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Copy pathACSAuto_1.4.ijm
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ACSAuto_1.4.ijm
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///////////////////////////////////////////////////////////
//// ACSAuto - Anatomical Cross-Sectional Area Analysis ////
//////////////////////////////////////////////////////////
// ACSAuto - Analysis of anatomical cross-sectional area of muscles
// Copyright (C), 2020, Paul Ritsche & Philipp Wirth
// This Macro Requires:
// Canny Edge Detector plugin (https://imagej.nih.gov/ij/plugins/canny/index.html - Tom Gibara)
// Ridge Detection plugin v.1.4.0 (https://imagej.net/Ridge_Detection - Thorsten Wagner, Mark Hiner)
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
// You should have received a copy of the GNU General Public License
// along with this program. If not, see <http://www.gnu.org/licenses/>.
#@ String (value = "----- ACSAuto - Automatic cross-sectional area analysis -----", visibility="MESSAGE") title
#@ String (label = "Type of analysis", choices= {"Folder", "Image"}, persist=true, style="radioButtonHorizontal", description="Analyse single image or several images. Medial muscle border needs to be on the (top) left, lateral on the (bottom) right. If not, use flipping.") analysis
#@ Boolean (label = "Export to excel", value = FALSE, persist = TRUE, description = "Wheter to export results to excel file on desktop. If name not changed, values will be added.") excel
#@ String (value = "------------------ Folder analysis ------------------", visibility="MESSAGE") text1
#@ File (label = "Input directory", style = "directory") input
#@ File (label = "Output directory", style = "directory") output
#@ String (value = "--------------- Mode selection ---------------", visibility="MESSAGE") text3
#@ String (label = "Mode Name", choices = {"Rectus femoris", "Vastus lateralis", "Quad RF", "Quad VL", "Quadriceps", "Gastro MED"}, description="Select muscle(s) to be analysed on picture") muscle
#@ String (value = "--------------- Outline finder -------------", visibility="MESSAGE") text4
#@ String (label = " ", choices= {"Manual", "Automatic", "Fixed Pixels"}, style = "directory", persist=true, description="Select outline-finder strategy. Choose at Manual. Absolute fixed at Fixed Pixels. Relative fixed at Automatic") select_outline
#@ Boolean (label = "Sorting of coordinates", value = true, persist = false, describtion = "Whether to sort found outline coordinates to avoid overlap") sorting
#@ String (value = "---------------- Pixel scaling ----------------", visibility="MESSAGE") text5
#@ String (label ="Scale measurements", choices = {"Automatic", "Manual"}, style="radioButtonHorizontal", persist=true, description="Muscle scaling, produce output in cm²") scaling
#@ String (label="Scan depth (cm)", choices = {3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9}, persist=true, description="Requires images in input folder to be taken at same depth") depth
#@ Boolean (label ="Flip horizontally", value = false, persist = true, description = "Whether to flip the image horizontally") flip_horizontal
#@ Boolean (label ="Flip vertically", value = false, persist = true, description = "Whether to flip the image vertically") flip_vertical
// starting xys for outline finder
var starting_xy = newArray();
// length of the scale line
var lineLength = 0;
