added the ImageJ macro course from January 2017

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/demo/test_arrays.ijm

+print("\\Clear");
+
+array = newArray(0, 1, 2);
+
+// print (array);
+
+// save as ijm
+
+Array.print(array)
+
+array[0] = 5
+
+Array.print(array)
+
+
+sum = array[0] + array[1] + array[2];
+print(sum)
+
+
+
+animals = newArray("dog", "cat");
+
+conc = Array.concat(array, animals);
+
+Array.print(conc);
+
+
+
+
+// ----------------------------
\ No newline at end of file

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/demo/test_loop.ijm

+start = 5;
+end = 25;
+print("\\Clear");
+
+
+// ... many empty lines
+
+
+
+
+
+for (i = start; i >= end; i++) {
+	
+	if (i > 5) {
+		print("i was " + i);
+	}
+}
\ No newline at end of file

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/demo/test_strings.ijm

+print("\\Clear");
+
+firstname = "Robert";
+lastname = "Haase";
+
+name = firstname + " " + lastname;
+
+print (name);
+
+//------------------------------------------
+
+a = "1";
+b = 1;
+
+sumAB = a + b;
+sumBA = b + a;
+
+print(sumAB);
+print(sumBA);
+
+
+//------------------------------------------
+
+
+print("\\Clear");
+
+text = "Hello world!";
+
+text = replace(text, "world", "universe");
+
+print(text);
\ No newline at end of file

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/demo/troubleshooting_error_message.ijm

+Sentence = "Can you can a can as a canner can can a can?";
+
+if (startsWith(Sentence, "Can") {
+	print(sentence);
+}
\ No newline at end of file

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/demo/troubleshooting_tracing.ijm

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

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/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");
+
+

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/code_highlights.ijm

+a = 5;
+b = 7;
+
+sum = a + b;
+ratio = a / b;
+
+print("The sum is + sum);
+print("The ratio is " + ratio);
+

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/custom_functions.ijm

+// point 1
+x1 = 3; 
+y1 = 5;
+
+// point 2
+x2 = 7;
+y2 = 8; 
+
+// point 3
+x3 = 14;
+y3 = 3; 
+
+printDistance(x1, y1, x2, y2, "between 1 and 2");
+printDistance(x2, y2, x3, y3, "between 2 and 3");
+printDistance(x1, y1, x3, y3, "between 1 and 3");
+
+function printDistance(xA, yA, xB, yB, description) {
+    d = sqrt(pow(xA - xB, 2) + pow(yA - yB, 2));
+    print("The distance " + description + " is " + d);
+}
+

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_analyse_folder_solution.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 < lengthOf(list); i++) {
+    filename = list[i];   
+       
+    if (endsWith(filename, ".tif") ||
+        endsWith(filename, ".gif")) {
+        
+        open(foldername + filename);
+
+        // analyse FOV
+        getDimensions (imageWidth, imageHeight, 
+                       channels, slices, frames);
+        getPixelSize (physicalUnitName, 
+                      pixelWidth, pixelHeight);
+        
+        // calculate FOV size
+        FOVwidth = (imageWidth * pixelWidth);
+        FOVheight = (imageHeight * pixelHeight);
+
+        // show results
+        print(filename);      
+        print("FOV width: " + FOVwidth + physicalUnitName);
+        print("FOV height: " + FOVheight + physicalUnitName);        
+        close();
+    }
+}

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_cubic_root.ijm

+// call build-in function
+variable1 = pow(2, 3);
+
+// call custom function
+variable2 = cubicRoot(variable1);
+
+print(variable2);
+

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_cubic_root_solution.ijm

+// call build-in function
+variable1 = pow(2, 3);
+
+// call custom function
+variable2 = cubicRoot(variable1);
+
+print(variable2);
+
+// define a self-made custom function
+function cubicRoot(x) {
+    return pow(x, 1 / 3);
+}

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_for_loop.ijm

+print("\\Clear");
+
+foldername = "/Users/rhaase/temp/";
+
+filelist = getFileList(foldername);
+
+for ( i = 0; i < lengthOf(filelist); i++) {
+	imagefilename = filelist[i];
+
+	if (endsWith(imagefilename, ".tif")) {
+		print(imagefilename);	
+	}
+
+	
+}
+
+

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_for_loop_solution.ijm

+// initialisation
+input_num = getNumber("Input a number", 5);
+
+// print 10 numbers
+for( i = input_num; i >= 0 ; i-- ){
+       print(i);
+}

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_german_grading_system_solution.ijm

+
+// initialise program
+numberOfTotalPoints = 50;
+numberOfReachedPoints_Robert = 40;
+
+// calculate percentage
+percentage = numberOfReachedPoints_Robert / numberOfTotalPoints * 100;
+
+// print out grade
+if (percentage >= 90) {
+	print("very good");
+}
+if (percentage >= 80 && percentage < 90) {
+	print("good");
+}
+if (percentage >= 65 && percentage < 80) {
+	print("satisfactory");
+}
+if (percentage >= 50 && percentage < 65) {
+	print("sufficient");
+}
+if (percentage > 0 && percentage < 50) {
+	print("insufficient");
+}
+if (percentage == 0) {
+	print("failed");
+}

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_join.ijm

+sentence = "Text processing is a pain.";
+
+words = split(sentence, " ");
+
+words[0] = "Image";
+words[4] = "big fun.";
+
+sentence = join(words, " ");
+
+print(sentence);

