def main():
parser = cli.parse_command_line()
args = parser.parse_args()
if args.task == "train" and args.mode == "slice":
args.mode_task = "cnn"
commandline = parser.parse_known_args()
arguments = vars(args)
if (arguments['task'] != 'preprocessing') \
and (arguments['task'] != 'extract') \
and (arguments['task'] != 'generate') \
and (arguments['task'] != 'tsvtool') \
and (arguments['task'] != 'quality_check') \
and (arguments['task'] != 'classify'):
commandline_to_json(commandline)
text_file = open(path.join(args.output_dir, 'environment.txt'), 'w')
text_file.write('Version of python: %s \n' % sys.version)
text_file.write('Version of pytorch: %s \n' % torch.__version__)
text_file.close()
if arguments['task'] in ['train', 'quality_check']:
if not args.use_cpu and not torch.cuda.is_available():
raise ValueError(
"No GPU is available. Please add the -cpu flag to run on CPU.")
args.func(args)
def main():
parser = cli.parse_command_line()
args = parser.parse_args()
if args.task == "train" and args.mode == "slice":
args.mode_task = "cnn"
commandline = parser.parse_known_args()
arguments = vars(args)
if (arguments['task'] != 'preprocessing') \
and (arguments['task'] != 'extract') \
and (arguments['task'] != 'generate') \
and (arguments['task'] != 'tsvtool') \
and (arguments['task'] != 'quality_check') \
and (arguments['task'] != 'classify'):
commandline_to_json(commandline)
write_requirements_version(args.output_dir)
if hasattr(args, "use_cpu"):
if not args.use_cpu and not torch.cuda.is_available():
raise ValueError(
"No GPU is available. Please add the -cpu flag to run on CPU.")
args.func(args)
def main():
parser = cli.parse_command_line()
args = parser.parse_args()
commandline = parser.parse_known_args()
if args.train_autoencoder:
model_type = 'autoencoder'
else:
model_type = 'cnn'
commandline_to_json(commandline, model_type)
args.func(args)
def main():
parser = cli.parse_command_line()
args = parser.parse_args()
print(args)
commandline = parser.parse_known_args()
if hasattr(args, 'train_autoencoder'):
model_type = 'autoencoder'
else:
model_type = 'cnn'
arguments = vars(args)
if arguments['task'] != 'preprocessing':
commandline_to_json(commandline, model_type)
args.func(args)
optimizer = eval("torch.optim." + params.optimizer)(
filter(lambda x: x.requires_grad, model.parameters()),
lr=params.learning_rate,
weight_decay=params.weight_decay)
setattr(params, 'beginning_epoch', 0)
# Define output directories
log_dir = os.path.join(params.output_dir, 'fold-%i' % fi,
'tensorboard_logs')
model_dir = os.path.join(params.output_dir, 'fold-%i' % fi, 'models')
print('Beginning the training task')
train(model, train_loader, valid_loader, criterion, optimizer, False,
log_dir, model_dir, params)
test_cnn(train_loader, "train", fi, criterion, options)
test_cnn(valid_loader, "validation", fi, criterion, options)
total_time = time() - total_time
print("Total time of computation: %d s" % total_time)
if __name__ == "__main__":
commandline = parser.parse_known_args()
commandline_to_json(commandline)
options = commandline[0]
if commandline[1]:
raise Exception("unknown arguments: %s" %
(parser.parse_known_args()[1]))
train_CNN_bad_data_split(options)
valid_df,
metrics_valid,
fi,
dataset='validation',
selection=selection)
soft_voting_to_tsvs(params.output_dir,
fi,
dataset='train',
selection=selection,
selection_threshold=params.selection_threshold)
soft_voting_to_tsvs(params.output_dir,
fi,
dataset='validation',
selection=selection,
selection_threshold=params.selection_threshold)
torch.cuda.empty_cache()
total_time = time() - total_time
print("Total time of computation: %d s" % total_time)
if __name__ == "__main__":
commandline = parser.parse_known_args()
commandline_to_json(commandline, "CNN")
options = commandline[0]
if commandline[1]:
raise Exception("unknown arguments: %s" %
(parser.parse_known_args()[1]))
train_CNN_bad_data_split(options)
def inference_from_model(caps_dir,
tsv_path,
model_path=None,
json_file=None,
prefix=None,
labels=True,
gpu=True,
num_workers=0,
batch_size=1,
prepare_dl=False,
selection_metrics=None,
diagnoses=None,
logger=None,
multi_cohort=False):
"""
Inference from previously trained model.