// sample by which the image is downsampled during preprocessing
var downSampleFac = 0.5;
// image ids
var IDraw;
var IDFoV;
var IDvessel1;
var IDvessel2;
var IDmask;
var IDScaling;
var IDScaling1;
var IDmaskScaling;
macro "ACSAutomated" {
//********************************
//********** FUNCTIONS ***********
//********************************
function getPreprocessingSettings(muscle) {
/*
Prompts user to adapt the preprocessing settings, default depends on muscle choice
*/
if (muscle == "Rectus femoris") {
defaultMinLengthFac = 0.6;
defaultTubenessSigma = 7;
defaultGaussianSigma= 0.5;
}
if (muscle == "Vastus lateralis") {
defaultMinLengthFac = 0.65;
defaultTubenessSigma = 7;
defaultGaussianSigma = 0.5;
}
if (muscle == "Gastro MED") {
defaultMinLengthFac = 0.5;
defaultTubenessSigma = 7;
defaultGaussianSigma= 1;
}
if (muscle == "Quad RF") {
defaultMinLengthFac = 0.055;
defaultTubenessSigma = 3;
defaultGaussianSigma = 0;
}
if (muscle == "Quad VL") {
defaultMinLengthFac = 0.3;
defaultTubenessSigma = 7;
defaultGaussianSigma = 0;
}
if (muscle == "Quadriceps") {
defaultMinLengthFac = 0.055;
defaultTubenessSigma = 3;
defaultGaussianSigma = 0;
defaultMinLengthFac1 = 0.2;
defaultTubenessSigma1 = 7;
defaultGaussianSigma1 = 0;
}
if (muscle == "Quadriceps") {
Dialog.create("Preprocessing Settings");
Dialog.addNumber("Min Length Fac RF", defaultMinLengthFac);
Dialog.addNumber("Tubeness Sigma RF", defaultTubenessSigma);
Dialog.addNumber("Gaussian Sigma RF", defaultGaussianSigma);
Dialog.addNumber("Min Length Fac VL", defaultMinLengthFac1);
Dialog.addNumber("Tubeness Sigma VL", defaultTubenessSigma1);
Dialog.addNumber("Gaussian Sigma VL", defaultGaussianSigma1);
Dialog.show();
settings = newArray(6);
settings[0] = Dialog.getNumber();
settings[1] = Dialog.getNumber();
settings[2] = Dialog.getNumber();
settings[3] = Dialog.getNumber();
settings[4] = Dialog.getNumber();
settings[5] = Dialog.getNumber();
return settings;
}
else {
Dialog.create("Preprocessing Settings");
Dialog.addNumber("Min Length Fac", defaultMinLengthFac);
Dialog.addNumber("Tubeness Sigma", defaultTubenessSigma);
Dialog.addNumber("Gaussian Sigma", defaultGaussianSigma);
Dialog.show();
settings = newArray(3);
settings[0] = Dialog.getNumber();
settings[1] = Dialog.getNumber();
settings[2] = Dialog.getNumber();
return settings;
}
}
function flipImage(axis) {
/*
Flips image horizontally (axis == 0) or vertically (axis == 1)
*/
if (axis == 0) {
run("Flip Horizontally");
} else {
run("Flip Vertically");
}
}
function clearDisplay () {
/*
Clears display after getlinelength()
*/
roiManager("delete");
roiManager("show none");
close("Log");
close("ROI Manager");
close("Summary");
close("Junctions");
close("Threshold");
run("Close");
}
function excel_expo () {
/*
Export results to excel
*/
if (excel == true) {
run("Read and Write Excel", "stack_results no_count_column dataset_label=Analysis_results");
}
}
function getlineLength () {
/*
Scales image automatically
*/
// flip image
if (flip_horizontal) {
flipImage(0);
}
if (flip_vertical) {
flipImage(1);
}
if (scaling == "Automatic") {
if (muscle == "Quad RF" || muscle == "Quadriceps" || muscle == "Quad VL") {
run("Duplicate...", " ");
//pre-processing for ridge-detection
run("8-bit");
run("Threshold...");
setThreshold(50, 255);
setOption("BlackBackground", true);
run("Convert to Mask");
// select active image
IDScaling = getImageID();
selectImage(IDScaling);
n0 = nResults;
