update

download_SegRap23.py

@@ -0,0 +1,176 @@
+import os
+import subprocess
+import shutil
+import argparse
+import zipfile
+import gdown
+
+
+# ====================================
+# Dataset Info [!]
+# ====================================
+# Dataset: SegRap23
+# Challenge: https://segrap2023.grand-challenge.org
+# Data: https://segrap2023.grand-challenge.org/dataset/
+# Format: .nii.gz
+# ====================================
+
+
+def download_and_extract(dataset_dir, dataset_name):
+    # Download files
+    current_dir = os.getcwd()
+    os.chdir(dataset_dir)
+    tmp_dir = os.path.join(dataset_dir, "tmp")
+    os.makedirs(tmp_dir, exist_ok=True)
+    os.chdir(tmp_dir)
+    print(f"Downloading {dataset_name} dataset to {dataset_dir}...")
+
+    # ====================================
+    # Add download logic here [!]
+    # ====================================
+    # Download dataset
+    folder_id = "115mzmNlZRIewnSR2QFDwW_-RkNM0LC9D"
+    url = f"https://drive.google.com/drive/folders/{folder_id}"
+    gdown.download_folder(url, quiet=False, use_cookies=False)
+
+    # Extract training set zip files
+    zip_files = [
+        "SegRap2023/SegRap2023_Training_Set_120cases_OneHot_Labels.zip",
+        "SegRap2023/SegRap2023_Training_Set_120cases.zip",
+    ]
+    passwords = [None, "segrap2023@uestc"]
+    for zip_file, password in zip(zip_files, passwords):
+        if os.path.exists(zip_file):
+            print(f"Extracting {zip_file}...")
+            if password:
+                # Use 7z for password-protected files
+                subprocess.run(["7z", "x", zip_file, f"-p{password}"], check=True)
+            else:
+                # Use zipfile for non-protected files
+                with zipfile.ZipFile(zip_file) as zf:
+                    zf.extractall()
+
+    # Create destination directories
+    for dir_name in ["Images-contrastCT", "Images-CT", "Masks-Task1", "Masks-Task2"]:
+        os.makedirs(dir_name, exist_ok=True)
+
+    # Move training images
+    training_dir = "SegRap2023_Training_Set_120cases"
+    if not os.path.exists(training_dir):
+        raise FileNotFoundError(f"Training directory '{training_dir}' does not exist")
+
+    for subject_id in os.listdir(training_dir):
+        subject_path = os.path.join(training_dir, subject_id)
+        if not os.path.isdir(subject_path):
+            continue
+        for img_type, filename in [
+            ("contrastCT", "image_contrast.nii.gz"),
+            ("CT", "image.nii.gz"),
+        ]:
+            src = os.path.join(subject_path, filename)
+            if os.path.exists(src):
+                dst = os.path.join(f"Images-{img_type}", f"{subject_id}.nii.gz")
+                shutil.move(src, dst)
+
+    # Move mask files
+    for task_num in [1, 2]:
+        labels_dir = os.path.join(
+            "SegRap2023_Training_Set_120cases_OneHot_Labels", f"Task00{task_num}"
+        )
+        if os.path.exists(labels_dir):
+            for file in os.listdir(labels_dir):
+                if file.endswith(".nii.gz"):
+                    shutil.move(
+                        os.path.join(labels_dir, file),
+                        os.path.join(f"Masks-Task{task_num}", file),
+                    )
+
+    # Move JSON files from SegRap2023 directory to current directory
+    segrap_dir = "SegRap2023"
+    if not os.path.exists(segrap_dir):
+        print(f"Error: Directory '{segrap_dir}' does not exist")
+    else:
+        for file in os.listdir(segrap_dir):
+            if file.endswith(".json"):
+                shutil.move(os.path.join(segrap_dir, file), file)
+
+    # Move folder to dataset_dir
+    folders_to_move = [
+        "Images-CT",
+        "Images-contrastCT",
+        "Masks-Task1",
+        "Masks-Task2",
+    ]
+    for folder in folders_to_move:
+        move_folder(
+            os.path.join(tmp_dir, folder),
+            os.path.join(dataset_dir, folder),
+            create_dest=True,
+        )
+    # ====================================
+
+    print(f"Download and extraction completed for {dataset_name}")
+    os.chdir(dataset_dir)
+    shutil.rmtree(tmp_dir)
+    os.chdir(current_dir)
+
+
+def move_folder(source_folder, destination_folder, create_dest=True):
+    """
+    Moves a folder from source to destination.
+
+    Args:
+        source_folder (str): Path to the source folder to move
+        destination_folder (str): Path to the destination location
+        create_dest (bool): Whether to create the destination parent directory if it doesn't exist
+
+    Returns:
+        bool: True if successful, False otherwise
+
+    Raises:
+        FileNotFoundError: If the source folder doesn't exist
+    """
+    # Check if source folder exists
+    if not os.path.exists(source_folder):
+        raise FileNotFoundError(f"Source folder does not exist: {source_folder}")
+
+    # Create destination directory if it doesn't exist and create_dest is True
+    if create_dest and not os.path.exists(os.path.dirname(destination_folder)):
+        os.makedirs(os.path.dirname(destination_folder), exist_ok=True)
+
+    try:
+        # Move the folder
+        shutil.move(source_folder, destination_folder)
+        print(f"Successfully moved '{source_folder}' to '{destination_folder}'")
+        return True
+    except Exception as e:
+        print(f"Failed to move folder: {e}")
+        return False
+
+
+if __name__ == "__main__":
+    # Set up argument parser
+    parser = argparse.ArgumentParser(description="Download and extract dataset")
+    parser.add_argument(
+        "-d",
+        "--dir_datasets_data",
+        help="Directory path where datasets will be stored",
+        required=True,
+    )
+    parser.add_argument(
+        "-n",
+        "--dataset_name",
+        help="Name of the dataset",
+        required=True,
+    )
+    args = parser.parse_args()
+
+    # Create dataset directory
+    dataset_dir = os.path.join(args.dir_datasets_data, args.dataset_name)
+    os.makedirs(dataset_dir, exist_ok=True)
+
+    # Change to dataset directory
+    os.chdir(dataset_dir)
+
+    # Download and extract dataset
+    download_and_extract(dataset_dir, args.dataset_name)