Pydicom

For handling compressed DICOM files, additional packages may be needed:

uv pip install pylibjpeg pylibjpeg-libjpeg pylibjpeg-openjpeg  # JPEG compression
uv pip install python-gdcm  # Alternative compression handler

Core Workflows

Reading DICOM Files

Read a DICOM file using pydicom.dcmread():

import pydicom

# Read a DICOM file
ds = pydicom.dcmread('path/to/file.dcm')

# Access metadata
print(f"Patient Name: {ds.PatientName}")
print(f"Study Date: {ds.StudyDate}")
print(f"Modality: {ds.Modality}")

# Display all elements
print(ds)

Key points:

• dcmread() returns a Dataset object
• Access data elements using attribute notation (e.g., ds.PatientName) or tag notation (e.g., ds[0x0010, 0x0010])
• Use ds.file_meta to access file metadata like Transfer Syntax UID
• Handle missing attributes with getattr(ds, 'AttributeName', default_value) or hasattr(ds, 'AttributeName')

Working with Pixel Data

Extract and manipulate image data from DICOM files:

import pydicom
import numpy as np
import matplotlib.pyplot as plt

# Read DICOM file
ds = pydicom.dcmread('image.dcm')

# Get pixel array (requires numpy)
pixel_array = ds.pixel_array

# Image information
print(f"Shape: {pixel_array.shape}")
print(f"Data type: {pixel_array.dtype}")
print(f"Rows: {ds.Rows}, Columns: {ds.Columns}")

# Apply windowing for display (CT/MRI)
if hasattr(ds, 'WindowCenter') and hasattr(ds, 'WindowWidth'):
    from pydicom.pixel_data_handlers.util import apply_voi_lut
    windowed_image = apply_voi_lut(pixel_array, ds)