Comparing two methods of measurement in Matalb or Octave

How to compare two methods that measure the same variable? How to check if one method produces results constantly higher than the other method and if the difference is significant? How to determine whether new method, can replace the old one? The anwser to these question lies in the analysis of bias between the two method of measurement [1]. Below is a Matlab implementation of Ordinary least products (OLP) regression analysis [1] that can be used to anwser to these questions.

function res = mgr(X,Y,varargin)
% res = mgr(X,Y)
% Mean Geometric Regression (i.e. Ordinary least products (OLP) regression)
%
% Used to evaluate two measurement methods in terms of fixed and
% proportional bias as described in [1].
%
% INPUT
% X - vector of values calculated by the first method.
% Y - vector of values calculated by the second method.
% boolean - plot or not scattergram of the values
% string - label of x axis of scattergram
% string - label of y axis of scattergram
%
%
% EXAMPLE from [1]:
%
% M1=[132 138 144 146 148 152 158 130 162 168 172 174 180 180 188 194 194 200 200 204 210 210 216 220 220];
% M2=[130 134 132 140 150 144 150 122 160 150 160 178 168 174 186 172 182 178 196 188 180 196 210 190 202];
%
% res=mgr(M1,M2)
%res =
%
% a: 13.9506
% b: 0.8611
% a_CI95: [-6.9476 32.3364]
% b_CI95: [0.7576 0.9788]
%
% res=mgr(M1,M2,true); % produces scattergram
% res=mgr(M1,M2,true,'SBP(M1)','SBP(M2)'); % produces scattergram with x and y axis
% % labels of 'SBP(M1)' and 'SBP(M2)'
%
% NOTE:
% The above calculated values of a and b agree with the values in [1]
% Values of CI95 are marginally different, becouse, as expalined in [1],
% they are calculated using approximate formulas.
%
%REFERENCE:
%[1] J Ludbrook, Comparing methods of measurement, Clinical and
% Experimental Pharmacology and Physiology, 1997:24,193-203
%
%
%Full code of the above script is here.
Script was tested on Matlab 2007a and in Octave 3.2. En example of the scattergram that is generated by the script is below. This scattergram is the same as an example given in [1].

References

[1] J Ludbrook, Comparing methods of measurement, Clinical and Experimental Pharmacology and Physiology, 1997:24,193-203.

Ten clicks to install Ubuntu 9.04

Update: My honest mistake: It should be Ubuntu 9.10, not 9.04. Thanks Tom!

Click 1

Click Enter for English language.

Clicks 2 and 3

Go to Install Ubuntu and Click Enter.

Click 4

Forward.

Click5

Forward.

Click 6

Forward

Click 7

Forward

Click 8

Forward (Typing username and password were not counted).

Click 9

Install

Waiting for installation to complete

Click 10

Restart Now and Ubuntu installation is finished.

So 10 clicks is enough to install Ubuntu 9.04 9.10. Is it much or not? You can compare it with the number of clicks in other systems [Image taken from Benchmarked: Ubuntu vs Vista vs Windows 7]:

How ImageMagick can save you time

ImageMagick is a great tool! Many times it has saved me from programming. Here is just one example of many applications of the ImageMagick that can save one's time.

Recently, I was asked to check whether a set of images (few hundreds of them) contains one particular image. So, basically I was given and image (called testImage.tiff), and I needed to check whether this image belongs to a set a few hundreds of images. En example of the images from the set is below:

So how to anwser this? You can do manual (i.e. visual comparison), you can also write some simple script in Python with PIL. All would take some time. But why to do this, if you can just write one for loop in bash with compare command from ImageMagick?

So first thing I did is to create the following folders:

The input folder contains all images from the set, the output folder will be where the results of my search will be stored, and the testImage.tiff is my test image.

So thanks to ImageMagick's, the only thing I had to do is to execute its compare command on all images from the set (i.e. input folder).  In other words, I compared, in a loop, an image from the set with the testImage.tiff and the results of the comparison went to output folder. Below is the bash for loop that was executed inside the input folder.

for f in *.tiff ; do
compare $f ../testImage.tiff ../output/$f ;
doneAfter loop finished, I could go to output folder, and quickly find out whether testImage.tiff is in the set:

As can be seen in the above picture, the testImage.tiff belongs this this set.

