Upload mri_autoencoder.ipynb

mri_autoencoder.ipynb

@@ -0,0 +1,1484 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Generating Train-Val Split from Dataset"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import shutil\n",
+    "import random\n",
+    "import multiprocessing\n",
+    "from copy import deepcopy\n",
+    "\n",
+    "def recursive_copy_dicom(src_folder, dest_folder, file_counter):\n",
+    "    \"\"\"\n",
+    "    Recursively finds and copies DICOM files from the source to the destination folder, renaming them sequentially.\n",
+    "    \n",
+    "    :param src_folder: The source folder containing DICOM files (including subdirectories).\n",
+    "    :param dest_folder: The destination folder where the files will be copied and renamed.\n",
+    "    :param file_counter: The sequential counter for renaming files.\n",
+    "    :return: List of renamed files for further splitting.\n",
+    "    \"\"\"\n",
+    "    renamed_files = []\n",
+    "\n",
+    "    for root, dirs, files in os.walk(src_folder):\n",
+    "        for dicom_file in files:\n",
+    "            if dicom_file.lower().endswith('.dcm'):\n",
+    "                # Get full path of the source file\n",
+    "                src_file_path = os.path.join(root, dicom_file)\n",
+    "                \n",
+    "                # Create the new file path in the destination folder\n",
+    "                dest_file_path = os.path.join(dest_folder, f\"{file_counter}.dcm\")\n",
+    "                \n",
+    "                # Copy and rename the file\n",
+    "                shutil.copy(src_file_path, dest_file_path)\n",
+    "                \n",
+    "                # Append the renamed file to the list\n",
+    "                renamed_files.append(f\"{file_counter}.dcm\")\n",
+    "                \n",
+    "                # Increment the file counter for the next file\n",
+    "                file_counter += 1\n",
+    "\n",
+    "    return renamed_files\n",
+    "\n",
+    "def split_and_transfer_files(file_list, dest_folder, split_factor):\n",
+    "    \"\"\"\n",
+    "    Splits the list of renamed files into train and val sets and moves them into the appropriate folders.\n",
+    "    \n",
+    "    :param file_list: List of renamed DICOM files.\n",
+    "    :param dest_folder: Destination folder where train and val subfolders will be created.\n",
+    "    :param split_factor: The ratio of files to go into the train subfolder.\n",
+    "    \"\"\"\n",
+    "    # Ensure the destination folder and subfolders exist\n",
+    "    train_folder = os.path.join(dest_folder, 'train')\n",
+    "    val_folder = os.path.join(dest_folder, 'val')\n",
+    "    \n",
+    "    if not os.path.exists(train_folder):\n",
+    "        os.makedirs(train_folder)\n",
+    "    \n",
+    "    if not os.path.exists(val_folder):\n",
+    "        os.makedirs(val_folder)\n",
+    "\n",
+    "    # Shuffle the files for randomness\n",
+    "    random.shuffle(file_list)\n",
+    "\n",
+    "    # Calculate the number of files for the train and validation sets\n",
+    "    split_index = int(len(file_list) * split_factor)\n",
+    "    \n",
+    "    # Split the files into train and val sets\n",
+    "    train_files = file_list[:split_index]\n",
+    "    val_files = file_list[split_index:]\n",
+    "\n",
+    "    # Move the files to the respective folders\n",
+    "    for file in train_files:\n",
+    "        src_file = os.path.join(dest_folder, file)\n",
+    "        dest_file = os.path.join(train_folder, file)\n",
+    "        shutil.move(src_file, dest_file)\n",
+    "        print(f\"Moved {file} to train folder\")\n",
+    "    \n",
+    "    for file in val_files:\n",
+    "        src_file = os.path.join(dest_folder, file)\n",
+    "        dest_file = os.path.join(val_folder, file)\n",
+    "        shutil.move(src_file, dest_file)\n",
+    "        print(f\"Moved {file} to val folder\")\n",
+    "\n",
+    "def process_dicom_files(src_folder, dest_folder, split_factor):\n",
+    "    \"\"\"\n",
+    "    Recursively finds, renames, copies DICOM files, and splits them into train and val sets.\n",
+    "    \n",
+    "    :param src_folder: The source folder containing DICOM files (including subdirectories).\n",
+    "    :param dest_folder: The destination folder where the renamed files and the train/val split will be created.\n",
+    "    :param split_factor: The ratio of files to go into the train subfolder.\n",
+    "    \"\"\"\n",
+    "    # Ensure the destination folder exists\n",
+    "    if not os.path.exists(dest_folder):\n",
+    "        os.makedirs(dest_folder)\n",
+    "\n",
+    "    # Initialize file counter\n",
+    "    file_counter = 1\n",
+    "\n",
+    "    # Recursively copy DICOM files and rename them\n",
+    "    renamed_files = recursive_copy_dicom(src_folder, dest_folder, file_counter)\n",
+    "\n",
+    "    # Step 2: Split the renamed files into train and val sets\n",
+    "    split_and_transfer_files(renamed_files, dest_folder, split_factor)\n",
+    "\n",
+    "# Example usage:\n",
+    "src_folder = r\"F:\\TCIA\"  # Replace with your source folder path\n",
+    "dest_folder = r\"F:\\TCIA_Split\"  # Destination folder for the renamed files and train/val split\n",
+    "split_factor = 0.9  # 90% of files will go to 'train', 10% will go to 'val'\n",
+    "\n",
+    "# Perform the entire process\n",
+    "process_dicom_files(src_folder, dest_folder, split_factor)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Basic U-Net"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import torch\n",
+    "import torch.nn as nn\n",
+    "import torch.nn.functional as F\n",
+    "import pydicom\n",
+    "import numpy as np\n",
+    "from torch.utils.data import Dataset, DataLoader\n",
+    "import os\n",
+    "from torch.utils.checkpoint import checkpoint\n",
+    "from tqdm import tqdm  # Import tqdm for progress bar\n",
+    "\n",
+    "device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')\n",
+    "\n",
+    "class MedicalImageDataset(Dataset):\n",
+    "    def __init__(self, dicom_dir):\n",
+    "        self.dicom_files = [os.path.join(dicom_dir, f) for f in os.listdir(dicom_dir) if f.endswith('.dcm')]\n",
+    "    \n",
+    "    def __len__(self):\n",
+    "        return len(self.dicom_files)\n",
+    "    \n",
+    "    def __getitem__(self, idx):\n",
+    "        # Read DICOM file and normalize\n",
+    "        dcm = pydicom.dcmread(self.dicom_files[idx])\n",
+    "        image = dcm.pixel_array.astype(float)\n",
+    "        image = (image - image.min()) / (image.max() - image.min())\n",
+    "        \n",
+    "        # Convert to tensor\n",
+    "        image_tensor = torch.from_numpy(image).float().unsqueeze(0)\n",
+    "        return image_tensor, image_tensor\n",
+    "\n",
+    "class UNetBlock(nn.Module):\n",
+    "    def __init__(self, in_channels, out_channels):\n",
+    "        super().__init__()\n",
+    "        self.conv1 = nn.Conv2d(in_channels, out_channels, 3, padding=1)\n",
+    "        self.bn1 = nn.BatchNorm2d(out_channels)\n",
+    "        self.conv2 = nn.Conv2d(out_channels, out_channels, 3, padding=1)\n",
+    "        self.bn2 = nn.BatchNorm2d(out_channels)\n",
+    "    \n",
+    "    def forward(self, x):\n",
+    "        x = F.relu(self.bn1(self.conv1(x)))\n",
+    "        x = F.relu(self.bn2(self.conv2(x)))\n",
+    "        return x\n",
+    "\n",
+    "class UNet(nn.Module):\n",
+    "    def __init__(self, in_channels=1, out_channels=1):\n",
+    "        super().__init__()\n",
+    "        # Encoder\n",
+    "        self.enc1 = UNetBlock(in_channels, 64)\n",
+    "        self.enc2 = UNetBlock(64, 128)\n",
+    "        self.enc3 = UNetBlock(128, 256)\n",
+    "        \n",
+    "        # Decoder\n",
+    "        self.dec3 = UNetBlock(256 + 128, 128)  # Adjust for concatenation with skip connection\n",
+    "        self.dec2 = UNetBlock(128 + 64, 64)    # Adjust for concatenation with skip connection\n",
+    "        self.dec1 = UNetBlock(64, out_channels)\n",
+    "        \n",
