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Olivier Burri
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adds new exercise examples to week 6
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‎Week-06/Macro_ROI_and_Results_v1.ijm

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/**
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* Regions of Interest & Results Tables
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* ----------------------------------------------
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*
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* In this short macro we showcase roiManager functions and how ROIs can be manipulated in ImageJ
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* This extended version of the macro covers how results tables can be accessed and customized
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*
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* Due to the simple nature of this code, no copyright is applicable
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*
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* Code created for Image Processing and Analysis For Life Scientists MOOC on EdX
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* https://www.edx.org/course/image-processing-and-analysis-for-life-scientists
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*
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* 2018 - Romain Guiet, Olivier Burri - EPFL - SV - BIOP
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* https://biop.epfl.ch
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*/
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// clear environment
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roiManager("Reset");
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run("Close All");
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run("Clear Results");
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// Create a new image
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newImage("User Drawing", "8-bit black", 512, 512, 1);
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// ask user to draw some ROIs
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waitForUser("Please Draw a Large Region Of Interest,\nThen Press 'OK'");
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Roi.setName("Large ROI");
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roiManager("Add");
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waitForUser("Please Draw a smaller ROI overlapping (partially) with the large one,\nThen Press 'OK'");
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Roi.setName("Small ROI");
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roiManager("Add");
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//
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roiManager("Select", newArray(0,1));
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roiManager("OR");
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roiManager("Add");
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roiManager("Select", (roiManager("Count")-1) ); // select the last ROI (newest one )
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roiManager("Rename", "OR");
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roiManager("Select", newArray(0,1));
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roiManager("AND");
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roiManager("Add");
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roiManager("Select", (roiManager("Count")-1) );
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roiManager("Rename", "AND");
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roiManager("Select", newArray(0,1));
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roiManager("XOR");
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roiManager("Add");
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roiManager("Select", (roiManager("Count")-1) );
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roiManager("Rename", "XOR");
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// Create an output image
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for(i=0;i<roiManager("Count");i++){
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if (i!=0) run("Add Slice");
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roiManager("Select",i);
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roiManager("Fill");
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}
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run("Make Composite", "display=Composite");
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Stack.setDisplayMode("color");
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// Do some measurement
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roiManager("Deselect");
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roiManager("Measure");
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// Create a nicer result table for the user with the areas
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// The simplest way, if there will only be one results table for one image
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// We can just grab the results at each row number and store it
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areaLargeRoi = getResult("Area",0) ;
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areaSmallRoi = getResult("Area",1) ;
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areaOrROI = getResult("Area",2) ;
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areaAndRoi = getResult("Area",3) ;
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areaXorROI = getResult("Area",4) ;
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// ########### The lines above only work for a Results table with a single image ###########
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// ########### Any result row after the 5th one would be ignored ###########
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// Because getResult and setResult only work with a window exactly called "Results",
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// we need to rename the old one before starting a new one.
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// We could also use run("Clear Results"); but this way we keep the raw data just in case
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IJ.renameResults("Raw"); // keep the raw measurements aside
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// Suppose we want to call our new measurements table "Custom" by the end of the processing
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// We need to make sure that Custom does not already exist from a previous run, as this might cause bugs.
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if( isOpen("Custom") ) {
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selectWindow("Custom");
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run("Close");
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}
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// Because there is no window called Results anymore, calling setResult will create a new one automatically
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// create a new table with "custom" values
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setResult("Label",0,"Measured Area") ; // Label for the given row, the 0 is the column
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// The next setResult will add data to the newly created Results window.
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// In the following cases, we are staying on the same row (0) and adding new columns
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setResult("Image Name",0 , getTitle());
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setResult("Large" ,0 , areaLargeRoi) ;
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setResult("Small" ,0 , areaSmallRoi) ;
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setResult("OR" ,0 , areaOrROI) ; // Union
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setResult("And" ,0 , areaAndRoi) ;// Intersection
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setResult("XOR" ,0 , areaXorROI) ;// Exclusion
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// And we can perform some computations to obtain custom values
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setResult("Large/OR Ratio",0 , (areaLargeRoi / areaOrROI) ) ;
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setResult("Small/OR Ratio",0 , (areaSmallRoi / areaOrROI) ) ;
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updateResults;
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// Here we will rename our results "Custom"
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IJ.renameResults("Custom");
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// And bring back the original results tables name
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IJ.renameResults("Raw","Results"); // bring back the raw measurements as a Results window. New results will be appended to this one and not to our custom one.
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// Our custom results are exactly behind the Results window, so we need to make it come to the front
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selectWindow("Custom");