run("Analyze Particles...", "size=650-Infinity show=Masks");
n1 = nResults;
IJ.deleteRows(n0, n1);
// Subtract and close unnecessary pictures
IDmaskScaling = getImageID(); // Mask of shorter lines
imageCalculator("Subtract create", IDScaling, IDmaskScaling);
selectImage(IDmaskScaling); close();
selectImage(IDScaling); close();
// current image
IDScaling1 = getImageID();
run("Gaussian Blur...", "sigma=1.50");
n0 = nResults;
print(n0);
roiManager("show none");
run("Ridge Detection", "line_width=1 high_contrast=128 low_contrast=70 show_ids displayresults add_to_manager method_for_overlap_resolution=NONE sigma=0.79 lower_threshold=9 upper_threshold=18 minimum_line_length=175 maximum=280");
// length of scaling line in picture and number of pixels per cm
n1 = nResults;
print(n1);
Length = getResult("Length", n0+1);
print(Length);
lineLength = Length/depth;
IJ.deleteRows(n0, n1);
clearDisplay();
}
if (muscle == "Vastus lateralis") {
run("Duplicate...", " ");
// pre-processing for ridge-detection
run("8-bit");
run("Threshold...");
setThreshold(50, 255);
setOption("BlackBackground", true);
run("Convert to Mask");
IDScaling = getImageID();
selectImage(IDScaling);
n0 = nResults;
run("Analyze Particles...", "size=550-Infinity show=Masks Clear");
n1 = nResults;
IJ.deleteRows(n0, n1);
//Subtract and close unnecessary pictures
IDmaskScaling = getImageID(); // Mask of shorter lines
imageCalculator("Subtract create", IDScaling, IDmaskScaling);
selectImage(IDmaskScaling); close();
selectImage(IDScaling); close();
// current image
IDScaling1 = getImageID();
run("Gaussian Blur...", "sigma=1.50");
n0 = nResults;
print(n0);
run("Ridge Detection", "line_width=1 high_contrast=128 low_contrast=70 show_ids displayresults add_to_manager method_for_overlap_resolution=NONE sigma=0.79 lower_threshold=9 upper_threshold=18 minimum_line_length=200 maximum=500");
// Length of scaling line in picture and number of pixels per cm
n1 = nResults;
print(n1);
Length = getResult("Length", n0+1);
print(Length);
lineLength = Length/depth;
IJ.deleteRows(n0, n1);
clearDisplay();
}
if (muscle == "Rectus femoris") {
run("Duplicate...", " ");
// pre-processing for ridge detection
run("8-bit");
run("Threshold...");
setThreshold(50, 255);
setOption("BlackBackground", true);
run("Convert to Mask");
IDScaling = getImageID();
selectImage(IDScaling);
n0 = nResults;
run("Analyze Particles...", "size=1150-Infinity show=Masks");
n1 = nResults;
IJ.deleteRows(n0, n1);
//Subtract and close unnecessary pictures
IDmaskScaling = getImageID(); // Mask of shorter lines
imageCalculator("Subtract create", IDScaling, IDmaskScaling);
selectImage(IDmaskScaling); close();
selectImage(IDScaling); close();
// current image
IDScaling1 = getImageID();
run("Gaussian Blur...", "sigma=1.50");
n0 = nResults;
print(n0);
run("Ridge Detection", "line_width=1 high_contrast=128 low_contrast=70 show_ids displayresults add_to_manager method_for_overlap_resolution=NONE sigma=0.79 lower_threshold=9 upper_threshold=20 minimum_line_length=350 maximum=700");
// length of scaling line in picture and number of pixels per cm
n1 = nResults;
print(n1);
Length = getResult("Length", n0+1);
print(Length);
lineLength = Length/depth;
IJ.deleteRows(n0, n1);
clearDisplay();
}
if (muscle == "Gastro MED") {
run("Duplicate...", " ");
// pre-processing for ridge-detection
run("8-bit");
run("Threshold...");
setThreshold(50, 255);
