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Python convert .dcm to .png, images are too bright

I have to convert some files which come by default as .dcm to .png, I've found some code samples to achieve that around here but the end results are too bright. Could anybody have a look at this, please?

 def convert_to_png(file):
    ds = pydicom.dcmread(file)

    shape = ds.pixel_array.shape

    # Convert to float to avoid overflow or underflow losses.
    image_2d = ds.pixel_array.astype(float)

    # Rescaling grey scale between 0-255
    image_2d_scaled = (np.maximum(image_2d,0) / image_2d.max()) * 255.0

    # Convert to uint
    image_2d_scaled = np.uint8(image_2d_scaled)

    # Write the PNG file
    with open(f'{file.strip(".dcm")}.png', 'wb') as png_file:
        w = png.Writer(shape[1], shape[0], greyscale=True)
        w.write(png_file, image_2d_scaled)

I've tweaked around the code but nothing seems to work.

This is how the actual thing looks like as dicom and on the right side is the result of running this code enter image description here

Solution

  • Some DICOM datasets require window center/width rescaling of the original pixel intensities (via the (0028,1050) Window Center and (0028,1051) Window Width elements in the VOI LUT Module) in order to reproduce the way they were "viewed".

    pydicom has a function apply_voi_lut() for applying this windowing:

    from pydicom import dcmread
from pydicom.pixel_data_handlers.util import apply_voi_lut

ds = dcmread(file)
if 'WindowWidth' in ds:
    print('Dataset has windowing')

windowed = apply_voi_lut(ds.pixel_array, ds)

# Add code for rescaling to 8-bit...

    Depending on the dataset type you may need to use apply_modality_lut() beforehand.