Merge pull request #171 from BerndDoser/rot-loss

Alternative rotational invariance and convolution neural networks

.gitignore

@@ -2,10 +2,11 @@ __pycache__
 .venv*/
 *.ckpt
 *.ncu-rep
+*.sarif
 config.yaml
 dist/
+docs/_build/
+docs/html/
 HiPSter/
 lightning_logs/
 wandb/
-docs/_build/
-docs/html/

experiments/pokemon.yaml

@@ -0,0 +1,66 @@
+seed_everything: 42
+
+model:
+  class_path: spherinator.models.RotationalVariationalAutoencoderPower
+  init_args:
+    encoder: 
+      class_path: spherinator.models.ConvolutionalEncoder
+    decoder: 
+      class_path: spherinator.models.ConvolutionalDecoder
+    h_dim: 256
+    z_dim: 3
+    image_size: 224
+    rotations: 1
+    beta: 1.0e-3
+
+data:
+  class_path: spherinator.data.ImagesDataModule
+  init_args:
+    data_directory: /local_data/doserbd/data/pokemon
+    extensions: ['jpg']
+    image_size: 224
+    batch_size: 32
+    shuffle: True
+    num_workers: 16
+
+optimizer:
+  class_path: torch.optim.Adam
+  init_args:
+    lr: 1.e-3
+
+lr_scheduler:
+  class_path: lightning.pytorch.cli.ReduceLROnPlateau
+  init_args:
+    mode: min
+    factor: 0.1
+    patience: 5
+    cooldown: 5
+    min_lr: 1.e-6
+    monitor: train_loss
+    verbose: True
+
+trainer:
+  max_epochs: -1
+  accelerator: gpu
+  devices: [3]
+  precision: 32
+  callbacks:
+    - class_path: spherinator.callbacks.LogReconstructionCallback
+      init_args:
+        num_samples: 6
+#   - class_path: lightning.pytorch.callbacks.ModelCheckpoint
+#     init_args:
+#       monitor: train_loss
+#       filename: "{epoch}-{train_loss:.2f}"
+#       save_top_k: 3
+#       mode: min
+#       every_n_epochs: 1
+  logger:
+    class_path: lightning.pytorch.loggers.WandbLogger
+    init_args:
+      project: spherinator
+      log_model: True
+      entity: ain-space
+      tags:
+        - rot-loss
+        - pokemon

src/spherinator/data/__init__.py

@@ -7,6 +7,8 @@
 from .illustris_sdss_data_module import IllustrisSdssDataModule
 from .illustris_sdss_dataset import IllustrisSdssDataset
 from .illustris_sdss_dataset_with_metadata import IllustrisSdssDatasetWithMetadata
+from .images_data_module import ImagesDataModule
+from .images_dataset import ImagesDataset
 from .shapes_data_module import ShapesDataModule
 from .shapes_dataset import ShapesDataset
 from .spherinator_data_module import SpherinatorDataModule
@@ -18,6 +20,8 @@
     "IllustrisSdssDataModule",
     "IllustrisSdssDataset",
     "IllustrisSdssDatasetWithMetadata",
+    "ImagesDataModule",
+    "ImagesDataset",
     "ShapesDataModule",
     "ShapesDataset",
     "SpherinatorDataModule",

src/spherinator/data/galaxy_zoo_data_module.py

@@ -65,7 +65,7 @@ def setup(self, stage: str):
         Args:
             stage (str): Defines for which stage the data is needed.
         """
-        if not stage in ["fit", "processing", "images", "thumbnail_images"]:
+        if stage not in ["fit", "processing", "images", "thumbnail_images"]:
             raise ValueError(f"Stage {stage} not supported.")
 
         if stage == "fit" and self.data_train is None:

src/spherinator/data/illustris_sdss_data_module.py

@@ -93,7 +93,7 @@ def setup(self, stage: str):
         Args:
             stage (str): Defines for which stage the data is needed.
         """
-        if not stage in ["fit", "processing", "images", "thumbnail_images"]:
+        if stage not in ["fit", "processing", "images", "thumbnail_images"]:
             raise ValueError(f"Stage {stage} not supported.")
 
