<div>Hi Luis,</div><div><br></div>Thanks very much for looking into the problem and sending me better codes, especially using iterator to access pixel values.<div><br></div><div>You are right that the problem comes from the image viewer I used. Actually I used Paraview to examine the generate image which was saved in vtk format. I have been trusting Paraview and could not believe it doesn't interpret 16-bit image properly.</div>
<div><br></div><div>For the random number generator, the reason I used RNG function is random generator on Windows XP (I don't have LINUX/UNIX) is a pseudo-random number generator. Perhaps random() on LINUX is working better. From what I found, RNG does give better results. </div>
<div><br></div><div>Thanks again,</div><div>Ming<br><br><div class="gmail_quote">On Tue, Feb 10, 2009 at 4:48 PM, Luis Ibanez <span dir="ltr"><<a href="mailto:luis.ibanez@kitware.com">luis.ibanez@kitware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><br>Hi Ming,<br><br>Thanks for your clear description of the problem and for posting the source code.<br><br>I just reformatted your code a bit, and ... <br>
it works for me.... :-)<br><br>Well,<br>I also replaced your RNG object with a call to the GNU/Linux function "random()".<br>
<br>It produces an image of the correct size (33x33) and the pixel values are indeed<br>0 and 1000, and distributed close to 50% versus 50%.<br><br>I'm wondering if the problem may be with the tool that you are using for looking<br>
at the output test.vtk file. It may be that the tool is not interpreting correctly the<br>fact that you have 16-bits values.<br><br>Independent of the problem that you are reporting, please not that your method<br>for accessing pixel values is quite inefficient. I have converted your code to use<br>
ITK iterators (which is the fastest way of visiting pixel data in ITK).<br><br>Please find attached to this email the following files:<br><br><ul><li>Random.cxx: your source code reformatted</li><li>Random2.cxx: converted to use ITK iterators</li>
<li>CMakeLists.txt file for building both</li></ul><br>Please give it a try to building these two files and let us know if you <br>still see any problem.<br><br>(in which case, please let us know what tool you are using for looking<br>
at the output image).<br><br><br> Thanks<br><br><br> Luis<br><br><br>------------------------------------------<br><br><div class="gmail_quote"><div><div></div><div class="Wj3C7c">On Mon, Feb 9, 2009 at 11:57 AM, Ming Chao <span dir="ltr"><<a href="mailto:mingchao2005@gmail.com" target="_blank">mingchao2005@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex"><div><div></div><div class="Wj3C7c">I tried to generate a binary image based on a random number. I observed something I haven't understood. What I did was quite simple. I generated a uniform random number between 0 and 1. If the random number is smaller than 0.5, then the image intensity value was set to zero, otherwise 1000. I tested the idea by generating a 2D image. What I found was that when the image sizes (both x and y) were set to 2^N (N= 1, 2, 3, 4....), the generated image was fine. With other image sizes, there were two interesting observations: (1) the generated image was not a binary image, ie, the image intensities were not 0 and 1000 but there were some intermediate values; (2) the sizes of the generated image were not the sizes I specified. For instance, if I specified a 3X3 region, but the generated image would have 4X4 sizes. I don't know what I did wrong here. Any help or suggestions would be appreciated! <div>
<br></div><div><br></div><div>Here is the code I used to generate the image.</div><div><br></div><div><div>#include "itkImage.h"</div><div><br></div><div>#include "itkImageFileReader.h"</div><div>#include "itkImageFileWriter.h"</div>
<div><br></div><div>#include <fstream></div><div>//#include <cstdlib></div><div>//#include <ctime></div><div><br></div><div>#include "rng.h"</div><div><br></div><div>//using namespace std;</div>
<div><br></div><div>//---------------------------------------------------------------------------------------</div><div>int main( )</div><div>{</div><div><br></div><div><span style="white-space:pre"> </span>const unsigned int Dimension = 2;</div>
<div> </div><div><span style="white-space:pre"> </span>typedef unsigned short PixelType;</div><div><span style="white-space:pre"> </span>typedef itk::Image< PixelType, Dimension ><span style="white-space:pre"> </span> ImageType;</div>
<div><br></div><div><span style="white-space:pre"> </span>ImageType::Pointer image = ImageType::New();</div><div><br></div><div><span style="white-space:pre"> </span>ImageType::IndexType start;</div>
<div><span style="white-space:pre"> </span>start[0] = 0; start[1] = 0; //start[2] = 0;</div><div><br></div><div><span style="white-space:pre"> </span>ImageType::SizeType size;</div>
