197 lines
7.9 KiB
Python
197 lines
7.9 KiB
Python
from collections import defaultdict
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from pathlib import Path
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from abc import ABC
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import torch
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import pandas as pd
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from ml_lib.modules.util import LightningBaseModule
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from util.loss_mixin import LossMixin
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from util.optimizer_mixin import OptimizerMixin
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class TrainMixin:
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def training_step(self, batch_xy, batch_nb, *args, **kwargs):
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assert isinstance(self, LightningBaseModule)
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batch_files, batch_x, batch_y = batch_xy
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y = self(batch_x).main_out
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if self.params.n_classes <= 2:
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loss = self.bce_loss(y.squeeze().float(), batch_y.float())
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else:
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if self.params.loss == 'focal_loss_rob':
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labels_one_hot = torch.nn.functional.one_hot(batch_y, num_classes=self.params.n_classes)
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loss = self.__getattribute__(self.params.loss)(y, labels_one_hot)
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else:
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loss = self.__getattribute__(self.params.loss)(y, batch_y.long())
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return dict(loss=loss)
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def training_epoch_end(self, outputs):
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assert isinstance(self, LightningBaseModule)
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keys = list(outputs[0].keys())
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summary_dict = {f'mean_{key}': torch.mean(torch.stack([output[key]
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for output in outputs]))
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for key in keys if 'loss' in key}
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summary_dict.update(epoch=self.current_epoch)
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self.log_dict(summary_dict)
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class ValMixin:
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def validation_step(self, batch_xy, batch_idx, *args, **kwargs):
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assert isinstance(self, LightningBaseModule)
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batch_files, batch_x, batch_y = batch_xy
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model_out = self(batch_x)
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y = model_out.main_out
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sorted_y = defaultdict(list)
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sorted_batch_y = dict()
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for idx, file_name in enumerate(batch_files):
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sorted_y[file_name].append(y[idx])
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sorted_batch_y.update({file_name: batch_y[idx]})
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sorted_y = dict(sorted_y)
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for file_name in sorted_y:
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sorted_y.update({file_name: torch.stack(sorted_y[file_name])})
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target_y = torch.stack(tuple(sorted_batch_y.values())).long()
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if self.params.n_classes <= 2:
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mean_sorted_y = torch.stack([x.mean(dim=0) if x.shape[0] > 1 else x for x in sorted_y.values()])
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self.metrics.update(mean_sorted_y, target_y)
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else:
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y_max = torch.stack(
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[torch.argmax(x.mean(dim=0)) if x.shape[0] > 1 else torch.argmax(x) for x in sorted_y.values()]
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).squeeze()
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y_one_hot = torch.nn.functional.one_hot(y_max, num_classes=self.params.n_classes).float()
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self.metrics.update(y_one_hot, target_y)
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if self.params.n_classes <= 2:
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val_loss = self.bce_loss(y.squeeze().float(), batch_y.float())
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else:
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val_loss = self.ce_loss(y, batch_y.long())
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return dict(batch_files=batch_files, val_loss=val_loss,
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batch_idx=batch_idx, y=y, batch_y=batch_y)
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def validation_epoch_end(self, outputs, *_, **__):
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assert isinstance(self, LightningBaseModule)
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summary_dict = dict()
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keys = list(outputs[0].keys())
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summary_dict.update({f'mean_{key}': torch.mean(torch.stack([output[key]
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for output in outputs]))
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for key in keys if 'loss' in key}
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)
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sorted_y = defaultdict(list)
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sorted_batch_y = dict()
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for output in outputs:
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for idx, file_name in enumerate(output['batch_files']):
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sorted_y[file_name].append(output['y'][idx])
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sorted_batch_y.update({file_name: output['batch_y'][idx]})
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sorted_y = dict(sorted_y)
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sorted_batch_y = torch.stack(tuple(sorted_batch_y.values())).long()
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for file_name in sorted_y:
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sorted_y.update({file_name: torch.stack(sorted_y[file_name])})
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if self.params.n_classes <= 2:
