tferr

/*
 * IJ BAR: https://github.com/tferr/Scripts#scripts
 *
 * Performs a t-test between two open images (http://thread.gmane.org/gmane.comp.java.imagej/35266) using
 * commons-math:
 * http://commons.apache.org/proper/commons-math/userguide/stat.html
 * http://commons.apache.org/proper/commons-math/apidocs/org/apache/commons/math3/stat/inference/TTest.html
 *
 */

tferr

// yet another multichannel profile plotter
// with smart(?) lookuptables

Stack.getDimensions(w, h, c, z, t);
p = getProfile();
getStatistics(null, null, min, max);
Plot.create("Multi-Channel Profile Plot", "Distance (pixels)", "Value");
Plot.setLimits(0,p.length,min,max);
for (i=1;i<=c;i++) {
Stack.setChannel(i);

tferr

// ImageJ1 macros that create X/Y mirrors of the active ROI
// http://thread.gmane.org/gmane.comp.java.imagej/35570

macro "Contralateral in X [F1]" {
	mirrorROI(-1, 1);
}
macro "Contralateral in Y [F2]" {
	mirrorROI(1, -1);
}

tferr

import java.util.regex.Matcher;
import java.util.regex.Pattern;

boolean validFile(String filename) {
	String FILE_PATTERN = "(.*(\\.(?i)(stk|tif))$)";
	Pattern pattern = Pattern.compile(FILE_PATTERN);
	Matcher matcher = pattern.matcher(filename);
	return matcher.matches();
}

tferr

function randomString(length, spacers) {
	template = "0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ";
	nChars = lengthOf(template);
	string = "";
	for (i=0; i<length; i++) {
		idx = maxOf(0, round(random()*nChars-1));
		string += substring(template, idx, idx+1);
		if (spacers && i%5==0) string += "_";
	}
	return string;

tferr

/**
 * Retrieves the Checkbox of a RadioButtonGroup() in an ImageJ1
 * GenericDialog associated with the specified label.
 */
Checkbox getRadioCheckbox(ij.gui.GenericDialog gd, String label) {
	Component[] gdComponents = gd.getComponents();
	for (Component c1 : gdComponents) {
		if (c1 instanceof Panel) {
			Component[] c1Components = ((Panel) c1).getComponents();
			for (Component c2 : c1Components) {

tferr

/* Polar_Plot_Demo.bsh
 * IJ BAR: https://github.com/tferr/Scripts#scripts
 *
 * Beanshell implementation of JFreeChart[1] PolarChartDemo[2] 
 * 
 * [1] http://www.jfree.org/jfreechart/api/javadoc/
 * [2] http://www.java2s.com/Code/Java/Chart/JFreeChartPolarChartDemo.htm
 */

import ij.gui.GUI;

tferr

import os
import re
from tracing import PathAndFillManager

# An example script showing how to convert all the .traces
# files in a directory to SWC files.  (The .traces format
# is the native file format of Simple Neurite Tracer.)

def run():
    d = IJ.getDirectory("Choose your directory of .traces files...")

tferr

# @ImageJ ij
# @Dataset data
# @String(label="Projection Type",choices={"Max","Mean","Median","Min", "StdDev", "Sum"}) proj_type


from net.imagej.axis import Axes
from net.imagej.ops import Ops


def proj_method(method):

tferr

ImageJ 2.0.0-rc-56/1.51j; Java 1.8.0_66 [x86_64]

-- Application: ImageJ --
Title = ImageJ
Version = 2.0.0-rc-56/1.51j
groupId = net.imagej
artifactId = imagej
Archiver-Version = Plexus Archiver
Build-Jdk = 1.8.0_111
Built-By = jenkins-maven