Working with Overlay Data

How to work with overlay data in pydicom.


Overlays in DICOM are present in what’s called a Repeating Group, where the group number of the element tags are defined over a range rather than a specific value. For example, the tag’s group number for (60xx,3000) Overlay Data may be (in hex) 6000, 6002, or any even value up to 601E. This allows a dataset to include multiple overlays, where the related elements for each overlay use the same group number. Because of this, the only way to access a particular element from an overlay is to use the Dataset[group, elem] method:

>>> import pydicom
>>> from import get_testdata_files
>>> fpath = get_testdata_files("MR-SIEMENS-DICOM-WithOverlays.dcm")[0]
>>> ds = pydicom.dcmread(fpath)
>>> elem = ds[0x6000, 0x3000]  # returns a DataElement
>>> print(elem)
(6000, 3000) Overlay Data                        OW: Array of 29282 elements

pydicom tends to be “lazy” in interpreting DICOM data. For example, by default it doesn’t do anything with overlay data except read in the raw bytes:

>>> elem.value 



Dataset.overlay_array() requires NumPy.

The Overlay Data element contains the raw bytes exactly as found in the file as bit-packed data. To unpack and get an overlay in a more useful form you can use the overlay_array() method to return a numpy.ndarray. To use it you simply pass the group number of the overlay elements you’re interested in:

>>> arr = ds.overlay_array(0x6000) 
>>> arr
array([[ 0, 0, 0, ...,  0,  0,  0],
       [ 0, 0, 0, ...,  0,  0,  0],
       [ 0, 0, 0, ...,  0,  0,  0],
       [ 0, 0, 0, ...,  0,  0,  0],
       [ 0, 0, 0, ...,  0,  0,  0],
       [ 0, 0, 0, ...,  0,  0,  0],], dtype=uint8)
>>> arr.shape
(484, 484)

One thing to remember when dealing with Overlay Data is that the top left of the overlay doesn’t necessarily have to line up with the top left of the related Pixel Data. The actual offset between them can be determined from (60xx,0050) Overlay Origin, where a value of [1, 1] indicates that the top left pixels are aligned and a value of [0, 0] indicates that the overlay pixels start 1 row above and 1 row to the left of the image pixels.

NumPy can be used to modify the pixels, but if the changes are to be saved, they must be bit-packed (using something like pack_bits()) and written back to the correct element:

# Add a line
arr[10, :] = 1

# Pack the data
from pydicom.pixel_data_handlers.numpy_handler import pack_bits
packed_bytes = pack_bits(arr)

# Update the element value
ds[0x6000, 0x3000].value = packed_bytes

Some changes may require other DICOM elements to be modified. For example, if the overlay data is reduced (e.g. a 512x512 image is collapsed to 256x256) then the corresponding (60xx,0010) Overlay Rows and (60xx,0011) Overlay Columns should be set appropriately. You must explicitly set these yourself; pydicom does not do so automatically.