+    "        # Pooling and upsampling\n",
+    "        self.pool = nn.MaxPool2d(2, 2)\n",
+    "        self.upsample = nn.Upsample(scale_factor=2, mode='bilinear', align_corners=True)\n",
+    "    \n",
+    "    def forward(self, x):\n",
+    "        # Encoder path\n",
+    "        e1 = checkpoint(self.enc1, x)\n",
+    "        e2 = checkpoint(self.enc2, self.pool(e1))\n",
+    "        e3 = checkpoint(self.enc3, self.pool(e2))\n",
+    "        \n",
+    "        # Decoder path with skip connections\n",
+    "        d3 = self.upsample(e3)\n",
+    "        d3 = torch.cat([d3, e2], dim=1)  # Concatenate along channels\n",
+    "        d3 = checkpoint(self.dec3, d3)\n",
+    "        \n",
+    "        d2 = self.upsample(d3)\n",
+    "        d2 = torch.cat([d2, e1], dim=1)  # Concatenate along channels\n",
+    "        d2 = checkpoint(self.dec2, d2)\n",
+    "        \n",
+    "        d1 = self.dec1(d2)  # No checkpointing for final output layer\n",
+    "        \n",
+    "        return d1\n",
+    "\n",
+    "def calculate_loss(model, dataloader, criterion):\n",
+    "    model.eval()\n",
+    "    total_loss = 0\n",
+    "    with torch.no_grad():\n",
+    "        for images, targets in dataloader:\n",
+    "            images, targets = images.to(device), targets.to(device)\n",
+    "            outputs = model(images)\n",
+    "            loss = criterion(outputs, targets)\n",
+    "            total_loss += loss.item()\n",
+    "    return total_loss / len(dataloader)\n",
+    "\n",
+    "def calculate_psnr(output, target, max_pixel=1.0):\n",
+    "    # Ensure the values are in the correct range\n",
+    "    mse = F.mse_loss(output, target)\n",
+    "    psnr = 20 * torch.log10(max_pixel / torch.sqrt(mse))\n",
+    "    return psnr.item()\n",
+    "\n",
+    "def calculate_loss_and_psnr(model, dataloader, criterion):\n",
+    "    model.eval()\n",
+    "    total_loss = 0\n",
+    "    total_psnr = 0\n",
+    "    num_batches = len(dataloader)\n",
+    "    \n",
+    "    with torch.no_grad():\n",
+    "        for images, targets in dataloader:\n",
+    "            images, targets = images.to(device), targets.to(device)\n",
+    "            outputs = model(images)\n",
+    "            \n",
+    "            # Calculate MSE loss\n",
+    "            loss = criterion(outputs, targets)\n",
+    "            total_loss += loss.item()\n",
+    "            \n",
+    "            # Calculate PSNR\n",
+    "            psnr = calculate_psnr(outputs, targets)\n",
+    "            total_psnr += psnr\n",
+    "    \n",
+    "    avg_loss = total_loss / num_batches\n",
+    "    avg_psnr = total_psnr / num_batches\n",
+    "    \n",
+    "    return avg_loss, avg_psnr\n",
+    "\n",
+    "best_val_loss = float('inf')\n",
+    "best_model_path = 'best_model.pth'\n",
+    "\n",
+    "def train_unet(dicom_dir, val_dicom_dir, epochs=50, batch_size=4, grad_accumulation_steps=2):\n",
+    "    # Dataset and DataLoader\n",
+    "    dataset = MedicalImageDataset(dicom_dir)\n",
+    "    train_dataloader = DataLoader(dataset, batch_size=batch_size, shuffle=True)\n",
+    "    val_dataset = MedicalImageDataset(val_dicom_dir)\n",
+    "    val_dataloader = DataLoader(val_dataset, batch_size=batch_size, shuffle=False)\n",
+    "    \n",
+    "    # Model, Loss, Optimizer\n",
+    "    model = UNet().to(device)\n",
+    "    criterion = nn.MSELoss()\n",
+    "    optimizer = torch.optim.Adam(model.parameters(), lr=0.0001)\n",
+    "    \n",
+    "    # Training loop with tqdm\n",
+    "    for epoch in range(epochs):\n",
+    "        model.train()\n",
+    "        total_loss = 0\n",
+    "        optimizer.zero_grad()\n",
+    "        \n",
+    "        with tqdm(train_dataloader, unit=\"batch\", desc=f\"Epoch {epoch+1}/{epochs}\") as tepoch:\n",
+    "            for i, (images, targets) in enumerate(tepoch):\n",
+    "                images, targets = images.to(device), targets.to(device)\n",
+    "                \n",
+    "                # Forward pass\n",
+    "                outputs = model(images)\n",
+    "                loss = criterion(outputs, targets)\n",
+    "                loss.backward()\n",
+    "                \n",
+    "                # Gradient accumulation\n",
+    "                if (i + 1) % grad_accumulation_steps == 0 or (i + 1) == len(tepoch):\n",
+    "                    optimizer.step()\n",
+    "                    optimizer.zero_grad()\n",
+    "                \n",
+    "                total_loss += loss.item()\n",
+    "                \n",
+    "                # Update the tqdm progress bar with the current loss\n",
+    "                tepoch.set_postfix(loss=total_loss / ((i + 1) * batch_size))\n",
+    "        \n",
+    "        avg_train_loss = total_loss / len(train_dataloader)\n",
+    "        avg_val_loss, avg_val_psnr = calculate_loss_and_psnr(model, val_dataloader, criterion)\n",
+    "        \n",
+    "        print(f\"Epoch [{epoch+1}/{epochs}] - Train Loss: {avg_train_loss:.4f}, Validation Loss: {avg_val_loss:.4f}, Validation PSNR: {avg_val_psnr:.4f}\")\n",
+    "\n",
+    "        if avg_val_loss < best_val_loss:\n",
+    "            best_val_loss = avg_val_loss\n",
+    "            torch.save(model.state_dict(), best_model_path)\n",
+    "            print(f\"Model saved with improved validation loss: {avg_val_loss:.4f}\")\n",
+    "    \n",
+    "    return model\n",
+    "\n",
+    "# Example usage with train and validation directories\n",
+    "model = train_unet(r\"D:\\PN_Split\\train\", r\"D:\\PN_Split\\val\", epochs=50, batch_size=4, grad_accumulation_steps=8)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### U-Net Inference"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import torch\n",
+    "import torch.nn as nn\n",
+    "import pydicom\n",
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt\n",
+    "import os\n",
+    "\n",
+    "# Import the UNet and related classes from the previous script\n",
+    "# Replace with the actual import method\n",
+    "\n",
+    "def load_dicom_image(dicom_path):\n",
+    "    \"\"\"\n",
+    "    Load and normalize a DICOM image\n",
+    "    \n",
+    "    Args:\n",
+    "        dicom_path (str): Path to the DICOM file\n",
+    "    \n",
+    "    Returns:\n",
+    "        torch.Tensor: Normalized image tensor\n",
+    "    \"\"\"\n",
+    "    # Read DICOM file\n",
+    "    dcm = pydicom.dcmread(dicom_path)\n",
+    "    image = dcm.pixel_array.astype(float)\n",
+    "    \n",
+    "    # Normalize image\n",
+    "    image = (image - image.min()) / (image.max() - image.min())\n",
+    "    \n",
+    "    # Convert to tensor\n",
+    "    image_tensor = torch.from_numpy(image).float().unsqueeze(0).unsqueeze(0)\n",
+    "    return image_tensor\n",
+    "\n",
+    "def calculate_psnr(output, target, max_pixel=1.0):\n",
+    "    \"\"\"\n",
+    "    Calculate Peak Signal-to-Noise Ratio (PSNR)\n",
+    "    \n",
+    "    Args:\n",
+    "        output (torch.Tensor): Reconstructed image\n",
+    "        target (torch.Tensor): Original image\n",
+    "        max_pixel (float): Maximum pixel value\n",
+    "    \n",
+    "    Returns:\n",
+    "        float: PSNR value\n",
+    "    \"\"\"\n",
+    "    # Ensure the values are in the correct range\n",
+    "    mse = torch.nn.functional.mse_loss(output, target)\n",
+    "    psnr = 20 * torch.log10(max_pixel / torch.sqrt(mse))\n",
+    "    return psnr.item()\n",
+    "\n",
+    "def visualize_reconstruction(original_image, reconstructed_image, psnr):\n",
+    "    \"\"\"\n",
+    "    Visualize original and reconstructed images\n",
+    "    \n",
+    "    Args:\n",
+    "        original_image (torch.Tensor): Original image tensor\n",
+    "        reconstructed_image (torch.Tensor): Reconstructed image tensor\n",
+    "        psnr (float): Peak Signal-to-Noise Ratio\n",
+    "    \"\"\"\n",
+    "    # Convert tensors to numpy for visualization\n",
+    "    original = original_image.squeeze().cpu().numpy()\n",
+    "    reconstructed = reconstructed_image.squeeze().cpu().numpy()\n",
+    "    \n",
