diff --git a/_templates/new_project/main.py b/_templates/new_project/main.py index c60cc87..692072e 100644 --- a/_templates/new_project/main.py +++ b/_templates/new_project/main.py @@ -9,7 +9,7 @@ from pytorch_lightning.callbacks import ModelCheckpoint, EarlyStopping from ml_lib.modules.util import LightningBaseModule from ml_lib.utils.config import Config -from ml_lib.utils.logging import Logger +from ml_lib.utils.loggers import Logger warnings.filterwarnings('ignore', category=FutureWarning) warnings.filterwarnings('ignore', category=UserWarning) diff --git a/additions/__init__.py b/additions/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/additions/losses.py b/additions/losses.py new file mode 100644 index 0000000..347770b --- /dev/null +++ b/additions/losses.py @@ -0,0 +1,43 @@ +import torch +import torch.nn as nn +import torch.nn.functional as F + + +class FocalLoss(nn.modules.loss._WeightedLoss): + def __init__(self, weight=None, gamma=2,reduction='mean'): + super(FocalLoss, self).__init__(weight,reduction=reduction) + self.gamma = gamma + self.weight = weight # weight parameter will act as the alpha parameter to balance class weights + + def forward(self, input, target): + + ce_loss = F.cross_entropy(input, target, reduction=self.reduction, weight=self.weight) + pt = torch.exp(-ce_loss) + focal_loss = ((1 - pt) ** self.gamma * ce_loss).mean() + return focal_loss + + +class FocalLossRob(nn.Module): + # taken from https://github.com/mathiaszinnen/focal_loss_torch/blob/main/focal_loss/focal_loss.py + def __init__(self, alpha=1, gamma=2, reduction: str = 'mean'): + super().__init__() + if reduction not in ['mean', 'none', 'sum']: + raise NotImplementedError('Reduction {} not implemented.'.format(reduction)) + self.reduction = reduction + self.alpha = alpha + self.gamma = gamma + + def forward(self, x, target): + x = x.clamp(1e-7, 1. - 1e-7) # own addition + p_t = torch.where(target == 1, x, 1-x) + fl = - 1 * (1 - p_t) ** self.gamma * torch.log(p_t) + fl = torch.where(target == 1, fl * self.alpha, fl) + return self._reduce(fl) + + def _reduce(self, x): + if self.reduction == 'mean': + return x.mean() + elif self.reduction == 'sum': + return x.sum() + else: + return x diff --git a/audio_toolset/audio_to_mel_dataset.py b/audio_toolset/audio_to_mel_dataset.py index f86e1aa..a98ce90 100644 --- a/audio_toolset/audio_to_mel_dataset.py +++ b/audio_toolset/audio_to_mel_dataset.py @@ -60,7 +60,8 @@ class LibrosaAudioToMelDataset(Dataset): self.mel_file_path.unlink(missing_ok=True) if not self.mel_file_path.exists(): self.mel_file_path.parent.mkdir(parents=True, exist_ok=True) - raw_sample, _ = librosa.core.load(self.audio_path, sr=self.sampling_rate) + with self.audio_path.open(mode='rb') as audio_file: + raw_sample, _ = librosa.core.load(audio_file, sr=self.sampling_rate) mel_sample = self._mel_transform(raw_sample) with self.mel_file_path.open('wb') as mel_file: pickle.dump(mel_sample, mel_file, protocol=pickle.HIGHEST_PROTOCOL) diff --git a/audio_toolset/mel_dataset.py b/audio_toolset/mel_dataset.py index 696359b..2f05d56 100644 --- a/audio_toolset/mel_dataset.py +++ b/audio_toolset/mel_dataset.py @@ -22,10 +22,12 @@ class TorchMelDataset(Dataset): self.mel_hop_len = int(mel_hop_len) self.sub_segment_hop_len = int(sub_segment_hop_len) self.n = int((self.sampling_rate / self.mel_hop_len) * self.audio_file_len + 1) - if self.sub_segment_len and self.sub_segment_hop_len: + if self.sub_segment_len and self.sub_segment_hop_len and (self.n - self.sub_segment_len) > 0: self.offsets = list(range(0, self.n - self.sub_segment_len, self.sub_segment_hop_len)) else: self.offsets = [0] + if len(self) == 0: + print('what happend here') self.label = label self.transform = transform diff --git a/metrics/multi_class_classification.py