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https://github.com/pydicom/pylibjpeg-rle
Fast DICOM RLE plugin for pylibjpeg
https://github.com/pydicom/pylibjpeg-rle
decoder dicom encoder packbits pydicom pylibjpeg python rle rle-decoder rle-encoder rust
Last synced: 9 days ago
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Fast DICOM RLE plugin for pylibjpeg
- Host: GitHub
- URL: https://github.com/pydicom/pylibjpeg-rle
- Owner: pydicom
- License: mit
- Created: 2020-03-18T00:35:37.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2024-02-01T22:32:07.000Z (10 months ago)
- Last Synced: 2024-10-30T02:03:27.967Z (16 days ago)
- Topics: decoder, dicom, encoder, packbits, pydicom, pylibjpeg, python, rle, rle-decoder, rle-encoder, rust
- Language: Python
- Homepage:
- Size: 123 KB
- Stars: 6
- Watchers: 3
- Forks: 3
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
## pylibjpeg-rle
A fast DICOM ([PackBits](https://en.wikipedia.org/wiki/PackBits)) RLE plugin for [pylibjpeg](https://github.com/pydicom/pylibjpeg), written in Rust with a Python 3.7+ wrapper.
Linux, MacOS and Windows are all supported.
### Installation
#### Installing the current release
```bash
pip install pylibjpeg-rle
```
#### Installing the development version
Make sure [Python](https://www.python.org/), [Git](https://git-scm.com/) and
[Rust](https://www.rust-lang.org/) are installed. For Windows, you also need to install
[Microsoft's C++ Build Tools](https://visualstudio.microsoft.com/thank-you-downloading-visual-studio/?sku=BuildTools&rel=16).
```bash
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 |
### Usage
#### Decoding
##### With pylibjpeg
```python
from pydicom import dcmread
from pydicom.data import get_testdata_file
ds = dcmread(get_testdata_file("OBXXXX1A_rle.dcm"))
arr = ds.pixel_array
```
##### Standalone with pydicom
Alternatively you can use the included functions to decode a given dataset:
```python
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)
```
#### Encoding
##### Standalone with pydicom
Convert uncompressed pixel data to RLE encoding and save:
```python
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')
```
### Benchmarks
#### Decoding
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 s |
#### Encoding
Time 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 s |