+    "    # Create subplot\n",
+    "    fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(10, 5))\n",
+    "    \n",
+    "    # Plot original image\n",
+    "    im1 = ax1.imshow(original, cmap='gray')\n",
+    "    ax1.set_title('Original Image')\n",
+    "    plt.colorbar(im1, ax=ax1)\n",
+    "    \n",
+    "    # Plot reconstructed image\n",
+    "    im2 = ax2.imshow(reconstructed, cmap='gray')\n",
+    "    ax2.set_title(f'Reconstructed Image\\nPSNR: {psnr:.2f} dB')\n",
+    "    plt.colorbar(im2, ax=ax2)\n",
+    "    \n",
+    "    plt.tight_layout()\n",
+    "    plt.show()\n",
+    "\n",
+    "def inference_single_image(model_path, test_dicom_path):\n",
+    "    \"\"\"\n",
+    "    Perform inference on a single DICOM image\n",
+    "    \n",
+    "    Args:\n",
+    "        model_path (str): Path to the saved model weights\n",
+    "        test_dicom_path (str): Path to the test DICOM file\n",
+    "    \"\"\"\n",
+    "    # Set device\n",
+    "    device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')\n",
+    "    \n",
+    "    # Initialize model\n",
+    "    model = UNet().to(device)\n",
+    "    \n",
+    "    # Load saved model weights\n",
+    "    model.load_state_dict(torch.load(model_path))\n",
+    "    model.eval()\n",
+    "    \n",
+    "    # Load and preprocess test image\n",
+    "    with torch.no_grad():\n",
+    "        test_image = load_dicom_image(test_dicom_path).to(device)\n",
+    "        \n",
+    "        # Perform reconstruction\n",
+    "        reconstructed_image = model(test_image)\n",
+    "        \n",
+    "        # Calculate PSNR\n",
+    "        psnr = calculate_psnr(reconstructed_image, test_image)\n",
+    "\n",
+    "        print(f\"PSNR: {psnr:.2f} dB\")\n",
+    "        \n",
+    "        # Visualize results\n",
+    "        visualize_reconstruction(test_image, reconstructed_image, psnr)\n",
+    "\n",
+    "# Example usage\n",
+    "if __name__ == \"__main__\":\n",
+    "    # Paths to model and test image\n",
+    "    MODEL_PATH = r\"D:\\VSCODE\\PreSense\\best_model.pth\"  # Path to your saved model\n",
+    "    TEST_DICOM_PATH = r\"D:\\VSCODE\\PreSense\\test.dcm\"  # Replace with actual path to test DICOM\n",
+    "    \n",
+    "    # Run inference\n",
+    "    inference_single_image(MODEL_PATH, TEST_DICOM_PATH)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### U-Net Inference for Complete Scan"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import torch\n",
+    "import torch.nn as nn\n",
+    "import pydicom\n",
+    "import numpy as np\n",
+    "import os\n",
+    "from tqdm import tqdm\n",
+    "\n",
+    "# Import the UNet and related classes from the previous script\n",
+    "\n",
+    "def load_dicom_image(dicom_path):\n",
+    "    \"\"\"\n",
+    "    Load and normalize a DICOM image\n",
+    "    \n",
+    "    Args:\n",
+    "        dicom_path (str): Path to the DICOM file\n",
+    "    \n",
+    "    Returns:\n",
+    "        torch.Tensor: Normalized image tensor\n",
+    "    \"\"\"\n",
+    "    # Read DICOM file\n",
+    "    dcm = pydicom.dcmread(dicom_path)\n",
+    "    image = dcm.pixel_array.astype(float)\n",
+    "    \n",
+    "    # Normalize image\n",
+    "    image = (image - image.min()) / (image.max() - image.min())\n",
+    "    \n",
+    "    # Convert to tensor\n",
+    "    image_tensor = torch.from_numpy(image).float().unsqueeze(0).unsqueeze(0)\n",
+    "    return image_tensor, dcm\n",
+    "\n",
+    "def save_reconstructed_dicom(image_tensor, original_dcm, output_path):\n",
+    "    \"\"\"\n",
+    "    Save reconstructed image as a DICOM file\n",
+    "    \n",
+    "    Args:\n",
+    "        image_tensor (torch.Tensor): Reconstructed image tensor\n",
+    "        original_dcm (pydicom.Dataset): Original DICOM dataset\n",
+    "        output_path (str): Path to save the reconstructed image\n",
+    "    \"\"\"\n",
+    "    # Convert tensor to numpy and scale back to original pixel range\n",
+    "    reconstructed_image = image_tensor.squeeze().cpu().numpy()\n",
+    "    \n",
+    "    # Scale to original pixel array range\n",
+    "    min_val = original_dcm.pixel_array.min()\n",
+    "    max_val = original_dcm.pixel_array.max()\n",
+    "    reconstructed_image = reconstructed_image * (max_val - min_val) + min_val\n",
+    "    \n",
+    "    # Create a copy of the original DICOM dataset\n",
+    "    ds = pydicom.Dataset()\n",
+    "    ds.update(original_dcm)\n",
+    "    \n",
+    "    # Set the new pixel data\n",
+    "    ds.PixelData = reconstructed_image.astype(original_dcm.pixel_array.dtype).tobytes()\n",
+    "    \n",
+    "    # Set transfer syntax to explicit VR little endian (common default)\n",
+    "    ds.file_meta = pydicom.Dataset()\n",
+    "    ds.file_meta.TransferSyntaxUID = pydicom.uid.ExplicitVRLittleEndian\n",
+    "    \n",
+    "    # Write the DICOM file\n",
+    "    pydicom.dcmwrite(output_path, ds)\n",
+    "\n",
+    "def calculate_psnr(output, target, max_pixel=1.0):\n",
+    "    \"\"\"\n",
+    "    Calculate Peak Signal-to-Noise Ratio (PSNR)\n",
+    "    \n",
+    "    Args:\n",
+    "        output (torch.Tensor): Reconstructed image\n",
+    "        target (torch.Tensor): Original image\n",
+    "        max_pixel (float): Maximum pixel value\n",
+    "    \n",
+    "    Returns:\n",
+    "        float: PSNR value\n",
+    "    \"\"\"\n",
+    "    # Ensure the values are in the correct range\n",
+    "    mse = torch.nn.functional.mse_loss(output, target)\n",
+    "    psnr = 20 * torch.log10(max_pixel / torch.sqrt(mse))\n",
+    "    return psnr.item()\n",
+    "\n",
+    "def batch_inference(model_path, input_dir, output_dir):\n",
+    "    \"\"\"\n",
+    "    Perform batch inference on all DICOM files in a directory\n",
+    "    \n",
+    "    Args:\n",
+    "        model_path (str): Path to the saved model weights\n",
+    "        input_dir (str): Directory containing input DICOM files\n",
+    "        output_dir (str): Directory to save reconstructed DICOM files\n",
+    "    \"\"\"\n",
+    "    # Create output directory if it doesn't exist\n",
+    "    os.makedirs(output_dir, exist_ok=True)\n",
+    "    \n",
+    "    # Set device\n",
+    "    device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')\n",
+    "    \n",
+    "    # Initialize model\n",
+    "    model = UNet().to(device)\n",
+    "    \n",
+    "    # Load saved model weights\n",
+    "    model.load_state_dict(torch.load(model_path))\n",
+    "    model.eval()\n",
+    "    \n",
+    "    # Get list of DICOM files\n",
+    "    dcm_files = [f for f in os.listdir(input_dir) if f.endswith('.dcm')]\n",
+    "    \n",
+    "    # Prepare for inference\n",
+    "    print(f\"Starting batch inference on {len(dcm_files)} DICOM files...\")\n",
+    "    \n",
+    "    # Store PSNR values\n",
+    "    psnr_values = {}\n",
+    "    \n",
+    "    # Perform inference\n",
+    "    with torch.no_grad():\n",
+    "        for dcm_file in tqdm(dcm_files, desc=\"Reconstructing Images\"):\n",
+    "            # Full paths\n",
+    "            input_path = os.path.join(input_dir, dcm_file)\n",
+    "            output_path = os.path.join(output_dir, dcm_file)\n",
+    "            \n",
+    "            # Load image\n",
+    "            test_image, original_dcm = load_dicom_image(input_path)\n",
+    "            test_image = test_image.to(device)\n",
+    "            \n",
+    "            # Perform reconstruction\n",
+    "            reconstructed_image = model(test_image)\n",
+    "            \n",
+    "            # Calculate PSNR\n",
+    "            psnr = calculate_psnr(reconstructed_image, test_image)\n",
+    "            psnr_values[dcm_file] = psnr\n",
+    "            \n",
+    "            # Save reconstructed image\n",
+    "            save_reconstructed_dicom(reconstructed_image, original_dcm, output_path)\n",
+    "    \n",
+    "    # Print PSNR values\n",
+    "    print(\"\\nPSNR Values:\")\n",
+    "    for filename, psnr in psnr_values.items():\n",
+    "        print(f\"{filename}: {psnr:.2f} dB\")\n",