         if stage == "fit" and self.data_train is None:

src/spherinator/data/images_data_module.py

@@ -0,0 +1,85 @@
+import torch
+import torchvision.transforms.v2 as transforms
+from lightning.pytorch import LightningDataModule
+from torch.utils.data import DataLoader
+
+from spherinator.data.images_dataset import ImagesDataset
+
+
+class ImagesDataModule(LightningDataModule):
+    """Defines access to the ImagesDataset."""
+
+    def __init__(
+        self,
+        data_directory: str,
+        extensions: list[str] = ["jpg"],
+        shuffle: bool = True,
+        image_size: int = 64,
+        batch_size: int = 32,
+        num_workers: int = 1,
+    ):
+        """Initializes the data loader
+
+        Args:
+            data_directory (str): The data directory
+            shuffle (bool, optional): Wether or not to shuffle whe reading. Defaults to True.
+            image_size (int, optional): The size of the images. Defaults to 64.
+            batch_size (int, optional): The batch size for training. Defaults to 32.
+            num_workers (int, optional): How many worker to use for loading. Defaults to 1.
+            download (bool, optional): Wether or not to download the data. Defaults to False.
+        """
+        super().__init__()
+
+        self.data_directory = data_directory
+        self.extensions = extensions
+        self.shuffle = shuffle
+        self.image_size = image_size
+        self.batch_size = batch_size
+        self.num_workers = num_workers
+
+        self.data_train = None
+        self.dataloader_train = None
+
+        self.transform_train = transforms.Compose(
+            [
+                transforms.Resize((self.image_size, self.image_size), antialias=True),
+                transforms.Lambda(  # Normalize
+                    lambda x: (x - torch.min(x)) / (torch.max(x) - torch.min(x))
+                ),
+            ]
+        )
+        self.transform_processing = self.transform_train
+        self.transform_images = self.transform_train
+        self.transform_thumbnail_images = transforms.Compose(
+            [
+                self.transform_train,
+                transforms.Resize((100, 100), antialias=True),
+            ]
+        )
+
+    def setup(self, stage: str):
+        """Sets up the data set and data loaders.
+
+        Args:
+            stage (str): Defines for which stage the data is needed.
+                         For the moment just fitting is supported.
+        """
+
+        if stage == "fit" and self.data_train is None:
+            self.data_train = ImagesDataset(
+                data_directory=self.data_directory,
+                extensions=self.extensions,
+                transform=self.transform_train,
+            )
+            self.dataloader_train = DataLoader(
+                self.data_train,
+                batch_size=self.batch_size,
+                shuffle=self.shuffle,
+                num_workers=self.num_workers,
+            )
+        else:
+            raise ValueError(f"Stage {stage} not supported.")
+
+    def train_dataloader(self):
+        """Gets the data loader for training."""
+        return self.dataloader_train

src/spherinator/data/images_dataset.py

@@ -0,0 +1,67 @@
+""" Create dataset with all image files in a directory.
+"""
+
+import os
+from pathlib import Path
+
+import skimage.io as io
+import torch
+from torch.utils.data import Dataset
+
+
+def get_all_filenames(data_directory: str, extensions: list[str]):
+    result = []
+    for dirpath, dirnames, filenames in os.walk(data_directory):
+        for filename in filenames:
+            if Path(filename).suffix[1:] in extensions:
+                result.append(os.path.join(dirpath, filename))
+        for dirname in dirnames:
+            result.extend(get_all_filenames(dirname, extensions))
+    return result
+
+
+class ImagesDataset(Dataset):
+    """Create dataset with all image files in a directory."""
+
+    def __init__(
+        self,
+        data_directory: str,
+        extensions: list[str] = ["jpg"],
+        transform=None,
+    ):
+        """Initializes the data set.
+
+        Args:
+            data_directory (str): The data directory.
+            transform (torchvision.transforms, optional): A single or a set of
+                transformations to modify the images. Defaults to None.
+        """
+
+        self.transform = transform
+        self.filenames = sorted(get_all_filenames(data_directory, extensions))
+
+    def __len__(self) -> int:
+        """Return the number of items in the dataset.
+
+        Returns:
+            int: Number of items in dataset.
+        """
+        return len(self.filenames)
+
+    def __getitem__(self, index: int) -> torch.Tensor:
+        """Retrieves the item/items with the given indices from the dataset.
+
+        Args:
+            index: The index of the item to retrieve.
+
+        Returns:
+            data: Data of the item/items with the given indices.
+
+        """
+        # Swap axis 0 and 2 to bring the color channel to the front
+        data = io.imread(self.filenames[index])
+        data = data.swapaxes(0, 2)
+        data = torch.Tensor(data)
+        if self.transform:
+            data = self.transform(data)
+        return data

src/spherinator/data/shapes_data_module.py

@@ -76,7 +76,7 @@ def setup(self, stage: str):
             stage (str): Defines for which stage the data is needed.
                          For the moment just fitting is supported.
         """
-        if not stage in ["fit", "processing", "images", "thumbnail_images"]:
+        if stage not in ["fit", "processing", "images", "thumbnail_images"]:
             raise ValueError(f"Stage {stage} not supported.")
 
