Insight Journal - Adapting the ITK Registration Framework to Fit Parametric Image Models

Adapting the ITK Registration Framework to Fit Parametric Image Models

Center for Computer Integrated Systems for Microscopy and Manipulation, University of North Carolina at Chapel Hill

Please use this identifier to cite or link to this publication: http://hdl.handle.net/10380/3167

Published in The Insight Journal - 2010 January-June.

Submitted by Cory Quammen on 04-20-2010.

The image registration framework in the Insight Tookit offers a powerful body of code for finding the optimal spatial transform that registers one image with another. However, ITK currently lacks a way to fit parametric models of image pixel values to an input image. This document describes new classes that enable use of the registration framework to provide this capability. We describe a new base class, itk::ParametricImageSource, that defines an interface for parametric image sources. An adapter class itk::ImageToParametricImageSourceMetric that enables itk::ParametricImageSources to be hooked into the registration framework is also described. An example adapter class that enables the existing itk::GaussianImageSource to be used for image fitting is presented, and we demonstrate use of the classes by fitting a 2D Gaussian function to an image generated by the itk::GaussianImageSource class.

Code

Automatic Testing Results by Insight-Journal Dashboard on Tue May 18 12:09:36 2010 for revision #1

expertise: 5 sensitivity: 5

Reviews

Using the Parametric Image Source for my own purposes by Robert Atwood on 2010-10-07 10:56:21 for revision #1

expertise: 3 sensitivity: 5

Summary:

The problem of choosing mathematical parameters to represent a model of an image is closely related to the problem of choosing parameters to transform one image into another, and the ITK registration framework provides a flexible toolbox for the latter. The authors have developed new classes within the ITK framework to enable the application of the image registration tools already available in ITK to the former problem. The class needs to calculate the image's value given the location and provide the required methods enabling the optimizer classes to act upon the parameters in the same way as they do for the standard registration problem. To this end the authors have provided a special metric class to compare a standard image to a calculated (parametric) image, and a parametric image source class to present the calculated data in the required manner. A facility for enabling or disabling specified parameters is implemented.

Evidence:

The authors provide an example which aligns a 2-dimensional Gaussian distribution of greyscale with a second Gaussian calculated function, and apply two different optimizers from the ITK toolkit to solve the problem.The test program generates the input image in memory from the same Gaussian function generator and perturbs the parameters to provide to the parametric image source. No images are input or output, just the initial and final parameters.

Open Science:

Yes. All the code and data required is included in the package. The example does not input any images as the test image is generated in memory.

Reproducibility:

Yes. Compiling and running the provided example worked immediately on my Red Hat 5 / 64bit system with relatively recent ITK build installed.

I have also implemented my own routine that makes use of the code for a real-world problem and initial results are encouraging.

In order to implement my own function it was necessary to derive a class and implement the function generation sections. If a class which only needs to be provided with the function could be developed, this would be even better. However, it would need to be able to accept a function with an arbirtrary number of parameters, and to know how many parameters it has, I am not sure myself how this could be done, whether it could be templated over a 'functor' or obtain the information from a ->SetFunctor() method? I may be out of my c++ depth !

Use of Open Source Software:

The package does not use any software other than ITK

Open source Contributions:

Yes, the code is usable and at for my purpose it was working immediately with my ITK installation. But, creating a new parametric image with my own fuction required some more c++ knowledge than I usually have ;-) , as above; it would be attractive to be able to just call a SetFunctor() method and only provide the formulae for the parametric image.

Code Quality :

The code appears to me to be coded in ITK compatible style, to the limit of my knowledge of the style guidelines.

Quality of the data :

The example does not use significant amount of data. To try the example with different parameters requires altering and compiling the code, to try with different functions for the parametric image requires creating a derived class and compiling that.

Interest:

It is broadly applicable. I intend to use this method to check the alignment of a calibration sample (sphere of known diameter and density moved to known positions in space ) in an X-ray beam imaging system, applying the formula for attenuation of the X-ray through the thickness of the sphere. In our lab it could be used to help track the change in size and shape of features in images where the nature of the shape is known i.e. growth of spherical particles or bubbles, as altertnative to segmentation of the boundaries -- often the boundary is not so clear but the overall variation in image intensity is clear and contains more information than just 'inside/outside' so it's an attractive approach .

Free comment :

I observed some issue with the interaction of the set of enabled/disabled parameters with the optimizer classes, this also appears to vary depending upon the optimizer class chosen.