b/metrics/multi_class_classification.py index 4bb77f6..0656376 100644 --- a/metrics/multi_class_classification.py +++ b/metrics/multi_class_classification.py @@ -2,7 +2,9 @@ from itertools import cycle import numpy as np import torch -from sklearn.metrics import f1_score, roc_curve, auc, roc_auc_score, ConfusionMatrixDisplay, confusion_matrix +from pytorch_lightning.metrics import Recall +from sklearn.metrics import f1_score, roc_curve, auc, roc_auc_score, ConfusionMatrixDisplay, confusion_matrix, \ + recall_score from ml_lib.metrics._base_score import _BaseScores from ml_lib.utils.tools import to_one_hot @@ -16,20 +18,21 @@ class MultiClassScores(_BaseScores): super(MultiClassScores, self).__init__(*args) pass - def __call__(self, outputs): + def __call__(self, outputs, class_names=None): summary_dict = dict() + class_names = class_names or range(self.model.params.n_classes) ####################################################################################### # Additional Score - UAR - ROC - Conf. Matrix - F1 ####################################################################################### # # INIT y_true = torch.cat([output['batch_y'] for output in outputs]).cpu().numpy() - y_true_one_hot = to_one_hot(y_true, self.model.n_classes) + y_true_one_hot = to_one_hot(y_true, self.model.params.n_classes) y_pred = torch.cat([output['y'] for output in outputs]).squeeze().cpu().float().numpy() y_pred_max = np.argmax(y_pred, axis=1) - class_names = {val: key for key, val in self.model.dataset.test_dataset.classes.items()} + class_names = {val: key for val, key in enumerate(class_names)} ###################################################################################### # # F1 SCORE @@ -38,7 +41,12 @@ class MultiClassScores(_BaseScores): macro_f1_score = f1_score(y_true, y_pred_max, labels=None, pos_label=1, average='macro', sample_weight=None, zero_division=True) summary_dict.update(dict(micro_f1_score=micro_f1_score, macro_f1_score=macro_f1_score)) - + ###################################################################################### + # + # Unweichted Average Recall + uar = recall_score(y_true, y_pred_max, labels=[0, 1, 2, 3, 4], average='macro', + sample_weight=None, zero_division='warn') + summary_dict.update(dict(uar_score=uar)) ####################################################################################### # # ROC Curve @@ -47,7 +55,7 @@ class MultiClassScores(_BaseScores): fpr = dict() tpr = dict() roc_auc = dict() - for i in range(self.model.n_classes): + for i in range(self.model.params.n_classes): fpr[i], tpr[i], _ = roc_curve(y_true_one_hot[:, i], y_pred[:, i]) roc_auc[i] = auc(fpr[i], tpr[i]) @@ -56,15 +64,15 @@ class MultiClassScores(_BaseScores): roc_auc["micro"] = auc(fpr["micro"], tpr["micro"]) # First aggregate all false positive rates - all_fpr = np.unique(np.concatenate([fpr[i] for i in range(self.model.n_classes)])) + all_fpr = np.unique(np.concatenate([fpr[i] for i in range(self.model.params.n_classes)])) # Then interpolate all ROC curves at this points mean_tpr = np.zeros_like(all_fpr) - for i in range(self.model.n_classes): + for i in range(self.model.params.n_classes): mean_tpr += np.interp(all_fpr, fpr[i], tpr[i]) # Finally average it and compute AUC - mean_tpr /= self.model.n_classes + mean_tpr /= self.model.params.n_classes fpr["macro"] = all_fpr tpr["macro"] = mean_tpr @@ -83,7 +91,7 @@ class MultiClassScores(_BaseScores): colors = cycle(['firebrick', 'orangered', 'gold', 'olive', 'limegreen', 'aqua', 'dodgerblue', 'slategrey', 'royalblue', 'indigo', 'fuchsia'], ) - for i, color in zip(range(self.model.n_classes), colors): + for i, color in zip(range(self.model.params.n_classes), colors): plt.plot(fpr[i], tpr[i], color=color, lw=2, label=f'{class_names[i]} ({round(roc_auc[i], 2)})') plt.plot([0, 1], [0, 1], 