+    "    \n",
+    "    # Calculate and print overall statistics\n",
+    "    psnr_list = list(psnr_values.values())\n",
+    "    print(f\"\\nPSNR Statistics:\")\n",
+    "    print(f\"Average PSNR: {np.mean(psnr_list):.2f} dB\")\n",
+    "    print(f\"Minimum PSNR: {np.min(psnr_list):.2f} dB\")\n",
+    "    print(f\"Maximum PSNR: {np.max(psnr_list):.2f} dB\")\n",
+    "\n",
+    "# Example usage\n",
+    "if __name__ == \"__main__\":\n",
+    "    # Paths to model, input, and output directories\n",
+    "    MODEL_PATH = r\"D:\\VSCODE\\PreSense\\best_model.pth\"  # Path to your saved model\n",
+    "    INPUT_DICOM_DIR = r\"D:\\Pancreatic Neuroendocrine\\manifest-1662644254281\\CTpred-Sunitinib-panNET\\PAN_01\\04-11-2001-NA-NA-29221\\3.000000-CEFC07AIDR 3D STD-16260\"  # Directory with input DICOM files\n",
+    "    OUTPUT_DICOM_DIR = r\"D:\\VSCODE\\PreSense\\reconstructed_dicom\"  # Directory to save reconstructed DICOM files\n",
+    "    \n",
+    "    # Run batch inference\n",
+    "    batch_inference(MODEL_PATH, INPUT_DICOM_DIR, OUTPUT_DICOM_DIR)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import torch\n",
+    "import torch.nn as nn\n",
+    "import pydicom\n",
+    "import numpy as np\n",
+    "import os\n",
+    "from tqdm import tqdm\n",
+    "from PIL import Image\n",
+    "\n",
+    "# Import the UNet and related classes from the previous script\n",
+    "\n",
+    "def load_dicom_image(dicom_path):\n",
+    "    \"\"\"\n",
+    "    Load and normalize a DICOM image\n",
+    "    \n",
+    "    Args:\n",
+    "        dicom_path (str): Path to the DICOM file\n",
+    "    \n",
+    "    Returns:\n",
+    "        torch.Tensor: Normalized image tensor\n",
+    "    \"\"\"\n",
+    "    # Read DICOM file\n",
+    "    dcm = pydicom.dcmread(dicom_path)\n",
+    "    image = dcm.pixel_array.astype(float)\n",
+    "    \n",
+    "    # Normalize image\n",
+    "    image = (image - image.min()) / (image.max() - image.min())\n",
+    "    \n",
+    "    # Convert to tensor\n",
+    "    image_tensor = torch.from_numpy(image).float().unsqueeze(0).unsqueeze(0)\n",
+    "    return image_tensor, dcm\n",
+    "\n",
+    "def save_reconstructed_image(image_tensor, output_path):\n",
+    "    \"\"\"\n",
+    "    Save reconstructed image as a JPEG file\n",
+    "    \n",
+    "    Args:\n",
+    "        image_tensor (torch.Tensor): Reconstructed image tensor\n",
+    "        output_path (str): Path to save the reconstructed JPEG image\n",
+    "    \"\"\"\n",
+    "    # Convert tensor to numpy array\n",
+    "    reconstructed_image = image_tensor.squeeze().cpu().numpy()\n",
+    "    \n",
+    "    # Scale back to the original pixel range (assuming input was normalized to [0, 1])\n",
+    "    reconstructed_image = np.uint8(reconstructed_image * 255)\n",
+    "    \n",
+    "    # Convert to PIL Image\n",
+    "    pil_image = Image.fromarray(reconstructed_image)\n",
+    "    \n",
+    "    # Save as JPEG\n",
+    "    pil_image.save(output_path, 'JPEG')\n",
+    "\n",
+    "def calculate_psnr(output, target, max_pixel=1.0):\n",
+    "    \"\"\"\n",
+    "    Calculate Peak Signal-to-Noise Ratio (PSNR)\n",
+    "    \n",
+    "    Args:\n",
+    "        output (torch.Tensor): Reconstructed image\n",
+    "        target (torch.Tensor): Original image\n",
+    "        max_pixel (float): Maximum pixel value\n",
+    "    \n",
+    "    Returns:\n",
+    "        float: PSNR value\n",
+    "    \"\"\"\n",
+    "    # Ensure the values are in the correct range\n",
+    "    mse = torch.nn.functional.mse_loss(output, target)\n",
+    "    psnr = 20 * torch.log10(max_pixel / torch.sqrt(mse))\n",
+    "    return psnr.item()\n",
+    "\n",
+    "def batch_inference(model_path, input_dir, output_dir):\n",
+    "    \"\"\"\n",
+    "    Perform batch inference on all DICOM files in a directory\n",
+    "    \n",
+    "    Args:\n",
+    "        model_path (str): Path to the saved model weights\n",
+    "        input_dir (str): Directory containing input DICOM files\n",
+    "        output_dir (str): Directory to save reconstructed JPEG images\n",
+    "    \"\"\"\n",
+    "    # Create output directory if it doesn't exist\n",
+    "    os.makedirs(output_dir, exist_ok=True)\n",
+    "    \n",
+    "    # Set device\n",
+    "    device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')\n",
+    "    \n",
+    "    # Initialize model\n",
+    "    model = UNet().to(device)\n",
+    "    \n",
+    "    # Load saved model weights\n",
+    "    model.load_state_dict(torch.load(model_path))\n",
+    "    model.eval()\n",
+    "    \n",
+    "    # Get list of DICOM files\n",
+    "    dcm_files = [f for f in os.listdir(input_dir) if f.endswith('.dcm')]\n",
+    "    \n",
+    "    # Prepare for inference\n",
+    "    print(f\"Starting batch inference on {len(dcm_files)} DICOM files...\")\n",
+    "    \n",
+    "    # Store PSNR values\n",
+    "    psnr_values = {}\n",
+    "    \n",
+    "    # Perform inference\n",
+    "    with torch.no_grad():\n",
+    "        for dcm_file in tqdm(dcm_files, desc=\"Reconstructing Images\"):\n",
+    "            # Full paths\n",
+    "            input_path = os.path.join(input_dir, dcm_file)\n",
+    "            output_path = os.path.join(output_dir, f\"{os.path.splitext(dcm_file)[0]}.jpg\")  # Save as .jpg\n",
+    "            \n",
+    "            # Load image\n",
+    "            test_image, original_dcm = load_dicom_image(input_path)\n",
+    "            test_image = test_image.to(device)\n",
+    "            \n",
+    "            # Perform reconstruction\n",
+    "            reconstructed_image = model(test_image)\n",
+    "            \n",
+    "            # Calculate PSNR\n",
+    "            psnr = calculate_psnr(reconstructed_image, test_image)\n",
+    "            psnr_values[dcm_file] = psnr\n",
+    "            \n",
+    "            # Save reconstructed image as JPEG\n",
+    "            save_reconstructed_image(reconstructed_image, output_path)\n",
+    "    \n",
+    "    # Print PSNR values\n",
+    "    print(\"\\nPSNR Values:\")\n",
+    "    for filename, psnr in psnr_values.items():\n",
+    "        print(f\"{filename}: {psnr:.2f} dB\")\n",
+    "    \n",
+    "    # Calculate and print overall statistics\n",
+    "    psnr_list = list(psnr_values.values())\n",
+    "    print(f\"\\nPSNR Statistics:\")\n",
+    "    print(f\"Average PSNR: {np.mean(psnr_list):.2f} dB\")\n",
+    "    print(f\"Minimum PSNR: {np.min(psnr_list):.2f} dB\")\n",
+    "    print(f\"Maximum PSNR: {np.max(psnr_list):.2f} dB\")\n",
+    "\n",
+    "# Example usage\n",
+    "if __name__ == \"__main__\":\n",
+    "    # Paths to model, input, and output directories\n",
+    "    MODEL_PATH = r\"D:\\VSCODE\\PreSense\\best_model.pth\"  # Path to your saved model\n",
+    "    INPUT_DICOM_DIR = r\"D:\\Pancreatic Neuroendocrine\\manifest-1662644254281\\CTpred-Sunitinib-panNET\\PAN_01\\04-11-2001-NA-NA-29221\\3.000000-CEFC07AIDR 3D STD-16260\"  # Directory with input DICOM files\n",
+    "    OUTPUT_JPEG_DIR = r\"D:\\VSCODE\\PreSense\\reconstructed_images\"  # Directory to save reconstructed JPEG images\n",
+    "    \n",
+    "    # Run batch inference\n",
+    "    batch_inference(MODEL_PATH, INPUT_DICOM_DIR, OUTPUT_JPEG_DIR)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Small Reconstructor and Denoiser U-Net (smallRD)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import torch\n",
+    "import torch.nn as nn\n",
+    "import torch.nn.functional as F\n",
+    "import pydicom\n",
+    "import numpy as np\n",
+    "from torch.utils.data import Dataset, DataLoader\n",
+    "import os\n",
+    "from torch.utils.checkpoint import checkpoint\n",
+    "from tqdm import tqdm  # Import tqdm for progress bar\n",
+    "\n",
+    "device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')\n",
+    "\n",
+    "class MedicalImageDataset(Dataset):\n",
+    "    def __init__(self, dicom_dir):\n",
+    "        self.dicom_files = [os.path.join(dicom_dir, f) for f in os.listdir(dicom_dir) if f.endswith('.dcm')]\n",
