Snippets
Dave Mason Image Feature Measurement from http://forum.imagej.net/t/image-features-measurement-in-batch-mode-not-working/11284
Created by
Dave Mason
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 | //@ File (label = "Input directory", style = "directory") input
//@ File (label = "Output directory", style = "directory") output
//@ String (label = "File suffix", value = ".tif") suffix
//-- Call the initial function to get a list of files
processFolder(input);
print("Done");
//-- FUNCTIONS ---
function processFolder(input) {
list = getFileList(input);
list = Array.sort(list);
for (i = 0; i < list.length; i++) {
if(endsWith(list[i], suffix))
//-- Call the file processing function
processFile(input, output, list[i]);
}
}
function processFile(input, output, file) {
print("Processing: " + input + File.separator + file);
//-- Open the file
open(input+File.separator+file);
title=getTitle();
//-- Your code here -------------------
//setAutoThreshold("Default");
//setThreshold(245, 255);
// Shape Analysis Macro for ImageJ
// Copyright of Liu, E.J., Cashman, K.V., & Rust, A.C., (2015). Optimising Shape Analysis to quantify volcanic ash morphology. GeoResJ
// INPUTS: this macro requires a binary image.
// OUTPUTS: Particle area, Particle perimeter, Convex hull (CH) area, Convex hull (CH) perimeter, Solidity, Convexity,
// Concavity Index, Form Factor, Major axis (of best fit ellipse), Minor axis (of best fit ellipse), Axial ratio (minor/major axis),
// Bounding box width (along x axis), Bounding box height (along y axis), Feret diameter, Minimum Feret diameter. All mathematical
// definitions given in Table 2 of Liu et al., (2015).
// Default variables: particle size range = 750-Infinity pixels per particle; 'exclude' edge-touching particles;
// 'include' holes in the particle area.
{
run("Set Measurements...", "area centroid perimeter bounding fit shape feret's redirect=None decimal=3");
run("Analyze Particles...", "size=750-Infinity pixel circularity=0.00-1.00 show=Outlines exclude clear include record stack");
n = nResults;
area1 = newArray(n);
length1 = newArray(n);
area2 = newArray(n);
length2 = newArray(n);
xstart = newArray(n);
ystart = newArray(n);
ff1 = newArray(n);
AR1 = newArray(n);
round1 = newArray(n);
BBX1 = newArray(n);
BBY1 = newArray(n);
major1 = newArray(n);
minor1 = newArray(n);
feret1 = newArray(n);
minferet1 = newArray(n);
solidity1 = newArray(n);
for (i=0; i<n; i++) {
area1[i] = getResult("Area", i);
length1[i] = getResult("Perim.", i);
xstart[i] = getResult("XStart", i);
ystart[i] = getResult("YStart", i);
ff1[i] = getResult("Circ.", i);
AR1[i] = getResult("Aspect", i);
round1[i] = getResult("Round", i);
BBX1[i] = getResult("Width", i);
BBY1[i] = getResult("Height", i);
minor1[i] = getResult("Minor", i);
major1[i] = getResult("Major", i);
feret1[i] = getResult("Feret", i);
minferet1[i] = getResult("MinFeret", i);
}
run("Clear Results");
for (i=0; i<n; i++) {
doWand(xstart[i], ystart[i]);
run("Convex Hull");
run("Measure");
area2[i] = getResult("Area", i);
length2[i] = getResult("Perim.", i);
}
run("Clear Results");
run("Select None");
for (i=0; i<n; i++) {
setResult("Area", i, area1[i]);
setResult("Perim.", i, length1[i]);
setResult("CH Area", i, area2[i]);
setResult("CH Perim.", i, length2[i]);
setResult("Solidity", i, area1[i]/area2[i]);
setResult("Convexity", i, length2[i]/length1[i]);
setResult("Concavity Index", i, sqrt((pow(1-(area1[i]/area2[i]),2)+(pow(1-(length2[i]/length1[i]),2)))));
setResult("FormFactor", i, ff1[i]);
setResult("Major axis", i, major1[i]);
setResult("Minor axis", i, minor1[i]);
setResult("Axial ratio", i, minor1[i]/major1[i]);
setResult("BX width", i, BBX1[i]);
setResult("BY height", i, BBY1[i]);
setResult("Feret d", i, feret1[i]);
setResult("MinFeret d", i, minferet1[i]);
}
updateResults();
}
//-- Save out the results table here:
selectWindow("Results");
saveAs("Results", output+File.separator+replace(file,suffix,"_results.csv"));
//run("Read and Write Excel");
//-- Save out your drawing here
selectWindow("Drawing of "+title);
saveAs("TIFF",output+File.separator+replace(file,suffix,"_drawing.tif"));
//-- Close everything before the next image is opened
close("*");
}
|
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