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/**
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* root_tools
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*
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* The root tools help to efficiently measure the following characteristics of plant roots:
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* - the angle of the opening of the whole root
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* - the depth to which it goes down
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* - the number of roots at 30 cm depth
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* - the diameters of the roots at depth
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*
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* written 2013 by Volker Baecker (INSERM) at Montpellier RIO Imaging (www.mri.cnrs.fr)
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*/
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var helpURL = "http://dev.mri.cnrs.fr/wiki/imagej-macros/Root_Tools";
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var KNOWN_DISTANCE = 40; // known distance for spatial calibration (there are 20mm between two nails)
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var RADIUS=75; // radius of the circle drawn around the root point
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var ROOT_POINT_LINE_WIDTH = 15; // line width of the circle drawn around the root point
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var COLOR_ROOT_POINT = "red"; // color of the circle drawn around the root point
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var COUNT_ROOT_DEPTH = 30; // depth from the root point at which the horizontal line is drawn. The number of roots will be counted at that depth
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var HALF_LINE_WIDTH = 10; // half of the width of the line drawn at count root depth
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var WIDTH_DEPTH = 8; // line width of the line drawn at count root depth
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var COLOR_DEPTH = "cyan"; // color of the line drawn at count root depth
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var DX_ANGLE = 300; // delta x for the angle tool that is added to the image
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var DY_ANGLE = 600; // delta y for the angle tool that is added to the image
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var ANGLE_COLOR = "red"; // the color for marking the measured angle
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var ANGLE_LINE_WIDTH = 8; // the line width for marking the measured angle
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var MEASURE_DEPTH_COLOR = "magenta"; // the color of the line indicating the max. depth to which the root goes down
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var MEASURE_DEPTH_WIDTH = 8; // the line width of the line indicating the max. depth to which the root goes down
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var ZOOM_RADIUS = 20; // radius of the region around the click that is copied and zoomed
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var DIAMETER_COLOR = "yellow"; // color of the line indicating the measured root diameters
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var DIAMETER_WIDTH = 2; // width of the line indicating the measured root diameters
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var USE_GLOBAL_SCALE = true;
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var rootX;
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var rootY;
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var deepX;
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var deepY;
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var UNIT = "mm";
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var X1;
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var X2;
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var Y;
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var MAX_ROOTS = 20;
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var DIAMETERS = newArray(MAX_ROOTS);
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var numberOfRootsAtThirty = 0;
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var DEPTH = 0;
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var ID = 0;
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var ANGLE = 0;
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var TITLE;
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var NUMBER = 0;
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var FOLDER;
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macro "zoomIn [f1]" {
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run("In [+]");
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}
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macro "zoomOut [f2]" {
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run("Out [-]");
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}
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macro "Root Tools Help Action Tool- 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" {
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run('URL...', 'url='+helpURL);
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}
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macro "Set Scale [f5]" {
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setScale();
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}
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macro "Define Root Point [f6]" {
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setTool("Define Root Point Tool");
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}
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macro "Angle [f7]" {
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measureAngle();
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}
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macro "Measure Depth [f8]" {
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setTool("Measure Depth Tool");
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}
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macro "Zoom Region [f9]" {
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setTool("Zoom region Tool");
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}
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macro "Measure Diameter [f10]" {
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measureDiameter();
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}
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macro "Write Report [f11]" {
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writeReport();
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}
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macro "Set Scale Action Tool- C000T4b12s"{
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setScale();
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}
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macro "Set Scale Action Tool Options" {
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Dialog.create("Root Tools - Set Scale - Options");
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Dialog.addNumber("known distance [cm]: ", KNOWN_DISTANCE);
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Dialog.addCheckbox("use global scale", USE_GLOBAL_SCALE);
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Dialog.show();
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KNOWN_DISTANCE = Dialog.getNumber();
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USE_GLOBAL_SCALE = Dialog.getCheckbox();
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}
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macro "Define Root Point Tool- C000T4b12r" {
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getCursorLoc(x, y, z, flags);
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ID = getImageID();
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TITLE = getTitle();
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FOLDER = getDirectory("image");