setOption("BlackBackground", true);
run("Convert to Mask");
IDScaling = getImageID();
selectImage(IDScaling);
n0 = nResults;
run("Analyze Particles...", "size=650-Infinity show=Masks Clear");
n1 = nResults;
IJ.deleteRows(n0, n1);
//Subtract and close unnecessary pictures
IDmaskScaling = getImageID(); // Mask of shorter lines
imageCalculator("Subtract create", IDScaling, IDmaskScaling);
selectImage(IDmaskScaling); close();
selectImage(IDScaling); close();
// current image
IDScaling1 = getImageID();
run("Gaussian Blur...", "sigma=1.50");
n0 = nResults;
print(n0);
run("Ridge Detection", "line_width=1 high_contrast=128 low_contrast=70 show_ids displayresults add_to_manager method_for_overlap_resolution=NONE sigma=0.79 lower_threshold=9 upper_threshold=18 minimum_line_length=200 maximum=500");
// Length of scaling line in picture and number of pixels per cm
n1 = nResults;
print(n1);
Length = getResult("Length", n0+1);
print(Length);
lineLength = Length/depth;
IJ.deleteRows(n0, n1);
clearDisplay();
}
}
}
function getFixedOutlineFinderStartingPoints(muscle) {
/*
Returns hardcoded starting points for the outline finder for each muscle
*/
if (muscle == "Rectus femoris") {
starting_xy = newArray(2);
starting_xy[0] = 170;
starting_xy[1] = 250;
}
if (muscle == "Vastus lateralis") {
starting_xy = newArray(6);
starting_xy[0] = 115;
starting_xy[1] = 180;
starting_xy[2] = 150;
starting_xy[3] = 340;
starting_xy[4] = 300;
starting_xy[5] = 400;
}
if (muscle == "Quad RF"){
starting_xy = newArray(2);
starting_xy[0] = 102;
starting_xy[1] = 240;
}
if (muscle == "Quad VL"){
starting_xy = newArray(6);
starting_xy[0] = 150;
starting_xy[1] = 340;
starting_xy[2] = 220;
starting_xy[3] = 360;
starting_xy[4] = 300;
starting_xy[5] = 335;
}
if (muscle == "Quadriceps"){
starting_xy = newArray(8);
starting_xy[0] = 102;
starting_xy[1] = 240;
starting_xy[2] = 150;
starting_xy[3] = 340;
starting_xy[4] = 220;
starting_xy[5] = 360;
starting_xy[6] = 310;
starting_xy[7] = 340;
}
if (muscle == "Gastro MED"){
starting_xy = newArray(6);
starting_xy[0] = 120;
starting_xy[1] = 215;
starting_xy[2] = 170;
starting_xy[3] = 360;
starting_xy[4] = 270;
starting_xy[5] = 390;
}
}
function getAutoOutlineFinderStartingPoints(muscle) {
/*
Returns automatically estimated starting points for the outline finder for each muscle
*/
// determine region of interest
run("Duplicate...", " ");
IDcopy1 = getImageID();
run("8-bit");
run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
run("Convolve...", "text1=[-1 -1 -1 -1 -1\n-1 -1 -1 -1 -1\n-1 -1 24 -1 -1\n-1 -1 -1 -1 -1\n-1 -1 -1 -1 -1\n] normalize");
run("Median...", "radius=2");
run("Auto Local Threshold", "method=Median radius=15 parameter_1=0 parameter_2=0 white");
run("Options...", "iterations=2 count=1 black do=Close");
run("Analyze Particles...", "size=10000-Infinity add");
roiManager("Select", 0);
getSelectionBounds(x, y, width, height);
roiManager("delete");
selectImage(IDcopy1);
close();
// determine starting points
if (muscle == "Rectus femoris") {
starting_xy = newArray(2);
starting_xy[1] = round(x + 0.5*width);
starting_xy[0] = round(y + 0.35*height);
}
if (muscle == "Vastus lateralis") {
starting_xy = newArray(6);
starting_xy[0] = round(y + 0.2*height);
starting_xy[1] = round(x + 0.2*width);
starting_xy[2] = round(y + 0.35*height);
starting_xy[3] = round(x + 0.6*width);
starting_xy[4] = round(y + 0.7*height);
starting_xy[5] = round(x + 0.85*width);
}
