print("\\Clear")
// MIT License
// Copyright (c) 2018 Nicholas Condon n.condon@uq.edu.au
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
// The above copyright notice and this permission notice shall be included in all
// copies or substantial portions of the Software.
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
// SOFTWARE.
//IMB Macro Splash screen (Do not remove this acknowledgement)
scripttitle="LLSM - Time-Point Dimension Changer";
version="1.2";
versiondate="10/03/2019";
description="This script takes LLSM files that have been split into individual timepoints using the UQ-RCC generated SButility.exe and updates the pixel size information for deskewing."
showMessage("Institute for Molecular Biosciences ImageJ Script", ""
+"ACRF: Cancer Biology Imaging Facility
+"The Institute for Molecular Bioscience
The University of Queensland
+"ACRF: Cancer Biology Imaging Facility<\h4>"
+"ImageJ Script Macro: "+scripttitle+"
"
+"Version: "+version+" ("+versiondate+")"
+"Created by Nicholas Condon
"
+" contact n.condon@uq.edu.au \n "
+" Available for use/modification/sharing under the "+"MIT License<\h4> "
+" <\h3>"
+""+description+""
+"
"
+" "
+"");
//Log Window Title and Acknowledgement
print("");
print("FIJI Macro: "+scripttitle);
print("Version: "+version+" ("+versiondate+")");
print("ACRF: Cancer Biology Imaging Facility");
print("By Nicholas Condon (2018) n.condon@uq.edu.au")
print("");
getDateAndTime(year, month, week, day, hour, min, sec, msec);
print("Script Run Date: "+day+"/"+(month+1)+"/"+year+" Time: " +hour+":"+min+":"+sec);
print("");
//Directory Warning panel
Dialog.create("Choosing your image location");
Dialog.addMessage("Use the next window to navigate to your directory of images.");
Dialog.addMessage("(Note a sub-directory will be made for each input image within this fodler) ");
Dialog.addMessage("Take note of your file extension (eg .tif, .czi)");
Dialog.show();
setBatchMode(true);
path = getDirectory("Choose Source Directory ");
list = getFileList(path);
ext = ".tiff";
Dialog.create("Pixel Size Information");
Dialog.addString("File Extension:", ext);
Dialog.addMessage("(For example .czi .lsm .nd2 .lif .ims)");
Dialog.addMessage(" ");
Dialog.addMessage("Input your pixel sizes below");
Dialog.addNumber("XY =", 0.104);
Dialog.addNumber("Voxel Depth= ", 0.495);
Dialog.addString("Unit", "microns");
Dialog.show();
ext = Dialog.getString();
XY=Dialog.getNumber();
depth = Dialog.getNumber();
Unit = Dialog.getString();
print("File Extension = "+ext);
print("XY Pixel Size = "+XY);
print("Z Pixel Size = "+depth);
print("Units = "+Unit);
start = getTime();
for (z=0; z