miura

//==============================================================================
//
// Project: EDF - Extended Depth of Focus
// 
// Author: Alex Prudencio
// 
// Organization: Biomedical Imaging Group (BIG)
// Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
//
// Information: http://bigwww.epfl.ch/demo/edf/

miura

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
	<key>charactersArray</key>
	<array>
		<dict>
			<key>beginString</key>
			<string>'</string>
			<key>endString</key>

miura

from edfgui import ExtendedDepthOfField
from edfgui import ExtendedDepthOfFieldHeadless
from edfgui import Parameters
from ij import IJ
print 'test'
imp = IJ.openImage('http://imagej/nih.gov/ij/images/mri-stack.zip')
edf = ExtendedDepthOfFieldHeadless(imp, Parameters())
# I added a test method in the java file only with IJ.log("test method") to see if instance is sucessfully made
edf.testpp()

miura

// LUT Inversion Test
// Created by Jeffrey N. Murphy on 2012.10.30
// Contact on Twitter: @MurphysLab
// http://murphyslab.ca/files/LUT_Inversion_Test.ijm
// added LUT stack output (miura@embl.de)

newImage("Test", "8-bit Ramp", 400, 400, 1);
imgid = getTitle();
print("Grays");

miura

<?xml version="1.0" encoding="UTF-8"?>
<!-- >
This pom.xml is for running Scala Script with ImageJ. 
run the script with the following command. 
mvn scala:script
<-->
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
		http://maven.apache.org/xsd/maven-4.0.0.xsd">
	<modelVersion>4.0.0</modelVersion>

miura

import ij._

println ("Hello from external script :-)")
IJ.log("test ij")
IJ.log(IJ.getVersion())
val imp = IJ.openImage("http://imagej.nih.gov/ij/images/blobs.gif")
imp.show()
IJ.wait(2000)
imp.close()

miura

//==============================================================================
//
// Project: EDF - Extended Depth of Focus
// 
// Author: Alex Prudencio (headless hack by Kota Miura and Christian Tischer, christian.tischer@embl.de)
// 
// Organization: Biomedical Imaging Group (BIG)
// Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
//
// Information: http://bigwww.epfl.ch/demo/edf/

miura

# requires https://github.com/cmci/CourseUtil and JmageJ
from emblcmci import URLSaver

us = URLSaver()
us.run("http://cmci.embl.de/sampleimages/macrocourse.zip")

miura

macro "create"{
	ww = 100;
	hh = 30;
	slices = 11;
	newImage("teststack.tif", "8-bit Black", ww, hh, slices);
	for (i = 0; i < slices; i++){
		setSlice(i+1);
		drawString(i+1, ww/2, hh/2 + 10);
	}
}

miura

// calculater based on an Image. 
// kota MIura

ww = 300;
hh = 600;
rows = 7;
newImage("Calc", "8-bit Black", ww, hh, 1);
setFont("Monospaced", 14, "bold");
setColor(255, 255, 255);
drawString("Exit: Right Click", 10, hh - 15);