+    "    \n",
+    "    def __len__(self):\n",
+    "        return len(self.dicom_files)\n",
+    "    \n",
+    "    def __getitem__(self, idx):\n",
+    "        # Read DICOM file and normalize\n",
+    "        dcm = pydicom.dcmread(self.dicom_files[idx])\n",
+    "        image = dcm.pixel_array.astype(float)\n",
+    "        image = (image - image.min()) / (image.max() - image.min())\n",
+    "        \n",
+    "        # Convert to tensor\n",
+    "        image_tensor = torch.from_numpy(image).float().unsqueeze(0)\n",
+    "        return image_tensor, image_tensor\n",
+    "\n",
+    "class UNetBlock(nn.Module):\n",
+    "    def __init__(self, in_channels, out_channels):\n",
+    "        super().__init__()\n",
+    "        self.conv1 = nn.Conv2d(in_channels, out_channels, 3, padding=1)\n",
+    "        self.bn1 = nn.BatchNorm2d(out_channels)\n",
+    "        self.conv2 = nn.Conv2d(out_channels, out_channels, 3, padding=1)\n",
+    "        self.bn2 = nn.BatchNorm2d(out_channels)\n",
+    "    \n",
+    "    def forward(self, x):\n",
+    "        x = F.relu(self.bn1(self.conv1(x)))\n",
+    "        x = F.relu(self.bn2(self.conv2(x)))\n",
+    "        return x\n",
+    "\n",
+    "class UNet(nn.Module):\n",
+    "    def __init__(self, in_channels=1, out_channels=1):\n",
+    "        super().__init__()\n",
+    "        # Encoder\n",
+    "        self.enc1 = UNetBlock(in_channels, 64)\n",
+    "        self.enc2 = UNetBlock(64, 128)\n",
+    "        self.enc3 = UNetBlock(128, 256)\n",
+    "        \n",
+    "        # Decoder\n",
+    "        self.dec3 = UNetBlock(256 + 128, 128)  # Adjust for concatenation with skip connection\n",
+    "        self.dec2 = UNetBlock(128 + 64, 64)    # Adjust for concatenation with skip connection\n",
+    "        self.dec1 = UNetBlock(64, out_channels)\n",
+    "        \n",
+    "        # Pooling and upsampling\n",
+    "        self.pool = nn.MaxPool2d(2, 2)\n",
+    "        self.upsample = nn.Upsample(scale_factor=2, mode='bilinear', align_corners=True)\n",
+    "    \n",
+    "    def forward(self, x):\n",
+    "        # Encoder path\n",
+    "        e1 = checkpoint(self.enc1, x)\n",
+    "        e2 = checkpoint(self.enc2, self.pool(e1))\n",
+    "        e3 = checkpoint(self.enc3, self.pool(e2))\n",
+    "        \n",
+    "        # Decoder path with skip connections\n",
+    "        d3 = self.upsample(e3)\n",
+    "        d3 = torch.cat([d3, e2], dim=1)  # Concatenate along channels\n",
+    "        d3 = checkpoint(self.dec3, d3)\n",
+    "        \n",
+    "        d2 = self.upsample(d3)\n",
+    "        d2 = torch.cat([d2, e1], dim=1)  # Concatenate along channels\n",
+    "        d2 = checkpoint(self.dec2, d2)\n",
+    "        \n",
+    "        d1 = self.dec1(d2)  # No checkpointing for final output layer\n",
+    "        \n",
+    "        return d1\n",
+    "\n",
+    "def calculate_loss(model, dataloader, criterion):\n",
+    "    model.eval()\n",
+    "    total_loss = 0\n",
+    "    with torch.no_grad():\n",
+    "        for images, targets in dataloader:\n",
+    "            images, targets = images.to(device), targets.to(device)\n",
+    "            outputs = model(images)\n",
+    "            loss = criterion(outputs, targets)\n",
+    "            total_loss += loss.item()\n",
+    "    return total_loss / len(dataloader)\n",
+    "\n",
+    "def calculate_psnr(output, target, max_pixel=1.0):\n",
+    "    # Ensure the values are in the correct range\n",
+    "    mse = F.mse_loss(output, target)\n",
+    "    psnr = 20 * torch.log10(max_pixel / torch.sqrt(mse))\n",
+    "    return psnr.item()\n",
+    "\n",
+    "def calculate_loss_and_psnr(model, dataloader, criterion):\n",
+    "    model.eval()\n",
+    "    total_loss = 0\n",
+    "    total_psnr = 0\n",
+    "    num_batches = len(dataloader)\n",
+    "    \n",
+    "    with torch.no_grad():\n",
+    "        for images, targets in dataloader:\n",
+    "            images, targets = images.to(device), targets.to(device)\n",
+    "            outputs = model(images)\n",
+    "            \n",
+    "            # Calculate MSE loss\n",
+    "            loss = criterion(outputs, targets)\n",
+    "            total_loss += loss.item()\n",
+    "            \n",
+    "            # Calculate PSNR\n",
+    "            psnr = calculate_psnr(outputs, targets)\n",
+    "            total_psnr += psnr\n",
+    "    \n",
+    "    avg_loss = total_loss / num_batches\n",
+    "    avg_psnr = total_psnr / num_batches\n",
+    "    \n",
+    "    return avg_loss, avg_psnr\n",
+    "\n",
+    "class UNet(nn.Module):\n",
+    "    def __init__(self, in_channels=1, out_channels=1):\n",
+    "        super().__init__()\n",
+    "        # Encoder\n",
+    "        self.enc1 = UNetBlock(in_channels, 64)\n",
+    "        self.enc2 = UNetBlock(64, 128)\n",
+    "        self.enc3 = UNetBlock(128, 256)\n",
+    "        \n",
+    "        # Decoder\n",
+    "        self.dec3 = UNetBlock(256 + 128, 128)  # Adjust for concatenation with skip connection\n",
+    "        self.dec2 = UNetBlock(128 + 64, 64)    # Adjust for concatenation with skip connection\n",
+    "        self.dec1 = UNetBlock(64, out_channels)\n",
+    "        \n",
+    "        # Pooling and upsampling\n",
+    "        self.pool = nn.MaxPool2d(2, 2)\n",
+    "        self.upsample = nn.Upsample(scale_factor=2, mode='bilinear', align_corners=True)\n",
+    "    \n",
+    "    def forward(self, x):\n",
+    "        # Encoder path\n",
+    "        e1 = checkpoint(self.enc1, x)\n",
+    "        e2 = checkpoint(self.enc2, self.pool(e1))\n",
+    "        e3 = checkpoint(self.enc3, self.pool(e2))\n",
+    "        \n",
+    "        # Decoder path with skip connections\n",
+    "        d3 = self.upsample(e3)\n",
+    "        d3 = torch.cat([d3, e2], dim=1)  # Concatenate along channels\n",
+    "        d3 = checkpoint(self.dec3, d3)\n",
+    "        \n",
+    "        d2 = self.upsample(d3)\n",
+    "        d2 = torch.cat([d2, e1], dim=1)  # Concatenate along channels\n",
+    "        d2 = checkpoint(self.dec2, d2)\n",
+    "        \n",
+    "        d1 = self.dec1(d2)  # No checkpointing for final output layer\n",
+    "        \n",
+    "        return d1\n",
+    "\n",
+    "class Reconstructor(nn.Module):\n",
+    "    def __init__(self, in_channels=1, out_channels=1):\n",
+    "        super().__init__()\n",
+    "        # Same UNet architecture for reconstruction\n",
+    "        self.unet = UNet(in_channels=in_channels, out_channels=out_channels)\n",
+    "    \n",
+    "    def forward(self, x):\n",
+    "        return self.unet(x)\n",
+    "\n",
+    "\n",
+    "class Denoiser(nn.Module):\n",
+    "    def __init__(self, in_channels=1, out_channels=1):\n",
+    "        super().__init__()\n",
+    "        # Same UNet architecture for denoising\n",
+    "        self.unet = UNet(in_channels=in_channels, out_channels=out_channels)\n",
+    "    \n",
+    "    def forward(self, x):\n",
+    "        return self.unet(x)\n",
+    "    \n",
+    "def train_reconstructor_and_denoiser(dicom_dir, val_dicom_dir, epochs=50, batch_size=4, grad_accumulation_steps=2):\n",
+    "    # Dataset and DataLoader\n",
+    "    dataset = MedicalImageDataset(dicom_dir)\n",
+    "    train_dataloader = DataLoader(dataset, batch_size=batch_size, shuffle=True)\n",
+    "    val_dataset = MedicalImageDataset(val_dicom_dir)\n",
+    "    val_dataloader = DataLoader(val_dataset, batch_size=batch_size, shuffle=False)\n",
+    "    \n",
+    "    # Initialize both models\n",
+    "    reconstructor = Reconstructor().to(device)\n",
+    "    denoiser = Denoiser().to(device)\n",
+    "    \n",
+    "    # Loss functions for both models\n",
+    "    reconstructor_criterion = nn.MSELoss()\n",
+    "    denoiser_criterion = nn.MSELoss()\n",
+    "    \n",
+    "    # Optimizers for both models\n",
+    "    reconstructor_optimizer = torch.optim.Adam(reconstructor.parameters(), lr=0.0001)\n",
+    "    denoiser_optimizer = torch.optim.Adam(denoiser.parameters(), lr=0.0001)\n",
+    "    \n",
