## Monday, June 25, 2007

### Matlab: Mandelbrot set

Recently I read article on Free Software Magazine titled Generating cool fractals. I was very pleased to find source code for generation of Mandelbrot set.
`function mandelFrac% MATLAB and Octave code to generate%a Mandelbrot fractal% Number of points in side of image and% number of iterations in the Mandelbrot% fractal calculationnpts=1000;niter=51;% Generating z = 0 (real and% imaginary part)zRe=zeros(npts,npts);zIm=zeros(npts,npts);% Generating the constant k (real and% imaginary part)kRe=repmat(linspace(-1.5,0.5,npts),npts,1);kIm=repmat(linspace(-1,1,npts)',1,npts);% Iteratingfor j=1:niter% Calculating q = z*z + k in complex space% q is a temporary variable to store the resultqRe=zRe.*zRe-zIm.*zIm+kRe;qIm=2.*zRe.*zIm+kIm;% Assigning the q values to z constraining between% -5 and 5 to avoid numerical divergenceszRe=qRe;qgtfive= find(qRe > 5.);zRe(qgtfive)=5.;qltmfive=find(qRe<-5.);zRe(qltmfive)=-5.;zIm=qIm;hgtfive=find(qIm>5.);zIm(hgtfive)=5.;hltmfive=find(qIm<-5.);zIm(hltmfive)=-5.;end% Lines below this one are commented out when making% the benchmark.% Generating plot% Generating the image to plotima=log( sqrt(zRe.*zRe+zIm.*zIm) + 1);% Plotting the imageimagesc(ima);` ## Sunday, June 24, 2007

### Lenne picture

The original photo of famous Lenna picture which is found in many papers and books conserning image processing:-) ## Sunday, June 17, 2007

### Ruby: Tk, select directory

Just quick code for selecting input/output directory```#!/usr/bin/env ruby require 'tk' bdir=Tk.chooseDirectory('initialdir'=>'./') puts bdir ```
Below an example that takes a directory and lists all txt files that contain string '_data' in their name. Than contents of each such file is copied to one output file ('allData.txt'):```#!/usr/bin/env ruby require 'tk' bdir=Tk.chooseDirectory('initialdir'=>'./') fout= open('allData.txt', 'w') Dir.foreach(bdir) { |x| next if x !~ /_data/ fpath=bdir+'/'+x File.open(fpath).each_line {|l| fout << l} } fout.close ```

## Thursday, June 14, 2007

### Excel: Visual Basic; mean value

Simple code in Microsoft VBA as a function in Excel. This function takes a range (x) and calculates mean value of the number lower than 0.
`Function mymeanLr(x)n = x.CountReDim xx(n + 1)Dim ind As Integerind = 0For i = 1 To n If x(i) < 0 Then xx(i - 1) = x(i) ind = ind + 1 End IfNext imymeanLr = WorksheetFunction.Average(xx)End Function`

## Monday, June 11, 2007

### bash: use sed and awk to calculate an awarage value in the file

`#!/bin/bashFD=`cat \$1 | sed -e 's/^[0-9.]*//g' -e 's/^\t//g' -e 's/^M\$//g' \ | awk '{for (i=1; i<=NF; i++) s=s+\$i}; END{print s/9/12}'`echo \$1 \$FD`
The script calculates avarage of values in a txt without values from the first column.
Example txt file:`0 2.7792 2.7876 2.8023 2.8248 2.8413 2.8551 2.8679 2.8593 2.853718.281 2.7619 2.7723 2.7864 2.7888 2.8105 2.8314 2.8697 2.8695 2.861526.719 2.749 2.7464 2.7622 2.7811 2.8145 2.8276 2.8359 2.8438 2.848245 2.7596 2.7601 2.7614 2.779 2.803 2.803 2.8207 2.8391 2.837463.281 2.778 2.7809 2.8013 2.8071 2.8408 2.8423 2.8478 2.8514 2.82671.719 2.7871 2.7927 2.8171 2.819 2.8366 2.8581 2.876 2.8826 2.864890 2.8007 2.8038 2.8219 2.8371 2.851 2.8628 2.8683 2.879 2.8719108.28 2.781 2.7835 2.7901 2.7982 2.8214 2.8314 2.8488 2.852 2.8416116.72 2.7731 2.7749 2.7784 2.7852 2.8077 2.8155 2.8226 2.8274 2.832135 2.7744 2.7826 2.7854 2.7998 2.8153 2.8154 2.8358 2.8627 2.8775153.28 2.7866 2.8011 2.8079 2.8253 2.8517 2.862 2.8727 2.8728 2.8644161.72 2.7906 2.8071 2.8278 2.8424 2.8674 2.8679 2.8709 2.8716 2.8635`