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_join_solution.ijm

+sentence = "Text processing is a pain.";
+
+words = split(sentence, " ");
+
+words[0] = "Image";
+words[4] = "big fun.";
+
+sentence = join(words, " ");
+
+print(sentence);
+
+// take an array and concatenate is elements. 
+// Put a separator between the elments.
+function join(array, separator) {
+    result = "";
+    for (i = 0; i < lengthOf(array); i++) {
+        // put the separator not before the first element.
+        if (i > 0) {
+            result += separator;
+        }
+        result += array[i];
+    }
+    return result;
+}

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_math.ijm

+
+// initialise program
+x1 = 3; 
+y1 = 5;
+
+x2 = 7;
+y2 = 8; 
+
+// run complicated algorithm
+
+d = 
+
+
+// show the result
+print("The distance is " + d);

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_math_solution.ijm

+
+// initialise program
+x1 = 3; 
+y1 = 5;
+
+x2 = 7;
+y2 = 8; 
+
+// run complicated algorithm
+
+d = sqrt(pow(x1 - x2, 2) +  
+         pow(y1 - y2, 2));
+
+
+// show the result
+print("The distance is " + d);

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_reading.ijm

+sentence = "double bubble gum bubbles double";
+
+words = split(sentence, " ");
+
+temp = words[0];
+words[0] = words[4];
+words[4] = temp;
+
+sentence = join(words, " ");
+
+print(sentence);
+
+function join(array, separator) {
+    result = "";
+    for (i = 0; i < lengthOf(array); i++) {
+        if (i > 0) {
+            result += separator;
+        }
+        result += array[i];
+    }
+    return result;
+}
\ No newline at end of file

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_string_manipulation.ijm

+// retrieve filename
+filename = "blobs_timepoint5_conditionB.gif";
+
+// cut out interesting parts
+filenameParts = split(filename, "_"); 
+timepoint = filenameParts[1];
+
+
+// remove unneccessary characters
+timepoint = replace(timepoint, "timepoint", "");
+
+
+// show result
+print("Timepoint was: " + timepoint);
+
+

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_string_manipulation_solution.ijm

+// retrieve filename
+filename = "blobs_timepoint5_conditionB.gif";
+
+// cut out interesting parts
+filenameParts = split(filename, "_"); 
+timepoint = filenameParts[1];
+condition = filenameParts[2];
+
+// remove unneccessary characters
+timepoint = replace(timepoint, "timepoint", "");
+condition = replace(condition, "condition", "");
+condition = replace(condition, ".gif", "");
+// show result
+print("Timepoint was: " + timepoint);
+print("Condition was: " + condition);
+

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/first_example.ijm

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

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/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 );
+

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/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();
+

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/mandelbrot.ijm

+
+window_size = 300;
+max_size = 4; 
+max_iterations = 64;
+
+speed = 0.95;
+
+
+imin = -1.25;
+imax = 1.25;
+rmin = -1.5;
+rmax = 1;
+
+title = "Suprise"
+
+newImage(title, "32-bit", window_size, window_size, 1);
+
+count = 0;
+while (isOpen(title)) {
+	imin = imin * speed;
+	imax = imax * speed;
+
+	rmax = rmin + (rmax-rmin) * speed;
+	
+	deltar=(rmax-rmin)/(window_size-1); 
+	deltai=(imax-imin)/(window_size-1); 
+	
+	arr = newArray(window_size * window_size);
+	count = 0;
+	for (row=0; row<window_size; row++) {
+		for (col=0; col<window_size; col++) {
+			x=0; 
+			y=0; 
+			ci=(imin+row*deltai);  
+			cr=(rmin+col*deltar);  
+			color=0;
+			do {
+				color++; 
+				xsq=x*x;
+				ysq=y*y;
+				if ((xsq+ysq)<(max_size)) {  
+				    y=x*2*y+ci;                
+				    x=xsq-ysq+cr;
+			    }
+			}
+			while ((color<max_iterations)&&((xsq+ysq)<(max_size)));
+			
+			if (color>=max_iterations) {
+				color=0;
+			}
+			arr[count] = color;
+			count++;
+		}              
+	}
+	
+	count = 0;
+	for (row=0; row<window_size; row++) {
+		for (col=0; col<window_size; col++) {
+			if (isOpen(title)) {
+				setPixel (col, row, arr[count]);
+			}
+			count++;
+		}
+	}
+	if (isOpen(title)) {
+		run("6 shades");
+		updateDisplay();
+		run("Enhance Contrast", "saturated=0.35");
+	}
+	count ++;
+}

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/math_with_strings.ijm

+
+// initialise program
+a = "1"; 
+b = 1;
+
+// calculate the sum
+sumAB = a + b;
+sumBA = b + a;
+
+// show the result
+print("The sumAB is " + sumAB);
+print("The sumBA is " + sumBA);
+

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/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 );
+}

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/quiz_formatting1.ijm

+measurements = newArray(34,67,32,9,22,37,22,5,12,78,51);
+threshold=50;count=0;
+minimum=measurements[0];maximum=measuremnts[0];
+for (i=0;i<lengthOf(measurements);i++){
+if(measurements[i]>threshold){count++;}
+if(measurements[i]<minimum){minimum=measurements[i]}
+if(measurements[i]>maximum){maximum=measurements[i]}
+}
\ No newline at end of file

ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/read_image_properties.ijm

+// initialise program
+imageFilename = "blobs.gif";
+open( imageFilename );
+
+// read image properties
+width = getWidth();
+height = getHeight();
+getPixelSize(unit, pixelWidth, pixelHeight);
+