+    "    # Best validation loss initialization\n",
+    "    best_reconstructor_val_loss = float('inf')\n",
+    "    best_denoiser_val_loss = float('inf')\n",
+    "    best_reconstructor_model_path = 'best_reconstructor_model.pth'\n",
+    "    best_denoiser_model_path = 'best_denoiser_model.pth'\n",
+    "\n",
+    "    # Training loop with tqdm\n",
+    "    for epoch in range(epochs):\n",
+    "        reconstructor.train()\n",
+    "        denoiser.train()\n",
+    "        \n",
+    "        reconstructor_total_loss = 0\n",
+    "        denoiser_total_loss = 0\n",
+    "        \n",
+    "        reconstructor_optimizer.zero_grad()\n",
+    "        denoiser_optimizer.zero_grad()\n",
+    "\n",
+    "        with tqdm(train_dataloader, unit=\"batch\", desc=f\"Epoch {epoch+1}/{epochs}\") as tepoch:\n",
+    "            for i, (images, targets) in enumerate(tepoch):\n",
+    "                images, targets = images.to(device), targets.to(device)\n",
+    "                \n",
+    "                # Training Reconstructor\n",
+    "                reconstructor_outputs = reconstructor(images)\n",
+    "                reconstructor_loss = reconstructor_criterion(reconstructor_outputs, targets)\n",
+    "                reconstructor_loss.backward(retain_graph=True)\n",
+    "\n",
+    "                # Gradient accumulation for reconstructor\n",
+    "                if (i + 1) % grad_accumulation_steps == 0 or (i + 1) == len(tepoch):\n",
+    "                    reconstructor_optimizer.step()\n",
+    "                    reconstructor_optimizer.zero_grad()\n",
+    "\n",
+    "                reconstructor_total_loss += reconstructor_loss.item()\n",
+    "\n",
+    "                # Training Denoiser (using output from Reconstructor as noisy input)\n",
+    "                noisy_images = reconstructor_outputs.detach()  # Detach from the computation graph to avoid in-place error\n",
+    "                denoiser_outputs = denoiser(noisy_images)\n",
+    "                denoiser_loss = denoiser_criterion(denoiser_outputs, targets)\n",
+    "                denoiser_loss.backward()\n",
+    "\n",
+    "                # Gradient accumulation for denoiser\n",
+    "                if (i + 1) % grad_accumulation_steps == 0 or (i + 1) == len(tepoch):\n",
+    "                    denoiser_optimizer.step()\n",
+    "                    denoiser_optimizer.zero_grad()\n",
+    "\n",
+    "                denoiser_total_loss += denoiser_loss.item()\n",
+    "\n",
+    "                # Update the tqdm progress bar with current loss\n",
+    "                tepoch.set_postfix(\n",
+    "                    reconstructor_loss=reconstructor_total_loss / ((i + 1) * batch_size),\n",
+    "                    denoiser_loss=denoiser_total_loss / ((i + 1) * batch_size)\n",
+    "                )\n",
+    "        \n",
+    "        # Calculate validation loss for both models\n",
+    "        avg_reconstructor_train_loss = reconstructor_total_loss / len(train_dataloader)\n",
+    "        avg_denoiser_train_loss = denoiser_total_loss / len(train_dataloader)\n",
+    "        \n",
+    "        avg_reconstructor_val_loss, avg_reconstructor_val_psnr = calculate_loss_and_psnr(reconstructor, val_dataloader, reconstructor_criterion)\n",
+    "        avg_denoiser_val_loss, avg_denoiser_val_psnr = calculate_loss_and_psnr(denoiser, val_dataloader, denoiser_criterion)\n",
+    "        \n",
+    "        print(f\"Epoch [{epoch+1}/{epochs}] - \"\n",
+    "              f\"Reconstructor Train Loss: {avg_reconstructor_train_loss:.4f}, \"\n",
+    "              f\"Denoiser Train Loss: {avg_denoiser_train_loss:.4f}, \"\n",
+    "              f\"Reconstructor Val Loss: {avg_reconstructor_val_loss:.4f}, \"\n",
+    "              f\"Denoiser Val Loss: {avg_denoiser_val_loss:.4f}, \"\n",
+    "              f\"Reconstructor Validation PSNR: {avg_reconstructor_val_psnr:.4f}, \"\n",
+    "              f\"Denoiser Validation PSNR: {avg_denoiser_val_psnr:.4f}\")\n",
+    "        \n",
+    "        # Save models if validation loss is improved\n",
+    "        if avg_reconstructor_val_loss < best_reconstructor_val_loss:\n",
+    "            best_reconstructor_val_loss = avg_reconstructor_val_loss\n",
+    "            torch.save(reconstructor.state_dict(), best_reconstructor_model_path)\n",
+    "            print(f\"Reconstructor model saved with improved validation loss: {avg_reconstructor_val_loss:.4f}\")\n",
+    "        \n",
+    "        if avg_denoiser_val_loss < best_denoiser_val_loss:\n",
+    "            best_denoiser_val_loss = avg_denoiser_val_loss\n",
+    "            torch.save(denoiser.state_dict(), best_denoiser_model_path)\n",
+    "            print(f\"Denoiser model saved with improved validation loss: {avg_denoiser_val_loss:.4f}\")\n",
+    "    \n",
+    "    return reconstructor, denoiser\n",
+    "\n",
+    "# Example usage with train and validation directories\n",
+    "reconstructor_model, denoiser_model = train_reconstructor_and_denoiser(\n",
+    "    r\"D:/PN_Split/train\", r\"D:/PN_Split/val\", epochs=50, batch_size=20, grad_accumulation_steps=2\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### smallRD Single Image Inference"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import torch\n",
+    "import pydicom\n",
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt\n",
+    "import os\n",
+    "\n",
+    "# Import the models from the previous script\n",
+    "# Assuming they are defined or imported correctly\n",
+    "\n",
+    "def load_dicom_image(dicom_path):\n",
+    "    \"\"\"\n",
+    "    Load and normalize a DICOM image\n",
+    "    \n",
+    "    Args:\n",
+    "        dicom_path (str): Path to the DICOM file\n",
+    "    \n",
+    "    Returns:\n",
+    "        torch.Tensor: Normalized image tensor\n",
+    "    \"\"\"\n",
+    "    # Read DICOM file\n",
+    "    dcm = pydicom.dcmread(dicom_path)\n",
+    "    image = dcm.pixel_array.astype(float)\n",
+    "    \n",
+    "    # Normalize image\n",
+    "    image = (image - image.min()) / (image.max() - image.min())\n",
+    "    \n",
+    "    # Convert to tensor\n",
+    "    image_tensor = torch.from_numpy(image).float().unsqueeze(0).unsqueeze(0)  # Add batch and channel dimensions\n",
+    "    return image_tensor\n",
+    "\n",
+    "def calculate_psnr(output, target, max_pixel=1.0):\n",
+    "    \"\"\"\n",
+    "    Calculate Peak Signal-to-Noise Ratio (PSNR)\n",
+    "    \n",
+    "    Args:\n",
+    "        output (torch.Tensor): Reconstructed image\n",
+    "        target (torch.Tensor): Original image\n",
+    "        max_pixel (float): Maximum pixel value\n",
+    "    \n",
+    "    Returns:\n",
+    "        float: PSNR value\n",
+    "    \"\"\"\n",
+    "    # Ensure the values are in the correct range\n",
+    "    mse = torch.nn.functional.mse_loss(output, target)\n",
+    "    psnr = 20 * torch.log10(max_pixel / torch.sqrt(mse))\n",
+    "    return psnr.item()\n",
+    "\n",
+    "def visualize_reconstruction(original_image, reconstructed_image, psnr):\n",
+    "    \"\"\"\n",
+    "    Visualize original and reconstructed images\n",
+    "    \n",
+    "    Args:\n",
+    "        original_image (torch.Tensor): Original image tensor\n",
+    "        reconstructed_image (torch.Tensor): Reconstructed image tensor\n",
+    "        psnr (float): Peak Signal-to-Noise Ratio\n",
+    "    \"\"\"\n",
+    "    # Convert tensors to numpy for visualization\n",
+    "    original = original_image.squeeze().cpu().numpy()\n",
+    "    reconstructed = reconstructed_image.squeeze().cpu().numpy()\n",
+    "    \n",
+    "    # Create subplot\n",
+    "    fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(10, 5))\n",
+    "    \n",
+    "    # Plot original image\n",
+    "    im1 = ax1.imshow(original, cmap='gray')\n",
+    "    ax1.set_title('Original Image')\n",
+    "    plt.colorbar(im1, ax=ax1)\n",
+    "    \n",
+    "    # Plot reconstructed image\n",
+    "    im2 = ax2.imshow(reconstructed, cmap='gray')\n",
+    "    ax2.set_title(f'Reconstructed Image\\nPSNR: {psnr:.2f} dB')\n",
