Merge branch 'main' into dataset-rework

Author: c-salomonsen

main.py

@@ -73,7 +73,7 @@ def main():
         "--dataset",
         type=str,
         default="svhn",
-        choices=["svhn", "usps_0-6", "uspsh5_7_9"],
+        choices=["svhn", "usps_0-6", "uspsh5_7_9", "mnist_0-3"],
         help="Which dataset to train the model on.",
     )
 
@@ -149,16 +149,15 @@ def main():
         transform=augmentations,
     )
 
-    # Find number of channels in the dataset
-    if len(traindata[0][0].shape) == 2:
-        channels = 1
-    else:
-        channels = traindata[0][0].shape[0]
+    # Find the shape of the data, if is 2D, add a channel dimension
+    data_shape = traindata[0][0].shape
+    if len(data_shape) == 2:
+        data_shape = (1, *data_shape)
 
     # load model
     model = load_model(
         args.modelname,
-        in_channels=channels,
+        image_shape=data_shape,
         num_classes=traindata.num_classes,
     )
     model.to(device)

tests/test_metrics.py

@@ -1,4 +1,4 @@
-from utils.metrics import Recall, F1Score
+from utils.metrics import F1Score, Recall
 
 
 def test_recall():

tests/test_models.py

@@ -4,11 +4,14 @@
 from utils.models import ChristianModel
 
 
-@pytest.mark.parametrize("in_channels, num_classes", [(1, 6), (3, 6)])
-def test_christian_model(in_channels, num_classes):
-    n, c, h, w = 5, in_channels, 16, 16
+@pytest.mark.parametrize(
+    "image_shape, num_classes",
+    [((1, 16, 16), 6), ((3, 16, 16), 6)],
+)
+def test_christian_model(image_shape, num_classes):
+    n, c, h, w = 5, *image_shape
 
-    model = ChristianModel(c, num_classes)
+    model = ChristianModel(image_shape, num_classes)
 
     x = torch.randn(n, c, h, w)
     y = model(x)

utils/dataloaders/__init__.py

@@ -1,4 +1,5 @@
-__all__ = ["USPSDataset0_6", "USPSH5_Digit_7_9_Dataset"]
+__all__ = ["USPSDataset0_6", "USPSH5_Digit_7_9_Dataset", "MNISTDataset0_3"]
 
+from .mnist_0_3 import MNISTDataset0_3
 from .usps_0_6 import USPSDataset0_6
-from .uspsh5_7_9 import USPSH5_Digit_7_9_Dataset
+from .uspsh5_7_9 import USPSH5_Digit_7_9_Dataset

utils/dataloaders/mnist_0_3.py

@@ -0,0 +1,151 @@
+import gzip
+import os
+import urllib.request
+from pathlib import Path
+
+import numpy as np
+from torch.utils.data import Dataset
+
+
+class MNISTDataset0_3(Dataset):
+    """
+    A custom dataset class for loading MNIST data, specifically for digits 0 through 3.
+    Parameters
+    ----------
+    data_path : Path
+        The root directory where the MNIST data is stored or will be downloaded.
+    train : bool, optional
+        If True, loads the training data, otherwise loads the test data. Default is False.
+    transform : callable, optional
+        A function/transform that takes in an image and returns a transformed version. Default is None.
+    download : bool, optional
+        If True, downloads the dataset if it is not already present in the specified data_path. Default is False.
+    Attributes
+    ----------
+    data_path : Path
+        The root directory where the MNIST data is stored.
+    mnist_path : Path
+        The directory where the MNIST data files are stored.
+    train : bool
+        Indicates whether the training data or test data is being used.
+    transform : callable
+        A function/transform that takes in an image and returns a transformed version.
+    download : bool
+        Indicates whether the dataset should be downloaded if not present.
+    images_path : Path
+        The path to the image file (training or test) based on the `train` flag.
+    labels_path : Path
+        The path to the label file (training or test) based on the `train` flag.
+    idx : numpy.ndarray
+        Indices of the labels that are less than 4.
+    length : int
+        The number of samples in the dataset.
+    Methods
+    -------
+    _parse_labels(train)
+        Parses the labels from the label file.
+    _chech_is_downloaded()
+        Checks if the dataset is already downloaded.
+    _download_data()
+        Downloads and extracts the MNIST dataset.
+    __len__()
+        Returns the number of samples in the dataset.
+    __getitem__(index)
+        Returns the image and label at the specified index.
+    """
+
+    def __init__(
+        self,
+        data_path: Path,
+        train: bool = False,
+        transform=None,
+        download: bool = False,
+    ):
+        super().__init__()
+
+        self.data_path = data_path
+        self.mnist_path = self.data_path / "MNIST"
+        self.train = train
+        self.transform = transform
+        self.download = download
+        self.num_classes = 4
+
+        if not self.download and not self._chech_is_downloaded():
+            raise ValueError(
+                "Data not found. Set --download-data=True to download the data."
+            )
+        if self.download and not self._chech_is_downloaded():
+            self._download_data()
+
+        self.images_path = self.mnist_path / (
+            "train-images-idx3-ubyte" if train else "t10k-images-idx3-ubyte"
+        )
+        self.labels_path = self.mnist_path / (
+            "train-labels-idx1-ubyte" if train else "t10k-labels-idx1-ubyte"
+        )
+
+        labels = self._parse_labels(train=self.train)
+
+        self.idx = np.where(labels < 4)[0]
+
+        self.length = len(self.idx)
+
+    def _parse_labels(self, train):
+        with open(self.labels_path, "rb") as f:
+            data = np.frombuffer(f.read(), dtype=np.uint8, offset=8)
+        return data
+
+    def _chech_is_downloaded(self):
+        if self.mnist_path.exists():
+            required_files = [
+                "train-images-idx3-ubyte",
+                "train-labels-idx1-ubyte",
+                "t10k-images-idx3-ubyte",
+                "t10k-labels-idx1-ubyte",
+            ]
+            if all([(self.mnist_path / file).exists() for file in required_files]):
+                print("MNIST Dataset already downloaded.")
+                return True
+            else:
+                return False
+        else:
+            self.mnist_path.mkdir(parents=True, exist_ok=True)
+            return False
+
+    def _download_data(self):
+        urls = {
+            "train_images": "https://storage.googleapis.com/cvdf-datasets/mnist/train-images-idx3-ubyte.gz",
+            "train_labels": "https://storage.googleapis.com/cvdf-datasets/mnist/train-labels-idx1-ubyte.gz",
+            "test_images": "https://storage.googleapis.com/cvdf-datasets/mnist/t10k-images-idx3-ubyte.gz",
+            "test_labels": "https://storage.googleapis.com/cvdf-datasets/mnist/t10k-labels-idx1-ubyte.gz",
+        }
+
+        for name, url in urls.items():
+            file_path = os.path.join(self.mnist_path, url.split("/")[-1])
+            if not os.path.exists(file_path.replace(".gz", "")):  # Avoid re-downloading
+                urllib.request.urlretrieve(url, file_path)
+                with gzip.open(file_path, "rb") as f_in:
+                    with open(file_path.replace(".gz", ""), "wb") as f_out:
+                        f_out.write(f_in.read())
+                os.remove(file_path)  # Remove compressed file
+
+    def __len__(self):
+        return self.length
+
+    def __getitem__(self, index):
+        with open(self.labels_path, "rb") as f:
+            f.seek(8 + index)  # Jump to the label position
+            label = int.from_bytes(f.read(1), byteorder="big")  # Read 1 byte for label
+
+        with open(self.images_path, "rb") as f:
+            f.seek(16 + index * 28 * 28)  # Jump to image position
+            image = np.frombuffer(f.read(28 * 28), dtype=np.uint8).reshape(
+                28, 28
+            )  # Read image data
+
+        image = np.expand_dims(image, axis=0)  # Add channel dimension
+
+        if self.transform:
+            image = self.transform(image)
+
+        return image, label