One limitation of this procedure is that I had to manually go through the output folder. But because all not matching images are in red, it was very quick to find, the one image that was not red. (if any). Additionally, if the testImage.tiff and images from the set were of different size or type additional code would be necessary.

So thanks to the ImageMagick, I could do the job in just a few minutes.

xampp / lampp: upgrade PHPUnit in lampp 1.7.1

The default PHPUnit that ships with lampp 1.7.1 is not suited for use with Zend Framework 1.9. The reason is that the PHPUnit version in lampp is to low. So it is necessary to upgrade it using pear. However, before it can be done, pear version that comes with lampp 1.7.1 needs to be also upgraded. The pear executable is in /opt/lampp/bin so I went to this folder.

First PHPUnit channel must be added sudo ./pear channel-discover pear.phpunit.de
Adding Channel "pear.phpunit.de" succeeded
Discovery of channel "pear.phpunit.de" succeeded

Then pear chanels can be updated sudo ./pear update-channels

Then we can try to install PHPUnit:sudo ./pear install phpunit/PHPUnit
phpunit/PHPUnit requires PEAR Installer (version >= 1.8.1), installed version is 1.7.1
phpunit/PHPUnit requires package "pear/Image_GraphViz" (version >= 1.2.1), installed version is 1.1.0
phpunit/PHPUnit can optionally use PHP extension "xdebug" (version >= 2.0.5)
No valid packages found
install failed

To upgrade pear I used sudo ./pear upgrade PEAR To check if upgrade was successful I used ./pear -V
PEAR Version: 1.9.0
PHP Version: 5.2.9
Zend Engine Version: 2.2.0
Running on: Linux arch 2.6.31-ARCH #1 SMP PREEMPT Tue Oct 13 13:36:23 CEST 2009 i686

Before PHPUnit can be upgraded, pear/Image_GraphViz package must be upgraded first. So sudo ./pear upgrade pear/Image_GraphViz
downloading Image_GraphViz-1.2.1.tgz ...
Starting to download Image_GraphViz-1.2.1.tgz (4,872 bytes)
.....done: 4,872 bytes
upgrade ok: channel://pear.php.net/Image_GraphViz-1.2.1
and install PHPUnit ./pear install -a phpunit/PHPUnit
phpunit/PHPUnit can optionally use PHP extension "xdebug" (version >= 2.0.5)
downloading PHPUnit-3.4.1.tgz ...
Starting to download PHPUnit-3.4.1.tgz (326,659 bytes)
...................................................................done: 326,659 bytes
install ok: channel://pear.phpunit.de/PHPUnit-3.4.1
After this, when I could use PHPUnit with Zend Framework as described in a tutorial here.

SPSS: create random binary variable

To create a random binary variable called e.g. new_var one can use the following code:COMPUTE new_var=RND(RV.UNIFORM(0,1)).
EXECUTE.or

Xampp: SQLSTATE[HY000] [2002] Invalid argument

I'm currently developing a web application using Zend Framework 1.9.x. For this purpose I used Xampp for linux (i.e. lampp 1.7.2). Most of the time I was using arch linux with xampp 1.7.2 and there was no problem. Then I changed my os to Ubuntu 9.04 and I installed the same xampp 1.7.2. Interestingly, when I wanted to run my application under Ubuntu I got an errorMessage: SQLSTATE[HY000] [2002] Invalid argumentAfter googling I found that the reason was that in my php.ini (i.e. for xampp it is /opt/lampp/etc/php.ini) the variable pdo_mysql.default_socket was not set: Therefore I set it to /opt/lampp/var/mysql/mysql.sockOf course, I also had to restart Xamppsudo /opt/lampp/lampp restartIt is interesting why Xampp 1.7.2 worked under Arch Linux, but it did not work under Ubuntu 9.04?

Gnome desktop icons disappear

I have gnome 2.26.3 and sometimes all my icons on the desktop disappear. I found that in Gnome, program called nautilus manages it. So for my case it was enough to restart/start itnautilus --no-default-window &Nautilus is the same program that you use for browsing folders under Gnome.