+    "    plt.colorbar(im2, ax=ax2)\n",
+    "    \n",
+    "    plt.tight_layout()\n",
+    "    plt.show()\n",
+    "\n",
+    "def inference_single_image(reconstructor_model_path, denoiser_model_path, test_dicom_path):\n",
+    "    \"\"\"\n",
+    "    Perform inference on a single DICOM image using both Reconstructor and Denoiser models.\n",
+    "    \n",
+    "    Args:\n",
+    "        reconstructor_model_path (str): Path to the saved Reconstructor model weights\n",
+    "        denoiser_model_path (str): Path to the saved Denoiser model weights\n",
+    "        test_dicom_path (str): Path to the test DICOM file\n",
+    "    \"\"\"\n",
+    "    # Set device\n",
+    "    device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')\n",
+    "    \n",
+    "    # Initialize models\n",
+    "    reconstructor = Reconstructor().to(device)\n",
+    "    denoiser = Denoiser().to(device)\n",
+    "    \n",
+    "    # Load saved model weights\n",
+    "    reconstructor.load_state_dict(torch.load(reconstructor_model_path))\n",
+    "    denoiser.load_state_dict(torch.load(denoiser_model_path))\n",
+    "    \n",
+    "    reconstructor.eval()\n",
+    "    denoiser.eval()\n",
+    "    \n",
+    "    # Load and preprocess test image\n",
+    "    with torch.no_grad():\n",
+    "        test_image = load_dicom_image(test_dicom_path).to(device)\n",
+    "        \n",
+    "        # Perform reconstruction\n",
+    "        reconstructed_image = reconstructor(test_image)\n",
+    "        \n",
+    "        # Perform denoising on the reconstructed image\n",
+    "        denoised_image = denoiser(reconstructed_image)\n",
+    "        \n",
+    "        # Calculate PSNR for both original and denoised outputs\n",
+    "        psnr_reconstructed = calculate_psnr(reconstructed_image, test_image)\n",
+    "        psnr_denoised = calculate_psnr(denoised_image, test_image)\n",
+    "\n",
+    "        print(f\"PSNR (Reconstructed): {psnr_reconstructed:.2f} dB\")\n",
+    "        print(f\"PSNR (Denoised): {psnr_denoised:.2f} dB\")\n",
+    "        \n",
+    "        # Visualize results\n",
+    "        visualize_reconstruction(test_image, reconstructed_image, psnr_reconstructed)\n",
+    "        visualize_reconstruction(test_image, denoised_image, psnr_denoised)\n",
+    "\n",
+    "# Example usage\n",
+    "if __name__ == \"__main__\":\n",
+    "    # Paths to models and test image\n",
+    "    RECONSTRUCTOR_MODEL_PATH = r\"D:/VSCODE/PreSense/small_reconstructor.pth\"  # Path to your saved Reconstructor model\n",
+    "    DENOISER_MODEL_PATH = r\"D:/VSCODE/PreSense/small_denoiser.pth\"  # Path to your saved Denoiser model\n",
+    "    TEST_DICOM_PATH = r\"D:/VSCODE/PreSense/test2.dcm\"  # Replace with actual path to test DICOM    \n",
+    "    # Run inference\n",
+    "    inference_single_image(RECONSTRUCTOR_MODEL_PATH, DENOISER_MODEL_PATH, TEST_DICOM_PATH)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Larger Reconstructor and Denoiser U-Net (largeRD)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import torch\n",
+    "import torch.nn as nn\n",
+    "import torch.nn.functional as F\n",
+    "import pydicom\n",
+    "import numpy as np\n",
+    "from torch.utils.data import Dataset, DataLoader\n",
+    "import os\n",
+    "from torch.utils.checkpoint import checkpoint\n",
+    "from tqdm import tqdm  # Import tqdm for progress bar\n",
+    "\n",
+    "device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')\n",
+    "\n",
+    "class MedicalImageDataset(Dataset):\n",
+    "    def __init__(self, dicom_dir):\n",
+    "        self.dicom_files = [os.path.join(dicom_dir, f) for f in os.listdir(dicom_dir) if f.endswith('.dcm')]\n",
+    "    \n",
+    "    def __len__(self):\n",
+    "        return len(self.dicom_files)\n",
+    "    \n",
+    "    def __getitem__(self, idx):\n",
+    "        # Read DICOM file and normalize\n",
+    "        dcm = pydicom.dcmread(self.dicom_files[idx])\n",
+    "        image = dcm.pixel_array.astype(float)\n",
+    "        image = (image - image.min()) / (image.max() - image.min())\n",
+    "        \n",
+    "        # Convert to tensor\n",
+    "        image_tensor = torch.from_numpy(image).float().unsqueeze(0)\n",
+    "        return image_tensor, image_tensor\n",
+    "\n",
+    "class UNetBlock(nn.Module):\n",
+    "    def __init__(self, in_channels, out_channels):\n",
+    "        super().__init__()\n",
+    "        self.conv1 = nn.Conv2d(in_channels, out_channels, 3, padding=1)\n",
+    "        self.bn1 = nn.BatchNorm2d(out_channels)\n",
+    "        self.conv2 = nn.Conv2d(out_channels, out_channels, 3, padding=1)\n",
+    "        self.bn2 = nn.BatchNorm2d(out_channels)\n",
+    "        self.conv2 = nn.Conv2d(out_channels, out_channels, 3, padding=1)\n",
+    "        self.bn2 = nn.BatchNorm2d(out_channels)\n",
+    "    \n",
+    "    def forward(self, x):\n",
+    "        x = F.relu(self.bn1(self.conv1(x)))\n",
+    "        x = F.relu(self.bn2(self.conv2(x)))\n",
+    "        return x\n",
+    "\n",
+    "class UNet(nn.Module):\n",
+    "    def __init__(self, in_channels=1, out_channels=1):\n",
+    "        super().__init__()\n",
+    "        # Encoder\n",
+    "        self.enc1 = UNetBlock(in_channels, 96)\n",
+    "        self.enc2 = UNetBlock(96, 192)\n",
+    "        self.enc3 = UNetBlock(192, 384)\n",
+    "        self.enc4 = UNetBlock(384, 784)\n",
+    "        \n",
+    "        # Decoder with learned upsampling (transposed convolutions)\n",
+    "        self.upconv4 = nn.ConvTranspose2d(784, 384, kernel_size=2, stride=2)  # Learnable upsampling\n",
+    "        self.dec4 = UNetBlock(384 + 384, 384)  # Adjust input channels after concatenation\n",
+    "\n",
+    "        self.upconv3 = nn.ConvTranspose2d(384, 192, kernel_size=2, stride=2)  # Learnable upsampling\n",
+    "        self.dec3 = UNetBlock(192 + 192, 192)  # Adjust input channels after concatenation\n",
+    "\n",
+    "        self.upconv2 = nn.ConvTranspose2d(192, 96, kernel_size=2, stride=2)  # Learnable upsampling\n",
+    "        self.dec2 = UNetBlock(96 + 96, 96)  # Adjust input channels after concatenation\n",
+    "\n",
+    "        self.dec1 = UNetBlock(96, out_channels)  # Final output\n",
+    "\n",
+    "        self.pool = nn.MaxPool2d(2, 2)\n",
+    "    \n",
+    "    def forward(self, x):\n",
+    "        # Encoder path\n",
+    "        e1 = checkpoint(self.enc1, x)\n",
+    "        e2 = checkpoint(self.enc2, self.pool(e1))\n",
+    "        e3 = checkpoint(self.enc3, self.pool(e2))\n",
+    "        e4 = checkpoint(self.enc4, self.pool(e3))\n",
+    "        \n",
+    "        # Decoder path with learned upsampling and skip connections\n",
+    "        d4 = self.upconv4(e4)  # Learnable upsampling\n",
+    "        d4 = torch.cat([d4, e3], dim=1)  # Concatenate with encoder features\n",
+    "        d4 = checkpoint(self.dec4, d4)\n",
+    "\n",
+    "        d3 = self.upconv3(d4)  # Learnable upsampling\n",
+    "        d3 = torch.cat([d3, e2], dim=1)  # Concatenate with encoder features\n",
+    "        d3 = checkpoint(self.dec3, d3)\n",
+    "\n",
+    "        d2 = self.upconv2(d3)  # Learnable upsampling\n",
+    "        d2 = torch.cat([d2, e1], dim=1)  # Concatenate with encoder features\n",
+    "        d2 = checkpoint(self.dec2, d2)\n",
+    "        \n",
+    "        d1 = self.dec1(d2)  # No checkpointing for final output layer\n",
+    "        \n",
+    "        return d1\n",
+    "\n",
+    "def calculate_loss(model, dataloader, criterion):\n",
+    "    model.eval()\n",
+    "    total_loss = 0\n",
+    "    with torch.no_grad():\n",
+    "        for images, targets in dataloader:\n",
+    "            images, targets = images.to(device), targets.to(device)\n",
+    "            outputs = model(images)\n",
+    "            loss = criterion(outputs, targets)\n",
+    "            total_loss += loss.item()\n",
+    "    return total_loss / len(dataloader)\n",
+    "\n",
+    "def calculate_psnr(output, target, max_pixel=1.0):\n",
+    "    # Ensure the values are in the correct range\n",