<div><span style="white-space:pre"> </span>size[0] = 33; size[1] = 33; //size[2] = 1;</div><div><br></div><div><span style="white-space:pre"> </span>ImageType::RegionType region;</div>
<div><span style="white-space:pre"> </span>region.SetSize( size ); region.SetIndex( start );</div><div><br></div><div><span style="white-space:pre"> </span>image->SetRegions( region );</div>
<div><span style="white-space:pre"> </span>image->Allocate(); </div><div><br></div><div><span style="white-space:pre"> </span>/*</div><div><span style="white-space:pre"> </span>ImageType::SpacingType spacing;</div>
<div><span style="white-space:pre"> </span>spacing[0] = 1.0; spacing[1] = 1.0; spacing[2] = 0.0;</div><div><span style="white-space:pre"> </span>image->SetSpacing( spacing );</div>
<div><br></div><div><span style="white-space:pre"> </span>ImageType::PointType origin;</div><div><span style="white-space:pre"> </span>origin[0] = 0.0; origin[1] = 0.0; origin[2] = 0.0;</div>
<div><span style="white-space:pre"> </span>image->SetOrigin( origin );</div><div><span style="white-space:pre"> </span>*/</div><div><span style="white-space:pre"> </span></div>
<div><br></div><div><span style="white-space:pre"> </span>RNG rdm;</div><div><span style="white-space:pre"> </span>int counter=0;</div><div><span style="white-space:pre"> </span>for ( int i = 0; i < size[0]; i++) {</div>
<div><span style="white-space:pre"> </span>for ( int j = 0; j < size[1]; j++ ) {</div><div><span style="white-space:pre"> </span>//for ( int k = 0; k < size[2]; k++ ) {</div>
<div><span style="white-space:pre"> </span></div><div><span style="white-space:pre"> </span>ImageType::IndexType pixelIndex;</div><div><span style="white-space:pre"> </span>pixelIndex[0] = i;</div>
<div><span style="white-space:pre"> </span>pixelIndex[1] = j;</div><div><span style="white-space:pre"> </span>//pixelIndex[2] = k;</div><div><br></div><div><span style="white-space:pre"> </span>double prob = rdm.uniform();</div>
<div><span style="white-space:pre"> </span>//std::cout << "probability = " << prob << std::endl;</div><div><span style="white-space:pre"> </span></div>
<div><span style="white-space:pre"> </span>if (prob <= 0.5) { </div><div><span style="white-space:pre"> </span>ImageType::PixelType pixelValue = itk::NumericTraits < PixelType >::Zero;</div>
<div><span style="white-space:pre"> </span>image->SetPixel( pixelIndex, pixelValue );</div><div><span style="white-space:pre"> </span>counter++;</div><div><span style="white-space:pre"> </span>} else { </div>
<div><span style="white-space:pre"> </span>ImageType::PixelType pixelValue = 1000;</div><div><span style="white-space:pre"> </span>image->SetPixel( pixelIndex, pixelValue );</div>
<div><span style="white-space:pre"> </span>}</div><div><span style="white-space:pre"> </span></div><div><span style="white-space:pre"> </span>//}</div>
<div><span style="white-space:pre"> </span>}</div><div><span style="white-space:pre"> </span>}</div><div><br></div><div><span style="white-space:pre"> </span></div>
<div><span style="white-space:pre"> </span>for ( int i = 0; i < size[0]; i++) {</div><div><span style="white-space:pre"> </span>for ( int j = 0; j < size[1]; j++ ) {</div>
<div><span style="white-space:pre"> </span>//for ( int k = 0; k < size[2]; k++ ) {</div><div><span style="white-space:pre"> </span></div><div><span style="white-space:pre"> </span>ImageType::IndexType pixelIndex;</div>
<div><span style="white-space:pre"> </span>pixelIndex[0] = i;</div><div><span style="white-space:pre"> </span>pixelIndex[1] = j;</div><div><span style="white-space:pre"> </span>//pixelIndex[2] = k;</div>
<div><br></div><div><span style="white-space:pre"> </span>ImageType::PixelType outPixel = image->GetPixel(pixelIndex); </div><div><span style="white-space:pre"> </span>//std::cout << "pixel value = " << outPixel << std::endl;</div>
<div><br></div><div><span style="white-space:pre"> </span>//}</div><div><span style="white-space:pre"> </span>}</div><div><span style="white-space:pre"> </span>}</div>
<div><span style="white-space:pre"> </span></div><div><br></div><div><span style="white-space:pre"> </span>std::cout << counter << " pixels of " << size[0]*size[1] << " have zero values." << std::endl;</div>
<div><br></div><div><br></div><div><span style="white-space:pre"> </span>typedef itk::ImageFileWriter< ImageType ><span style="white-space:pre"> </span> WriterType;</div>
<div><span style="white-space:pre"> </span>WriterType::Pointer imgWriter = WriterType::New();</div><div><span style="white-space:pre"> </span>imgWriter->SetInput( image );</div>
<div><span style="white-space:pre"> </span>imgWriter->SetFileName( "test.vtk" );</div><div><span style="white-space:pre"> </span>imgWriter->Update();</div><div>
<br></div><div> </div><div><br></div><div><br></div><div><br></div><div> <span style="white-space:pre"> </span>return EXIT_SUCCESS;</div><div>}</div></div>
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