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checkpoint_converter_.ijm
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checkpoint_converter_.ijm
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/*
* Converts an image stack into a \*.ckpt file and its associated tiff-stack for the Stratovan Checkpoint (TM) landmarking software.
*
* Tested for Checkpoint (TM) Version 2020.10.13.0859 and some earlier versions on Win x64.
*
* Additional features:
* - reads pixel size from tiffs (user can change the value if wrong)
* - optional contrast enhancement & reduction to 8-bit
*
* Should run on Linux, Win & iOS.
*
* v. 1.1.0
*
* Please cite the following paper when you use this macro:
* Rühr et al. (2021.): Juvenile ecology drives adult morphology in two insect orders.
* Proc B 288: 20210616. https://doi.org/10.1098/rspb.2021.0616
*
*
* If you experience any issues, please contact me at [email protected]
*
* Happy landmarking!
* Peter T. Rühr
* BSD 3-Clause License
* Copyright (c) 2021, Peter-T-Ruehr
* All rights reserved.
*
*/
requires("1.39l");
ROI_def_start = getTime();
if (isOpen("Log")) {
selectWindow("Log");
run("Close");
}
if (isOpen("Results")) {
selectWindow("Results");
run("Close");
}
while (nImages>0) {
selectImage(nImages);
close();
}
plugins = getDirectory("plugins");
unix = '/plugins/';
windows = '\\plugins\\';
if(endsWith(plugins, unix)){
print("Running on Unix...");
dir_sep = "/";
}
else if(endsWith(plugins, windows)){
print("Running on Windows...");
dir_sep = "\\";
}
//get source dir from user and define other directories
source_dir = getDirectory("Select source Directory");
parent_dir_name = File.getName(source_dir);
print("Loading directory: "+parent_dir_name+"...");
setBatchMode(true);
open(source_dir);
getPixelSize(unit, px_size, ph, pd);
print("Pixel size: "+ px_size,".");
Dialog.create("Settings");
Dialog.addMessage("___________________________________");
Dialog.addString("File name: ", parent_dir_name);
Dialog.addMessage("___________________________________");
Dialog.addString("Name of ROI:", "ROI");
Dialog.addMessage("___________________________________");
Dialog.addNumber("Correct pixel size?:", px_size, 9, 10, "um")
Dialog.addMessage("___________________________________");
Dialog.addNumber("Scale to [MB]: ", 280);
Dialog.addMessage("___________________________________");
Dialog.addCheckbox("Convert to 8-bit*? ", false);
Dialog.addMessage("___________________________________");
Dialog.addCheckbox("Enhance contrast*?", false);
Dialog.addMessage("___________________________________");
Dialog.addMessage("*calibrated Hounsfield units will be lost!");
Dialog.addMessage("___________________________________");
Dialog.addMessage("Rühr et al. (2021): Proc B 288: 20210616.");
Dialog.addMessage("doi: 10.1098/rspb.2021.0616");
Dialog.addMessage("In case of any issues: please contact [email protected]");
Dialog.addMessage("___________________________________");
Dialog.show();
specimen_name = Dialog.getString();
ROI_name = Dialog.getString();
px_size = Dialog.getNumber();
d_size = Dialog.getNumber()/1024;
conv_8bit = Dialog.getCheckbox();
enhance_contrast = Dialog.getCheckbox();
print("Working on "+specimen_name+"...");
// calculate if scaling is necessary later
Stack.getDimensions(width_orig, height_orig, channels, slices, frames);
o_size = width_orig*height_orig*slices/(1024*1024*1024);
print("Target directory loaded. Stack size: "+o_size+" GB.");
d = pow(d_size/o_size,1/3);
perc_d = round(100 * d);
d = perc_d/100;
print(d);
run("Properties...", "unit=um pixel_width="+px_size+" pixel_height="+px_size+" voxel_depth="+px_size);
print("Pixel size set to "+px_size+".");
if(bitDepth() != 8 && conv_8bit == true){
run("8-bit");
}
if(perc_d < 100){
print("Scaling stack to "+perc_d+"%. to reach stack size of "+d_size+" GB...");
