Thursday, September 13, 2012

Rotating 3D Figures in Octave

When is executed, input the followings
> close all 
> setenv ("GNUTERM", "x11") 

There you go.

I'm sharing this original post from

Delaunay Triangulation and a Plane

When reconstructing a surface especially in three dimensional, its almost inevitable that you need to generate planes based on a set of vertices. In the case, when the facets are unknown, we basically have a cloud of three dimensional points. Based on the cloud of points, our eyes may be able to tell us what the sillouette or the contour of the three dimensional model in question is; however it is quite difficult or this is not trivial and it is a well-studied problem in computational geometry.

Certainly, there are a lot of recently proposed and well-developed methodologies for estimating or reconstructing a surface based on a given cloud of points. This post is written just to provide an idea of one of the basics: delaunay triangulation.  In short delaunay triangulation is to create a triangular mesh for a set of vertices that meets the Delaunay conditions(the main idea is to prevent any surface-within-a-surface).

In matlab, it is fair easy to follow the example (provided by Matlab).  Or if you want to explore further, you can try to make a cube. Basically you just need to write down the vertices and let Matlab do its job. I will leave the readers to do this on your own.

X, Y, Z are the column vectors of a cube(meaning all the x coords, y coords and z coords, say you have 2 vertices (0,0,0) and (0,0,1), X=[0 0]; Y=[0 0]; Z=[0 1];).

> dt = delaunay(X,Y,Z); 
> trimesh(dt,X,Y,Z); 

Now, that's pretty straightforward. However, if you have a problem similar to mine, when you only want to create a 3D plane with delaunay(you have your own reasons, i don't have to tell you mine). In the above example, if you only specify one of the faces of the cube, Matlab will probably tell you that they cannot proceed because all vertices are on a plane or are co-linear.

In order to do so, you need to trick Matlab into thinking the plane is no longer a plane; basically you just have to 'extrapolate' the plane in the perpendicular direction

X =[0 1 1 0];
Y =[0 1 1 0];
Z =[0 0 1 1];

X =[ 0 1 1.01 1.01 1 0];
Y =[0 1 0.99 0.99 1 0];
Z =[0 0 0 1 1 1];

Running the same command in the previous section should give you the following rendering.

Tuesday, July 31, 2012

(Medical) Imaging / PACS / DICOM / Health Informatics Conferences

Month-view of conference submission deadlines (on-going update)
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Journal of Medical Imaging (SPIE) (

Journal  Field IF
JACC: Cardiovas Img MI 5.528
Circulation: Cardiovas Img MI 4.757
Med Img Analysis MI 3.681
IEEE T Med Img MI 3.799
J American Med Inf. Asso. MI 3.609
IEEE T Img Pro CV 3.111
Int J Cardiovas Img CV 2.539
Int J Med Inf HI 2.414
J of Dig Img MI/CV/HI 1.421
IEEE T Pattern Anal CV 4.908
Pattern Recogn CV 2.292
J Mach Learn Res CV 2.561
Ultrasound in Med & Bio MI/CV 2.455
Ann Biomed Eng MI/CV 2.575
Int J Cars MI MI 1.364
SIAM J Imaging Sci MI 2.867
EUR HEART J Cardiac Imaging MI 3.669

HI      Health Informatics
MI     Medical Images, Radiography, DICOM, PACS
CV    Computer Vision, Pattern Recognition, Machine Learning

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- other details

last updated (2014-10-07)

Wednesday, July 11, 2012

From Microsoft Word to Latex

As much as I want to work on my papers in Microsoft Word, its been proven minutes by minutes that working on an academic research paper is not feasible without the use of LaTex.  Here, in this article, from a 'noob's perspective, I will lay down some of the fundamentals that you will need in order to have  your latex environment setup, ready, runnin' & gunnin'.  Since i am writing a paper for an upcoming SPIE conference, i'll take SPIE style class as a reference. (

Assuming you have been working on papers using the followings:
1) Microsoft Word
2) Endnote

At the end of this article, you will be dropping the above two, and will then be using the followings extensively hereafter.
1) Miktex (Think of this as a Compiler/Interpreter)
2) TeXnicCenter (Think of this as an IDE)
3) JabRef (Think of this as a Reference Manager)

I) Download and Install

Download and Install the followings (All of the followings will be done with a 'default' installation) Note: The version numbers are as of writing.

  • Miktex 2.9 (
  • TeXnicCenter 1 RC 1 Installer (
  • JabRef 2.8.1 (
Download from "HansonHub" (see above) and save them in a folder
  • spie.cls
  • spiebib.bst
  • ifthen.sty
  • cite.sty
  • article.tex
  • report.bib
  • mcr3b.eps

II) Setup Search Path for Miktex
  1. Start > All Programs > MikTex 2.9 > Maintenance > Settings > Roots [tab]
  2. Add the path, in my case, i added the path to "My Documents"\[Papers]\[Conference_Name]\[Year]\tex\latex\"
  3. Go back to General [tab]
  4. Click Refresh FNDB

III) Get TeXnicCenter going

When you first load TeXnicCenter, it will ask you for the root path to all your tex-related executables, in my case, i specified "C:\Program Files\miktex\miktex\bin".  It will then fill in the blanks for Yap and the rest.  

4) Start writing with the SPIE format

1) Open up article.tex (you can rename this to a more sensible filename)
2) Then, click on Project > Create with active file as main file
3) Press Ctrl F7, and then Press Ctrl F5, you shall see the LaTex with SPIE format 
(if you have any errors in the output window, post it up here as comments) You can also try refreshing FNDB, to see if some of the errors are resolved.

IV) EndNote to Bibtex

  1. Open up Endnote
  2. Click on Edit > Output Styles > select "BibTex Export" or go to Style Manager, and enable "BibTex Export" Click Apply/OK
  3. While you are still in Endnote, select all your citations, Click on File > Export  > In the output style selection list, choose BibTex Export
  4. Give it a sensible file name (it has to be in .txt, you will need to rename to .bib as you as its done saving)
  5. Save it to the folder along with your article.tex in step 3

JabRef Now
  1. Open up JabRef
  2. Open the .bib file you created and renamed in the previous step
  3. It will prompt errors saying none of the citations has BibTex Key
  4. You will need to auto-generate, while you are in JabRef, press Ctrl-G, and you will see your BibtexKey columns being filled
  5. Save the .bib
V) Completing the Circle

  1. Go back to TeXnicCenter
  2. Scroll to the bottom where you should see \bibliography{report}
  3. Change it to the .bib you saved in the previous step but without .bib (at this step, i suggest you refresh FNDB, again)
  4. Press Ctrl F7, and then Press Ctrl F5, you shall see the LaTex with SPIE format (if you have any errors in the output window, post it up here as comments) You can also try refreshing FNDB, to see if some of the errors are resolved.   You might also want to try to give a testing citation or two, just add \cite{ONE_OF_YOUR_BIBTEX_KEY} in any of the paragraphs reasonably. 

This should be it !