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ImageProcessor.ijm
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ImageProcessor.ijm
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// ImageProcessor.ijm -
// batch process all images in a given directory.
// converts images to TIFF and saves the acquisition dates.
run("Bio-Formats Macro Extensions");
// ask the user for the directory with images to process
dir = getDirectory("Choose directory");
// note start time, for benchmarking
start = getTime();
num = 0;
// get file listing
list = getFileList(dir);
newlist = list;
// expand directories -- we only recurse one level deep
// (i.e. main directory with subdirs for each experiment
for(i = 0; i < list.length; i++) {
if (endsWith(list[i], '/')) {
files = getFileList(dir + list[i]);
for (n = 0; n < files.length; n++) {
files[n] = list[i] + '/' + files[n];
}
newlist = Array.concat(newlist, files);
}
}
list = newlist;
// only process image files
images = newArray(0);
for(w = 0; w < list.length; w++) {
fn = dir + '/' + list[w];
Ext.isThisType(fn, type)
if (type == "true") {
images = Array.concat(images, fn);
}
}
// process images
for (n = 0; n < images.length; n++) {
Ext.setId(images[n]);
Ext.getSeriesCount(count);
if (count == 1) {
// file contains only one image
run("Bio-Formats Windowless Importer", "open=[" + images[n] + "]");
saveAs("tiff", images[n] + ".tif");
Ext.getImageCreationDate(crdate);
File.saveString(crdate, images[n] + ".tif.time");
num++;
close();
} else {
// file contains several images; save each separately
for (i = 1; i < count + 1; i++) {
Ext.setSeries(i - 1);
Ext.getSeriesName(sname);
Ext.getImageCreationDate(crdate);
run("Bio-Formats Importer", "open=[" + images[n] + "] series_" + i);
saveAs("tiff", dir + File.separator + sname + ".tif");
File.saveString(crdate, dir + '/' + sname + ".tif.time");
num++;
close();
}
}
}
elapsed = (getTime() - start) / 1000;
print("Processed " + num + " images in " + elapsed + " seconds.");