## Saturday, June 09, 2007

Reading of Excel files (*.xls) can be done using roo package for Ruby.One function that I write for myself was function that reads Excel file (fragment seen on the below picture) to a Hash table, where first column (image file name) is a key. Moreover, a key is only base name of the file,i.e., no extension. The line #(1) is very interesting, as I found out that roo reads x-rays in a way that each character is separated by '0'. Thus, to get correct String, it is necessary to remove zeros from the string. This is I think due to encoding shame. Excel uses Unicode 16, instead of ASCI; hence, each character is represented by two bites: firt byte is a character, and the second byte is '0'. Hence, to read the file name to ASCI, it is necessary to skip ever second byte. It must be done, because otherwise gsub does not want to work. `def readExcelToHash foo = Excel.new(f)oo.default_sheet = 1xcl=Hash.new0.upto(oo.last_row) { |line|r=oo.row(line)next if r.to_s.length==0rs= String.new r.to_sa=String.newrs.each_byte{|x| a+= x.chr if x!=0} #(1)next if rs =~ /^#/xcl[a.gsub(/\.tif+\$/,'')]=r}xclend`
As far as creating spreadsheets is concerned, roo does not provide this functionality.

## Monday, June 04, 2007

### Noise and blur effect on the image

Adding noise to an image adds hight frequency components to it. High frequency components are those that are responsible for image sharpness, i.e., pixel to pixel distances. In other words, the smallest components of the image like edges. On the other hand, blur removes high frequency components from the image. Bellow, the picture presents image (left column) and its Fourier transforms (right column). P.S
Above Fourier transforms were calculated using free ImageJ software.

## Saturday, June 02, 2007

### Ruby: Plotting with gnuplot in Mac X

To plot in Ruby, one can use rgplot interface to gnuplot. To install it, just download gnuplot-gem and install by`sudo gem install ./gnuplot-2.2.gem`
If you have gnuplot already installed it is good, if not install it by`sudo port install gnuplot`.
Assuming that everything went well, one can now plot and save figures using Ruby.
Simple example of Ruby code that plots simple data and saves (do not display) it to png file.
`#!/usr/bin/env ruby#testGnuplot.rbrequire 'rubygems'require 'gnuplot'outFname='graph.png'xData=[1, 2, 3, 4,5]yData=[2, 3 ,4, 2,3]#xData=(0..10).collect { |v| v.to_f }#yData= xData.collect { |v| v ** 2 }Gnuplot.open do |gp|Gnuplot::Plot.new( gp ) do |plot| plot.output outFname plot.terminal 'png' plot.title "Array Plot Example" plot.ylabel "y" plot.xlabel "x" x= xData y= yData plot.data << Gnuplot::DataSet.new( [x, y] ) do |ds| ds.with = "linespoints" ds.notitle endendend`
This is especially useful when one want to plot a lot of figures contained in a data file. Of corese, this is the simples example, and more complicated things require to do some experimenting before desired plots are obtained. Nonetheless, this is good start.

To plot two data on one graph and to save it as png one can do as below:
`#!/usr/bin/env ruby#test.rbrequire 'rubygems'require 'gnuplot'outFname='graph.png'xData=[1, 2, 3, 4,5]yData=[2, 3 ,4, 2,3]yData2=[1, 2 ,3, 3,4]Gnuplot.open do |gp|Gnuplot::Plot.new( gp ) do |plot| plot.output outFname plot.terminal 'png' plot.title "Array Plot Example" plot.ylabel "y" plot.xlabel "x" x= xData y= yData plot.data =[ Gnuplot::DataSet.new( [x, y] ) do |ds| ds.with = "linespoints" ds.notitle end,Gnuplot::DataSet.new( [xData, yData2] ) do |ds| ds.with = "linespoints" ds.notitle end ]endend`
Results is (graph.png): 