv_folds'],
upload_source_files=get_filepaths(),
properties={'experiment_dir': EXPERIMENT_DIR}):
cv = utils.KFoldBySortedValue(n_splits=PARAMS.n_cv_splits, shuffle=PARAMS.shuffle, random_state=SEED)
fold_iou, fold_iout, out_of_fold_train_predictions, out_of_fold_test_predictions = [], [], [], []
for fold_id, (train_idx, valid_idx) in enumerate(cv.split(meta_train[DEPTH_COLUMN].values.reshape(-1))):
train_data_split, valid_data_split = meta_train.iloc[train_idx], meta_train.iloc[valid_idx]
if USE_AUXILIARY_DATA:
auxiliary = pd.read_csv(PARAMS.auxiliary_metadata_filepath)
train_auxiliary = auxiliary[auxiliary[ID_COLUMN].isin(valid_data_split[ID_COLUMN].tolist())]
train_data_split = pd.concat([train_data_split, train_auxiliary], axis=0)
LOGGER.info('Started fold {}'.format(fold_id))
iou, iout, out_of_fold_prediction, test_prediction = fold_fit_evaluate_predict_loop(train_data_split,
valid_data_split,
meta_test,
fold_id)
LOGGER.info('Fold {} IOU {}'.format(fold_id, iou))
neptune.send_metric('Fold {} IOU'.format(fold_id), iou)
LOGGER.info('Fold {} IOUT {}'.format(fold_id, iout))
neptune.send_metric('Fold {} IOUT'.format(fold_id), iout)
fold_iou.append(iou)
fold_iout.append(iout)
out_of_fold_train_predictions.append(out_of_fold_prediction)
out_of_fold_test_predictions.append(test_prediction)
train_ids, train_predictions = [], []
for idx_fold, train_pred_fold in out_of_fold_train_predictions:
train_ids.extend(idx_fold)
train_predictions.extend(train_pred_fold)
iou_mean, iou_std = np.mean(fold_iou), np.std(fold_iou)
iout_mean, iout_std = np.mean(fold_iout), np.std(fold_iout)
log_scores(iou_mean, iou_std, iout_mean, iout_std)
save_predictions(train_ids, train_predictions, meta_test, out_of_fold_test_predictions)
def evaluate_cv():
meta = pd.read_csv(PARAMS.metadata_filepath)
if DEV_MODE:
meta = meta.sample(PARAMS.dev_mode_size, random_state=SEED)
meta_train = meta[meta['is_train'] == 1]
with neptune.create_experiment(name=EXPERIMENT_NAME,
params=PARAMS,
tags=TAGS + ['evaluate', 'on_cv_folds'],
upload_source_files=get_filepaths(),
properties={'experiment_dir': EXPERIMENT_DIR}):
cv = utils.KFoldBySortedValue(n_splits=PARAMS.n_cv_splits, shuffle=PARAMS.shuffle, random_state=SEED)
fold_iou, fold_iout = [], []
for fold_id, (train_idx, valid_idx) in enumerate(cv.split(meta_train[DEPTH_COLUMN].values.reshape(-1))):
valid_data_split = meta_train.iloc[valid_idx]
LOGGER.info('Started fold {}'.format(fold_id))
iou, iout, _ = fold_evaluate_loop(valid_data_split, fold_id)
LOGGER.info('Fold {} IOU {}'.format(fold_id, iou))
neptune.send_metric('Fold {} IOU'.format(fold_id), iou)
LOGGER.info('Fold {} IOUT {}'.format(fold_id, iout))
neptune.send_metric('Fold {} IOUT'.format(fold_id), iout)
fold_iou.append(iou)
fold_iout.append(iout)
iou_mean, iou_std = np.mean(fold_iou), np.std(fold_iou)
iout_mean, iout_std = np.mean(fold_iout), np.std(fold_iout)
log_scores(iou_mean, iou_std, iout_mean, iout_std)
def evaluate_predict_cv():
meta = pd.read_csv(PARAMS.metadata_filepath)
if DEV_MODE:
meta = meta.sample(PARAMS.dev_mode_size, random_state=SEED)
meta_train = meta[meta['is_train'] == 1]
meta_test = meta[meta['is_train'] == 0]
with neptune.create_experiment(name=EXPERIMENT_NAME,
params=PARAMS,
tags=TAGS + ['evaluate', 'predict', 'on_cv_folds'],
upload_source_files=get_filepaths(),
properties={'experiment_dir': EXPERIMENT_DIR}):
cv = utils.KFoldBySortedValue(n_splits=PARAMS.n_cv_splits, shuffle=PARAMS.shuffle, random_state=SEED)
fold_iou, fold_iout, out_of_fold_train_predictions, out_of_fold_test_predictions = [], [], [], []
for fold_id, (train_idx, valid_idx) in enumerate(cv.split(meta_train[DEPTH_COLUMN].values.reshape(-1))):
valid_data_split = meta_train.iloc[valid_idx]