When I optimize my 5-parameter image with Amoeba optimizer, but suppress some parameters, the optimizer still reports and adjusts 5 parameters, but when I use the Powell optimizer, the reduced number of parameters is reported.

The inital parameter set gets passed to the optimizer in such a way that the first parameter appears to be given to the first enabled parameter, thus the initial guess could be very poor compared to what was intended!

Certain parameter choices cause the optimizer to return an error message that all points map outside the target image, but it's unclear to me what this means in the context of the parametric image

Comment by Cory Quammen: Issues with disabling some parameters with the Amoeba optimizer

The Amoeba optimizer fixes the number of parameters to optimize when the method AmoebaOptimizer::SetCostFunction() is set. Specifically, it sets the number of parameters to the number reported by ImageToParametricImageSourceMetric::GetNumberOfParameters(). Now, because the ImageToParametricImageSourceMetric::GetNumberOfParameters() method reports the number of enabled parameters, this number may change. Therefore, if you disable a parameter in the metric after calling AmoebaOptimizer::SetCostFunction(), you'll get the strange behavior your describe. I'll look into submitting a patch for the AmoebaOptimizer to ITK.

The PowerOptimizer obtains the number of parameters just prior to optimization, so you are free to enable/disable parameters after calling PowerOptimizer::SetCostFunction().

I've updated the source code (revision 2) to show the necessary order of initialization and method calls when using the AmoebaOptimizer, and changed it to optimize only 4 of the 5 parameters for the ParametricGaussianImageSource to better show the capabilities of the ImageToParametricImageSourceMetric.

Add a new review

Quick Comments

Comment by Nagah Stone

كليوباترا ستون للحجر الهاشمي
http://cleopatra-stone.com/
حجر هاشمي كليوباترا ستون

http://cleopatra-stone.com/View_Item.php?ID=85
ديكورات حجر هاشمي كليوباترا

http://cleopatra-stone.com/View_Item.php?ID=84
واجهات حجر هاشمي كليوباترا

http://cleopatra-stone.com/View_Item.php?ID=83
توريد وتركيب حجر هاشمي

http://cleopatra-stone.com/View_Item.php?ID=82
اسعار حجر هاشمي 2020

===========================================
النجاح ستون لديكورات الحجر الهاشمي
http://elnagahstone.com/"مقاول حجر هاشمي النجاح ستون

http://elnagahstone.com/View_Item.php?ID=271
اسعار الحجر الهاشمي النجاح ستون

http://elnagahstone.com/View_Item.php?ID=270
حجر هاشمي النجاح ستون

http://elnagahstone.com/View_Item.php?ID=269
توريد وتركيب حجر هاشمي
http://elnagahstone.com/View_Item.php?ID=209
مميزات وعيوب الحجر الهاشمي
http://elnagahstone.com/index.php#contact
واجهات فلل وقصور
http://elnagahstone.com/categories.php?cat_id=7&pagename=%D8%A7%D9%84%D8...
تشطيب واجهات حجر هاشمي
http://elnagahstone.com/View_Item.php?ID=26
حجر هاشمي هيصم وكريمي
http://elnagahstone.com/View_Item.php?ID=29
انواع الحجر الهاشمي واشكال مختلفة للحجر الهاشمي
http://elnagahstone.com/View_Item.php?ID=209
ديكورات وواجهات حجر هاشمي النجاح ستون
http://elnagahstone.com/View_Item.php?ID=210
تصميمات حديثة لواجهات الحجر الهاشمي
http://elnagahstone.com/View_Item.php?ID=211
ديكورات فلل وقصور وعماير
http://elnagahstone.com/View_Item.php?ID=212
احدث ديكورات الحجر الهاشمي
http://elnagahstone.com/View_Item.php?ID=201
مهندسين حجر هاشمي ومقاولين حجر هاشمي

Comment by Altheqa Stone

واجهات حجر هاشمىحجر هاشمىواجهات حجر هاشمى هيصمحجر هاشمى هيصماسعار حجر هاشمىاسعار حجر هاشمى هيصمتركيب حجر هاشمىتركيب حجر هاشمى هيصمواجهات فلل حجر هاشمى هيصمانواع الحجر الهاشمىأشكال الحجر الهاشمىسعر متر الحجر الهاشمىواجهات حجر هاشمياسعار الحجر الهاشمى فى مصر.واجهات حجر هاشمى مصرواجهات حجر هاشمى2020.واجهات منازل حجر هاشمىواجهات عمارات حجر هاشمىاشكال واجهات حجر هاشمىاحدث واجهات حجر هاشمىديكورات حجر هاشمى سعر متر الحجر الهاشمي في مصر 2020 اسعار تركيب الحجر الهاشمي اسعار الحجر الهاشمى بمصر اسعار توريد وتركيب الحجر الهاشمى

