Create Dynamic 3D Model from DICOM Fields

author: OpenTPS team

This example shows how to read a DICOM CT and deformation fields, create a dynamic 3D model with the mid-position CT and the deformation fields, and print the model information.

running time: ~ 5 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
import sys

import the needed opentps.core packages

from opentps.core.io.dataLoader import readData
from opentps.core.data.images._deformation3D import Deformation3D
from opentps.core.data.dynamicData._dynamic3DModel import Dynamic3DModel

Load DICOM CT

inputPaths = 'Path_to_your_CT_data/'  # replace with the path to your CT data folder
dataList = readData(inputPaths, maxDepth=0)
midP = dataList[0]
print(type(midP))

Load DICOM Deformation Fields

inputPaths = 'Path_to_your_deformation_fields/'  # replace with the path to your deformation fields folder
defList = readData(inputPaths, maxDepth=0)

Transform VectorField3D to deformation3D

deformationList = []
for df in defList:
    df2 = Deformation3D()
    df2.initFromVelocityField(df)
    deformationList.append(df2)
del defList
print(deformationList)

patient_name = 'OpenTPS_Patient'

Create Dynamic 3D Model

model3D = Dynamic3DModel(name=patient_name, midp=midP, deformationList=deformationList)
print(model3D)