import torch
from torch.utils.data import DataLoader
import os
from biobb_common.tools.file_utils import launchlogger
from biobb_common.tools import file_utils as fu
from biobb_pytorch.mdae.utils.log_utils import get_size
from biobb_common.generic.biobb_object import BiobbObject
from mlcolvar.data import DictDataset
import numpy as np
[docs]
class EvaluateEncoder(BiobbObject):
"""
| biobb_pytorch EvaluateEncoder
| Encode data with a Molecular Dynamics AutoEncoder (MDAE) model.
| Evaluates a PyTorch autoencoder from the given properties.
Args:
input_model_pth_path (str): Path to the trained model file whose encoder will be used. File type: input. `Sample file <https://github.com/bioexcel/biobb_pytorch/raw/master/biobb_pytorch/test/reference/mdae/output_model.pth>`_. Accepted formats: pth (edam:format_2333).
input_dataset_pt_path (str): Path to the input dataset file (.pt) to encode. File type: input. `Sample file <https://github.com/bioexcel/biobb_pytorch/raw/master/biobb_pytorch/test/reference/mdae/output_model.pt>`_. Accepted formats: pt (edam:format_2333).
output_results_npz_path (str): Path to the output latent-space results file (compressed NumPy archive, typically containing 'z'). File type: output. `Sample file <https://github.com/bioexcel/biobb_pytorch/raw/master/biobb_pytorch/test/reference/mdae/output_results.npz>`_. Accepted formats: npz (edam:format_2333).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **Dataset** (*dict*) - ({}) mlcolvar DictDataset / DataLoader options (e.g. batch_size, shuffle).
Examples:
This example shows how to use the EvaluateEncoder class to evaluate a PyTorch autoencoder model::
from biobb_pytorch.mdae.evaluate_model import encode_model
input_model_pth_path='input_model.pth'
input_dataset_pt_path='input_dataset.npy'
output_results_npz_path='output_results.npz'
prop={
'Dataset': {
'batch_size': 32
}
}
encode_model(input_model_pth_path=input_model.pth,
input_dataset_pt_path=input_dataset.npy,
output_results_npz_path=output_results.npz,
properties=prop)
Info:
* wrapped_software:
* name: PyTorch
* version: >=1.6.0
* license: BSD 3-Clause
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(
self,
input_model_pth_path: str,
input_dataset_pt_path: str,
output_results_npz_path: str,
properties: dict,
**kwargs,
) -> None:
properties = properties or {}
super().__init__(properties)
self.input_model_pth_path = input_model_pth_path
self.input_dataset_pt_path = input_dataset_pt_path
self.output_results_npz_path = output_results_npz_path
self.properties = properties.copy()
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
"in": {
"input_model_pth_path": input_model_pth_path,
"input_dataset_pt_path": input_dataset_pt_path,
},
"out": {
"output_results_npz_path": output_results_npz_path,
},
}
self.Dataset = self.properties.get('Dataset', {})
self.results = None
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
def load_model(self):
return torch.load(self.io_dict["in"]["input_model_pth_path"],
weights_only=False)
[docs]
def load_dataset(self):
dataset = torch.load(self.io_dict["in"]["input_dataset_pt_path"],
weights_only=False)
return DictDataset(dataset)
[docs]
def create_dataloader(self, dataset):
ds_cfg = self.properties['Dataset']
return DataLoader(
dataset,
batch_size=ds_cfg.get('batch_size', 16),
shuffle=ds_cfg.get('shuffle', False),
)
[docs]
def evaluate_encoder(self, model, dataloader):
"""Evaluate the encoder part of the model."""
model.eval()
with torch.no_grad():
z_all = []
for batch in dataloader:
z = model.forward_cv(batch['data'])
z_all.append(z)
return {"z": torch.cat(z_all, dim=0)}
[docs]
@launchlogger
def launch(self) -> int:
"""
Execute the :class:`EvaluateEncoder <mdae.encode_model.EvaluateEncoder>` object.
"""
fu.log('## BioBB Model Evaluator ##', self.out_log)
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Start Pipeline
# load the model
fu.log(f'Load model from {os.path.abspath(self.io_dict["in"]["input_model_pth_path"])}', self.out_log)
model = self.load_model()
# load the dataset
fu.log(f'Load dataset from {os.path.abspath(self.io_dict["in"]["input_dataset_pt_path"])}', self.out_log)
dataset = self.load_dataset()
# create the dataloader
fu.log('Start evaluating...', self.out_log)
dataloader = self.create_dataloader(dataset)
# evaluate the model
results = self.evaluate_encoder(model, dataloader)
# Save the results
np.savez_compressed(self.io_dict["out"]["output_results_npz_path"], **results)
fu.log(f'Evaluation Results saved to {os.path.abspath(self.io_dict["out"]["output_results_npz_path"])}', self.out_log)
fu.log(f'File size: {get_size(self.io_dict["out"]["output_results_npz_path"])}', self.out_log)
# Copy files to host
self.copy_to_host()
# Remove temporal files
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return 0
[docs]
def encode_model(
properties: dict,
input_model_pth_path: str,
input_dataset_pt_path: str,
output_results_npz_path: str,
**kwargs,
) -> int:
"""Create the :class:`EvaluateEncoder <mdae.encode_model.EvaluateEncoder>` class and
execute the :meth:`launch() <mdae.encode_model.EvaluateEncoder.launch>` method."""
return EvaluateEncoder(**dict(locals())).launch()
encode_model.__doc__ = EvaluateEncoder.__doc__
main = EvaluateEncoder.get_main(encode_model, "Encode data with a Molecular Dynamics AutoEncoder (MDAE) model.")
if __name__ == "__main__":
main()