اسعار الحجر الهاشمى بمصر اسعار الحجر الهاشمى فرز اول وتانى
https://www.altheqa-eg.com/stone-prices/
الحجر الهاشمي الاختيار الأفضل لواجهات المنازل والفلل أفضل صنعة تركيب وأقل سعرًا
https://www.dekorishn-altheqa.com/decoration/
أنواع الحجر الهاشمي بمصر مميزات وعيوب كل نوع وما الأفضل لك
https://www.altheqa-eg.com/stone-types/
تعرف على أسعار الحجر الهاشمي في مصر بأشكاله المختلفة
https://www.altheqa-stone.com/hashmi-stone-prices/
حجر هاشمي هيصم بأقل تكاليف انتقال فرز أول للديكورات الخارجية والداخلية
https://www.decoration-altheqa.com/stone-facades/
حجر هاشمي فرز أول لواجهات الفلل والقصور والعمائر
https://www.altheqa-stone.com/stone-2020/
حجر هاشمى هيصم لواجهات المنازل والعمائر فى مصر 2020
https://www.dekorishn-altheqa.com/modern-stone-2/
تركيب الحجر الفرعوني لواجهات المنازل والفلل 2020
https://www.dekorishn-altheqa.com/stone-houses/
واجهات الحجر الفرعوني في مصر تركيبها بأقل الأسعار
https://www.altheqa-stone.com/altheqa-stone/
أفضل شركة لتركيب الحجر البازلت في مصر بأسعار مناسبة واستخدامات متعددة
https://www.altheqa-eg.com/black-basalt/
أنواع الحجر البازلت أسعار تركيب الحجر البازلت في مصر 2020
https://www.decoration-altheqa.com/basalt-altheqa/
هل الحجر الهاشمى يتوقف استخدامه فى الواجهات فحسب؟
https://www.altheqa-eg.com/stone-work/
سعر متر الحجر الهاشمى خامة مصنع فرز اول
https://www.dekorishn-altheqa.com/stone-meter-price/
شركة الثقه للمقاولات
https://www.altheqa-eg.com
أهم الشركات لوظيفة تركيب حجر هاشمى هيصم
https://www.altheqa-eg.com/%d8%a3%d9%87%d9%85-%d8%a7%d9%84%d8%b4%d8%b1%d9%83%d8%a7%d8%aa-%d9%84%d9%88%d8%b8%d9%8a%d9%81%d8%a9-%d8%aa%d8%b1%d9%83%d9%8a%d8%a8-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5/
حجر هاشمى هيصم هو الافضل دائما لماذا؟
https://www.altheqa-eg.com/%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85-%d9%87%d9%88-%d8%a7%d9%84%d8%a7%d9%81%d8%b6%d9%84-%d8%af%d8%a7%d8%a6%d9%85%d8%a7-%d9%84%d9%85%d8%a7%d8%b0%d8%a7%d8%9f/
تركيب حجر هاشمى هيصم خطوة بخطوة
https://www.altheqa-eg.com/%d8%aa%d8%b1%d9%83%d9%8a%d8%a8-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85-%d8%ae%d8%b7%d9%88%d8%a9-%d8%a8%d8%ae%d8%b7%d9%88%d8%a9/
واجهات جذابه من الحجر الهاشمى
https://www.altheqa-eg.com/%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d8%ac%d8%b0%d8%a7%d8%a8%d9%87-%d9%85%d9%86-%d8%a7%d9%84%d8%ad%d8%ac%d8%b1-%d8%a7%d9%84%d9%87%d8%a7%d8%b4%d9%85%d9%89/
شركة الثقه للمقاولات
https://www.altheqa-stone.com/
معرض صور حجر هاشمى
https://www.altheqa-stone.com/stone-decorations/
تعرف على اسعار الحجر الهاشمى
https://www.altheqa-stone.com/%d8%aa%d8%b9%d8%b1%d9%81-%d8%b9%d9%84%d9%89-%d8%a7%d8%b3%d8%b9%d8%a7%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85/
تصدير حجر هاشمى
https://www.altheqa-stone.com/export/
سعر حجر هاشمى وطريقه تركيبه
https://www.altheqa-stone.com/%d8%b3%d8%b9%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85-%d9%88%d8%b7%d8%b1%d9%8a%d9%82%d9%87-%d8%aa%d8%b1%d9%83%d9%8a%d8%a8%d8%a9/
لمعرفه اسعار الحجر الهاشمى فى مصر
https://www.altheqa-stone.com/%d8%a7%d8%b3%d8%b9%d8%a7%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
اسعار حجر هاشمى
https://www.dekorishn-altheqa.com/%D8%A7%D8%B3%D8%B9%D8%A7%D8%B1-%D8%AD%D8%AC%D8%B1-%D9%87%D8%A7%D8%B4%D9%85%D9%89/
واجهات فلل حجر هاشمى
https://www.dekorishn-altheqa.com/%D9%88%D8%A7%D8%AC%D9%87%D8%A7%D8%AA-%D9%81%D9%84%D9%84-%D8%AD%D8%AC%D8%B1-%D9%87%D8%A7%D8%B4%D9%85%D9%8A/
اشكال واجهات عمارات حجر هاشمى هيصم
https://www.dekorishn-altheqa.com/modern-homes/
كتالوج صور واجهات بيوت مصرية ريفية
https://www.dekorishn-altheqa.com/happy-home/
اشكال واجهات منازل | اشكال واجهات عمارات
https://www.dekorishn-altheqa.com/home-decor/
اسعار البازلت فى مصر
https://www.dekorishn-altheqa.com/%D8%A7%D8%B3%D8%B9%D8%A7%D8%B1-%D8%A7%D9%84%D8%A8%D8%A7%D8%B2%D9%84%D8%AA-%D9%81%D9%89-%D9%85%D8%B5%D8%B1/
واجهات منازل وفلل بتصيمات حجر هاشمى فخمة
https://www.altheqa-eg.com/modern-homes/
اشكال وصور واجهات منازل وبيوت بالحجر الهاشمى بطريقة حديثة
https://www.dekorishn-altheqa.com/stone-altheqa/