'k--', lw=2) @@ -116,9 +124,9 @@ class MultiClassScores(_BaseScores): fig1, ax1 = plt.subplots(dpi=96) cm = confusion_matrix([class_names[x] for x in y_true], [class_names[x] for x in y_pred_max], labels=[class_names[key] for key in class_names.keys()], - normalize='all') + normalize='true') disp = ConfusionMatrixDisplay(confusion_matrix=cm, - display_labels=[class_names[i] for i in range(self.model.n_classes)] + display_labels=[class_names[i] for i in range(self.model.params.n_classes)] ) disp.plot(include_values=True, ax=ax1) diff --git a/modules/blocks.py b/modules/blocks.py index d4c425b..3bde036 100644 --- a/modules/blocks.py +++ b/modules/blocks.py @@ -22,8 +22,8 @@ DEVICE = torch.device('cuda' if torch.cuda.is_available() else 'cpu') ################### class LinearModule(ShapeMixin, nn.Module): - def __init__(self, in_shape, out_features, bias=True, activation=None, - norm=False, dropout: Union[int, float] = 0, **kwargs): + def __init__(self, in_shape, out_features, use_bias=True, activation=None, + use_norm=False, dropout: Union[int, float] = 0, **kwargs): if list(kwargs.keys()): warnings.warn(f'The following arguments have been ignored: \n {list(kwargs.keys())}') super(LinearModule, self).__init__() @@ -31,8 +31,8 @@ class LinearModule(ShapeMixin, nn.Module): self.in_shape = in_shape self.flat = Flatten(self.in_shape) if isinstance(self.in_shape, (tuple, list)) else F_x(in_shape) self.dropout = nn.Dropout(dropout) if dropout else F_x(self.flat.shape) - self.norm = nn.BatchNorm1d(self.flat.shape) if norm else F_x(self.flat.shape) - self.linear = nn.Linear(self.flat.shape, out_features, bias=bias) + self.norm = nn.LayerNorm(self.flat.shape) if use_norm else F_x(self.flat.shape) + self.linear = nn.Linear(self.flat.shape, out_features, bias=use_bias) self.activation = activation() if activation else F_x(self.linear.out_features) def forward(self, x): @@ -47,13 +47,14 @@ class LinearModule(ShapeMixin, nn.Module): class ConvModule(ShapeMixin, nn.Module): def __init__(self, in_shape, conv_filters, conv_kernel, activation: nn.Module = nn.ELU, pooling_size=None, - bias=True, norm=False, dropout: Union[int, float] = 0, trainable: bool = True, + bias=True, use_norm=False, dropout: Union[int, float] = 0, trainable: bool = True, conv_class=nn.Conv2d, conv_stride=1, conv_padding=0, **kwargs): super(ConvModule, self).__init__() assert isinstance(in_shape, (tuple, list)), f'"in_shape" should be a [list, tuple], but was {type(in_shape)}' assert len(in_shape) == 3, f'Length should be 3, but was {len(in_shape)}' - warnings.warn(f'The following arguments have been ignored: \n {list(kwargs.keys())}') - if norm and not trainable: + if len(kwargs.keys()): + warnings.warn(f'The following arguments have been ignored: \n {list(kwargs.keys())}') + if use_norm and not trainable: warnings.warn('You set this module to be not trainable but the running norm is active.\n' + 'We set it to "eval" mode.\n' + 'Keep this in mind if you do a finetunning or retraining step.' @@ -72,9 +73,9 @@ class ConvModule(ShapeMixin, nn.Module): # Modules self.activation = activation() or F_x(None) + self.norm = nn.LayerNorm(self.in_shape, eps=1e-04) if use_norm else F_x(None) self.dropout = nn.Dropout2d(dropout) if dropout else F_x(None) self.pooling = nn.MaxPool2d(pooling_size) if pooling_size else F_x(None) - self.norm = nn.BatchNorm2d(in_channels, eps=1e-04) if norm else F_x(None) self.conv = conv_class(in_channels, self.conv_filters, self.conv_kernel, bias=bias, padding=self.padding, stride=self.stride ) @@ -134,7 +135,7 @@ class DeConvModule(ShapeMixin, nn.Module): def __init__(self, in_shape, conv_filters, conv_kernel, conv_stride=1, conv_padding=0, dropout: Union[int, float] = 0, autopad=0, activation: Union[None, nn.Module] = nn.ReLU, interpolation_scale=0, - bias=True, norm=False, **kwargs): + bias=True, use_norm=False, **kwargs): super(DeConvModule, self).