         if stage == "fit" and self.data_train is None:

src/spherinator/models/__init__.py

@@ -13,9 +13,15 @@
 """
 
 from .convolutional_decoder import ConvolutionalDecoder
+from .convolutional_decoder_2 import ConvolutionalDecoder2
 from .convolutional_decoder_224 import ConvolutionalDecoder224
 from .convolutional_decoder_256 import ConvolutionalDecoder256
 from .convolutional_encoder import ConvolutionalEncoder
+from .convolutional_encoder_2 import ConvolutionalEncoder2
+from .rotational2_autoencoder import Rotational2Autoencoder
+from .rotational2_variational_autoencoder_power import (
+    Rotational2VariationalAutoencoderPower,
+)
 from .rotational_autoencoder import RotationalAutoencoder
 from .rotational_variational_autoencoder_power import (
     RotationalVariationalAutoencoderPower,
@@ -24,9 +30,13 @@
 
 __all__ = [
     "ConvolutionalDecoder",
+    "ConvolutionalDecoder2",
     "ConvolutionalDecoder224",
     "ConvolutionalDecoder256",
     "ConvolutionalEncoder",
+    "ConvolutionalEncoder2",
+    "Rotational2Autoencoder",
+    "Rotational2VariationalAutoencoderPower",
     "RotationalAutoencoder",
     "RotationalVariationalAutoencoderPower",
     "SpherinatorModule",

src/spherinator/models/convolutional_decoder.py

@@ -5,10 +5,10 @@
 
 
 class ConvolutionalDecoder(pl.LightningModule):
-    def __init__(self, h_dim: int = 256):
+    def __init__(self, latent_dim: int):
         super().__init__()
 
-        self.fc = nn.Linear(h_dim, 256 * 4 * 4)
+        self.fc = nn.Linear(latent_dim, 256 * 4 * 4)
         self.deconv1 = nn.ConvTranspose2d(
             in_channels=256, out_channels=128, kernel_size=(4, 4), stride=2, padding=1
         )  # 8x8

src/spherinator/models/convolutional_decoder_2.py

@@ -0,0 +1,47 @@
+import torch
+import torch.nn as nn
+
+
+class ConvolutionalDecoder2(nn.Module):
+    def __init__(self, latent_dim: int):
+        super().__init__()
+
+        self.dec1 = nn.Sequential(
+            nn.Linear(latent_dim, 1024 * 4 * 4),
+            nn.Unflatten(1, (1024, 4, 4)),
+            nn.BatchNorm2d(1024),
+            nn.ReLU(),
+        )  # 512 x 8 x 8
+        self.dec2 = nn.Sequential(
+            nn.ConvTranspose2d(1024, 512, 4, stride=2, padding=1),
+            nn.BatchNorm2d(512),
+            nn.ReLU(),
+        )  # 512 x 8 x 8
+        self.dec3 = nn.Sequential(
+            nn.ConvTranspose2d(512, 512, 4, stride=2, padding=1),
+            nn.BatchNorm2d(512),
+            nn.ReLU(),
+        )  # 512 x 16 x 16
+        self.dec4 = nn.Sequential(
+            nn.ConvTranspose2d(512, 256, 4, stride=2, padding=1),
+            nn.BatchNorm2d(256),
+            nn.ReLU(),
+        )  # 256 x 32 x 32
+        self.dec5 = nn.Sequential(
+            nn.ConvTranspose2d(256, 128, 4, stride=2, padding=1),
+            nn.BatchNorm2d(128),
+            nn.ReLU(),
+        )  # 128 x 64 x 64
+        self.dec6 = nn.Sequential(
+            nn.ConvTranspose2d(128, 3, 4, stride=2, padding=1),
+            nn.BatchNorm2d(3),
+        )  # 3 x 128 x 128
+
+    def forward(self, x: torch.tensor) -> torch.tensor:
+        x = self.dec1(x)
+        x = self.dec2(x)
+        x = self.dec3(x)
+        x = self.dec4(x)
+        x = self.dec5(x)
+        x = self.dec6(x)
+        return x

src/spherinator/models/convolutional_decoder_224.py

@@ -5,15 +5,15 @@
 
 
 class ConvolutionalDecoder224(pl.LightningModule):
-    def __init__(self, h_dim: int = 256):
+    def __init__(self, latent_dim: int):
         """Convolutional decoder for 224x224 images.
         Input: h_dim
         Output: 3x224x224
         H_out = (H_in - 1) * stride[0] - 2 * padding[0] + dilation[0] * (kernel_size[0] - 1) + output_padding[0] + 1
         """
         super().__init__()
 
-        self.fc = nn.Linear(h_dim, 256 * 4 * 4)
+        self.fc = nn.Linear(latent_dim, 256 * 4 * 4)
         self.deconv1 = nn.ConvTranspose2d(
             in_channels=256, out_channels=128, kernel_size=(3, 3), stride=2, padding=1
         )  # 7 = 6 - 2 + 2 + 1