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<font class="Apple-style-span" face="Tahoma">Hi Seth,</font><div style="font-family: Tahoma; ">why should i need to <span class="Apple-style-span" style="color: rgb(42, 42, 42); font-family: 'Segoe UI', Tahoma, Verdana, Arial, sans-serif; ">find the maximum and minimum pixel values and then normalize the vector pixel components by these values? </span></div><div><font class="Apple-style-span" color="#2A2A2A" face="'Segoe UI', Tahoma, Verdana, Arial, sans-serif">in my case i iterate through a image of tensors, with the pixel type being a DiffusionTensor3D. should i do it as well?</font></div><div><font class="Apple-style-span" color="#2A2A2A" face="'Segoe UI', Tahoma, Verdana, Arial, sans-serif">Thanks and sorry for my ignorance, im a beginner :( </font></div><div><div style="font-family: Tahoma; ">
<p align="center"><font color="#000000"><img height="2" src="http://graphics.hotmail.com/greypixel.gif" width="100%" vspace="9"></font></p></div><br><br><br><br><div id="SkyDrivePlaceholder" style="font-family: Tahoma; "></div><hr id="stopSpelling" style="font-family: Tahoma; "><font class="Apple-style-span" face="Tahoma">From: seth@mech.ubc.ca</font><br><font class="Apple-style-span" face="Tahoma">Date: Mon, 14 Feb 2011 15:50:38 -0800</font><br><font class="Apple-style-span" face="Tahoma">Subject: Re: [Insight-users] map the colours from the eigenvector</font><br><font class="Apple-style-span" face="Tahoma">To: albagarin1986@hotmail.com</font><br><font class="Apple-style-span" face="Tahoma">CC: insight-users@itk.org</font><br><br><font class="Apple-style-span" face="Tahoma">Hi Alba,</font><br><font class="Apple-style-span" face="Tahoma">A program I wrote which I think should do something like you want is below. I'm working in Linux, but it should compile for you.</font><br><br><font class="Apple-style-span" face="Tahoma">#include <iostream></font><br><font class="Apple-style-span" face="Tahoma">#include <stdlib.h></font><br><font class="Apple-style-span" face="Tahoma">#include "itkVector.h"</font><br><font class="Apple-style-span" face="Tahoma">
#include "itkImage.h"</font><br><font class="Apple-style-span" face="Tahoma">#include "itkImageFileWriter.h"</font><br><font class="Apple-style-span" face="Tahoma">#include "itkRGBPixel.h"</font><br><font class="Apple-style-span" face="Tahoma">#include "itkImageRegionIterator.h"</font><br><font class="Apple-style-span" face="Tahoma">#include <time.h></font><br><font class="Apple-style-span" face="Tahoma">#include <limits></font><br>
<br><font class="Apple-style-span" face="Tahoma">int main(int argc, char** argv)</font><br><font class="Apple-style-span" face="Tahoma">{</font><br><font class="Apple-style-span" face="Tahoma"> if ( argc < 2 || argc > 2){ //Check for correct number of inputs</font><br><font class="Apple-style-span" face="Tahoma"> std::cout<<"Usage:"<<std::endl;</font><br><font class="Apple-style-span" face="Tahoma"> std::cout<<argv[0]<<" [Output File Name] "<<std::endl<<std::endl;</font><br><font class="Apple-style-span" face="Tahoma">
return EXIT_FAILURE;</font><br><font class="Apple-style-span" face="Tahoma"> }</font><br><font class="Apple-style-span" face="Tahoma"> /* Create the Images.*/</font><br><font class="Apple-style-span" face="Tahoma"> typedef double VectorComponentType;</font><br><font class="Apple-style-span" face="Tahoma"> typedef unsigned short RGBComponentType; // many image formats have limited pixel types</font><br><font class="Apple-style-span" face="Tahoma"> typedef itk::Vector< VectorComponentType, 3> VectorPixelType;</font><br><font class="Apple-style-span" face="Tahoma">
typedef itk::RGBPixel< RGBComponentType > RGBPixelType;</font><br><font class="Apple-style-span" face="Tahoma"> </font><br><font class="Apple-style-span" face="Tahoma"> typedef itk::Image< VectorPixelType, 3 > VectorImageType;</font><br><font class="Apple-style-span" face="Tahoma"> typedef itk::Image< RGBPixelType, 3 > RGBImageType;</font><br><font class="Apple-style-span" face="Tahoma">