__init__() warnings.warn(f'The following arguments have been ignored: \n {list(kwargs.keys())}') in_channels, height, width = in_shape[0], in_shape[1], in_shape[2] @@ -146,7 +147,7 @@ class DeConvModule(ShapeMixin, nn.Module): self.autopad = AutoPad() if autopad else lambda x: x self.interpolation = Interpolate(scale_factor=interpolation_scale) if interpolation_scale else lambda x: x - self.norm = nn.BatchNorm2d(in_channels, eps=1e-04) if norm else F_x(self.in_shape) + self.norm = nn.LayerNorm(in_channels, eps=1e-04) if use_norm else F_x(self.in_shape) self.dropout = nn.Dropout2d(dropout) if dropout else F_x(self.in_shape) self.de_conv = nn.ConvTranspose2d(in_channels, self.conv_filters, self.conv_kernel, bias=bias, padding=self.padding, stride=self.stride) @@ -166,14 +167,13 @@ class DeConvModule(ShapeMixin, nn.Module): class ResidualModule(ShapeMixin, nn.Module): - def __init__(self, in_shape, module_class, n, norm=False, **module_parameters): + def __init__(self, in_shape, module_class, n, use_norm=False, **module_parameters): assert n >= 1 super(ResidualModule, self).__init__() self.in_shape = in_shape module_parameters.update(in_shape=in_shape) - if norm: - norm = nn.BatchNorm1d if len(self.in_shape) <= 2 else nn.BatchNorm2d - self.norm = norm(self.in_shape if isinstance(self.in_shape, int) else self.in_shape[0]) + if use_norm: + self.norm = nn.LayerNorm(self.in_shape if isinstance(self.in_shape, int) else self.in_shape[0]) else: self.norm = F_x(self.in_shape) self.activation = module_parameters.get('activation', None) @@ -216,13 +216,14 @@ class RecurrentModule(ShapeMixin, nn.Module): class FeedForward(nn.Module): - def __init__(self, dim, hidden_dim, dropout=0.): + def __init__(self, dim, hidden_dim, dropout=0., activation=nn.GELU): super().__init__() self.net = nn.Sequential( nn.Linear(dim, hidden_dim), - nn.GELU(), + activation() or F_x(None), nn.Dropout(dropout), nn.Linear(hidden_dim, dim), + activation() or F_x(None), nn.Dropout(dropout) ) @@ -272,18 +273,20 @@ class Attention(nn.Module): class TransformerModule(ShapeMixin, nn.Module): - def __init__(self, in_shape, depth, heads, mlp_dim, dropout=None, use_norm=False, activation='gelu'): + def __init__(self, in_shape, depth, heads, mlp_dim, dropout=None, use_norm=False, + activation=nn.GELU, use_residual=True): super(TransformerModule, self).__init__() self.in_shape = in_shape + self.use_residual = use_residual self.flat = Flatten(self.in_shape) if isinstance(self.in_shape, (tuple, list)) else F_x(in_shape) - self.layers = nn.ModuleList([]) self.embedding_dim = self.flat.flat_shape - self.norm = nn.LayerNorm(self.embedding_dim) + self.norm = nn.LayerNorm(self.embedding_dim) if use_norm else F_x(self.embedding_dim) self.attns = nn.ModuleList([Attention(self.embedding_dim, heads=heads, dropout=dropout) for _ in range(depth)]) - self.mlps = nn.ModuleList([FeedForward(self.embedding_dim, mlp_dim, dropout=dropout) for _ in range(depth)]) + self.mlps = nn.ModuleList([FeedForward(self.embedding_dim, mlp_dim, dropout=dropout, activation=activation) + for _ in range(depth)]) def forward(self, x, mask=None, return_attn_weights=False, **_): tensor = self.flat(x) @@ -297,11 +300,11 @@ class TransformerModule(ShapeMixin, nn.Module): attn_weights.append(attn_weight) else: attn_tensor = attn(attn_tensor, mask=mask) - tensor = attn_tensor + tensor + tensor = tensor + attn_tensor if self.use_residual else attn_tensor # MLP mlp_tensor = self.norm(tensor) mlp_tensor = mlp(mlp_tensor) - tensor = tensor + mlp_tensor + tensor = tensor + mlp_tensor if self.use_residual else mlp_tensor return (tensor, attn_weights) if return_attn_weights else tensor diff --git a/modules/model_parts.py b/modules/model_parts.py index 7b4dada..b076d9c 100644 --- a/modules/model_parts.py +++ b/modules/model_parts.py @@ -183,10 +183,11 @@ class BaseCNNEncoder(ShapeMixin, nn.Module): # noinspection PyUnresolvedReferences def __init__(self, in_shape, lat_dim=256, use_bias=True, use_norm=False, dropout: Union[int, float] = 0, latent_activation: Union[nn.Module, None] = None, activation: nn.Module = nn.ELU, - filters: List[int] = None, kernels: List[int] = None, **kwargs): + filters: List[int] = None, kernels: Union[List[int], int, None] = None, **kwargs): super(BaseCNNEncoder, self).