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mean_sorted_y = torch.stack([x.mean(dim=0) if x.shape[0] > 1 else x for x in sorted_y.values()]).squeeze()
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max_vote_loss = self.bce_loss(mean_sorted_y.float(), sorted_batch_y.float())
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# Sklearn Scores
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additional_scores = self.additional_scores(dict(y=mean_sorted_y, batch_y=sorted_batch_y))
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else:
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y_max = torch.stack(
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[torch.argmax(x.mean(dim=0)) if x.shape[0] > 1 else torch.argmax(x) for x in sorted_y.values()]
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).squeeze()
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y_one_hot = torch.nn.functional.one_hot(y_max, num_classes=self.params.n_classes).float()
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max_vote_loss = self.ce_loss(y_one_hot, sorted_batch_y)
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# Sklearn Scores
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additional_scores = self.additional_scores(dict(y=y_one_hot, batch_y=sorted_batch_y))
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summary_dict.update(val_max_vote_loss=max_vote_loss, **additional_scores)
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summary_dict.update({f'mean_{key}': torch.mean(torch.stack([output[key]
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for output in outputs]))
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for key in keys if 'loss' in key}
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)
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pl_metrics, pl_images = self.metrics.compute_and_prepare()
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self.metrics.reset()
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summary_dict.update(**pl_metrics)
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summary_dict.update(epoch=self.current_epoch)
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self.log_dict(summary_dict)
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# For Debugging:
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# print(f'Summary Metrics are: {summary_dict}')
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for name, image in pl_images.items():
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self.logger.log_image(name, image, step=self.global_step)
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pass
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class TestMixin:
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def test_step(self, batch_xy, batch_idx, *_, **__):
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assert isinstance(self, LightningBaseModule)
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batch_files, batch_x, batch_y = batch_xy
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model_out = self(batch_x)
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y = model_out.main_out
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return dict(batch_files=batch_files, batch_idx=batch_idx, y=y)
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def test_epoch_end(self, outputs, *_, **__):
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assert isinstance(self, LightningBaseModule)
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# No logging, just inference.
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sorted_y = defaultdict(list)
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for output in outputs:
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for idx, file_name in enumerate(output['batch_files']):
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sorted_y[file_name].append(output['y'][idx].cpu())
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sorted_y = dict(sorted_y)
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for file_name in sorted_y:
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sorted_y.update({file_name: torch.stack(sorted_y[file_name])})
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if self.params.n_classes > 2:
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pred = torch.stack(
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[torch.argmax(x.mean(dim=0)) if x.shape[0] > 1 else torch.argmax(x) for x in sorted_y.values()]
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).squeeze().cpu()
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class_names = {val: key for val, key in
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enumerate(['background', 'chimpanze', 'geunon', 'mandrille', 'redcap'])}
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else:
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pred = torch.stack([x.mean(dim=0) if x.shape[0] > 1 else x for x in sorted_y.values()]).squeeze()
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pred = torch.where(pred > 0.5, 1, 0)
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class_names = {val: key for val, key in enumerate(['negative', 'positive'])}
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df = pd.DataFrame(data=dict(filename=[Path(x).name for x in sorted_y.keys()],
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prediction=[class_names[x.item()] for x in pred.cpu()]))
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result_file = Path(self.logger.log_dir / 'predictions.csv')
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if result_file.exists():
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try:
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result_file.unlink()
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except:
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print('File already existed')
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pass
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with result_file.open(mode='wb') as csv_file:
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df.to_csv(index=False, path_or_buf=csv_file)
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with result_file.open(mode='rb') as csv_file:
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try:
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self.logger.neptunelogger.log_artifact(csv_file)
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except:
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print('No possible to send to neptune')
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pass
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class CombinedModelMixins(LossMixin,
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TrainMixin,
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ValMixin,
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TestMixin,
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OptimizerMixin,
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LightningBaseModule,
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ABC):
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pass
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