if (muscle == "Quad RF") {
starting_xy = newArray(2);
starting_xy[0] = round(y + 0.15*height);
starting_xy[1] = round(x + 0.25*width);
}
if (muscle == "Quad VL") {
starting_xy = newArray(6);
starting_xy[0] = round(y + 0.3*height);
starting_xy[1] = round(x + 0.73*width);
starting_xy[2] = round(y + 0.5*height);
starting_xy[3] = round(x + 0.8*width);
starting_xy[4] = round(y + 0.75*height);
starting_xy[5] = round(x + 0.65*width);
}
if (muscle == "Quadriceps") {
starting_xy = newArray(8);
starting_xy[0] = round(y + 0.15*height);
starting_xy[1] = round(x + 0.25*width);
starting_xy[2] = round(y + 0.3*height);
starting_xy[3] = round(x + 0.73*width);
starting_xy[4] = round(y + 0.5*height);
starting_xy[5] = round(x + 0.8*width);
starting_xy[6] = round(y + 0.75*height);
starting_xy[7] = round(x + 0.65*width);
}
if (muscle== "Gastro MED"){
starting_xy = newArray(6);
starting_xy[0] = round(y + 0.25*height);
starting_xy[1] = round(x + 0.33*width);
starting_xy[2] = round(y + 0.35*height);
starting_xy[3] = round(x + 0.7*width);
starting_xy[4] = round(x + 0.6*height);
starting_xy[5] = round(x + 0.73*width);
}
for (i = 0; i < starting_xy.length; i++) {
starting_xy[i] = downSampleFac * starting_xy[i];
}
}
function getManualOutlineFinderStartingPoints(muscle) {
/*
Lets the user choose the starting points for the outline finder
*/
if (muscle == "Rectus femoris") {
starting_xy = newArray(2);
setTool("point");
waitForUser("Select Outline Finder Starting Point.");
if (selectionType() > 0) {
Roi.getCoordinates(x, y);
do_continue = x.length != 1;
} else {
do_continue = 1;
}
while (do_continue) {
run("Select None");
setTool("point");
waitForUser("Select Outline Finder Starting Point.");
if (selectionType() > 0) {
Roi.getCoordinates(x, y);
do_continue = x.length != 1;
}
if (nImages > 0) {
do_continue = 1;
} else {
do_continue = 0;
}
}
Roi.getCoordinates(x, y);
}
if (muscle == "Vastus lateralis") {
starting_xy = newArray(6);
setTool("multipoint");
waitForUser("Select 3 Outline Finder Starting Points.");
if (selectionType() > 0) {
Roi.getCoordinates(x, y);
do_continue = x.length != 3;
} else {
do_continue = 1;
}
while (do_continue) {
run("Select None");
setTool("multipoint");
waitForUser("Select 3 Outline Finder Starting Points.");
if (selectionType() > 0) {
Roi.getCoordinates(x, y);
do_continue = x.length != 3;
}
if (nImages > 0) {
do_continue = 1;
} else {
do_continue = 0;
}
}
Roi.getCoordinates(x, y);
}
if (muscle == "Quad RF") {
starting_xy = newArray(2);
setTool("point");
waitForUser("Select Outline Finder Starting Point.");
if (selectionType() >= 0) {
Roi.getCoordinates(x, y);
do_continue = x.length != 1;
} else {
do_continue = 1;
}
while (do_continue) {
run("Select None");
setTool("point");
waitForUser("Select Outline Finder Starting Point.");
if (selectionType() >= 0) {
Roi.getCoordinates(x, y);
do_continue = x.length != 1;
}
if (nImages > 0) {
do_continue = 1;
} else {
do_continue = 0;
}
}
Roi.getCoordinates(x, y);
}
if (muscle == "Quad VL") {
starting_xy = newArray(6);
setTool("multipoint");
waitForUser("Select 3 Outline Finder Starting Points.");
if (selectionType() > 0) {
Roi.getCoordinates(x, y);
do_continue = x.length != 3;
} else {
do_continue = 1;
}
while (do_continue) {
run("Select None");
setTool("multipoint");
waitForUser("Select 3 Outline Finder Starting Points.");
if (selectionType() > 0) {
Roi.getCoordinates(x, y);
do_continue = x.length != 3;
}
if (nImages > 0) {
