Merge branch 'imagej_macro' into 'master'

Imagej macro

See merge request !2

05_example_code_and_data/analyse_banana.ijm

+// 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);

05_example_code_and_data/arrays.ijm

+// 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");
+
+

05_example_code_and_data/csv_test.py

+
+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
+
+

05_example_code_and_data/first_example.ijm

+//
+// This program is our first example
+// 
+// Author: Robert Haase, MPI-CBG,
+// rhaase@mpi-cbg.de
+// July 2015
+
+print("Hello world");
+

05_example_code_and_data/good_comments.ijm

+// 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 );
+

05_example_code_and_data/good_comments.py

+#
+# 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 )
+

05_example_code_and_data/image_statistics.ijm

+// 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();
+

05_example_code_and_data/process_folder.ijm

+// 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 );
+}

05_example_code_and_data/read_image_properties.ijm

+// 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();

05_example_code_and_data/string_variables.ijm

+
+// initialise program
+firstname = "Robert"; 
+lastname = "Haase"; 
+
+// run complicated algorithm
+name = firstname + " " + lastname; 
+
+// show the result
+print("Hello " + name + "!");
+

05_example_code_and_data/troubleshooting_tracing.ijm

+start = 0;
+end = 10;
+
+
+// print numbers
+for ( i = start; i < end; i++ ) {
+    if (i > 5) {
+        print(i);
+    }
+}

05_example_code_and_data/variables.ijm

+
+// initialise program
+a = 1; 
+b = 2.5; 
+
+// run complicated algorithm
+c = a + b;
+
+// show the result
+print(c);

05_example_code_and_data/yin_yang.ijm

+// 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");
+    }
+}