</font><br><font class="Apple-style-span" face="Tahoma"> VectorImageType::RegionType region;</font><br><font class="Apple-style-span" face="Tahoma"> VectorImageType::RegionType::SizeType regionSize;</font><br><font class="Apple-style-span" face="Tahoma"> VectorImageType::RegionType::IndexType regionStart;</font><br><font class="Apple-style-span" face="Tahoma"> VectorImageType::PointType origin;</font><br><font class="Apple-style-span" face="Tahoma">
VectorImageType::SpacingType spacing;</font><br><font class="Apple-style-span" face="Tahoma"> </font><br><font class="Apple-style-span" face="Tahoma"> regionSize[0] = 100;</font><br><font class="Apple-style-span" face="Tahoma"> regionSize[1] = 100;</font><br><font class="Apple-style-span" face="Tahoma"> regionSize[2] = 100;</font><br><font class="Apple-style-span" face="Tahoma"> regionStart[0] = 0;</font><br><font class="Apple-style-span" face="Tahoma"> regionStart[1] = 0;</font><br><font class="Apple-style-span" face="Tahoma"> regionStart[2] = 0;</font><br><font class="Apple-style-span" face="Tahoma">
region.SetSize(regionSize);</font><br><font class="Apple-style-span" face="Tahoma"> region.SetIndex(regionStart);</font><br><font class="Apple-style-span" face="Tahoma"> origin[0] = 0;</font><br><font class="Apple-style-span" face="Tahoma"> origin[1] = 0;</font><br><font class="Apple-style-span" face="Tahoma"> origin[2] = 0;</font><br><font class="Apple-style-span" face="Tahoma"> spacing[0] = 1;</font><br><font class="Apple-style-span" face="Tahoma"> spacing[1] = 1;</font><br><font class="Apple-style-span" face="Tahoma"> spacing[2] = 1;</font><br><font class="Apple-style-span" face="Tahoma"> </font><br><font class="Apple-style-span" face="Tahoma"> VectorImageType::Pointer vectorIm = VectorImageType::New();</font><br><font class="Apple-style-span" face="Tahoma">
RGBImageType::Pointer rgbIm = RGBImageType::New();</font><br><font class="Apple-style-span" face="Tahoma"> </font><br><font class="Apple-style-span" face="Tahoma"> vectorIm->SetRegions(region);</font><br><font class="Apple-style-span" face="Tahoma"> vectorIm->SetOrigin(origin);</font><br><font class="Apple-style-span" face="Tahoma"> vectorIm->SetSpacing(spacing);</font><br><font class="Apple-style-span" face="Tahoma"> rgbIm->SetRegions(region);</font><br><font class="Apple-style-span" face="Tahoma">
rgbIm->SetOrigin(origin);</font><br><font class="Apple-style-span" face="Tahoma"> rgbIm->SetSpacing(spacing);</font><br><font class="Apple-style-span" face="Tahoma"> </font><br><font class="Apple-style-span" face="Tahoma"> vectorIm->Allocate();</font><br><font class="Apple-style-span" face="Tahoma"> rgbIm->Allocate();</font><br><font class="Apple-style-span" face="Tahoma"> </font><br><font class="Apple-style-span" face="Tahoma"> /*Create the Iterators */</font><br><font class="Apple-style-span" face="Tahoma"> typedef itk::ImageRegionIterator< VectorImageType > VectorIteratorType;</font><br><font class="Apple-style-span" face="Tahoma">
typedef itk::ImageRegionIterator< RGBImageType > RGBIteratorType;</font><br><font class="Apple-style-span" face="Tahoma"> </font><br><font class="Apple-style-span" face="Tahoma"> VectorIteratorType vIt(vectorIm, vectorIm->GetLargestPossibleRegion() );</font><br><font class="Apple-style-span" face="Tahoma"> RGBIteratorType cIt(rgbIm, vectorIm->GetLargestPossibleRegion() );</font><br><font class="Apple-style-span" face="Tahoma">
</font><br><font class="Apple-style-span" face="Tahoma"> /* Let's fill the vector image with random numbers between -1 and 1 */</font><br><font class="Apple-style-span" face="Tahoma"> srand( time(NULL) );</font><br><font class="Apple-style-span" face="Tahoma"> </font><br><font class="Apple-style-span" face="Tahoma"> for( vIt.GoToBegin(); !vIt.IsAtEnd(); ++vIt ){</font><br><font class="Apple-style-span" face="Tahoma"> VectorPixelType setPixel;</font><br><font class="Apple-style-span" face="Tahoma">
setPixel[0] = (VectorComponentType) rand()/RAND_MAX; // Random value</font><br><font class="Apple-style-span" face="Tahoma">
setPixel[1] = (VectorComponentType) rand()/RAND_MAX;</font><br><font class="Apple-style-span" face="Tahoma"> setPixel[2] = (VectorComponentType) rand()/RAND_MAX;</font><br><font class="Apple-style-span" face="Tahoma"> </font><br><font class="Apple-style-span" face="Tahoma"> setPixel[0] = rand() > RAND_MAX/2 ? setPixel[0] : -1 * setPixel[0]; //Randomly +'ve or -'ve</font><br><font class="Apple-style-span" face="Tahoma">
setPixel[1] = rand() > RAND_MAX/2 ? setPixel[1] : -1 * setPixel[1];</font><br><font class="Apple-style-span" face="Tahoma"> setPixel[2] = rand() > RAND_MAX/2 ? setPixel[2] : -1 * setPixel[2];</font><br><font class="Apple-style-span" face="Tahoma"> </font><br><font class="Apple-style-span" face="Tahoma"> vIt.Set(setPixel);</font><br><font class="Apple-style-span" face="Tahoma"> }</font><br><font class="Apple-style-span" face="Tahoma"> </font><br><font class="Apple-style-span" face="Tahoma">
/* Here you might need to find the maximum and minimum pixel values</font><br><font class="Apple-style-span" face="Tahoma"> * and then normalize the vector pixel components by these values.</font><br><font class="Apple-style-span" face="Tahoma"> * Presumably your vectors are unit vectors so it is likely that the max and </font><br><font class="Apple-style-span" face="Tahoma">
* min values are -1 and 1, but I don't know. */</font><br><font class="Apple-style-span" face="Tahoma"> </font><br><font class="Apple-style-span" face="Tahoma"> for( cIt.GoToBegin(), vIt.GoToBegin(); !vIt.IsAtEnd(); ++cIt, ++vIt ){</font><br><font class="Apple-style-span" face="Tahoma"> VectorPixelType getPixel;</font><br><font class="Apple-style-span" face="Tahoma"> getPixel = vIt.Get();</font><br><br><font class="Apple-style-span" face="Tahoma">
RGBPixelType rgbPixel; // since abs(values) of vector are 0-1, multiply by RGB pixel max</font><br><font class="Apple-style-span" face="Tahoma"> rgbPixel[0] = std::numeric_limits< RGBComponentType >::max() * fabs (getPixel[0]);</font><br><font class="Apple-style-span" face="Tahoma"> rgbPixel[1] = std::numeric_limits< RGBComponentType >::max() * fabs (getPixel[1]);</font><br><font class="Apple-style-span" face="Tahoma">
rgbPixel[2] = std::numeric_limits< RGBComponentType >::max() * fabs (getPixel[2]);</font><br><font class="Apple-style-span" face="Tahoma"> </font><br><font class="Apple-style-span" face="Tahoma"> cIt.Set(rgbPixel);</font><br><font class="Apple-style-span" face="Tahoma"> }</font><br><font class="Apple-style-span" face="Tahoma"> </font><br><font class="Apple-style-span" face="Tahoma"> typedef itk::ImageFileWriter< RGBImageType > RGBWriterType;</font><br><font class="Apple-style-span" face="Tahoma">
RGBWriterType::Pointer writer = RGBWriterType::New();</font><br><font class="Apple-style-span" face="Tahoma"> writer->SetInput( rgbIm );</font><br><font class="Apple-style-span" face="Tahoma"> std::string fileName = argv[1];</font><br><font class="Apple-style-span" face="Tahoma"> writer->SetFileName( fileName );</font><br><font class="Apple-style-span" face="Tahoma"> </font><br><font class="Apple-style-span" face="Tahoma"> writer->Update(); </font><br><font class="Apple-style-span" face="Tahoma">
</font><br><font class="Apple-style-span" face="Tahoma"> return 0;</font><br><font class="Apple-style-span" face="Tahoma">}</font><br><br><br><div class="ecxgmail_quote" style="font-family: Tahoma; ">On Mon, Feb 14, 2011 at 8:42 AM, alba garin <span dir="ltr"><<a href="mailto:albagarin1986@hotmail.com">albagarin1986@hotmail.com</a>></span> wrote:<br>
<blockquote class="ecxgmail_quote" style="padding-left:1ex">
<div>
<br><font face="Tahoma" size="2">Hello Seth</font><div style="font-family:Tahoma;font-size:10pt"><br></div><div><font face="Tahoma" size="2">the error is "Unhandled exception at 0x012cb166 in tesImageReaderExample.exe: 0xC0000094: Integer division by zero." now in doing like this </font></div>
<div><font face="Tahoma" size="2"><code></font></div><div><font face="Tahoma" size="2"><div><span style="white-space:pre-wrap"> </span>rgb.SetRed(x);</div><div><span style="white-space:pre-wrap"> </span>rgb.SetGreen(y);</div>
<div><span style="white-space:pre-wrap"> </span>rgb.SetBlue(z);</div><div><div><span style="white-space:pre-wrap"> </span>indexIt=itRGB.GetIndex();</div><div><span style="white-space:pre-wrap"> </span>rgbImage->SetPixel(indexIt,rgb);</div>