do_continue = 1;
} else {
do_continue = 0;
}
}
Roi.getCoordinates(x, y);
}
if (muscle == "Quadriceps"){
starting_xy = newArray(8);
setTool("multipoint");
waitForUser("Select 4 Outline Finder Starting Points.");
if (selectionType() > 0) {
Roi.getCoordinates(x, y);
do_continue = x.length != 4;
} else {
do_continue = 1;
}
while (do_continue) {
run("Select None");
setTool("multipoint");
waitForUser("Select 4 Outline Finder Starting Points.");
if (selectionType() > 0) {
Roi.getCoordinates(x, y);
do_continue = x.length != 4;
} if (nImages >= 1) {
do_continue = 1;
} else {
do_continue = 0;
}
}
Roi.getCoordinates(x, y);
}
if (muscle == "Gastro MED") {
starting_xy = newArray(6);
setTool("multipoint");
waitForUser("Select 3 Outline Finder Starting Points.");
if (selectionType() > 0) {
Roi.getCoordinates(x, y);
do_continue = x.length != 3;
} else {
do_continue = 1;
}
while (do_continue) {
run("Select None");
setTool("multipoint");
waitForUser("Select 3 Outline Finder Starting Points.");
if (selectionType() > 0) {
Roi.getCoordinates(x, y);
do_continue = x.length != 3;
}
if (nImages > 0) {
do_continue = 1;
} else {
do_continue = 0;
}
}
Roi.getCoordinates(x, y);
}
for (i = 0; i < x.length; i++) {
starting_xy[2*i + 1] = x[i];
starting_xy[2*i] = y[i];
}
}
function sqDistance(x0, x1, y0, y1) {
/*
Return the squared distance between (x0, y0) and (x1, y1)
*/
return (x1 - x0) * (x1 - x0) + (y1 - y0) * (y1 - y0);
}
function swap(xs, ys, i, j) {
/*
Swaps the coordinates of xs and ys
*/
tmp_x = xs[i];
tmp_y = ys[i];
xs[i] = xs[j];
ys[i] = ys[j];
xs[j] = tmp_x;
ys[j] = tmp_y;
}
function sortCoordinatesClockwise(xs, ys) {
/*
Sorts depending on squared distance
*/
for (i = 0; i < xs.length - 1; i++) {
squared_distance_to_neighbor = sqDistance(xs[i], xs[i+1], ys[i], ys[i+1]);
for (j = i+1; j < xs.length - 1; j++) {
squared_distance = sqDistance(xs[i], xs[j] , ys[i], ys[j]);
if (squared_distance < squared_distance_to_neighbor) {
swap(xs, ys, i+1, j);
squared_distance_to_neighbor = squared_distance;
}
}
}
}
function measureRectusArea(nbeams, R, N, thresh) {
/*
Measures the area of the isolated rectus femoris
*/
xs = newArray(nbeams);
ys = newArray(nbeams);
// define x and y
x = starting_xy[1];
y = starting_xy[0];
// do a radial scan around (x,y)
count = circScanLine(x, y, xs, ys, 0, nbeams, R, N, thresh, 0, 360);
// select raw image and rescale outline
selectImage(IDFoV); close();
selectImage(IDraw);
// make selection and measure
upscaleAndLocalSearch(xs, ys, 4);
makeSelection("polygon", xs, ys);
run("Set Scale...", "distance=lineLength known=1 pixel=1 unit=cm");
waitForUser("Adjust Region of Interest. Click OK when done");
roiManager("add");
roiManager("measure");
roiManager("delete");
Overlay.addSelection("red", 4);
}
function measureVastusLatArea(nbeams, nsteps, R, N, thresh) {
/*
Measures the area of the isolated vastus lateralis
*/
xs = newArray(2 * (nbeams + nsteps + nsteps));
ys = newArray(2 * (nbeams + nsteps + nsteps));
// upper side
count = 0;
count = circScanLine(starting_xy[1], starting_xy[0], xs, ys, count, nbeams, R, 10000, thresh, 90, 270);
count = verticalScanLine(starting_xy[1], starting_xy[0], starting_xy[3], starting_xy[2], xs, ys, count, nsteps, R, N, thresh, 1);
count = horizontalScanLine(starting_xy[3], starting_xy[2], starting_xy[5], starting_xy[4], xs, ys, count, nsteps, R, N, thresh, 1);
count = circScanLine(starting_xy[5], starting_xy[4], xs, ys, count, nbeams, R, 10000, thresh, 0, 180);