‎Week-06/Macro_ROI_and_Results_v2.ijm

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/**
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* Lookup Tables (LUTs)
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* ----------------------------------------------
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*
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* This short macro showcases different way to use the Lookup Tables, the while loop, the window dialog getBoolean()
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*
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* Due to the simple nature of this code, no copyright is applicable
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*
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* Code created for Image Processing and Analysis For Life Scientists MOOC on EdX
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* https://www.edx.org/course/image-processing-and-analysis-for-life-scientists
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*
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* 2018 - Romain Guiet, EPFL - SV - BIOP
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* https://biop.epfl.ch
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*/
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// clear environment
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roiManager("Reset");
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run("Close All");
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run("Clear Results");
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// Create a new image with a unique ID
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id = round( random() * 100 );
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newImage("User Drawing - "+id, "8-bit black", 512, 512, 1);
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// ask user to draw some ROIs
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waitForUser("Please Draw a Large Region Of Interest,\nThen Press 'OK'");
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Roi.setName("Large ROI");
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roiManager("Add");
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waitForUser("Please Draw a smaller ROI overlapping (partially) with the large one,\nThen Press 'OK'");
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Roi.setName("Small ROI");
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roiManager("Add");
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//
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roiManager("Select", newArray(0,1));
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roiManager("OR");
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roiManager("Add");
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roiManager("Select", (roiManager("Count")-1) ); // select the last ROI (newest one )
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roiManager("Rename", "OR");
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roiManager("Select", newArray(0,1));
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roiManager("AND");
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roiManager("Add");
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roiManager("Select", (roiManager("Count")-1) );
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roiManager("Rename", "AND");
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roiManager("Select", newArray(0,1));
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roiManager("XOR");
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roiManager("Add");
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roiManager("Select", (roiManager("Count")-1) );
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roiManager("Rename", "XOR");
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// Create an output image
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for(i=0;i<roiManager("Count");i++){
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if (i!=0) run("Add Slice");
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roiManager("Select",i);
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roiManager("Fill");
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}
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run("Make Composite", "display=Composite");
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Stack.setDisplayMode("color");
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// Do some measurement
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roiManager("Deselect");
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roiManager("Measure");
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// Create a nicer result table for the user with the areas
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// Our goal is to have a table with one line == one observation
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// We can make our custom table a bit more flexible by using loops and getting the column names directly from the ROI names in the Label column
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// We will recover the names of the images and the areas for further processing
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n = nResults; // how many rows we have to recover
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// Create an array that will contain the areas
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areas = newArray(n);
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// Create an array that will contain the ROI names
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roiNames = newArray(n);
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for(i=0; i<n; i++) {
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// Pick up the label
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name = getResultLabel(i);
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// The name is like this 'Image_Name:ROI name:Slice'
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// We do not care about the Slice here, only the image name and the ROI name
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// Split the names at the colon
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splitName = split(name, ':');
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// Keep the roiName, which is at index 1
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roiNames[i] = splitName[1];
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// Recover the value of the area
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areas[i] = getResult("Area", i);
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}
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// Now that everything is set, we can create a new results table
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// Because getResult and setResult only work with a window exactly called "Results",
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// we need to rename the old one before starting a new one.
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// We could also use run("Clear Results"); but this way we keep the raw data just in case
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IJ.renameResults("Raw"); // keep the raw measurements aside
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// Suppose we want to call our new measurements table "Custom" by the end of the processing
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// We need to check first if there is already a table called "Custom", so that we can APPEND to it
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row= 0;
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if( isOpen("Custom") ) {
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IJ.renameResults("Custom", "Results");
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row = nResults; // get the current number of rows
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}
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// Append data to the table at the correct row
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setResult("Label", row, "Measured Area") ; // Label for the given row, the 0 is the column
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setResult("Image Name", row, getTitle()); // Add the image name to the table
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// Now we go through all the columns we have created
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for(i=0; i<n; i++) {
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// We make a new column for each ROI name and add the corresponding area
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setResult(roiNames[i], row, areas[i]);
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}
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// Now we can do some custom calculations
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// For instance compute how much of the Large ROI is contributing to the overlap
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// The formula would be (In column names) AND / LARGE ROI * 100 or (the area both have in common divided by the area of the large roi time 100 to have it percent
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area_large = getResult("Large ROI", row);
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area_and = getResult("AND", row);
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// Create new measurement
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large_ratio = area_and / area_large * 100;
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// Add the new column
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setResult("Large ROI % Overlap", row, large_ratio);
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updateResults;
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// Here we will rename our results "Custom"
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IJ.renameResults("Custom");
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// And bring back the original results tables name
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IJ.renameResults("Raw","Results"); // bring back the raw measurements as a Results window. New results will be appended to this one and not to our custom one.
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// Our custom results are exactly behind the Results window, so we need to make it come to the front
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selectWindow("Custom");

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