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https://github.com/pydicom/pylibjpeg
A Python framework for decoding JPEG images, with a focus on supporting pydicom
https://github.com/pydicom/pylibjpeg
dcm decoding dicom j2k jls jp2 jpeg jpeg-ls jpeg-xt jpeg2000 jpg pydicom python
Last synced: 1 day ago
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A Python framework for decoding JPEG images, with a focus on supporting pydicom
- Host: GitHub
- URL: https://github.com/pydicom/pylibjpeg
- Owner: pydicom
- License: mit
- Created: 2020-02-21T11:18:03.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2024-06-17T03:06:42.000Z (5 months ago)
- Last Synced: 2024-10-30T02:03:28.252Z (15 days ago)
- Topics: dcm, decoding, dicom, j2k, jls, jp2, jpeg, jpeg-ls, jpeg-xt, jpeg2000, jpg, pydicom, python
- Language: Python
- Homepage:
- Size: 50 MB
- Stars: 46
- Watchers: 6
- Forks: 5
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
## pylibjpeg
A Python 3.8+ framework for decoding JPEG images and decoding/encoding RLE datasets, with a focus on providing support for [pydicom](https://github.com/pydicom/pydicom).
### Installation
#### Installing the current release
```
pip install pylibjpeg
```
##### Installing extra requirements
The package can be installed with extra requirements to enable support for JPEG (with `libjpeg`), JPEG 2000 (with `openjpeg`) and Run-Length Encoding (RLE) (with `rle`), respectively:
```
pip install pylibjpeg[libjpeg,openjpeg,rle]
```
Or alternatively with just `all`:
```
pip install pylibjpeg[all]
```
#### Installing the development version
Make sure [Git](https://git-scm.com/) is installed, then
```bash
git clone https://github.com/pydicom/pylibjpeg
python -m pip install pylibjpeg
```
### Plugins
One or more plugins are required before *pylibjpeg* is able to handle JPEG images or RLE datasets. To handle a given format or DICOM Transfer Syntax
you first have to install the corresponding package:
#### Supported Image Formats
|Format |Decode?|Encode?|Plugin | License |Based on |
|--- |------ |--- |--- |--- |--- |
|JPEG, JPEG-LS and JPEG XT|Yes |No |[pylibjpeg-libjpeg][1] | GPLv3 |[libjpeg][2] |
|JPEG 2000 |Yes |Yes |[pylibjpeg-openjpeg][3]| MIT |[openjpeg][4]|
|RLE Lossless (PackBits) |Yes |Yes |[pylibjpeg-rle][5] | MIT |- |
#### Supported DICOM Transfer Syntaxes
|UID | Description | Plugin |
|--- |--- |---- |
|1.2.840.10008.1.2.4.50 |JPEG Baseline (Process 1) |[pylibjpeg-libjpeg][1] |
|1.2.840.10008.1.2.4.51 |JPEG Extended (Process 2 and 4) |[pylibjpeg-libjpeg][1] |
|1.2.840.10008.1.2.4.57 |JPEG Lossless, Non-Hierarchical (Process 14) |[pylibjpeg-libjpeg][1] |
|1.2.840.10008.1.2.4.70 |JPEG Lossless, Non-Hierarchical, First-Order Prediction(Process 14, Selection Value 1) | [pylibjpeg-libjpeg][1]|
|1.2.840.10008.1.2.4.80 |JPEG-LS Lossless |[pylibjpeg-libjpeg][1] |
|1.2.840.10008.1.2.4.81 |JPEG-LS Lossy (Near-Lossless) Image Compression |[pylibjpeg-libjpeg][1] |
|1.2.840.10008.1.2.4.90 |JPEG 2000 Image Compression (Lossless Only) |[pylibjpeg-openjpeg][3]|
|1.2.840.10008.1.2.4.91 |JPEG 2000 Image Compression |[pylibjpeg-openjpeg][3]|
|1.2.840.10008.1.2.4.201|High-Throughput JPEG 2000 Image Compression (Lossless Only) |[pylibjpeg-openjpeg][3]|
|1.2.840.10008.1.2.4.202|High-Throughput JPEG 2000 with RPCL Options Image Compression (Lossless Only) |[pylibjpeg-openjpeg][3]|
|1.2.840.10008.1.2.4.203|High-Throughput JPEG 2000 Image Compression |[pylibjpeg-openjpeg][3]|
|1.2.840.10008.1.2.5 |RLE Lossless |[pylibjpeg-rle][5] |
If you're not sure what the dataset's *Transfer Syntax UID* is, it can be
determined with:
```python
>>> from pydicom import dcmread
>>> ds = dcmread('path/to/dicom_file')
>>> ds.file_meta.TransferSyntaxUID.name
```
[1]: https://github.com/pydicom/pylibjpeg-libjpeg
[2]: https://github.com/thorfdbg/libjpeg
[3]: https://github.com/pydicom/pylibjpeg-openjpeg
[4]: https://github.com/uclouvain/openjpeg
[5]: https://github.com/pydicom/pylibjpeg-rle
### Usage
#### Decoding
##### With pydicom
Assuming you have *pydicom* v2.1+ and suitable plugins installed:
```python
from pydicom import dcmread
from pydicom.data import get_testdata_file
# With the pylibjpeg-libjpeg plugin
ds = dcmread(get_testdata_file('JPEG-LL.dcm'))
jpg_arr = ds.pixel_array
# With the pylibjpeg-openjpeg plugin
ds = dcmread(get_testdata_file('JPEG2000.dcm'))
j2k_arr = ds.pixel_array
# With the pylibjpeg-rle plugin and pydicom v2.2+
ds = dcmread(get_testdata_file('OBXXXX1A_rle.dcm'))
# pydicom defaults to the numpy handler for RLE so need
# to explicitly specify the use of pylibjpeg
ds.decompress("pylibjpeg")
rle_arr = ds.pixel_array
```
##### Standalone JPEG decoding
You can also just use *pylibjpeg* to decode JPEG images to a [numpy ndarray](https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html), provided you have a suitable plugin installed:
```python
from pylibjpeg import decode
# Can decode using the path to a JPG file as str or path-like
arr = decode('filename.jpg')
# Or a file-like...
with open('filename.jpg', 'rb') as f:
arr = decode(f)
# Or bytes...
with open('filename.jpg', 'rb') as f:
arr = decode(f.read())
```
#### Encoding
##### With pydicom
Assuming you have *pydicom* v2.2+ and suitable plugins installed:
```python
from pydicom import dcmread
from pydicom.data import get_testdata_file
from pydicom.uid import RLELossless
ds = dcmread(get_testdata_file("CT_small.dcm"))
# Encode in-place using RLE Lossless and update the dataset
# Updates the Pixel Data, Transfer Syntax UID and Planar Configuration
ds.compress(RLELossless)
# Save compressed
ds.save_as("CT_small_rle.dcm")
```