tag:blogger.com,1999:blog-31969655276426498512012-02-22T13:18:19.325+01:00Articles about topics ranging from technology and software to scientific research. Occasional book reviews. Topics of general interest such as lifestyle, and nutrition. Exploration of blogs and the technical side of blogging.Benjamin Auffarthhttps://profiles.google.com/118440342400845052454noreply@blogger.comBlogger12125tag:blogger.com,1999:blog-3196965527642649851.post-51946514645360563592010-12-03T16:16:00.004+01:002011-02-02T11:55:00.553+01:00

You spent a long time extracting statistics from data and creating meaningful figures with appropriate line-styles and markers. Now you want to create a video by just concatenating these figures. Some lines of matlab code and you are done. Just spent too much time to create a movie in matlab. This script takes 10 figures which are already displayed, resizes them to full screen resolution (all

Benjamin Auffarthhttps://profiles.google.com/118440342400845052454noreply@blogger.com3tag:blogger.com,1999:blog-3196965527642649851.post-272575041658916892009-10-28T17:55:00.012+01:002009-12-16T22:12:15.091+01:00

In articles about programming it is very important to embed source code so that people can see the code and even download it directly. Sometimes I include code snippets in my posts and the code reads much nicer if the syntax is highlighted. There are different ways to embed source code from different programming languages in HTML and in this post I comment on them. The different methods for

Benjamin Auffarthhttps://profiles.google.com/118440342400845052454noreply@blogger.com9tag:blogger.com,1999:blog-3196965527642649851.post-69427887610096911732009-09-01T15:43:00.009+02:002010-12-24T00:05:37.564+01:00

When you are doing some computations in C++ you might not want to write everything yourself including optimizing advanced algorithms. You would want to reuse code or write it in a numerical computing environment such as matlab, octave, R, or python. In this post I link to sources that explain how to include such high-level code in C++ or to call it from a C++ program. How to embed matlab code

Benjamin Auffarthhttps://profiles.google.com/118440342400845052454noreply@blogger.com4tag:blogger.com,1999:blog-3196965527642649851.post-60358989018396662502009-08-04T10:52:00.009+02:002010-01-10T18:35:31.659+01:00

In my last post I showed how to write mex functions with the armadillo library to get both fast and clean mex functions. Armadillo is a library for C++ that has a syntax similar to matlab. Here I give an example of a mex function using armadillo. It computes the Mahalanobis distance and is based on the template from the last post. Code snippet - Mex Function for Mahalanobis Function on

Benjamin Auffarthhttps://profiles.google.com/118440342400845052454noreply@blogger.com0tag:blogger.com,1999:blog-3196965527642649851.post-46250578877189323542009-08-02T11:35:00.014+02:002010-01-02T23:59:46.547+01:00

Typical situation: you run a matlab script for some simulation or experiment and need to run it faster. You find out with the profiler that there is a function that takes a lot of time and want to optimize that function. You want to write it in C/C++ and wrap it as a mex. In an earlier post I did a review of different C/C++ libraries for scientific computing (among them IT++, GSL, and others)

Benjamin Auffarthhttps://profiles.google.com/118440342400845052454noreply@blogger.com4tag:blogger.com,1999:blog-3196965527642649851.post-15812249710646050172009-07-21T20:00:00.033+02:002011-01-29T17:59:35.423+01:00

This post explains how to create print-quality figures in Matlab. The process is efficient and results in editable vector-graphics that you can include in any document including Microsoft Word, Open Office, or latex. Before you create your figures you might also want to check my article on combinations of linestyles and markers to have clear plots in black-and-white and color. IntroductionThere

Benjamin Auffarthhttps://profiles.google.com/118440342400845052454noreply@blogger.com6tag:blogger.com,1999:blog-3196965527642649851.post-64836577897556453712009-03-16T18:20:00.010+01:002011-02-02T11:53:55.860+01:00

For creating figures for print, lines and markers should be distinguishable by both, color and style. Matlab offers a variety of styles and colors, but the plot command when given a matrix as y input, only changes colors. You can spend a lot of time checking what looks good and what not. Here I present a script which can help to generate plots where each curve is distinguishable by marker, color,

Benjamin Auffarthhttps://profiles.google.com/118440342400845052454noreply@blogger.com0tag:blogger.com,1999:blog-3196965527642649851.post-1956748966041231152009-01-09T14:53:00.020+01:002010-01-10T18:52:14.165+01:00

Matlab has been used for years. In recent years, with the rise of linux, open source community projects such as python and GNU R have found increasing use and a recent article in NY times wrote about the rise of R. I took the time to create graphs to compare trends in popularity of three algebra computing platforms. This could help in predicting which is the future platform for scientific

Benjamin Auffarthhttps://profiles.google.com/118440342400845052454noreply@blogger.com0tag:blogger.com,1999:blog-3196965527642649851.post-73892221003369708792008-11-21T17:05:00.011+01:002010-12-24T02:10:29.324+01:00

You want to use a classifier, for example a support vector machine, to distinguish between different classes. When making binary decisions you want to make sure that your decision criterion is sensitive to your target class and that it is specific to the target class. Say you want to detect cancer, but only cancer. That's why there are roc curves and the area under the curve. I searched for

Benjamin Auffarthhttps://profiles.google.com/118440342400845052454noreply@blogger.com0tag:blogger.com,1999:blog-3196965527642649851.post-36210063259344629072008-11-20T18:00:00.015+01:002010-12-24T02:08:14.600+01:00

The most used implementations for SVM (support vector machines) are currently svmlight and libsvm. While libsvm comes with interfaces for many different programming languages, svmlight (svm-light perf) has the advantage that you can specify the loss function. I have very disproportionate classes in my training data, so using the area under the curve (AUC), the area under the receiver operating

Benjamin Auffarthhttps://profiles.google.com/118440342400845052454noreply@blogger.com10tag:blogger.com,1999:blog-3196965527642649851.post-60058259158655954612008-11-07T10:46:00.015+01:002011-02-02T11:56:18.685+01:00

Image via Wikipedia There are many different ways to export and import data from matlab. You can import and export data from and to matlab binary formats (MAT files), text files, Excel spreadsheet (works only on Windows), XML, several special purpose formats, and a lot of image, audio, and video file formats. Text formats are very useful, because they very portable in that they can be read and

Benjamin Auffarthhttps://profiles.google.com/118440342400845052454noreply@blogger.com13tag:blogger.com,1999:blog-3196965527642649851.post-76908342231141522682008-10-08T12:53:00.041+02:002009-11-09T18:39:32.359+01:00

I put myself to the task of setting up our beowulf computing cluster for parallel distributed processing. A reminder: a beowulf cluster is a compute cluster dedicated to scientific calculations. In earlier posts I explained the hardware part of how to build a beowulf, then software installation and administration, and cloning of setups, and now it's time to make the cluster do some work. In

Benjamin Auffarthhttps://profiles.google.com/118440342400845052454noreply@blogger.com6