PlotNIfTI

Table of contents

• General info
• Example
• Dependencies

General info

Features	Status
List of segmentations	✅
Align to centroid of first seg.	✅
Show filled with transparency	✅
Show contour	✅
Seg. list for colormap	✅
Crop CT/CBCT using body	✅

Bastien Rigaud, PhD Laboratoire Traitement du Signal et de l'Image (LTSI), INSERM U1099 Campus de Beaulieu, Université de Rennes 1 35042 Rennes, FRANCE bastien.rigaud@univ-rennes1.fr

Example

from PlotNIfTI import PlotNifti

def main():
    image_path = r"C:\Data\Data_test\plot_cervix_ct\image.nii.gz"
    segmentation_paths = [r"C:\Data\Data_test\plot_cervix_ct\CTVT.nii.gz",
                          r"C:\Data\Data_test\plot_cervix_ct\Bladder.nii.gz",
                          r"C:\Data\Data_test\plot_cervix_ct\Rectum.nii.gz",
                          r"C:\Data\Data_test\plot_cervix_ct\Sigmoid.nii.gz",
                          r"C:\Data\Data_test\plot_cervix_ct\BowelBag.nii.gz"]
    # segmentation_names is optional, but usefull to add a colormap
    plot_object = PlotNifti(image_path=image_path, segmentation_paths=segmentation_paths,
              show_contour=True, show_filled=True, transparency=0.20, get_at_centroid=True,
              segmentation_names=['CTVT', 'Bladder', 'Rectum', 'Sigmoid', 'BowelBag'])

    for view in ['sagittal', 'axial', 'coronal']:
        output_path = r"C:\Data\Data_test\plot_cervix_ct\screenshot_{}.png".format(view)
        plot_object.set_view(view)
        plot_object.set_output_path(output_path)
        plot_object.generate_plot()

Example to run PlotNifti in with threading and to lock the "generate_plot()" function because Matplotlib is not thread safe.

import os
from threading import Thread, Lock
from multiprocessing import cpu_count
from queue import *

lock = Lock()

from PlotNIfTI.PlotNIfTI import PlotNifti


def worker_def(A):
    q = A
    while True:
        item = q.get()
        if item is None:
            break
        else:
            image_path, segmentation_paths, output_dir, segmentation_names, views = item
            try:
                plot_object = PlotNifti(image_path=image_path, segmentation_paths=segmentation_paths,
                                        show_contour=True, show_filled=True, transparency=0.20,
                                        get_at_centroid=True, segmentation_names=segmentation_names, crop_scan=True)
                for view in views:
                    plot_object.set_view(view)
                    plot_object.set_output_path(os.path.join(output_dir, 'screenshot_{}.png'.format(view)))
                    lock.acquire()
                    plot_object.generate_plot()
                    lock.release()
            except:
                print('     failed on {}'.format(image_path))
            q.task_done()

Dependencies

pip install -r requirements.txt