Working with DICOM images in Python
Trigger
At the Kaggle Competition, CT scan images and DICOM images of the chest came out and I didn't know how to handle them.
What you can do
・ What is a DICOM image? ・ How to display DICOM images and handle data
What is a DICOM image?
DICOM is a standard that defines the formats of medical images taken by CT, MRI, CR, etc. and the communication protocol between the medical image devices that handle them. wiki
Example of use
Installation
%pip install pydicom
dataset contains metadata
import pydicom
import matplotlib.pyplot as plt
from pydicom.data import get_testdata_files
filename = get_testdata_files('CT_small.dcm')[0]
dataset = pydicom.dcmread(filename)
print(dataset)
The value can be displayed and accessed by key name (.Rows) or number (0x0010,0x0010).
dataset[0x0010, 0x0010]
dataset.Rows
Until the image is displayed
pat_name = dataset.PatientName
display_name = pat_name.family_name + ", " + pat_name.given_name
print("Patient's name...:", display_name)
print("Patient id.......:", dataset.PatientID)
print("Modality.........:", dataset.Modality)
print("Study Date.......:", dataset.StudyDate)
print(dataset[0x0018, 0x0050])
if 'PixelData' in dataset:
rows = int(dataset.Rows)
cols = int(dataset.Columns)
print("Image size.......: {rows:d} x {cols:d}, {size:d} bytes".format(
rows=rows, cols=cols, size=len(dataset.PixelData)))
if 'PixelSpacing' in dataset:
print("Pixel spacing....:", dataset.PixelSpacing)
# use .get() if not sure the item exists, and want a default value if missing
print("Slice location...:", dataset.get('SliceLocation', "(missing)"))
# plot the image using matplotlib
plt.imshow(dataset.pixel_array, cmap=plt.cm.bone)
plt.show()
reference
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