A fast DICOM (PackBits) RLE plugin for pylibjpeg, written in Rust with a Python 3.7+ wrapper.
Linux, MacOS and Windows are all supported.
Installing the current releasepip install pylibjpeg-rleInstalling the development version
Make sure Python, Git and Rust are installed. For Windows, you also need to install Microsoft's C++ Build Tools.
git clone https://github.com/pydicom/pylibjpeg-rle cd pylibjpeg-rle python -m pip install .Supported Transfer Syntaxes UID Description Decoding Encoding 1.2.840.10008.1.2.5 RLE Lossless Yes Yes
from pydicom import dcmread
from pydicom.data import get_testdata_file
ds = dcmread(get_testdata_file("OBXXXX1A_rle.dcm"))
arr = ds.pixel_array
Alternatively you can use the included functions to decode a given dataset:
from rle import pixel_array, generate_frames
# Return the entire Pixel Data as an ndarray
arr = pixel_array(ds)
# Generator function that only processes 1 frame at a time,
# may help reduce memory usage when dealing with large Pixel Data
for arr in generate_frames(ds):
print(arr.shape)
Convert uncompressed pixel data to RLE encoding and save:
from pydicom import dcmread
from pydicom.data import get_testdata_file
from pydicom.uid import RLELossless
from rle import pixel_data
# Get the uncompressed pixel data
ds = dcmread(get_testdata_file("OBXXXX1A.dcm"))
arr = ds.pixel_array
# RLE encode and encapsulate `arr`
ds.PixelData = pixel_data(arr, ds)
# Set the correct *Transfer Syntax UID*
ds.file_meta.TransferSyntaxUID = RLELossless
ds.save_as('as_rle.dcm')
Time per 1000 decodes, pydicom's default RLE handler vs. pylibjpeg-rle
Dataset Pixels Bytes pydicom pylibjpeg-rle OBXXXX1A_rle.dcm 480,000 480,000 4.89 s 0.79 s OBXXXX1A_rle_2frame.dcm 960,000 960,000 9.89 s 1.65 s SC_rgb_rle.dcm 10,000 30,000 0.20 s 0.15 s SC_rgb_rle_2frame.dcm 20,000 60,000 0.32 s 0.18 s MR_small_RLE.dcm 4,096 8,192 0.35 s 0.13 s emri_small_RLE.dcm 40,960 81,920 1.13 s 0.28 s SC_rgb_rle_16bit.dcm 10,000 60,000 0.33 s 0.17 s SC_rgb_rle_16bit_2frame.dcm 20,000 120,000 0.56 s 0.21 s rtdose_rle_1frame.dcm 100 400 0.12 s 0.13 s rtdose_rle.dcm 1,500 6,000 0.53 s 0.26 s SC_rgb_rle_32bit.dcm 10,000 120,000 0.56 s 0.19 s SC_rgb_rle_32bit_2frame.dcm 20,000 240,000 1.03 s 0.28 sTime per 1000 encodes, pydicom's default RLE handler vs. pylibjpeg-rle
Dataset Pixels Bytes pydicom pylibjpeg-rle OBXXXX1A.dcm 480,000 480,000 30.7 s 1.36 s SC_rgb.dcm 10,000 30,000 1.80 s 0.09 s MR_small.dcm 4,096 8,192 2.29 s 0.04 s SC_rgb_16bit.dcm 10,000 60,000 3.57 s 0.17 s rtdose_1frame.dcm 100 400 0.19 s 0.003 s SC_rgb_32bit.dcm 10,000 120,000 7.20 s 0.33 sRetroSearch is an open source project built by @garambo | Open a GitHub Issue
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