TOP PHP frameworks in terms of number of books published on a given framework

To begin with, I would like to say that I'm not new to PHP 4 and 5, but I would not call myself an expert. The reason is that for a few years now, PHP and web applications are things that I do only in my spare time. I also haven't used all the PHP frameworks, nor I'm the expert in any of them. I'm basically looking for a framework that is worth looking into and which would save me a time, as I don't want to spend much time on weekends coding e.g. only user authorization or registration form validation. So far, I did some small jobs using Prado, CakePHP and now I'm starting to learn Zend Framework. I also heard lots of good about CodeIgniter and Symfony. Since, I couldn't learn all of them, I just wanted to find some way of determining which of them seems to be the most popular. I decided to check how many books on a given framework are available in amazon.com?

I chose this criterion because for a person that wants to learn a framework, examples along with explanation can be valuable. Apart from official tutorials, quick start guides and reference manuals, that are available on the websites of the frameworks, books can provide good introduction along with example applications. Additionally, a number of books, also shows to some extend, how popular a given framework is. I would imaging that not many authors would write books about unpopular frameworks. Off course, there are many other possible criteria that can be used to rank or compare PHP frameworks, such as documentation, community support, performance, fast availability of updates etc., but I think that the number of books somehow translates to the the popularity of a framework.

Method of comparison

I went to amazon.com and I performed advanced searches for books on a given framework written in English and published after 2007. A year 2007 was chosen because books older than two years may contain highly outdated information. A framework name was a keyword. Than, the number of books found was counted.

En example of a search criteria used is given below:

Results

The results are as follows:

	Zend Framework - 10 books (see the books)
	Symfony - 9 books (see the books)
	CakePHP - 3 books (see the books)
	CodeIgniter - 2 book (see the books)
	Prado - 0 books (see the books)

My personal opinion

From my perspective, the experience that I had with Prado (I used v. 3.1.4) was the worst one, although it's concept was interesting. I found it difficult to learn and use, because the documentation was sparse, there were not many tutorials, and even if I was wiling to invest some money and buy a book about it, I could not find any books about it.

After Prado I tried CakePHP (I was using v. 1.2). I found it very good, easy to learn and fast to use, as long as I adhered to all the naming conventions. Especially, I liked the ORM (Object-Relational Mapping) which was very useful and saved me a lot of time. The problem I had with it, was that it uses PHP 4, which already has been discontinued. Off course, sooner or later CakePHP will move to PHP 5, but I wanted to use a PHP 5. I think it would be better to use something in PHP 5, rather than something that is developed in a version of language that is already not supported. Off course, CakePHP runs smoothly on PHP 5. It is only CakePHP's core that does not use features of PHP 5. Additionally, I wanted to have more freedom when programming, and CakePHP does not allow for much of it due to it's "convention over configuration paradigm". But this is a price that you pay in CakePHP.

At the moment I'm learning Zend Framework v1.9 which is build using PHP 5. For now, I can say that it is definitely more difficult to learn at the beginning. The biggest issue that I had at the beginning, and still have but to a lesser extend, is a bootstrap class, which is difficult to understand. It really took me a long time to begin to understand how to use it at the simplest level. However, what I like is, that Zend Framework is less rigid than CakePHP, it uses PHP 5, and it has a vast number of tools (e.g. for working with PDF files or captcha) that CakePHP does not have.

I don't have experience with Symfony and CodeIgniter, so I cannot say anything apart from what I read in the Internet. CodeIgniter is considered to be faster than CakePHP and just like CakePHP, it is written for PHP 4, whereas Symfony is for PHP 5 only.

In conclusion, it seems that when you look only at the number of books on a given framework, Zend Framework is the winner with eight books. At the moment, I'm trying to get to know it, hopping that it will not be a waste of time. It must be remembered though, that there are many other criteria that can be used to compare PHP frameworks. However the final decision which framework to choose, if any, should be based on the specific needs of a project that we want to developed.

imagemagick: resize all image files in a current folder

Example:mogrify -resize 60% *.JPG

Arch linux: RGB to CMYK

To convert RGB files to CMYK files (for printing) one can install Separate+ Gimp plugin.

My gimp version was 2.6.6. I downloaded Separate+ plugin sources (now version 0.54) and unpacked them. Than I installed littleCMS library sudo pacman -S lcms. After that I compiled the Separate+ plugin and installed it: make
sudo make install I also needed Adobe ICC Profiles that can be found here (does not meter that they are for Windows). I unpacked the downloaded archive and I copied the contents of RGB and CMYK folders to usr/share/color/icc/ folder. That's it!