__init__() assert filters, '"Filters" has to be a list of int' - assert kernels, '"Kernels" has to be a list of int' + kernels = kernels or [3] * len(filters) + kernels = kernels if not isinstance(kernels, int) else [kernels] * len(filters) assert len(kernels) == len(filters), 'Length of "Filters" and "Kernels" has to be same.' # Optional Padding for odd image-sizes diff --git a/modules/util.py b/modules/util.py index 6492bc2..2c29fb4 100644 --- a/modules/util.py +++ b/modules/util.py @@ -1,7 +1,5 @@ -import inspect -from argparse import ArgumentParser - from functools import reduce +from matplotlib import pyplot as plt from abc import ABC from pathlib import Path @@ -12,14 +10,77 @@ from pytorch_lightning.utilities import argparse_utils from torch import nn from torch.nn import functional as F, Unfold +from sklearn.metrics import ConfusionMatrixDisplay + # Utility - Modules ################### from ..utils.model_io import ModelParameters -from ..utils.tools import locate_and_import_class, add_argparse_args +from ..utils.tools import add_argparse_args try: import pytorch_lightning as pl + class PLMetrics(pl.metrics.Metric): + + def __init__(self, n_classes, tag=''): + super(PLMetrics, self).__init__() + + self.n_classes = n_classes + self.tag = tag + + self.accuracy_score = pl.metrics.Accuracy(compute_on_step=False) + self.precision = pl.metrics.Precision(num_classes=self.n_classes, average='macro', compute_on_step=False) + self.recall = pl.metrics.Recall(num_classes=self.n_classes, average='macro', compute_on_step=False) + self.confusion_matrix = pl.metrics.ConfusionMatrix(self.n_classes, normalize='true', compute_on_step=False) + # self.precision_recall_curve = pl.metrics.PrecisionRecallCurve(self.n_classes, compute_on_step=False) + # self.average_prec = pl.metrics.AveragePrecision(self.n_classes, compute_on_step=True) + # self.roc = pl.metrics.ROC(self.n_classes, compute_on_step=False) + self.fbeta = pl.metrics.FBeta(self.n_classes, average='macro', compute_on_step=False) + self.f1 = pl.metrics.F1(self.n_classes, average='macro', compute_on_step=False) + + def __iter__(self): + return iter(((name, metric) for name, metric in self._modules.items())) + + def update(self, preds, target) -> None: + for _, metric in self: + metric.update(preds, target) + + def reset(self) -> None: + for _, metric in self: + metric.reset() + + def compute(self) -> dict: + tag = f'{self.tag}_' if self.tag else '' + return {f'{tag}{metric_name}_score': metric.compute() for metric_name, metric in self} + + def compute_and_prepare(self): + pl_metrics = self.compute() + images_from_metrics = dict() + for metric_name in list(pl_metrics.keys()): + if 'curve' in metric_name: + continue + roc_curve = pl_metrics.pop(metric_name) + print('debug_point') + + elif 'matrix' in metric_name: + matrix = pl_metrics.pop(metric_name) + fig1, ax1 = plt.subplots(dpi=96) + disp = ConfusionMatrixDisplay(confusion_matrix=matrix.cpu().numpy(), + display_labels=[i for i in range(self.n_classes)] + ) + disp.plot(include_values=True, ax=ax1) + images_from_metrics[metric_name] = fig1 + + elif 'ROC' in metric_name: + continue + roc = pl_metrics.pop(metric_name) + print('debug_point') + else: + pl_metrics[metric_name] = pl_metrics[metric_name].cpu().item() + + return