Reading *.mhd/*.raw format in python

Reading *.mhd/*.raw format in python

To read medical image data stored in the .mhd (MetaImage) and .raw format in Python, you can use libraries like SimpleITK or Pydicom. These libraries are commonly used in the medical imaging field to handle various medical image formats.

Here's how you can read .mhd and .raw files using SimpleITK:

import SimpleITK as sitk # Path to the .mhd file mhd_path = 'path/to/your/image.mhd' # Read the image using SimpleITK image = sitk.ReadImage(mhd_path) # Convert the image to a numpy array image_array = sitk.GetArrayFromImage(image) # Access metadata if needed spacing = image.GetSpacing() origin = image.GetOrigin() direction = image.GetDirection() # Print the shape of the numpy array print(image_array.shape)

And here's how you can read .mhd and .raw files using Pydicom:

import pydicom # Path to the .mhd file (Pydicom does not directly support .mhd, but you can use .dcm or .dicom) mhd_path = 'path/to/your/image.dcm' # Read the DICOM file using Pydicom ds = pydicom.dcmread(mhd_path) # Get pixel data as a numpy array pixel_array = ds.pixel_array # Print the shape of the numpy array print(pixel_array.shape)

Please note that .mhd and .raw are file pairs commonly used in the ITK framework for medical imaging. The .mhd file contains metadata information while the .raw file contains raw pixel data. You might need to adapt the code according to the specifics of your image data and the libraries you choose.

Examples

  1. Reading a .mhd/.raw File in Python

    • This snippet demonstrates how to read a .mhd/.raw file and extract image data using the SimpleITK library.
    # Install `SimpleITK` if needed !pip install SimpleITK 
    import SimpleITK as sitk # Load the .mhd file image = sitk.ReadImage("image.mhd") # Convert the image to a numpy array image_array = sitk.GetArrayFromImage(image) print("Image Shape:", image_array.shape)

  2. Visualizing a .mhd/.raw Image in Python

    • This snippet shows how to visualize a .mhd/.raw image using matplotlib.
    # Install `matplotlib` and `SimpleITK` if needed !pip install matplotlib SimpleITK 
    import SimpleITK as sitk import matplotlib.pyplot as plt # Load the .mhd file image = sitk.ReadImage("image.mhd") # Convert to numpy array image_array = sitk.GetArrayFromImage(image) # Visualize a slice of the image plt.imshow(image_array[0], cmap="gray") plt.title("MHD Image") plt.show()

  3. Reading Multiple .mhd/.raw Files in Python

    • This snippet demonstrates how to read multiple .mhd/.raw files and process them.
    import os import SimpleITK as sitk # Path to the directory containing .mhd files directory = "path/to/mhd_files" for file_name in os.listdir(directory): if file_name.endswith(".mhd"): # Read the .mhd file image = sitk.ReadImage(os.path.join(directory, file_name)) image_array = sitk.GetArrayFromImage(image) print(f"Read {file_name}, Shape:", image_array.shape)

  4. Converting .mhd/.raw to Other Formats in Python

    • This snippet demonstrates how to convert .mhd/.raw images to other formats like PNG or JPEG.
    import SimpleITK as sitk # Load the .mhd file image = sitk.ReadImage("image.mhd") # Convert to PNG sitk.WriteImage(image, "image.png") print("Converted .mhd to PNG.")

  5. Processing Medical Images from .mhd/.raw Files in Python

    • This snippet shows how to perform basic processing on a .mhd/.raw image, like resizing or cropping.
    import SimpleITK as sitk # Load the .mhd file image = sitk.ReadImage("image.mhd") # Resize the image new_size = [100, 100, 100] # New size for each dimension resized_image = sitk.Resample( image, new_size, sitk.Transform(), sitk.sitkLinear, image.GetOrigin(), image.GetSpacing(), image.GetDirection(), 0.0, image.GetPixelID(), ) print("Resized image.")

  6. Creating a 3D Visualization from .mhd/.raw Files in Python

    • This snippet demonstrates how to create a 3D visualization from .mhd/.raw files using mayavi.
    # Install `mayavi` if needed !pip install mayavi 
    import SimpleITK as sitk from mayavi import mlab # Load the .mhd file image = sitk.ReadImage("image.mhd") # Convert to numpy array image_array = sitk.GetArrayFromImage(image) # Visualize the 3D image mlab.contour3d(image_array, contours=10, opacity=0.5) mlab.show()

  7. Applying Filters to .mhd/.raw Images in Python

    • This snippet demonstrates how to apply filters to .mhd/.raw images using SimpleITK.
    import SimpleITK as sitk # Load the .mhd file image = sitk.ReadImage("image.mhd") # Apply Gaussian smoothing smoothed_image = sitk.SmoothingRecursiveGaussian(image, sigma=1.0) # Convert to numpy array smoothed_array = sitk.GetArrayFromImage(smoothed_image) print("Applied Gaussian smoothing.")

  8. Combining Multiple .mhd/.raw Images in Python

    • This snippet shows how to combine multiple .mhd/.raw images into a single 3D volume.
    import SimpleITK as sitk # Load multiple .mhd files and combine them images = [sitk.ReadImage(f"image_{i}.mhd") for i in range(1, 4)] # Combine images into a single volume combined_image = sitk.JoinSeries(images) print("Combined multiple images into a single volume.")

  9. Extracting Metadata from .mhd Files in Python

    • This snippet demonstrates how to extract metadata (like dimensions, spacing, origin) from a .mhd file.
    import SimpleITK as sitk # Load the .mhd file image = sitk.ReadImage("image.mhd") # Extract metadata dimensions = image.GetSize() spacing = image.GetSpacing() origin = image.GetOrigin() print("Dimensions:", dimensions) print("Spacing:", spacing) print("Origin:", origin)

  10. Saving .mhd/.raw Files with Custom Metadata in Python

    • This snippet demonstrates how to save a .mhd/.raw file with custom metadata in Python.
    import SimpleITK as sitk # Create a sample image image = sitk.GaussianSource(size=[100, 100, 100], mean=[50, 50, 50], sigma=[10, 10, 10]) # Set custom metadata image.SetSpacing([1.0, 1.0, 1.0]) image.SetOrigin([0, 0, 0]) # Save as .mhd/.raw sitk.WriteImage(image, "custom_image.mhd") print("Saved .mhd with custom metadata.")

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