Create a Dicom from multiple jpg images

Question

I've successfully built dicoms with one images but I cannot find a way to add more... I think the problem may be in my pixel array, can anyone help me correct it?

# Populate required values for file meta information
meta = pydicom.Dataset()
meta.TransferSyntaxUID = pydicom.uid.ExplicitVRLittleEndian
meta.MediaStorageSOPClassUID = pydicom._storage_sopclass_uids.MRImageStorage
meta.MediaStorageSOPInstanceUID = pydicom.uid.generate_uid()

# build dataset
ds = Dataset()
ds.file_meta = meta
ds.fix_meta_info()

# unknown options
ds.is_little_endian = True
ds.is_implicit_VR = False
ds.SOPClassUID = pydicom._storage_sopclass_uids.MRImageStorage
ds.SeriesInstanceUID = pydicom.uid.generate_uid()
ds.StudyInstanceUID = pydicom.uid.generate_uid()
ds.FrameOfReferenceUID = pydicom.uid.generate_uid()
ds.BitsStored = 16
ds.BitsAllocated = 16
ds.SamplesPerPixel = 1
ds.HighBit = 15
ds.ImagesInAcquisition = "1"
ds.InstanceNumber = 1
ds.ImagePositionPatient = r"0\0\1"
ds.ImageOrientationPatient = r"1\0\0\0\-1\0"
ds.ImageType = r"ORIGINAL\PRIMARY\AXIAL"
ds.RescaleIntercept = "0"
ds.RescaleSlope = "1"
ds.PixelRepresentation = 1

# Case options
ds.PatientName = "Anonymous"
ds.PatientID = "123456"
ds.Modality = "MR"
ds.StudyDate = '20200225'
ds.ContentDate = '20200225'

def ensure_even(stream):
    # Very important for some viewers
    if len(stream) % 2:
        return stream + b"\x00"
    return stream

pixel_data_list = []
for root, dir, filenames in walk(folder):
    filenames.sort(key=natural_keys)
    for filename in filenames:
        filename = folder + filename
        # convert image to grayscale
        img = Image.open(filename).convert('L')
        img.save(filename)

        # open image, decode and ensure_even stream
        with open(filename, 'rb') as f:
            arr = decode(f)

        pixel_data_list.append(arr.tobytes())

# required for pixel handler
ds.BitsStored = 8
ds.BitsAllocated = 8
ds.HighBit = 7
ds.PixelRepresentation = 0

# grayscale without compression
ds.PhotometricInterpretation = "MONOCHROME2"
ds.SamplesPerPixel = 1  # 1 color = 1 sampleperpixel
ds.file_meta.TransferSyntaxUID = pydicom.uid.ExplicitVRLittleEndian
ds.PixelData = array(pixel_data_list)
ds.NumberOfFrames = len(pixel_data_list)

# Image shape
ds['PixelData'].is_undefined_length = False
ds.Columns = img.width
ds.Rows = img.height

# validate and save
pydicom.dataset.validate_file_meta(ds.file_meta, enforce_standard=True)
new_filename = filename.replace('.jpg', name + '.dcm')
ds.save_as(new_filename, write_like_original=False)

Also can't seem to compress the images, only monochrome works (see tries here https://stackoverflow.com/a/68939321/1827162 )... That's not as problematic though, the most important thing is to be able to add multiple images. Thanks for any pointer !

Answer 1

Pixel Data should be bytes . If your transfer syntax is uncompressed then you need to concatenate the data together and if the length of the concatenated data is odd then you must add a trailing padding byte:

# For uncompressed transfer syntaxes only!
pixel_data = b"".join(pixel_data_list)
ds.PixelData = pixel_data + b"\x00" if len(pixel_data) % 2 else pixel_data

For compressed transfer syntaxes you must use encapsulation