// motionStructure-v2
// this version replaces and extends the latest imageToObject 0.1

// Description:
// This macro creates a digital 3D object from an image sequence
// It asks for a directory path, then impots all images, converts them to 8-bit, substracts background, applies a smooth filter and runs the 3D viewer with some predefined parameters

// To run the macro: open ImageJ, from the top menu Plugin, select Macros then Run… choose the file from your local disk.

// For information on how to use imageJ, see
// http://rsbweb.nih.gov/ij/

// Created: October 29, 2015, in Paris.
// By: Everardo Reyes Garcia
// http://ereyes.net


dir = getDirectory("Choose image sequence");
list = getFileList(dir);

print("directory contains " + list.length + " files");

run("Image Sequence...", dir);

name = getTitle; 
print(name);

run("8-bit");
run("Subtract Background...", "rolling=50 stack");
run("Smooth", "stack");

// Display as Volume (last parameter in 0). Goes faster if no immediate need to export as OBJ
run("3D Viewer");
call("ij3d.ImageJ3DViewer.add", name, "None", name, "0", "true", "true", "true", "2", "0");
selectWindow(name);

// Display as Surface (last parameter in 2). 1 as threshold value… higher values mean less shapes because only pixels above such threshold are taken into account.
//run("3D Viewer");
//call("ij3d.ImageJ3DViewer.add", name, "None", name, "1", "true", "true", "true", "2", "2");
//selectWindow(name);

// Display as Surface (last parameter in 2). 10 as threshold value… higher values handle better large images sequences
//run("3D Viewer");
//call("ij3d.ImageJ3DViewer.add", name, "None", name, "10", "true", "true", "true", "2", "2");
//selectWindow(name);