Applying Baseline Shift to a Model

author: OpenTPS team

This example demonstrates how to apply a baseline shift to a model and visualize the results.

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 numpy as np
import matplotlib.pyplot as plt
import logging
import os

import the needed opentps.core packages

from opentps.core.data.images import CTImage
from opentps.core.data.images import ROIMask
from opentps.core.processing.imageProcessing.syntheticDeformation import applyBaselineShift
from opentps.core.data.dynamicData._dynamic3DModel import Dynamic3DModel
from opentps.core.data.dynamicData._dynamic3DSequence import Dynamic3DSequence
from opentps.core.examples.syntheticData import *

logger = logging.getLogger(__name__)

Output path

output_path = os.path.join(os.getcwd(), 'Output', 'ExampleApplyBaselineShiftToModel')
if not os.path.exists(output_path):
        os.makedirs(output_path)
logger.info('Files will be stored in {}'.format(output_path))

Generate synthetic 4DCT, mask, and MidP

# GENERATE SYNTHETIC 4DCT
CT4D = createSynthetic4DCT()

# GENERATE MASK
mask = np.full(CT4D.dyn3DImageList[0].gridSize, 0)
mask[38:52, 87:103, 39:54] = 1
roi = ROIMask(imageArray=mask, origin=[0, 0, 0], spacing=[1, 1, 1.5])

# GENERATE MIDP
Model = Dynamic3DModel()
Model.computeMidPositionImage(CT4D, 0, tryGPU=True)

Dynamic 3D Sequence Created with  0 images

Apply baseline shift

ModelShifted, maskShifted = applyBaselineShift(Model, roi, [5, 0, 10])

Regenerate 4D sequences from models

CT4DRegen = Dynamic3DSequence()
for i in range(len(CT4D.dyn3DImageList)):
    CT4DRegen.dyn3DImageList.append(Model.generate3DImage(i / len(CT4D.dyn3DImageList), amplitude=1))
CT4DShifted = Dynamic3DSequence()
for i in range(len(CT4D.dyn3DImageList)):
    CT4DShifted.dyn3DImageList.append(ModelShifted.generate3DImage(i/len(CT4D.dyn3DImageList), amplitude=1))

Dynamic 3D Sequence Created with  0 images
Dynamic 3D Sequence Created with  0 images

Display results

fig, ax = plt.subplots(3, 7)
fig.tight_layout()
y_slice = 95
ax[1, 0].imshow(Model.midp.imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[1, 0].title.set_text('MidP')
ax[2, 0].imshow(ModelShifted.midp.imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[2, 0].title.set_text('MidP shifted')

average = CT4D.dyn3DImageList[0].copy()
for i in range(len(CT4D.dyn3DImageList)-1):
    average._imageArray += CT4D.dyn3DImageList[i+1]._imageArray
average._imageArray = average.imageArray/len(CT4D.dyn3DImageList)
averageRegen = CT4DRegen.dyn3DImageList[0].copy()
for i in range(len(CT4DRegen.dyn3DImageList) - 1):
    averageRegen._imageArray += CT4DRegen.dyn3DImageList[i + 1]._imageArray
averageRegen._imageArray = averageRegen.imageArray / len(CT4DRegen.dyn3DImageList)
averageShifted = CT4DShifted.dyn3DImageList[0].copy()
for i in range(len(CT4DShifted.dyn3DImageList) - 1):
    averageShifted._imageArray += CT4DShifted.dyn3DImageList[i + 1]._imageArray
averageShifted._imageArray = averageShifted.imageArray / len(CT4DShifted.dyn3DImageList)

ax[0, 1].imshow(average.imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[0, 1].title.set_text('Average')
ax[1, 1].imshow(averageRegen.imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[1, 1].title.set_text('Gen average')
ax[2, 1].imshow(averageShifted.imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[2, 1].title.set_text('Gen average shifted')

averageRegen._imageArray -= average._imageArray
averageShifted._imageArray -= average._imageArray
average._imageArray -= average._imageArray
ax[0, 0].imshow(average.imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[0, 0].title.set_text('-')
ax[0, 2].imshow(average.imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[0, 2].title.set_text('-')
ax[1, 2].imshow(averageRegen.imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[1, 2].title.set_text('Gen average diff')
ax[2, 2].imshow(averageShifted.imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[2, 2].title.set_text('Gen average shifted diff')

ax[0, 3].imshow(CT4D.dyn3DImageList[0].imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[0, 3].title.set_text('Phase 0')
ax[1, 3].imshow(CT4DRegen.dyn3DImageList[0].imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[1, 3].title.set_text('Gen phase 0')
ax[2, 3].imshow(CT4DShifted.dyn3DImageList[0].imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[2, 3].title.set_text('Gen phase 0 shifted')

ax[0, 4].imshow(CT4D.dyn3DImageList[1].imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[0, 4].title.set_text('Phase 1')
ax[1, 4].imshow(CT4DRegen.dyn3DImageList[1].imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[1, 4].title.set_text('Gen phase 1')
ax[2, 4].imshow(CT4DShifted.dyn3DImageList[1].imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[2, 4].title.set_text('Gen phase 1 shifted')

ax[0, 5].imshow(CT4D.dyn3DImageList[2].imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[0, 5].title.set_text('Phase 2')
ax[1, 5].imshow(CT4DRegen.dyn3DImageList[2].imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[1, 5].title.set_text('Gen phase 2')
ax[2, 5].imshow(CT4DShifted.dyn3DImageList[2].imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[2, 5].title.set_text('Gen phase 2 shifted')

ax[0, 6].imshow(CT4D.dyn3DImageList[3].imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[0, 6].title.set_text('Phase 3')
ax[1, 6].imshow(CT4DRegen.dyn3DImageList[3].imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[1, 6].title.set_text('Gen phase 3')
ax[2, 6].imshow(CT4DShifted.dyn3DImageList[3].imageArray[:, y_slice, :].T[::-1, ::1], cmap='gray', origin='upper', vmin=-1000, vmax=1000)
ax[2, 6].title.set_text('Gen phase 3 shifted')

plt.savefig(os.path.join(output_path, 'BaselinesSHift.png'))
print('done')
plt.show()

done