This script compute and exports the mean intensity and the standard deviation for a complete folder of image into a single excel file. If the image contains a region of interest the script uses it to localize the mean intensity and standard deviation calculation.
importClass(Packages.icy.roi.ROI2DRectangle)
importClass(Packages.icy.roi.ROIUtil)
importClass(Packages.icy.sequence.Sequence)
importClass(Packages.icy.util.XLSUtil)
importClass(Packages.icy.file.Loader)
importClass(Packages.icy.file.FileUtil)
importClass(Packages.plugins.tprovoost.scripteditor.uitools.filedialogs.FileDialog)
importClass(Packages.plugins.tprovoost.scripteditor.uitools.userdialogs.Dialog)
// select input folder
inputFolder = FileDialog.openFolder()
// cancelled
if (inputFolder == null) throw "Cancelled..."
// create output file name for XLS file
xlsFileName = inputFolder.getAbsolutePath() + "/result.xls"
// create excel document
wb = XLSUtil.createWorkbook(xlsFileName)
// create a new page in the excel document
ws = XLSUtil.createNewPage(wb, "result")
// set excel headers
XLSUtil.setCellString(ws, 0, 0, "filename")
XLSUtil.setCellString(ws, 2, 0, "average")
XLSUtil.setCellString(ws, 3, 0, "st dev")
// get all files from input folder
files = FileUtil.getFiles(inputFolder, null, false, false, false)
for(i = 0; i < files.length; i++)
{
// get current file
f = files[i]
// load image
seq = Loader.loadSequence(f.getAbsolutePath(), 0, false)
if (seq != null)
{
// get image rois
rois = seq.getROIs()
// we only take the first roi
if (rois.size() > 0) roi = rois.get(0)
// use the whole sequence as rectangular ROI
else roi = new ROI2DRectangle(seq.getBounds2D())
// compute the mean intensity for the whole roi
// be careful, if the image has severals channels
mean = ROIUtil.getMeanIntensity(seq, roi)
// compute the standard deviation for the whole roi
// be careful, if the image has severals channels
stdev = ROIUtil.getStandardDeviation(seq, roi)
// write results in excel file
XLSUtil.setCellString(ws, 0, i + 1, f.getAbsolutePath())
XLSUtil.setCellNumber(ws, 2, i + 1, mean)
XLSUtil.setCellNumber(ws, 3, i + 1, stdev)
}
}
// close and save the excel file
XLSUtil.saveAndClose(wb)