This functions uses a previously trained model to classify the input(s).
The model is stored in the variable model_path and it assumes the folder
structure given by the training stage. Particullary to have a prediction at
image level, it assumes that results of the validation set are stored in
the model_path folder in order to perform soft-voiting at the slice/patch
level and also for multicnn.
Args:
caps_dir: folder containing the tensor files (.pt version of MRI)
tsv_path: file with the name of the MRIs to process (single or multiple)
model_path: file with the model (pth format).
json_file: file containing the training parameters.
prefix: prefix of all classification outputs.
labels: by default is True. If False no metrics tsv files will be written.
measurements.tsv
gpu: if true, it uses gpu.
num_workers: num_workers used in DataLoader
batch_size: batch size of the DataLoader
prepare_dl: if true, uses extracted patches/slices otherwise extract them
on-the-fly.
selection_metrics: list of metrics to find best models to be evaluated.
diagnoses: list of diagnoses to be tested if tsv_path is a folder.
logger: Logger instance.
multi_cohort (bool): If True caps_directory is the path to a TSV file linking cohort names and paths.
Returns:
Files written in the output folder with prediction results and metrics. By
default the output folder is named cnn_classification and it is inside the
model_folder.
Raises:
"""
import argparse
import logging
if logger is None:
logger = logging
parser = argparse.ArgumentParser()
parser.add_argument("model_path",
type=str,
help="Path to the trained model folder.")
options = parser.parse_args([model_path])
options = read_json(options, json_path=json_file)
logger.debug("Load model with these options:")
logger.debug(options)
# Overwrite options with user input
options.use_cpu = not gpu
options.nproc = num_workers
options.batch_size = batch_size
if diagnoses is not None:
options.diagnoses = diagnoses
options = translate_parameters(options)
if options.mode_task == "multicnn":
num_cnn = compute_num_cnn(caps_dir, tsv_path, options, "test")
else:
num_cnn = None
# Define the path
currentDirectory = pathlib.Path(model_path)
# Search for 'fold-*' pattern
currentPattern = "fold-*"
# loop depending the number of folds found in the model folder
for fold_dir in currentDirectory.glob(currentPattern):
fold = int(str(fold_dir).split("-")[-1])
out_path = join(fold_dir, 'models')
for selection_metric in selection_metrics:
if options.mode_task == 'multicnn':
for cnn_dir in listdir(out_path):
if not exists(
join(out_path, cnn_dir, "best_%s" %
selection_metric, 'model_best.pth.tar')):
raise FileNotFoundError(
errno.ENOENT, strerror(errno.ENOENT),
join(out_path, cnn_dir,
"best_%s" % selection_metric,
'model_best.pth.tar'))
else:
full_model_path = join(out_path, "best_%s" % selection_metric)
if not exists(join(full_model_path, 'model_best.pth.tar')):
raise FileNotFoundError(
errno.ENOENT, strerror(errno.ENOENT),
join(full_model_path, 'model_best.pth.tar'))
performance_dir = join(fold_dir, 'cnn_classification',
'best_%s' % selection_metric)
makedirs(performance_dir, exist_ok=True)
commandline_to_json(
{
"output_dir": model_path,
"caps_dir": caps_dir,
"tsv_path": tsv_path,
"prefix": prefix,
"labels": labels
},
filename=f"commandline_classify-{prefix}")
# It launch the corresponding function, depending on the mode.
inference_from_model_generic(caps_dir,
tsv_path,
out_path,
options,
prefix,
currentDirectory,
fold,
"best_%s" % selection_metric,
labels=labels,
num_cnn=num_cnn,
logger=logger,
multi_cohort=multi_cohort,
prepare_dl=prepare_dl)
# Soft voting
if hasattr(options, 'selection_threshold'):
selection_thresh = options.selection_threshold
else:
selection_thresh = 0.8
# Write files at the image level (for patch, roi and slice).
# It assumes the existance of validation files to perform soft-voting
if options.mode in ["patch", "roi", "slice"]:
soft_voting_to_tsvs(currentDirectory,
fold,
"best_%s" % selection_metric,
options.mode,
prefix,
num_cnn=num_cnn,
selection_threshold=selection_thresh,
use_labels=labels,
logger=logger)
logger.info("Prediction results and metrics are written in the "
"following folder: %s" % performance_dir)