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run("Remove Overlay");
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rootX = x;
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rootY = y;
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setColor(COLOR_ROOT_POINT);
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setLineWidth(ROOT_POINT_LINE_WIDTH);
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Overlay.drawEllipse(rootX-RADIUS, rootY-RADIUS, 2*RADIUS+1, 2*RADIUS+1);
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Overlay.show();
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run("Select None");
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lineAtThirtyCM();
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angleSelection();
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setTool("Angle tool");
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}
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macro "Define Root Point Tool Options" {
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Dialog.create("Root Tools - Define Root Point - Options");
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Dialog.addNumber("radius: ", RADIUS);
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Dialog.addNumber("line width: ", ROOT_POINT_LINE_WIDTH);
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Dialog.addString("root point color: ", COLOR_ROOT_POINT);
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Dialog.addNumber("depth [cm]: ", COUNT_ROOT_DEPTH);
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Dialog.addNumber("half of length [cm]: ", HALF_LINE_WIDTH);
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Dialog.addNumber("line width for depth: ", WIDTH_DEPTH);
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Dialog.addString("depth line color: ", COLOR_DEPTH);
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Dialog.addNumber("dx angle: ", DX_ANGLE);
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Dialog.addNumber("dy angle: ", DY_ANGLE);
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Dialog.show();
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RADIUS = Dialog.getNumber();
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ROOT_POINT_LINE_WIDTH = Dialog.getNumber();
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COLOR_ROOT_POINT = Dialog.getString();
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COUNT_ROOT_DEPTH = Dialog.getNumber();
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HALF_LINE_WIDTH = Dialog.getNumber();
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WIDTH_DEPTH = Dialog.getNumber();
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COLOR_DEPTH = Dialog.getString();
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DX_ANGLE = Dialog.getNumber();
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DY_ANGLE = Dialog.getNumber();
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}
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macro "Angle Action Tool- C000T4b12a" {
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measureAngle();
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}
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macro "Angle Action Tool Options" {
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Dialog.create("Root Tools - Angle - Options");
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Dialog.addString("angle color: ", ANGLE_COLOR);
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Dialog.addNumber("line width: ", ANGLE_LINE_WIDTH);
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Dialog.show();
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ANGLE_COLOR = Dialog.getString();
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ANGLE_LINE_WIDTH = Dialog.getNumber();
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}
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macro "Measure Depth Tool- C000T4b12d" {
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getCursorLoc(x, y, z, flags);
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deepX = x;
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deepY = y;
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DEPTH = deepY - rootY;
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toScaled(DEPTH);
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setColor(MEASURE_DEPTH_COLOR);
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setLineWidth(MEASURE_DEPTH_WIDTH);
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Overlay.drawLine(rootX, rootY, rootX, deepY);
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Overlay.drawLine(rootX, deepY, deepX, deepY);
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Overlay.show();
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run("Select None");
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setTool("Zoom region Tool");
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}
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macro "Measure Depth Tool Options" {
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Dialog.create("Root Tools - Measure Depth - Options");
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Dialog.addString("line color: ", MEASURE_DEPTH_COLOR);
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Dialog.addNumber("line width: ", MEASURE_DEPTH_WIDTH);
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Dialog.show();
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MEASURE_DEPTH_COLOR = Dialog.getString();
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MEASURE_DEPTH_WIDTH = Dialog.getNumber();
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}
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macro "Zoom region Tool- C000T4b12z" {
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title = getTitle();
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getCursorLoc(x, y, z, flags);
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makeRectangle(x-ZOOM_RADIUS, y-ZOOM_RADIUS, 2*ZOOM_RADIUS+1, 2*ZOOM_RADIUS+1);
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run("Duplicate...", "title="+title+"box");
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run("Remove Overlay");
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run("In [+]");
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run("In [+]");
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run("In [+]");
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run("In [+]");
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run("In [+]");
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run("In [+]");
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setTool("line");
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}
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macro "Zoom region Tool Options" {
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Dialog.create("Root Tools - Zoom region - Options");
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Dialog.addNumber("radius ", ZOOM_RADIUS);
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Dialog.show();
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ZOOM_RADIUS = Dialog.getNumber();
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}
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macro "Measure diameter Action Tool- C000T4b12m" {
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measureDiameter();
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}
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macro "Measure diameter Action Tool Options" {
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Dialog.create("Root Tools - Measure diameter - Options");
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Dialog.addString("line color: ", DIAMETER_COLOR);
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Dialog.addNumber("line width", "DIAMETER_WIDTH);
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Dialog.show();
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DIAMETER_COLOR = Dialog.getString();
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DIAMETER_WIDTH = Dialog.getNumber();
