Prerequisite : MatplotlibĀ
DICOM stands for Digital Imaging and Communications in Medicine. DICOM files were introduced to maintain uniformity among varied types of medical image modalities. It is a standard format to view, store, share and retrieve medical images.
Python offers a powerful module, pydicom to work with the DICOM files such as medical images, reports and radiotherapy objects. pydicom reads, modifies and write data in DICOM files.Ā
Installation
Run the following commands in the command prompt:
pip install dicom
pip install matplotlib
pydicom enables us to work with DICOM files, in this article we will discuss the mechanism of viewing the DICOM file using pydicom and matplotlib. For reading the DICOM files we use pydicom package and to view the result we use matplotlib.
Input given
The path where the dicom file is stored is passed as an argument to data_manager.get_files method.
Using pydicom with matplotlibĀ
Explanation:
- Import module
- Read DICOM file using pydicom.data.data_manager.get_files() method
Syntax :Ā
pydicom.data.data_manager.get_files(base,pass_dicom)[0]
Parameter:
- Base : is base directory to recursively search as a string.
- Pattern : By default it is ā*ā. It is a string pattern which is used to filter the files.
- Provide 2 arguments: base and pattern
- Displays the data as image i.e. on 2D regular raster.
- Display image
Note : Enter the location of the dcm file excluding the file name in the variable names base and enter the file name in the pass_dicom variable. In this case the file is stored at a directory named dicom_image as shown:
Download the dcm file from here and rename it to: 1-12.dcm
Compare the path shown in the address bar with the values stored in the variable base and pass_dicom
Program:
Python3
import matplotlib.pyplot as plt import pydicom import pydicom.data Ā Ā # Full path of the DICOM file is passed in base base = r"C:\Users\Ajit Gupta\Documents\dicom image"pass_dicom = "1-12.dcm"Ā # file name is 1-12.dcm Ā Ā # enter DICOM image name for pattern # result is a list of 1 element filename = pydicom.data.data_manager.get_files(base, pass_dicom)[0] Ā Ā ds = pydicom.dcmread(filename) Ā Ā plt.imshow(ds.pixel_array, cmap=plt.cm.bone)Ā # set the color map to bone plt.show() |
Output:
