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Gabor 过滤器脚本

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Example of a two-dimensional Gabor filter kernel (with a spectrum LUT). Example of a two-dimensional Gabor filter kernel (with a spectrum LUT).

This is an example of how to create Gabor filters in Fiji using Beanshell scripting. The script will create and apply a set of Gabor filters to the currently selected image.

可以调整五个不同的参数：

  • Sigma，定义高斯包网络的大小
  • Psi，相位偏移
  • Gamma，空间纵横比，指定Gabor函数的支撑度的圆度。
  • Fx，正弦数量的频率
  • nAngles，滤波器方向的数量

结果，脚本将显示一组过滤器、每个方向的原始图像的过滤版本以及过滤图像堆栈的投影（简单、顶部、均值和透视）。

示例

这是使用 Leaf 示例图像 (File › Open Samples › Leaf (36K)) 和 sigma = 8.0、gamma = 0.25、psi = 0.0、Fx = 3.0、nAngles = 5 的脚本结果示例。<div class="thumbnail" > Example of a two-dimensional Gabor filter kernel (with a spectrum LUT). Example of a two-dimensional Gabor filter kernel (with a spectrum LUT). </div>

代码

import ij.*;
import ij.process.*;
import ij.plugin.filter.*;
import ij.plugin.ContrastEnhancer;
import ij.plugin.ZProjector;

/**
* This script calculates a set of Gabor filters over the selected image.
*
* Parameters: sigma, gamma, psi, Fx, nAngles
*/

// Sigma defining the size of the Gaussian envelope
sigma = 8.0;
// Aspect ratio of the Gaussian curves
gamma = 0.25;
// Phase
psi = Math.PI / 4.0 * 0;
// Frequency of the sinusoidal component
Fx = 3.0;

// Number of diferent orientation angles to use
nAngles = 5;

// copy original image and transform it to 32 bit 
originalImage = IJ.getImage();
originalImage = new ImagePlus(originalImage.getTitle(), originalImage.getProcessor().convertToFloat());
width = originalImage.getWidth();
height = originalImage.getHeight();

// Apply aspect ratio to the Gaussian curves
sigma_x = sigma;
sigma_y = sigma / gamma;

// Decide size of the filters based on the sigma
largerSigma = (sigma_x > sigma_y) ? (int) sigma_x : (int) sigma_y;
if(largerSigma < 1)
    largerSigma = 1;
    
ip = originalImage.getProcessor().duplicate();

sigma_x2 = sigma_x * sigma_x;
sigma_y2 = sigma_y * sigma_y;

// Create set of filters

filterSizeX = 19; //6 * largerSigma + 1;
filterSizeY = 19; //6 * largerSigma + 1;


middleX = (int) Math.round(filterSizeX / 2);
middleY = (int) Math.round(filterSizeY / 2);

is = new ImageStack(width, height);
kernels = new ImageStack(filterSizeX, filterSizeY);

rotationAngle = Math.PI/(double)nAngles;
// Rotate kernel from 0 to 180 degrees
for (i=0; i<nAngles; i++)
{   
    theta = rotationAngle * i;
    filter = new FloatProcessor(filterSizeX, filterSizeY);  
    for (int x=-middleX; x<=middleX; x++)
    {
        for (int y=-middleY; y<=middleY; y++)
        {           
            xPrime = (double)x * Math.cos(theta) + (double)y * Math.sin(theta);
                yPrime = (double)y * Math.cos(theta) - (double)x * Math.sin(theta);
                
            a = 1.0 / ( 2.0 * Math.PI * sigma_x * sigma_y ) *
                            Math.exp(-0.5 * (xPrime*xPrime / sigma_x2 + yPrime*yPrime / sigma_y2) );
            c = Math.cos( 2.0 * Math.PI * (Fx * xPrime) / filterSizeX + psi); 
            
            filter.setf(x+middleX, y+middleY, (float)(a*c) );
        }
    }
    kernels.addSlice("kernel angle = " + theta, filter);
}

// Show kernels
ip_kernels = new ImagePlus("kernels", kernels);
ip_kernels.show();

// Apply kernels
for (i=0; i<nAngles; i++)
{
    theta = rotationAngle * i;      
    c = new Convolver();                
    
    kernel = (float[]) kernels.getProcessor(i+1).getPixels();
    ip = originalImage.getProcessor().duplicate();      
    c.convolveFloat(ip, kernel, filterSizeX, filterSizeY);      

    is.addSlice("gabor angle = " + i, ip);
}
                
            

// Normalize filtered stack
c = new ContrastEnhancer();
for(int i=1 ; i <= is.getSize(); i++)
{
    c.stretchHistogram(is.getProcessor(i), 0.4);
}


projectStack = new ImagePlus("filtered stack",is);
IJ.run(projectStack, "Enhance Contrast", "saturated=0.4 normalize normalize_all");
                
resultStack = new ImageStack(width, height);
                
zp = new ZProjector(projectStack);
zp.setStopSlice(is.getSize());
for (int i=0;i<=5; i++)
{
    zp.setMethod(i);
    zp.doProjection();
    resultStack.addSlice("Gabor_" + i 
            +"_"+sigma+"_" + gamma + "_"+ (int) (psi / (Math.PI/4) ) +"_"+Fx, 
            zp.getProjection().getChannelProcessor());
}

// Display filtered images
(new ImagePlus("gabor, sigma="+sigma+" gamma="+gamma+ " psi="+psi, is)).show();

result= new ImagePlus ("Gabor stack projections", resultStack) ;
IJ.run(result, "Enhance Contrast", "saturated=0.4 normalize normalize_all");
result.show();

另请参阅