count = horizontalScanLine(starting_xy[5], starting_xy[4], starting_xy[3], starting_xy[2], xs, ys, count, nsteps, R, N, thresh, -1);
count = verticalScanLine(starting_xy[3], starting_xy[2], starting_xy[1], starting_xy[0], xs, ys, count, nsteps, R, N, thresh, -1);
real_xs = newArray(count);
real_ys = newArray(count);
for (i = 0; i < count; i++) {
real_xs[i] = xs[i];
real_ys[i] = ys[i];
}
//switch to raw image
selectImage(IDFoV); close();
selectImage(IDraw);
// make selection and measure
upscaleAndLocalSearch(real_xs, real_ys, 32);
if (sorting == true){
sortCoordinatesClockwise(real_xs, real_ys);
}
makeSelection("polygon", real_xs, real_ys);
run("Set Scale...", "distance=lineLength known=1 pixel=1 unit=cm");
waitForUser("Adjust Region of Interest. Click OK when done");
roiManager("add");
roiManager("measure");
roiManager("delete");
Overlay.addSelection("red", 4);
}
function measureQuadRFArea(nbeams, R, N, thresh) {
/*
Measures the area of the rectus femoris
*/
xs = newArray(nbeams);
ys = newArray(nbeams);
// define x and y
x = starting_xy[1];
y = starting_xy[0];
count = circScanLine(x, y, xs, ys, 0, nbeams, R, N, thresh, 0, 360);
// switch to raw image
selectImage(IDFoV); close();
selectImage(IDraw);
// make selection and measure
upscaleAndLocalSearch(xs, ys, 32);
makeSelection("polygon", xs, ys);
run("Set Scale...", "distance=lineLength known=1 pixel=1 unit=cm");
run("To Selection");
run("Out [-]");
waitForUser("Adjust Region of Interest. Click OK when done");
roiManager("add");
roiManager("measure");
roiManager("delete");
Overlay.addSelection("red", 4);
}
function measureQuadVLArea(nbeams, nsteps, R, N, thresh) {
/*
Measures the area of the vastus lateralis
*/
xs = newArray(2 * (nbeams + nsteps + nsteps));
ys = newArray(2 * (nbeams + nsteps + nsteps));
// upper side
count = 0;
count = circScanLine(starting_xy[1], starting_xy[0], xs, ys, count, nbeams, R, 10000, thresh, 180, 360);
count = horizontalScanLine(starting_xy[1], starting_xy[0], starting_xy[3], starting_xy[2], xs, ys, count, nsteps, R, N, thresh, 1);
count = horizontalScanLine(starting_xy[3], starting_xy[2], starting_xy[5], starting_xy[4], xs, ys, count, nsteps, R, N, thresh, 1);
count = circScanLine(starting_xy[5], starting_xy[4], xs, ys, count, nbeams, R, 10000, thresh, 0, 180);
count = horizontalScanLine(starting_xy[5], starting_xy[4], starting_xy[3], starting_xy[2], xs, ys, count, nsteps, R, N, thresh, -1);
count = horizontalScanLine(starting_xy[3], starting_xy[2], starting_xy[1], starting_xy[0], xs, ys, count, nsteps, R, N, thresh, -1);
real_xs = newArray(count);
real_ys = newArray(count);
for (i = 0; i < count; i++) {
real_xs[i] = xs[i];
real_ys[i] = ys[i];
}
// switch to raw image
selectImage(IDFoV); close();
selectImage(IDraw);
//make selection and measure
upscaleAndLocalSearch(real_xs, real_ys, 32);
if (sorting == true){
sortCoordinatesClockwise(real_xs, real_ys);
}
makeSelection("polygon", real_xs, real_ys);
run("Set Scale...", "distance=lineLength known=1 pixel=1 unit=cm");
run("To Selection");
waitForUser("Adjust Region of Interest. Click OK when done");
roiManager("add");
roiManager("measure");
roiManager("delete");
Overlay.addSelection("red", 4);
}
function measureQuadricepsArea(nbeams_r, R_r, N_r, thresh_r, nbeams_v, nsteps_v, R_v, N_v, thresh_v) {
/*
Measures the area of both, rectus femoris and vastus lateralis
*/
// measure Rectus
