Commit 4624726c authored by rhaase's avatar rhaase

initial version examples for ImageJ macro

parent b35e6247
// This ImageJ macro analyses a folder of 2D MRI
// images showing a banana slice by slice. It measures
// the position of the banana and writes it in a CSV file.
//
// Usage: run it in Fiji (http://fiji.sc)
//
// Robert Haase, MPI CBG, rhaase@mpi-cbg.de
// April 2019
//
folder = "C:/structure/teaching/lecture_applied_bioimage_analysis/05_example_data/banana/"
// access the folder
filelist = getFileList(folder);
for (i = 0; i < lengthOf(filelist); i++) {
// get the nth entry from the filelist array
file = filelist[i];
if (endsWith(file, ".tif")) {
// open the image
open(folder + file);
// segment the object in the image
setAutoThreshold("Default dark");
setOption("BlackBackground", true);
run("Convert to Mask");
run("Fill Holes");
// measure the position of this one single object
run("Set Measurements...", "centroid redirect=None decimal=3");
run("Create Selection");
run("Measure");
// close the image
close();
}
}
// save the positions as CSV to disc
result_filename = "Position.csv"
saveAs("Results", folder + result_filename);
// numeric arrays
v = newArray(3, -4, 0);
Array.print(v);
// create an array with three elements containing zeros
v = newArray(3);
Array.print(v);
// manipulate arrays
v[0] = 3.5
Array.print(v);
// access array elements
print( v[2] );
// string arrayss
animals = newArray("dog", "cat", "mouse");
// combining arrays
mixed = Array.concat(v, animals);
Array.print(mixed);
// get length of an array
numberOfElements = lengthOf(v);
print("v has " + numberOfElements + " elements");
import csv
with open("test.csv", newline='') as csvfile:
reader = csv.reader(csvfile, delimiter=',')
linecount = 0;
for row in reader:
if (linecount > 0):
print("The square of " + row[0] + " is " + row[1]);
linecount = linecount + 1
//
// This program is our first example
//
// Author: Robert Haase, MPI-CBG,
// rhaase@mpi-cbg.de
// July 2015
print("Hello world");
// This program is our second example.
// It sums up two numbers.
//
// Usage:
// * Run it in FIJI (www.fiji.sc)
//
// Author: Robert Haase, MPI CBG,
// rhaase@extern.mpi-cbg.de
// July 2016
// initialise program
a = 1;
b = 2.5;
// run complicated algorithm
final_result = a + b;
print( final_result );
#
# This program sums up two numbers.
#
# Usage:
# * Run it in Python (python.org)
#
# Author: Robert Haase, MPI CBG,
# rhaase@mpi-cbg.de
# April 2019
# initialise program
a = 1
b = 2.5
# run complicated algorithm
final_result = a + b
# print the final result
print( final_result )
// initialise program
imageFilename = "blobs.gif";
open( imageFilename );
// get image statistics
getStatistics(area, mean, min, max, std);
// show results
print("The grey value ranges from " + min + " to " + max + ". ");
print("It has an average of " + mean + " +- " + std + ". ");
close();
// initialise program
foldername = "/Users/rhaase/temp/";
// get all files in the folder as list
list = getFileList( foldername );
// print out the list; item by item
for (i = 0; i < list.length; i++) {
filename = list[i];
print( filename );
}
// initialise program
imageFilename = "blobs.gif";
open( imageFilename );
// read image properties
width = getWidth();
height = getHeight();
getPixelSize(unit, pixelWidth, pixelHeight);
// show results
print("The image is " + width + " times " + height + " pixels wide");
print("Each pixels has a size of " + pixelWidth +
" times " + pixelHeight + " " + unit + "^2");
close();
// initialise program
firstname = "Robert";
lastname = "Haase";
// run complicated algorithm
name = firstname + " " + lastname;
// show the result
print("Hello " + name + "!");
start = 0;
end = 10;
// print numbers
for ( i = start; i < end; i++ ) {
if (i > 5) {
print(i);
}
}
// initialise program
a = 1;
b = 2.5;
// run complicated algorithm
c = a + b;
// show the result
print(c);
// initialise program
a = 5;
b = 3;
c = 8;
// execute algorithm
d = (a + b) / c;
// evaluate result
if (b > 0) {
if (a == 5) {
print("Yin");
}
else {
if (c < 5) {
}
}
if (d != 0) {
print("Yang");
}
}
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