utils/load_data.py

@@ -1,13 +1,16 @@
 from torch.utils.data import Dataset
 
-from .dataloaders import USPSDataset0_6, USPSH5_Digit_7_9_Dataset
+from .dataloaders import (MNISTDataset0_3, USPSDataset0_6,
+                          USPSH5_Digit_7_9_Dataset)
 
 
 def load_data(dataset: str, *args, **kwargs) -> Dataset:
     match dataset.lower():
         case "usps_0-6":
             return USPSDataset0_6(*args, **kwargs)
+        case "mnist_0-3":
+            return MNISTDataset0_3(*args, **kwargs)
         case "usps_7-9":
-            return  USPSH5_Digit_7_9_Dataset(*args, **kwargs)
+            return USPSH5_Digit_7_9_Dataset(*args, **kwargs)
         case _:
             raise ValueError(f"Dataset: {dataset} not implemented.")

utils/load_model.py

@@ -1,6 +1,6 @@
 import torch.nn as nn
 
-from .models import ChristianModel, MagnusModel, SolveigModel
+from .models import ChristianModel, JanModel, MagnusModel, SolveigModel
 
 
 def load_model(modelname: str, *args, **kwargs) -> nn.Module:
@@ -9,6 +9,8 @@ def load_model(modelname: str, *args, **kwargs) -> nn.Module:
             return MagnusModel(*args, **kwargs)
         case "christianmodel":
             return ChristianModel(*args, **kwargs)
+        case "janmodel":
+            return JanModel(*args, **kwargs)
         case "solveigmodel":
             return SolveigModel(*args, **kwargs)
         case _:

utils/metrics/F1.py

@@ -84,4 +84,3 @@ def compute(self):
         )
 
         return f1_score
-

utils/models/__init__.py

@@ -1,5 +1,6 @@
-__all__ = ["MagnusModel", "ChristianModel", "SolveigModel"]
+__all__ = ["MagnusModel", "ChristianModel", "JanModel", "SolveigModel"]
 
 from .christian_model import ChristianModel
+from .jan_model import JanModel
 from .magnus_model import MagnusModel
 from .solveig_model import SolveigModel

utils/models/christian_model.py

@@ -27,8 +27,8 @@ class ChristianModel(nn.Module):
 
     Args
     ----
-    in_channels : int
-        Number of input channels.
+    image_shape : tuple(int, int, int)
+        Shape of the input image (C, H, W).
     num_classes : int
         Number of classes in the dataset.
 
@@ -49,10 +49,12 @@ class ChristianModel(nn.Module):
     FC Output Shape: (5, num_classes)
     """
 
-    def __init__(self, in_channels, num_classes):
+    def __init__(self, image_shape, num_classes):
         super().__init__()
 
-        self.cnn1 = CNNBlock(in_channels, 50)
+        C, *_ = image_shape
+
+        self.cnn1 = CNNBlock(C, 50)
         self.cnn2 = CNNBlock(50, 100)
 
         self.fc1 = nn.Linear(100 * 4 * 4, num_classes)