rectus_xs = newArray(nbeams_r);
rectus_ys = newArray(nbeams_r);
// define x and y
x = starting_xy[1];
y = starting_xy[0];
count = circScanLine(x, y, rectus_xs, rectus_ys, 0, nbeams_r, R_r, N_r, thresh_r, 0, 360);
//measure Vastus
xs = newArray(2 * (nbeams_v + nsteps_v + nsteps_v));
ys = newArray(2 * (nbeams_v + nsteps_v + nsteps_v));
// upper side
count = 0;
count = circScanLine(starting_xy[3], starting_xy[2], xs, ys, count, nbeams_v, R_v, 10000, thresh_v, 180, 360);
count = horizontalScanLine(starting_xy[3], starting_xy[2], starting_xy[5], starting_xy[4], xs, ys, count, nsteps_v, R_v, N_v, thresh_v, 1);
count = horizontalScanLine(starting_xy[5], starting_xy[4], starting_xy[7], starting_xy[6], xs, ys, count, nsteps_v, R_v, N_v, thresh_v, 1);
count = circScanLine(starting_xy[7], starting_xy[6], xs, ys, count, nbeams_v, R_v, 10000, thresh_v, 0, 180);
count = horizontalScanLine(starting_xy[7], starting_xy[6], starting_xy[5], starting_xy[4], xs, ys, count, nsteps_v, R_v, N_v, thresh_v, -1);
count = horizontalScanLine(starting_xy[5], starting_xy[4], starting_xy[3], starting_xy[2], xs, ys, count, nsteps_v, R_v, N_v, thresh_v, -1);
real_xs = newArray(count);
real_ys = newArray(count);
for (i = 0; i < count; i++) {
real_xs[i] = xs[i];
real_ys[i] = ys[i];
}
// switch to raw image
selectImage(IDFoV); close();
selectImage(IDraw);
//measure rectus
upscaleAndLocalSearch(rectus_xs, rectus_ys, 32);
makeSelection("polygon", rectus_xs, rectus_ys);
run("Set Scale...", "distance=lineLength known=1 pixel=1 unit=cm");
run("To Selection");
run("Out [-]");
waitForUser("Adjust Region of Interest. Click OK when done");
roiManager("add");
roiManager("measure");
roiManager("delete");
Overlay.addSelection("red", 4);
//measure vastus
upscaleAndLocalSearch(real_xs, real_ys, 32);
if (sorting == true){
sortCoordinatesClockwise(real_xs, real_ys);
}
makeSelection("polygon", real_xs, real_ys);
run("Set Scale...", "distance=lineLength known=1 pixel=1 unit=cm");
run("To Selection");
waitForUser("Adjust Region of Interest. Click OK when done");
roiManager("add");
roiManager("measure");
roiManager("delete");
Overlay.addSelection("red", 4);
}
function measureGastroMedArea(nbeams, nsteps, R, N, thresh) {
/*
Measures the area of the isolated vastus lateralis
*/
xs = newArray(2 * (nbeams + nsteps + nsteps));
ys = newArray(2 * (nbeams + nsteps + nsteps));
// upper side
count = 0;
count = circScanLine(starting_xy[1], starting_xy[0], xs, ys, count, nbeams, R, 10000, thresh, 90, 270);
count = verticalScanLine(starting_xy[1], starting_xy[0], starting_xy[3], starting_xy[2], xs, ys, count, nsteps, R, N, thresh, 1);
count = horizontalScanLine(starting_xy[3], starting_xy[2], starting_xy[5], starting_xy[4], xs, ys, count, nsteps, R, N, thresh, 1);
count = circScanLine(starting_xy[5], starting_xy[4], xs, ys, count, nbeams, R, 10000, thresh, 0, 180);
count = horizontalScanLine(starting_xy[5], starting_xy[4], starting_xy[3], starting_xy[2], xs, ys, count, nsteps, R, N, thresh, -1);
count = verticalScanLine(starting_xy[3], starting_xy[2], starting_xy[1], starting_xy[0], xs, ys, count, nsteps, R, N, thresh, -1);
real_xs = newArray(count);
real_ys = newArray(count);
for (i = 0; i < count; i++) {
real_xs[i] = xs[i];
real_ys[i] = ys[i];
}
//switch to raw image
selectImage(IDFoV); close();
selectImage(IDraw);
// make selection and measure
upscaleAndLocalSearch(real_xs, real_ys, 32);
if (sorting == true){