Gradient Decode Dicom Tensorflow Operation

Getting started

1. Install the DCMTK toolkit

   sudo apt-get install libdcmtk-dev

2. Install gradient_decode_dicom

   pip3 install gradient-decode-dicom

3. Example Colab notebook

Documentation

The gradient_decode_dicom package has two operations, decode_dicom_image which decodes the pixel data from DICOM files, and decode_dicom_data which decodes tag information. tags contains useful DICOM tags such as tags.PatientsName. We borrow the same tag notation from the pydicom dicom package.

Getting DICOM Image Data

gradient_decode_dicom.decode_dicom_image(
    contents,
    color_dim=False,
    on_error='skip',
    scale='preserve'
    dtype=tf.uint16
    name=None
)

• contents: A Tensor of type string. 0-D. The byte string encoded DICOM file
• color_dim: An optional bool. Defaults to False. If True, a third channel will be appended to all images forming a 3-D tensor. A 1024 x 1024 grayscale image will be 1024 x 1024 x 1
• on_error: Defaults to skip. This attribute establishes the behavior in case an error occurs on opening the image or if the output type cannot accomodate all the possible input values. For example if the user sets the output dtype to tf.uint8, but a dicom image stores a tf.uint16 type. strict throws an error. skip returns a 1-D empty tensor. lossy continues with the operation scaling the value via the scale attribute.
• scale: Defaults to preserve. This attribute establishes what to do with the scale of the input values. auto will autoscale the input values, if the output type is integer, auto will use the maximum output scale for example a uint8 which stores values from [0, 255] can be linearly stretched to fill a uint16 that is [0,65535]. If the output is float, auto will scale to [0,1]. preserve keeps the values as they are, an input value greater than the maximum possible output will be clipped.
• dtype: An optional tf.DType from: tf.uint8, tf.uint16, tf.uint32, tf.uint64, tf.float16, tf.float32, tf.float64. Defaults to tf.uint16.
• name: A name for the operation (optional).

Returns

A Tensor of type dtype and the shape is determined by the DICOM file.

Getting DICOM Tag Data

gradient_decode_dicom.decode_dicom_data(
    contents,
    tags=None,
    name=None
)

• contents: A Tensor of type string. 0-D. The byte string encoded DICOM file
• tags: A Tensor of type tf.uint32 of any dimension. These uint32 numbers map directly to DICOM tags
• name: A name for the operation (optional).

Returns

A Tensor of type tf.string and same shape as tags. If a dicom tag is a list of strings, they are combined into one string and seperated by a double backslash \\. There is a bug in DCMTK if the tag is a list of numbers, only the zeroth element will be returned as a string.