كيف يمكنك تحديد سعر متر الحجر الهاشمى فى واجهات الفلل والمنازل
https://www.decoration-altheqa.com/%d9%83%d9%8a%d9%81-%d9%8a%d9%85%d9%83%d9%86%d9%83-%d8%aa%d8%ad%d8%af%d9%8a%d8%af-%d8%b3%d8%b9%d8%b1-%d9%85%d8%aa%d8%b1-%d8%a7%d9%84%d8%ad%d8%ac%d8%b1-%d8%a7%d9%84%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%81/

Resources


Download All
Download Paper , View Paper
Download Source code
Github

Statistics more


Global rating:
Review rating:	[review]
Code rating:
Views:	92
Downloads:	4763
Paper Quality:
2 comments

Information more


Paper Id:	727
Categories:	Optimization, Registration metrics
Keywords:	parametric image models, Gaussian fitting
Toolkits:	ITK, CMake
Revision:
Export citation:
Status:	Open for public review

Share

Linked Publications more


Diffeomorphic Demons Using ITK's Finite Difference Solver Hierarchy by Vercauteren T., Pennec X., Perchant A., Ayache N.
A Label Geometry Image Filter for Multiple Object Measurement by Padfield D., Miller J.
Importing Contours from DICOM-RT Structure Sets by Dowling J., Malaterre M., Greer P.B., Salvado O.
Anisotropic Fast Marching in ITK by Mirebeau J.
Scalable Simple Linear Iterative Clustering (SSLIC) Using a Generic and Parallel Approach by Lowekamp B., Chen D., Yaniv Z., Yoo T.
InsightToolkit Kinetic Analysis (itk::ka) Library by Dowson N., Baker C., Raffelt D., Smith J., Thomas P., Salvado O., Rose S.
ITK in Biomedical Research and Commercial Applications by McCormick M., Aylward S., Johnson H., Lowekamp B.
An OpenCL implementation of the Gaussian pyramid and the resampler by Shamonin D., Staring M.
Computing Bone Morphometric Feature Maps from 3-Dimensional Images by Vimort J., McCormick M., Paniagua B.
A Skull-Stripping Filter for ITK by Bauer S., Fejes T., Reyes M.

View license

Loading license...

Send a message to the author