</div></font></div><div><font face="Tahoma" size="2"></code></font></div><div><font face="Tahoma" size="2">but first i tried like this</font></div><div><font face="Tahoma" size="2"><code></font></div><div><font face="Tahoma" size="2"><span style="white-space:pre-wrap"> rgb.SetRed(x);
rgb.SetGreen(y);
rgb.SetBlue(z);</span></font></div><div><font face="Tahoma" size="2"><span style="white-space:pre-wrap"> itRGB.Set(rgb);</span></font></div><div><font face="Tahoma" size="2"></code><br></font>where rgb is itk::RGBPixel<double>, x,y and z are the values extracted from the eigenvector, itRGB is the iterator that goes through the itk::Image<RGBPixelType,3>.</div>
<div>thanks,<div><br><br><br><br><div style="font-family:Tahoma;font-size:10pt"></div><hr style="font-family:Tahoma;font-size:10pt"><font face="Tahoma" size="2">From: <a href="mailto:seth@mech.ubc.ca">seth@mech.ubc.ca</a></font><br>
</div><font face="Tahoma" size="2">Date: Mon, 14 Feb 2011 08:14:57 -0800</font><div><br><font face="Tahoma" size="2">Subject: Re: [Insight-users] map the colours from the eigenvector</font><br></div><font face="Tahoma" size="2">To: <a href="mailto:albagarin1986@hotmail.com">albagarin1986@hotmail.com</a></font><br>
<font face="Tahoma" size="2">CC: <a href="mailto:insight-users@itk.org">insight-users@itk.org</a></font><div><div></div><div><br><br><font face="Tahoma" size="2">Hi alba,</font><br><font face="Tahoma" size="2">What's the error?</font><br>
<br><font face="Tahoma" size="2">Seth</font><br><br><div style="font-family:Tahoma;font-size:10pt">On Mon, Feb 14, 2011 at 3:09 AM, alba garin <span dir="ltr"><<a href="mailto:albagarin1986@hotmail.com">albagarin1986@hotmail.com</a>></span> wrote:<br>
<blockquote style="padding-left:1ex">
<div>
Hi again,<div><br></div><div>the problem is that i got an error at doing itRGB.Set(rgbPixel).</div><div>why is that happening?</div><div>Thanks,</div><div><br><div>
<p align="center"><font color="#000000"><img src="http://" height="2" vspace="9" width="100%"></font></p></div><br><br><br><br><hr>From: <a href="mailto:albagarin1986@hotmail.com">albagarin1986@hotmail.com</a><br>
To: <a href="mailto:seth@mech.ubc.ca">seth@mech.ubc.ca</a>; <a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br>Date: Mon, 14 Feb 2011 07:52:29 +0000<br>Subject: Re: [Insight-users] map the colours from the eigenvector<div>
<br><br>
<br><div>Thanks, I needed to save each component in RGB pixels so your pseudo code is useful. </div><div><br>
<p align="center"><font color="#000000"><img src="http://" height="2" vspace="9" width="100%"></font></p></div><br><br><br><br><hr>From: <a href="mailto:seth@mech.ubc.ca">seth@mech.ubc.ca</a><br>Date: Fri, 11 Feb 2011 13:25:25 -0800<br>
Subject: [Insight-users] map the colours from the eigenvector<br>To: <a href="mailto:insight-users@itk.org">insight-users@itk.org</a>; <a href="mailto:albagarin1986@hotmail.com">albagarin1986@hotmail.com</a><br>
<br></div><div><div></div><div>Hi Alba,<br>I'm not sure if I understand, is it the magnitude that you want mapped or the direction? You can use ParaView to create visualizations of both from an image of vectors, and that my be the best way to go. ParaView makes some very pretty pictures!<br>
<br>If you want to save each component of the vector to the components of an RGB pixel, you could use iterators to move through the image and save each component of the eigenvector to an RGB pixel as in the following pseudo code (more details in the Software Guide, page 738 on).<br>
<br>RBGIteratorType itRGB(rbgImage, vectorImage->GetLargestPossibleRegion());<br>ConstVectorIteratorType constItVec(vectorImage, vectorImage->GetLargestPossibleRegion());<br><br>for ([the whole region])<br>{<br> VectorImageType::PixelType currentVectorPixel = constItVec.Get();<br>
<br> RGBImageType::PixelType currentRGBPixel;<br> currentRGBPixel->SetBlue(currentVectorPixel[0]); // make sure your vector component type and pixel type match<br> currentRGBPixel->SetGreen(currentVectorPixel[1]); // you will also want to normalize your vector components by the largest in the image. <br>
currentRGBPixel->SetRed(currentVectorPixel[2]);<br> <br> itRGB.Set(currentRGBPixel);<br>}<br><br><br>
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