Crop 3D Data Around ROI

author: OpenTPS team

This example shows how to: - Read a serialized patient with a Dynamic3DSequence, a Dynamic3DModel and an RTStruct !! The data is not given in the test data folder of the project !! - Select an ROI from the RTStruct object - Get the ROI as an ROIMask - Get the box around the ROI in scanner coordinates - Crop the dynamic sequence and the dynamic model around the box

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
import sys

import the needed opentps.core packages

from opentps.core.processing.imageProcessing.resampler3D import crop3DDataAroundBox
from opentps.core.processing.segmentation.segmentation3D import getBoxAroundROI
from opentps.core.io.serializedObjectIO import loadDataStructure

Load the serialized patient data

dataPath = 'Path_to_your_serialized_patient_data/'  # replace with the path to your serialized patient data
patient = loadDataStructure(dataPath)[0]

dynSeq = patient.getPatientDataOfType("Dynamic3DSequence")[0]
dynMod = patient.getPatientDataOfType("Dynamic3DModel")[0]
rtStruct = patient.getPatientDataOfType("RTStruct")[0]

get the ROI and mask on which we want to apply the motion signal

print('Available ROIs')
rtStruct.print_ROINames()
bodyContour = rtStruct.getContourByName('body')
ROIMask = bodyContour.getBinaryMask(origin=dynMod.midp.origin, gridSize=dynMod.midp.gridSize, spacing=dynMod.midp.spacing)

get the box around the ROI

box = getBoxAroundROI(ROIMask)
marginInMM = [10, 10, 10]

crop the dynamic sequence and the dynamic model around the box

crop3DDataAroundBox(dynSeq, box, marginInMM=marginInMM)
print('-'*50)
crop3DDataAroundBox(dynMod, box, marginInMM=marginInMM)