+    "    mse = F.mse_loss(output, target)\n",
+    "    psnr = 20 * torch.log10(max_pixel / torch.sqrt(mse))\n",
+    "    return psnr.item()\n",
+    "\n",
+    "def calculate_loss_and_psnr(model, dataloader, criterion):\n",
+    "    model.eval()\n",
+    "    total_loss = 0\n",
+    "    total_psnr = 0\n",
+    "    num_batches = len(dataloader)\n",
+    "    \n",
+    "    with torch.no_grad():\n",
+    "        for images, targets in dataloader:\n",
+    "            images, targets = images.to(device), targets.to(device)\n",
+    "            outputs = model(images)\n",
+    "            \n",
+    "            # Calculate MSE loss\n",
+    "            loss = criterion(outputs, targets)\n",
+    "            total_loss += loss.item()\n",
+    "            \n",
+    "            # Calculate PSNR\n",
+    "            psnr = calculate_psnr(outputs, targets)\n",
+    "            total_psnr += psnr\n",
+    "    \n",
+    "    avg_loss = total_loss / num_batches\n",
+    "    avg_psnr = total_psnr / num_batches\n",
+    "    \n",
+    "    return avg_loss, avg_psnr\n",
+    "\n",
+    "class Reconstructor(nn.Module):\n",
+    "    def __init__(self, in_channels=1, out_channels=1):\n",
+    "        super().__init__()\n",
+    "        # Same UNet architecture for reconstruction\n",
+    "        self.unet = UNet(in_channels=in_channels, out_channels=out_channels)\n",
+    "    \n",
+    "    def forward(self, x):\n",
+    "        return self.unet(x)\n",
+    "\n",
+    "\n",
+    "class Denoiser(nn.Module):\n",
+    "    def __init__(self, in_channels=1, out_channels=1):\n",
+    "        super().__init__()\n",
+    "        # Same UNet architecture for denoising\n",
+    "        self.unet = UNet(in_channels=in_channels, out_channels=out_channels)\n",
+    "    \n",
+    "    def forward(self, x):\n",
+    "        return self.unet(x)\n",
+    "    \n",
+    "def train_reconstructor_and_denoiser(dicom_dir, val_dicom_dir, epochs=50, batch_size=4, grad_accumulation_steps=2):\n",
+    "    # Dataset and DataLoader\n",
+    "    dataset = MedicalImageDataset(dicom_dir)\n",
+    "    train_dataloader = DataLoader(dataset, batch_size=batch_size, shuffle=True)\n",
+    "    val_dataset = MedicalImageDataset(val_dicom_dir)\n",
+    "    val_dataloader = DataLoader(val_dataset, batch_size=batch_size, shuffle=False)\n",
+    "    \n",
+    "    # Initialize both models\n",
+    "    reconstructor = Reconstructor().to(device)\n",
+    "    denoiser = Denoiser().to(device)\n",
+    "    \n",
+    "    # Loss functions for both models\n",
+    "    reconstructor_criterion = nn.MSELoss()\n",
+    "    denoiser_criterion = nn.MSELoss()\n",
+    "    \n",
+    "    # Optimizers for both models\n",
+    "    reconstructor_optimizer = torch.optim.Adam(reconstructor.parameters(), lr=0.0001)\n",
+    "    denoiser_optimizer = torch.optim.Adam(denoiser.parameters(), lr=0.0001)\n",
+    "    \n",
+    "    # Best validation loss initialization\n",
+    "    best_reconstructor_val_loss = float('inf')\n",
+    "    best_denoiser_val_loss = float('inf')\n",
+    "    best_reconstructor_model_path = 'best_reconstructor_model.pth'\n",
+    "    best_denoiser_model_path = 'best_denoiser_model.pth'\n",
+    "\n",
+    "    # Training loop with tqdm\n",
+    "    for epoch in range(epochs):\n",
+    "        reconstructor.train()\n",
+    "        denoiser.train()\n",
+    "        \n",
+    "        reconstructor_total_loss = 0\n",
+    "        denoiser_total_loss = 0\n",
+    "        \n",
+    "        reconstructor_optimizer.zero_grad()\n",
+    "        denoiser_optimizer.zero_grad()\n",
+    "\n",
+    "        with tqdm(train_dataloader, unit=\"batch\", desc=f\"Epoch {epoch+1}/{epochs}\") as tepoch:\n",
+    "            for i, (images, targets) in enumerate(tepoch):\n",
+    "                images, targets = images.to(device), targets.to(device)\n",
+    "                \n",
+    "                # Training Reconstructor\n",
+    "                reconstructor_outputs = reconstructor(images)\n",
+    "                reconstructor_loss = reconstructor_criterion(reconstructor_outputs, targets)\n",
+    "                reconstructor_loss.backward(retain_graph=True)\n",
+    "\n",
+    "                # Gradient accumulation for reconstructor\n",
+    "                if (i + 1) % grad_accumulation_steps == 0 or (i + 1) == len(tepoch):\n",
+    "                    reconstructor_optimizer.step()\n",
+    "                    reconstructor_optimizer.zero_grad()\n",
+    "\n",
+    "                reconstructor_total_loss += reconstructor_loss.item()\n",
+    "\n",
+    "                # Training Denoiser (using output from Reconstructor as noisy input)\n",
+    "                noisy_images = reconstructor_outputs.detach()  # Detach from the computation graph to avoid in-place error\n",
+    "                denoiser_outputs = denoiser(noisy_images)\n",
+    "                denoiser_loss = denoiser_criterion(denoiser_outputs, targets)\n",
+    "                denoiser_loss.backward()\n",
+    "\n",
+    "                # Gradient accumulation for denoiser\n",
+    "                if (i + 1) % grad_accumulation_steps == 0 or (i + 1) == len(tepoch):\n",
+    "                    denoiser_optimizer.step()\n",
+    "                    denoiser_optimizer.zero_grad()\n",
+    "\n",
+    "                denoiser_total_loss += denoiser_loss.item()\n",
+    "\n",
+    "                # Update the tqdm progress bar with current loss\n",
+    "                tepoch.set_postfix(\n",
+    "                    reconstructor_loss=reconstructor_total_loss / ((i + 1) * batch_size),\n",
+    "                    denoiser_loss=denoiser_total_loss / ((i + 1) * batch_size)\n",
+    "                )\n",
+    "        \n",
+    "        # Calculate validation loss for both models\n",
+    "        avg_reconstructor_train_loss = reconstructor_total_loss / len(train_dataloader)\n",
+    "        avg_denoiser_train_loss = denoiser_total_loss / len(train_dataloader)\n",
+    "        \n",
+    "        avg_reconstructor_val_loss, _ = calculate_loss_and_psnr(reconstructor, val_dataloader, reconstructor_criterion)\n",
+    "        avg_denoiser_val_loss, _ = calculate_loss_and_psnr(denoiser, val_dataloader, denoiser_criterion)\n",
+    "        \n",
+    "        print(f\"Epoch [{epoch+1}/{epochs}] - \"\n",
+    "              f\"Reconstructor Train Loss: {avg_reconstructor_train_loss:.4f}, \"\n",
+    "              f\"Denoiser Train Loss: {avg_denoiser_train_loss:.4f}, \"\n",
+    "              f\"Reconstructor Val Loss: {avg_reconstructor_val_loss:.4f}, \"\n",
+    "              f\"Denoiser Val Loss: {avg_denoiser_val_loss:.4f}\")\n",
+    "        \n",
+    "        # Save models if validation loss is improved\n",
+    "        if avg_reconstructor_val_loss < best_reconstructor_val_loss:\n",
+    "            best_reconstructor_val_loss = avg_reconstructor_val_loss\n",
+    "            torch.save(reconstructor.state_dict(), best_reconstructor_model_path)\n",
+    "            print(f\"Reconstructor model saved with improved validation loss: {avg_reconstructor_val_loss:.4f}\")\n",
+    "        \n",
+    "        if avg_denoiser_val_loss < best_denoiser_val_loss:\n",
+    "            best_denoiser_val_loss = avg_denoiser_val_loss\n",
+    "            torch.save(denoiser.state_dict(), best_denoiser_model_path)\n",
+    "            print(f\"Denoiser model saved with improved validation loss: {avg_denoiser_val_loss:.4f}\")\n",
+    "    \n",
+    "    return reconstructor, denoiser\n",
+    "\n",
+    "# Example usage with train and validation directories\n",
+    "reconstructor_model, denoiser_model = train_reconstructor_and_denoiser(\n",
+    "    r\"D:\\PN_Split\\train\", r\"D:\\PN_Split\\val\", epochs=50, batch_size=1, grad_accumulation_steps=64\n",
+    ")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "tf",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.11"
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+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}