pl_metrics, images_from_metrics + + class LightningBaseModule(pl.LightningModule, ABC): @classmethod @@ -49,6 +110,9 @@ try: self._weight_init = weight_init self.params = ModelParameters(model_parameters) + self.metrics = PLMetrics(self.params.n_classes, tag='PL') + pass + def size(self): return self.shape diff --git a/utils/_basedatamodule.py b/utils/_basedatamodule.py index c2e0a2f..fa26276 100644 --- a/utils/_basedatamodule.py +++ b/utils/_basedatamodule.py @@ -25,5 +25,12 @@ class _BaseDataModule(LightningDataModule): self.datasets = dict() def transfer_batch_to_device(self, batch, device): - return batch.to(device) - + if isinstance(batch, list): + for idx, item in enumerate(batch): + try: + batch[idx] = item.to(device) + except (AttributeError, RuntimeError): + continue + return batch + else: + return batch.to(device) diff --git a/utils/config.py b/utils/config.py index 06f8635..492a574 100644 --- a/utils/config.py +++ b/utils/config.py @@ -1,6 +1,9 @@ import ast +import configparser from pathlib import Path +from typing import Mapping, Dict +import torch from copy import deepcopy from abc import ABC @@ -9,8 +12,67 @@ from argparse import Namespace, ArgumentParser from collections import defaultdict from configparser import ConfigParser, DuplicateSectionError import hashlib +from pytorch_lightning import Trainer -from ml_lib.utils.tools import locate_and_import_class +from ml_lib.utils.loggers import Logger +from ml_lib.utils.tools import locate_and_import_class, auto_cast + + +# Argument Parser and default Values +# ============================================================================= +def parse_comandline_args_add_defaults(filepath, overrides=None): + + # Parse Command Line + parser = ArgumentParser() + parser.add_argument('--model_name', type=str) + parser.add_argument('--data_name', type=str) + + # Load Defaults from _parameters.ini file + config = configparser.ConfigParser() + config.read(str(filepath)) + + new_defaults = dict() + for key in ['project', 'train', 'data']: + defaults = config[key] + new_defaults.update({key: auto_cast(val) for key, val in defaults.items()}) + + if new_defaults['debug']: + new_defaults.update( + max_epochs=2, + max_steps=2 # The seems to be the new "fast_dev_run" + ) + + args, _ = parser.parse_known_args() + overrides = overrides or dict() + default_data = overrides.get('data_name', None) or new_defaults['data_name'] + default_model = overrides.get('model_name', None) or new_defaults['model_name'] + + data_name = args.__dict__.get('data_name', None) or default_data + model_name = args.__dict__.get('model_name', None) or default_model + + new_defaults.update({key: auto_cast(val) for key, val in config[model_name].items()}) + + found_data_class = locate_and_import_class(data_name, 'datasets') + found_model_class = locate_and_import_class(model_name, 'models') + + for module in [Logger, Trainer, found_data_class, found_model_class]: + parser = module.add_argparse_args(parser) + + args, _ = parser.parse_known_args(namespace=Namespace(**new_defaults)) + + args = vars(args) + args.update({key: auto_cast(val) for key, val in args.items()}) + args.update(gpus=[0] if torch.cuda.is_available() and not args['debug'] else None, + row_log_interval=1000, # TODO: Better Value / Setting + log_save_interval=10000, # TODO: Better Value / Setting + auto_lr_find=not args['debug'], + weights_summary='top', + check_val_every_n_epoch=1 if args['debug'] else args.get('check_val_every_n_epoch', 1) + ) + + if overrides is not None and isinstance(overrides, (Mapping, Dict)): + args.update(**overrides) + return args, found_data_class, found_model_class def is_jsonable(x): diff --git a/utils/equal_sampler.py b/utils/equal_sampler.py new file mode 100644 index 0000000..27b414e --- /dev/null +++ b/utils/equal_sampler.py @@ -0,0 +1,30 @@ + +import random +from typing import Iterator, Sequence + +from torch.utils.data import Sampler +from torch.utils.data.sampler import T_co + + +# noinspection PyMissingConstructor +class EqualSampler(Sampler): + + def __init__(self, idxs_per_class: Sequence[Sequence[float]], replacement: bool = True) -> None: + + self.replacement = replacement + self.idxs_per_class = idxs_per_class + self.len_largest_class = max([len(x) for x in self.idxs_per_class]) + + def __iter__(self) -> Iterator[T_co]: + return iter(random.choice(self.idxs_per_class[random.randint(0, len(self.idxs_per_class)-1)]) + for _ in range(len(self))) + + def __len__(self): + return self.len_largest_class * len(self.idxs_per_class) + + +if __name__ == '__main__': + es = EqualSampler([list(range(5)), list(range(5, 10)), list(range(10, 12))]) + for i in es: + print(i) + pass diff --git a/utils/logging.py b/utils/loggers.py similarity index 63% rename from utils/logging.py rename to utils/loggers.py index f9ef373..5d9118b 100644 --- a/utils/logging.py +++ b/utils/loggers.py @@ -1,5 +1,6 @@ -import inspect -from argparse import ArgumentParser +from copy import deepcopy + +import hashlib from pathlib import Path import os @@ -17,11 +18,34 @@ class Logger(LightningLoggerBase): @classmethod def from_argparse_args(cls, args, **kwargs): - return argparse_utils.from_argparse_args(cls, args, **kwargs) + cleaned_args = deepcopy(args.__dict__) + + # Clean Seed and other attributes + # TODO: Find a better way in cleaning this + for attr in ['seed', 'num_worker', 'debug', 'eval', 'owner', 'data_root', 'check_val_every_n_epoch', + 'reset', 'outpath', 'version', 'gpus', 'neptune_key', 'num_sanity_val_steps', 'tpu_cores', + 'progress_bar_refresh_rate', 'log_save_interval', 'row_log_interval']: + + try: + del cleaned_args[attr] + except KeyError: + pass + + kwargs.update(params=cleaned_args) + new_logger = argparse_utils.from_argparse_args(cls, args, **kwargs) + return new_logger @property - def name(self) -> str: - return self._name + def fingerprint(self): + h = hashlib.md5() + h.update(self._finger_print_string.encode()) + fingerprint = h.hexdigest() + return fingerprint + + @property + def name(self): + short_name = "".join(c for c in self.model_name if c.isupper()) + return f'{short_name}_{self.fingerprint}' media_dir = 'media' @@ -42,7 +66,12 @@ class Logger(LightningLoggerBase): @property def project_name(self): - return f"{self.owner}/{self.name.replace('_', '-')}" + return f"{self.owner}/{self.projeect_root.replace('_', '-')}" + + @property + def projeect_root(self): + root_path = Path(os.getcwd()).name if not self.debug else 'test' + return root_path @property def version(self): @@ -56,7 +85,7 @@ class Logger(LightningLoggerBase): def outpath(self): return Path(self.root_out) / self.model_name - def __init__(self, owner, neptune_key, model_name, project_name='', outpath='output', seed=69, debug=False): + def __init__(self, owner, neptune_key, model_name, outpath='output', seed=69, debug=False, params=None): """ params (dict|None): Optional. Parameters of the experiment. After experiment creation params are read-only. Parameters are displayed in the experiment’s Parameters section and each key-value pair can be @@ -71,51 +100,67 @@ class Logger(LightningLoggerBase): super(Logger, self).