LOGGER.info('Started fold {}'.format(fold_id))
iou, iout, out_of_fold_prediction, test_prediction = fold_evaluate_predict_loop(valid_data_split,
meta_test,
fold_id)
LOGGER.info('Fold {} IOU {}'.format(fold_id, iou))
neptune.send_metric('Fold {} IOU'.format(fold_id), iou)
LOGGER.info('Fold {} IOUT {}'.format(fold_id, iout))
neptune.send_metric('Fold {} IOUT'.format(fold_id), iout)
fold_iou.append(iou)
fold_iout.append(iout)
out_of_fold_train_predictions.append(out_of_fold_prediction)
out_of_fold_test_predictions.append(test_prediction)
train_ids, train_predictions = [], []
for idx_fold, train_pred_fold in out_of_fold_train_predictions:
train_ids.extend(idx_fold)
train_predictions.extend(train_pred_fold)
iou_mean, iou_std = np.mean(fold_iou), np.std(fold_iou)
iout_mean, iout_std = np.mean(fold_iout), np.std(fold_iout)
log_scores(iou_mean, iou_std, iout_mean, iout_std)
save_predictions(train_ids, train_predictions, meta_test, out_of_fold_test_predictions)
def fold_fit_evaluate_predict_loop(train_data_split, valid_data_split, test, fold_id):
iou, iout, predicted_masks_valid = fold_fit_evaluate_loop(train_data_split, valid_data_split, fold_id)
test_pipe_input = {'input': {'meta': test
},
'callback_input': {'meta_valid': None
}
}
pipeline_network = network(config=CONFIG, suffix='_fold_{}'.format(fold_id), train_mode=False)
LOGGER.info('Start pipeline transform on test')
pipeline_network.clean_cache()
predicted_masks_test = pipeline_network.transform(test_pipe_input)
utils.clean_object_from_memory(pipeline_network)
predicted_masks_test = predicted_masks_test['resized_images']
return iou, iout, predicted_masks_valid, predicted_masks_test
def fold_fit_evaluate_loop(train_data_split, valid_data_split, fold_id):
train_pipe_input = {'input': {'meta': train_data_split
},
'callback_input': {'meta_valid': valid_data_split
}
}
valid_pipe_input = {'input': {'meta': valid_data_split
},
'callback_input': {'meta_valid': None
}
}
valid_ids = valid_data_split[ID_COLUMN].tolist()
LOGGER.info('Start pipeline fit and transform on train')
config = add_fold_id_suffix(CONFIG, fold_id)
pipeline_network = network(config=config, suffix='_fold_{}'.format(fold_id), train_mode=True)
pipeline_network.clean_cache()
pipeline_network.fit_transform(train_pipe_input)
utils.clean_object_from_memory(pipeline_network)
LOGGER.info('Start pipeline transform on valid')
pipeline_network = network(config=config, suffix='_fold_{}'.format(fold_id), train_mode=False)
pipeline_postprocessing = pipelines.mask_postprocessing(config=config, suffix='_fold_{}'.format(fold_id))
pipeline_network.clean_cache()
pipeline_postprocessing.clean_cache()
predicted_masks_valid = pipeline_network.transform(valid_pipe_input)
valid_pipe_masks = {'input_masks': predicted_masks_valid
}
output_valid = pipeline_postprocessing.transform(valid_pipe_masks)
utils.clean_object_from_memory(pipeline_network)
y_pred_valid = output_valid['binarized_images']
y_true_valid = utils.read_masks(valid_data_split[Y_COLUMN].values)
iou, iout = calculate_scores(y_true_valid, y_pred_valid)
predicted_masks_valid = predicted_masks_valid['resized_images']
return iou, iout, (valid_ids, predicted_masks_valid)
def fold_evaluate_predict_loop(valid_data_split, test, fold_id):
iou, iout, predicted_masks_valid = fold_evaluate_loop(valid_data_split, fold_id)
test_pipe_input = {'input': {'meta': test
},
'callback_input': {'meta_valid': None
}
}
pipeline_network = network(config=CONFIG, suffix='_fold_{}'.format(fold_id), train_mode=False)
LOGGER.info('Start pipeline transform on test')
pipeline_network.clean_cache()
predicted_masks_test = pipeline_network.transform(test_pipe_input)
utils.clean_object_from_memory(pipeline_network)
