Create 3D Sequence from DICOM

author: OpenTPS team

This example shows how to read data from a 4DCT folder, create a dynamic 3D sequence with the 4DCT data, and save this sequence in serialized format on the drive.

running time: ~ 10 minutes

Setting up the environment in google collab

import sys
if "google.colab" in sys.modules:
    from IPython import get_ipython
    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
    get_ipython().system('pip install ./opentps')
    get_ipython().system('pip install scipy==1.10.1')
    import opentps

imports

import os
from pathlib import Path
import sys

import the needed opentps.core packages

from opentps.core.io.dataLoader import readData
from opentps.core.data.dynamicData._dynamic3DSequence import Dynamic3DSequence
from opentps.core.io.serializedObjectIO import saveSerializedObjects

Get the current working directory, its parent, then add the testData folder at the end of it

testDataPath = os.path.join(Path(os.getcwd()).parent.absolute(), 'testData/')

# read a serialized dynamic sequence

dataPath = 'Path_to_your_4DCT_data/'  # replace with the path to your 4DCT data folder

print('Datas present in ' + dataPath + 'are loaded.')
dataList = readData(dataPath)
print(len(dataList), 'images found in the folder')
print('Image type =', type(dataList[0]))

create a Dynamic3DSequence and change its name

dynseq = Dynamic3DSequence(dyn3DImageList=dataList)
print('Type of the created object =', type(dynseq))
print('Sequence name =', dynseq.name)
dynseq.name = 'Light4DCT'
print('Sequence name = ', dynseq.name)
print('Sequence lenght =', len(dynseq.dyn3DImageList))

save it as a serialized object

savingPath = testDataPath + 'lightDynSeq'
saveSerializedObjects(dynseq, savingPath)