animation with bspline registration

henrisco82 · May 9, 2018, 6:19pm

Please I would like to make an animation suitable in gif format to see the different stages the registration does.
I am using the example from here http://simpleitk.readthedocs.io/en/master/Examples/ImageRegistrationMethodBSpline2/Documentation.html
please how can I do this?

Thank you

blowekamp · May 9, 2018, 6:26pm

We have done something similar for the SimpleITK notebooks:

You can find the script that was used to generate it here:

github.com

InsightSoftwareConsortium/SimpleITK-Notebooks/blob/master/Utilities/intro_animation.py

#
# Script for generating images illustrating the movement of images and change in
# similarity metric during registration.
#

import SimpleITK as sitk

import matplotlib
matplotlib.use('agg')

import matplotlib.pyplot as plt
import numpy as np

# Paste the two given images together. On the left will be image1 and on the right image2.
# image2 is also centered vertically in the combined image.
def write_combined_image(image1, image2, horizontal_space, file_name):
    combined_image = sitk.Image((image1.GetWidth() + image2.GetWidth() + horizontal_space,
                                max(image1.GetHeight(), image2.GetHeight())), 
                                image1.GetPixelID(), image1.GetNumberOfComponentsPerPixel())
    combined_image = sitk.Paste(combined_image, image1, image1.GetSize(), (0, 0), (0, 0))

This file has been truncated. show original

You should be able to adapt is to your particular registration method easily enough.

henrisco82 · May 9, 2018, 9:39pm

sitk_reg_bspline1.py (6.6 KB)

henrisco82 · May 9, 2018, 10:05pm

please I still get some errors
RuntimeError: Exception thrown in SimpleITK ImageRegistrationMethod_Execute: C:\d\VS14-Win64-pkg\SimpleITK\Wrapping\Python\sitkPyCommand.cxx:135:
sitk::ERROR: There was an error executing the Python Callable.

blowekamp · May 9, 2018, 10:10pm

You will need to add try-except inside you Python callable used in the events to get the error encountered. It may even be a syntax error the callables can be skittle tricky to debug and get right.

henrisco82 · May 10, 2018, 7:38am

The error is with the save_plot function. It says tuple index out of range. Please any ideas on how I can fix this?

central_index = round((f.GetSize())[2] / 2)

IndexError: tuple index out of range

blowekamp · May 10, 2018, 1:31pm

Perhaps len(f) is only 2?

I have not looked closely at your script ( or the original for a while), maybe your image is a different dimension that what is expected?

henrisco82 · May 10, 2018, 2:00pm

The files used in the example has .mha extension like training_001_mr_T1.mha but I am testing with .png files.
Do you think this is the problem?

blowekamp · May 10, 2018, 2:12pm

Have you inspect the original image and your images? Do you know their dimensions, sizes, pixel types?

henrisco82 · May 10, 2018, 3:03pm

The size of my image is 256 by 256 and it is a gray scale image

henrisco82 · May 10, 2018, 3:59pm

yeah that is the problem. The test image has width, height and color values, but my image just have width and height. Is there a way I can make it work without the color values?

Thanks

zivy · May 10, 2018, 4:20pm

@henrisco82 ,
The original script dealt with 3D scalar images, no color values. The blended slices are combined and converted to color by repeating the scalar value in all channels (see the line saying "convert grayscale image to color (r,g,b)). As you are working in 2D you will have to modify the code to deal with it (e.g. you don’t need all of the slice extraction, see references to central_index in the script).

The need for using color is because we wanted the similarity metric graph to be in color, so the alpha blended grayscale extracted slices were also converted to color.

 hope this clarifies things
         Ziv