predicted_masks_test = predicted_masks_test['resized_images']
return iou, iout, predicted_masks_valid, predicted_masks_test
def fold_evaluate_loop(valid_data_split, fold_id):
valid_pipe_input = {'input': {'meta': valid_data_split
},
'callback_input': {'meta_valid': None
}
}
valid_ids = valid_data_split[ID_COLUMN].tolist()
LOGGER.info('Start pipeline transform on valid')
pipeline_network = network(config=CONFIG, suffix='_fold_{}'.format(fold_id), train_mode=False)
pipeline_postprocessing = pipelines.mask_postprocessing(config=CONFIG, suffix='_fold_{}'.format(fold_id))
pipeline_network.clean_cache()
pipeline_postprocessing.clean_cache()
predicted_masks_valid = pipeline_network.transform(valid_pipe_input)
valid_pipe_masks = {'input_masks': predicted_masks_valid
}
output_valid = pipeline_postprocessing.transform(valid_pipe_masks)
utils.clean_object_from_memory(pipeline_network)
y_pred_valid = output_valid['binarized_images']
y_true_valid = utils.read_masks(valid_data_split[Y_COLUMN].values)
iou, iout = calculate_scores(y_true_valid, y_pred_valid)
predicted_masks_valid = predicted_masks_valid['resized_images']
return iou, iout, (valid_ids, predicted_masks_valid)
# __ __ .___________. __ __ _______.
# | | | | | || | | | / |
# | | | | `---| |----`| | | | | (----`
# | | | | | | | | | | \ \
# | `--' | | | | | | `----.----) |
# \______/ |__| |__| |_______|_______/
#
def calculate_scores(y_true, y_pred):
iou = metrics.intersection_over_union(y_true, y_pred)
iout = metrics.intersection_over_union_thresholds(y_true, y_pred)
return iou, iout
def add_fold_id_suffix(config, fold_id):
config['model']['network']['callbacks_config']['neptune_monitor']['model_name'] = 'network_{}'.format(fold_id)
checkpoint_filepath = config['model']['network']['callbacks_config']['model_checkpoint']['filepath']
fold_checkpoint_filepath = checkpoint_filepath.replace('network/best.torch',
'network_{}/best.torch'.format(fold_id))
config['model']['network']['callbacks_config']['model_checkpoint']['filepath'] = fold_checkpoint_filepath
return config
def log_scores(iou_mean, iou_std, iout_mean, iout_std):
LOGGER.info('IOU mean {}, IOU std {}'.format(iou_mean, iou_std))
neptune.send_metric('IOU', iou_mean)
neptune.send_metric('IOU STD', iou_std)
LOGGER.info('IOUT mean {}, IOUT std {}'.format(iout_mean, iout_std))
neptune.send_metric('IOUT', iout_mean)
neptune.send_metric('IOUT STD', iout_std)
def save_predictions(train_ids, train_predictions, meta_test, out_of_fold_test_predictions):
averaged_mask_predictions_test = np.mean(np.array(out_of_fold_test_predictions), axis=0)
pipeline_postprocessing = pipelines.mask_postprocessing(config=CONFIG)
pipeline_postprocessing.clean_cache()
test_pipe_masks = {'input_masks': {'resized_images': averaged_mask_predictions_test}
}
y_pred_test = pipeline_postprocessing.transform(test_pipe_masks)['binarized_images']
LOGGER.info('Saving predictions')
out_of_fold_train_predictions_path = os.path.join(EXPERIMENT_DIR, 'out_of_fold_train_predictions.pkl')
joblib.dump({'ids': train_ids,
'images': train_predictions}, out_of_fold_train_predictions_path)
out_of_fold_test_predictions_path = os.path.join(EXPERIMENT_DIR, 'out_of_fold_test_predictions.pkl')
joblib.dump({'ids': meta_test[ID_COLUMN].tolist(),
'images': averaged_mask_predictions_test}, out_of_fold_test_predictions_path)
submission = utils.create_submission(meta_test, y_pred_test)
submission_filepath = os.path.join(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()))
# .___ ___. ___ __ .__ __.
# | \/ | / \ | | | \ | |
# | \ / | / ^ \ | | | \| |
# | |\/| | / /_\ \ | | | . ` |
# | | | | / _____ \ | | | |\ |
# |__| |__| /__/ \__\ |__| |__| \__|
#
if __name__ == '__main__':
train_evaluate_predict_cv()