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}
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macro "Write report Action Tool- C000T4b12w" {
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writeReport();
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}
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function lineAtThirtyCM() {
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setColor(COLOR_DEPTH);
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setLineWidth(WIDTH_DEPTH);
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tenUnscaled = HALF_LINE_WIDTH;
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toUnscaled(tenUnscaled);
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thirtyUnscaled = COUNT_ROOT_DEPTH;
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toUnscaled(thirtyUnscaled);
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X1 = rootX - tenUnscaled;
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X2 = rootX + tenUnscaled;
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Y = rootY + thirtyUnscaled;
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Overlay.drawLine(X1, Y, X2, Y);
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Overlay.show();
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}
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function angleSelection() {
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xCoords = newArray(3);
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yCoords = newArray(3);
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xCoords[0] = rootX - DX_ANGLE;
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xCoords[1] = rootX;
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xCoords[2] = rootX + DX_ANGLE;
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yCoords[0] = rootY + DY_ANGLE;
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yCoords[1] = rootY;
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yCoords[2] = rootY + DY_ANGLE;
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makeSelection("angle", xCoords, yCoords);
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}
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function setScale() {
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getLine(x1, y1, x2, y2, lineWidth);
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dx = x2-x1;
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dy = y2-y1;
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length = sqrt(dx*dx+dy*dy);
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options = "distance=" + length+" known="+KNOWN_DISTANCE+" pixel=1 unit="+UNIT;
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if (USE_GLOBAL_SCALE) options = options + " global";
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run("Set Scale...", options);
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run("Select None");
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setTool("Define Root Point Tool");
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}
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function measureAngle() {
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run("Measure");
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ANGLE = getResult("Angle", nResults-1);
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selectWindow("Results");
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run("Close");
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getSelectionCoordinates(xCoordinates, yCoordinates);
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run("Select None");
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setColor(ANGLE_COLOR);
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setLineWidth(ANGLE_LINE_WIDTH);
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Overlay.drawLine(xCoordinates[0], yCoordinates[0], xCoordinates[1], yCoordinates[1]);
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Overlay.drawLine(xCoordinates[1], yCoordinates[1], xCoordinates[2], yCoordinates[2]);
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Overlay.show();
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setTool("Measure Depth Tool");
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}
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function measureDiameter() {
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getLine(x1, y1, x2, y2, lineWidth);
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dx = x2-x1;
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dy = y2-y1;
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length = sqrt(dx*dx+dy*dy);
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toScaled(length);
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DIAMETERS[numberOfRootsAtThirty++] = length;
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close();
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selectImage(ID);
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getSelectionBounds(x, y, width, height);
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run("Select None");
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setColor(DIAMETER_COLOR);
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setLineWidth(DIAMETER_WIDTH);
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Overlay.drawLine(x+x1, y+y1, x+x2, y+y2);
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Overlay.show();
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setTool("Zoom region Tool");
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}
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function writeReport() {
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NUMBER++;
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getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);
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title = "root measurements - " + year + "-" + month + "-" + dayOfMonth + ".txt";
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ref = "[" + title + "]";
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if (!isOpen(title)) {
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run("Table...", "name="+ref+" width=250 height=600");
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header = "\\Headings:" + "nr." + "\t" + "image" + "\t" + "root x" + "\t" + "root y" + "\t" + "angle" + "\t" + "depth" + "\t" + "nr at 30cm";
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for (i=0; i<MAX_ROOTS; i++) {
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header = header + "\t" + "d" + (i+1);
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}
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print(ref, header);
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}
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row = "" + NUMBER + "\t" + TITLE + "\t" + rootX + "\t" + rootY + "\t" + ANGLE + "\t" + DEPTH + "\t" + numberOfRootsAtThirty;
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for (i=0; i<numberOfRootsAtThirty; i++) {
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row = row + "\t" + DIAMETERS[i];
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}
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print(ref, row);
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resetMeasurements();
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if (!File.exists(FOLDER + "/" + "control/")) File.makeDirectory(FOLDER + "/" + "control/");
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path = FOLDER + "/" + "control/" + TITLE;
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saveAs("tiff", path);
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Overlay.remove;
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setTool("line");
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}
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function resetMeasurements() {
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numberOfRootsAtThirty = 0;
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DIAMETERS = newArray(MAX_ROOTS);
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}
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