__init__() self.debug = debug - self._name = project_name or Path(os.getcwd()).name if not self.debug else 'test' self.owner = owner if not self.debug else 'testuser' self.neptune_key = neptune_key if not self.debug else 'XXX' self.root_out = outpath if not self.debug else 'debug_out' + + self.params = params + self.seed = seed self.model_name = model_name + if self.params: + _, fingerprint_tuple = zip(*sorted(self.params.items(), key=lambda tup: tup[0])) + self._finger_print_string = str(fingerprint_tuple) + else: + self._finger_print_string = str((self.owner, self.root_out, self.seed, self.model_name, self.debug)) + self.params.update(fingerprint=self.fingerprint) + self._csvlogger_kwargs = dict(save_dir=self.outpath, version=self.version, name=self.name) self._neptune_kwargs = dict(offline_mode=self.debug, + params=self.params, api_key=self.neptune_key, experiment_name=self.name, + # tags=?, project_name=self.project_name) try: self.neptunelogger = NeptuneLogger(**self._neptune_kwargs) except ProjectNotFound as e: - print(f'The project "{self.project_name}"') + print(f'The project "{self.project_name}" does not exist! Create it or check your spelling.') print(e) self.csvlogger = CSVLogger(**self._csvlogger_kwargs) + if self.params: + self.log_hyperparams(self.params) + + def close(self): + self.csvlogger.close() + self.neptunelogger.close() + + def set_fingerprint_string(self, fingerprint_str): + self._finger_print_string = fingerprint_str + + def log_text(self, name, text, **_): + # TODO Implement Offline variant. + self.neptunelogger.log_text(name, text) def log_hyperparams(self, params): self.neptunelogger.log_hyperparams(params) self.csvlogger.log_hyperparams(params) pass + def log_metric(self, metric_name, metric_value, step=None, **kwargs): + self.csvlogger.log_metrics(dict(metric_name=metric_value, **kwargs), step=step, **kwargs) + self.neptunelogger.log_metric(metric_name, metric_value, step=step, **kwargs) + pass + def log_metrics(self, metrics, step=None): self.neptunelogger.log_metrics(metrics, step=step) self.csvlogger.log_metrics(metrics, step=step) pass - def close(self): - self.csvlogger.close() - self.neptunelogger.close() - - def log_text(self, name, text, **_): - # TODO Implement Offline variant. - self.neptunelogger.log_text(name, text) - - def log_metric(self, metric_name, metric_value, **kwargs): - self.csvlogger.log_metrics(dict(metric_name=metric_value)) - self.neptunelogger.log_metric(metric_name, metric_value, **kwargs) - - def log_image(self, name, image, ext='png', **kwargs): - step = kwargs.get('step', None) - image_name = f'{step}_{name}' if step is not None else name + def log_image(self, name, image, ext='png', step=None, **kwargs): + image_name = f'{"0" * (4 - len(str(step)))}{step}_{name}' if step is not None else name image_path = self.log_dir / self.media_dir / f'{image_name}.{ext[1:] if ext.startswith(".") else ext}' (self.log_dir / self.media_dir).mkdir(parents=True, exist_ok=True) image.savefig(image_path, bbox_inches='tight', pad_inches=0) diff --git a/utils/tools.py b/utils/tools.py index 08e2c20..3119f0e 100644 --- a/utils/tools.py +++ b/utils/tools.py @@ -2,7 +2,7 @@ import importlib import inspect import pickle import shelve -from argparse import ArgumentParser +from argparse import ArgumentParser, ArgumentError from ast import literal_eval from pathlib import Path, PurePath from typing import Union @@ -70,14 +70,17 @@ def add_argparse_args(cls, parent_parser): full_arg_spec = inspect.getfullargspec(cls.__init__) n_non_defaults = len(full_arg_spec.args) - (len(full_arg_spec.defaults) if full_arg_spec.defaults else 0) for idx, argument in enumerate(full_arg_spec.args): - if argument == 'self': + try: + if argument == 'self': + continue + if idx < n_non_defaults: + parser.add_argument(f'--{argument}', type=int) + else: + argument_type = type(argument) + parser.add_argument(f'--{argument}', + type=argument_type, + default=full_arg_spec.defaults[idx - n_non_defaults] + ) + except ArgumentError: continue - if idx < n_non_defaults: - parser.add_argument(f'--{argument}', type=int) - else: - argument_type = type(argument) - parser.add_argument(f'--{argument}', - type=argument_type, - default=full_arg_spec.defaults[idx - n_non_defaults] - ) return parser