run("Scale...", "x="+d+" y="+d+" z="+d+" interpolation=Bicubic average process create");
px_size = px_size/d;
print("New px size = "+px_size+" um.");
//tiff_name = source_dir+parent_dir_name+"_red"+perc_d;
tiff_name = specimen_name+"_"+ROI_name+"_red"+perc_d;
file_name = tiff_name+".tif";
ckpt_name = specimen_name+"_"+ROI_name+"_red"+perc_d+".ckpt";
}
else{
print("No scaling necessary; stack is already smaller than "+d_size+" GB.");
tiff_name = specimen_name+"_"+ROI_name;
file_name = tiff_name+".tif";
ckpt_name = specimen_name+"_"+ROI_name+".ckpt";
}
saveAs("Tiff", source_dir+tiff_name);
print("Saved stack as "+file_name+".");
checkpoint_file = File.open(source_dir+dir_sep+ckpt_name);
print(checkpoint_file, "Version 5");
print(checkpoint_file, "Stratovan Checkpoint (TM)");
print(checkpoint_file, "");
print(checkpoint_file, "[Specimen Information]");
print(checkpoint_file, "Name: "+parent_dir_name+", .ckpt");
print(checkpoint_file, parent_dir_name);
print(checkpoint_file, "Birthdate: ");
print(checkpoint_file, "Sex: ");
print(checkpoint_file, "");
print(checkpoint_file, "[Specimen Study]");
print(checkpoint_file, "StudyInstanceUID: ");
print(checkpoint_file, "StudyID: ");
print(checkpoint_file, "StudyDate: ");
print(checkpoint_file, "StudyTime: ");
print(checkpoint_file, "StudyDescription: ");
print(checkpoint_file, "");
print(checkpoint_file, "[Specimen Series]");
print(checkpoint_file, "SeriesInstanceUID: ");
print(checkpoint_file, "SeriesNumber: ");
print(checkpoint_file, "SeriesDate: ");
print(checkpoint_file, "SeriesTime: ");
print(checkpoint_file, "SeriesModality: ");
print(checkpoint_file, "SeriesProtocol: ");
print(checkpoint_file, "SeriesPart: ");
print(checkpoint_file, "SeriesDescription: ");
print(checkpoint_file, "");
print(checkpoint_file, "[Specimen File(s)]");
print(checkpoint_file, "NumberOfFolders: 1");
print(checkpoint_file, "Folder: "+source_dir);
print(checkpoint_file, "");
print(checkpoint_file, "[Surface Information]");
print(checkpoint_file, "NumberOfSurfaces: 0");
print(checkpoint_file, "");
print(checkpoint_file, "[Templates]");
print(checkpoint_file, "NumberOfTemplates: 0");
print(checkpoint_file, "");
print(checkpoint_file, "[Landmarks]");
print(checkpoint_file, "NumberOfPoints: 0");
print(checkpoint_file, "Units: um");
print(checkpoint_file, "");
print(checkpoint_file, "[SinglePoints]");
print(checkpoint_file, "NumberOfSinglePoints: 0");
print(checkpoint_file, "");
print(checkpoint_file, "[Curves]");
print(checkpoint_file, "NumberOfCurves: 0");
print(checkpoint_file, "");
print(checkpoint_file, "[Patches]");
print(checkpoint_file, "NumberOfPatches: 0");
print(checkpoint_file, "");
print(checkpoint_file, "[Joints]");
print(checkpoint_file, "NumberOfJoints: 0");
print(checkpoint_file, "");
print(checkpoint_file, "[Lengths]");
print(checkpoint_file, "NumberOfLengths: 0");
print(checkpoint_file, "");
print(checkpoint_file, "[Lines]");
print(checkpoint_file, "NumberOfLines: 0");
print(checkpoint_file, "");
print(checkpoint_file, "[Angles]");
print(checkpoint_file, "NumberOfAngles: 0");
print(checkpoint_file, "");
print(checkpoint_file, "[Planes]");
print(checkpoint_file, "NumberOfPlanes: 0");
print(checkpoint_file, "");
print(checkpoint_file, "[Image Stack]");
print(checkpoint_file, "Units: um");
print(checkpoint_file, "Spacing: "+px_size+" "+px_size+" "+px_size+" ");
print(checkpoint_file, "NumberOfFiles: 1");
print(checkpoint_file, "Files: \""+file_name);
print(checkpoint_file, "");
print(checkpoint_file, "[Contrast and Brightness]");
print(checkpoint_file, "Width: 82");
print(checkpoint_file, "Level: -19");
print(checkpoint_file, "");
print(checkpoint_file, "[Landmark Size]");
print(checkpoint_file, "Size: 2");
print("Saved checkpoint file as "+source_dir+dir_sep+ckpt_name+".ckpt.");
print("All done!");