Pure python package for DICOM medical file reading and writing
Project description
pydicom
pydicom is a pure Python package for working with DICOM files. It lets you read, modify and write DICOM data in an easy "pythonic" way.
As a pure Python package, pydicom can run anywhere Python runs without any other requirements, although if you're working with Pixel Data then we recommend you also install NumPy.
If you're looking for a Python library for DICOM networking then you might be interested in another of our projects: pynetdicom.
Installation
Using pip:
pip install pydicom
Using conda:
conda install -c conda-forge pydicom
For more information, including installation instructions for the development version, see the installation guide.
Documentation
The pydicom user guide, tutorials, examples and API reference documentation is available for both the current release and the development version on GitHub Pages.
Pixel Data
Compressed and uncompressed Pixel Data is always available to be read, changed and written as bytes:
>>> from pydicom import dcmread
>>> from pydicom.data import get_testdata_file
>>> path = get_testdata_file("CT_small.dcm")
>>> ds = dcmread(path)
>>> type(ds.PixelData)
<class 'bytes'>
>>> len(ds.PixelData)
32768
>>> ds.PixelData[:2]
b'\xaf\x00'
If NumPy is installed, Pixel Data can be converted to an ndarray using the Dataset.pixel_array property:
>>> arr = ds.pixel_array
>>> arr.shape
(128, 128)
>>> arr
array([[175, 180, 166, ..., 203, 207, 216],
[186, 183, 157, ..., 181, 190, 239],
[184, 180, 171, ..., 152, 164, 235],
...,
[906, 910, 923, ..., 922, 929, 927],
[914, 954, 938, ..., 942, 925, 905],
[959, 955, 916, ..., 911, 904, 909]], dtype=int16)
Compressed Pixel Data
JPEG, JPEG-LS and JPEG 2000
Converting JPEG compressed Pixel Data to an ndarray requires installing one or more additional Python libraries. For information on which libraries are required, see the pixel data handler documentation.
Compressing data into one of the JPEG formats is not currently supported.
RLE
RLE encoded Pixel Data only requires NumPy, and compression and decompression are both supported.
Examples
More examples are available in the documentation.
Change a patient's ID
from pydicom import dcmread
ds = dcmread("/path/to/file.dcm")
# Edit the (0010,0020) 'Patient ID' element
ds.PatientID = "12345678"
ds.save_as("/path/to/file_updated.dcm")
Display the Pixel Data
With NumPy and matplotlib
import matplotlib.pyplot as plt
from pydicom import dcmread
from pydicom.data import get_testdata_file
# The path to a pydicom test dataset
path = get_testdata_file("CT_small.dcm")
ds = dcmread(path)
# `arr` is a numpy.ndarray
arr = ds.pixel_array
plt.imshow(arr, cmap="gray")
plt.show()
Contributing
To contribute to pydicom, read our contribution guide.
To contribute an example or extension of pydicom that doesn't belong with the core software, see our contribution repository: contrib-pydicom.
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