Hi,
I have been working a little bit on a macro to batch convert DM3 to TIFF. This is what it does:
- Gets as input a folder (and sub folders) and a export file type.
- Batch converts ALL the DM3 to the file type.
- The Images obtain a Scale bar which is always around 1/3 of the width of the image, with nice numbers, such as 1, 2, 5, 10, 20, 50, 100, 200, 500…
- The diffractions obtain the same scale bar but with 1/nm instead of nm units.
- The EELS obtain NO scale bar. Instead, they are saved as 2 different documents:
- A 2-column text file, with the Energy and counts
- A image which lets you see how the spectrum looks like when digging in the folder, BUT just for that. This image is not calibrated nor has good quality, is just for easy seeking.
This macro is made up with pieces of several other macros/plugins, and I hope all of them are correctly refereed on it.
The macro requires CSI Spectrum reader, because it is the only way I found to get the data from the DM3.
If anyone has time and wants to dig in the macro, to find possible improvements, I would be happy.
Right now it makes what I need, it is a little bit slow (needs like 0.3s for each image) but it is enought for me.
I do not know how to attach files, so I just post it here:
// This macro batch processes .dm3 images saved with Gatan software
// for Transmission Electron Microscope (TEM) imaging. It adds scale bar to each image
// and converts them from .dm3 to different types of image
// the diffractions obtain a scalebar with 1/nm , and the EELS are saved
//as crappy image for track, and 2-column txt file
// global author: Oliver Dieste, 21.01.2016, JRC-ITU (Karlsruhe)
// last modification: 27.01.2016, 14:24
//REQUIRES CSI DM3 Reader plugin http://code.google.com/p/cornell-spectrum-imager/wiki/Home
// partially copied from: Amirhossein Khalajhedayati, 12/10/2013, University of California Irvine, USA
// Some other parts of this code were obtained from multiple resources on the web.
requires("1.33n");
dir = getDirectory("Choose a directory that contains dm3 files");
//i removed the output place, I prefer to have the tif where the dm3 are
format = getFormat();
start = getTime();
setBatchMode(true);
print("\\Clear")
//start the process: lets find the images in the folder and SUBFOLDERS
find(dir);
//print a count of the time
print("Processing time: " + (getTime() - start) / 1000 + " Seconds");
//END
/////////////////////////////////////////
function find(dir) {
print("Entering "+dir);
//showStatus("enter " + dir);
//this function iterates in the sub-folders to find the dm3 files
// copied from the ListFilesRecursively macro
list = getFileList(dir);
for (i = 0; i < list.length; i++) {
if (endsWith(list[i], "/")) {
//if you find a dir, go deep on it
// print("Entering "+dir+list[i]);
find("" + dir + list[i]);
}
else if (endsWith(list[i], "dm3")) {
//if you find a dm3, convert it!
convert_image(list[i], dir);
showProgress(i, list.length);
}
}
}
function convert_image(file_dm3, dir_dm3) {
imagestart=getTime();
>
//partially borrowed from ser2tiff plugin
//by J Kaelber at National University of Singapore on 20 July 2012
//this function converts the image
path = dir_dm3 + file_dm3;
outputDirectory = dir_dm3;
outFile = outputDirectory + file_dm3;
IJ.redirectErrorMessages();
open(path);
getPixelSize(unit, pixelWidth, pixelHeight);
//we check if it is EELS with the signal value
eels = getTag("ImageTags.Meta Data.Signal");
//if it is not EELS
if (eels != " EELS") {
//now we check if image or diffraction
modo = getTag("ImageTags.Microscope Info.Operation Mode");
if (modo != " IMAGING") {
//for diffraction change scale unit
run("Set Scale...", "unit=1/nm");
}
//for both images and diffraction create a scale bar
//and save the images
crea_bar(pixelWidth);
// windows does not like tiff with 16bit.
run("8-bit");
saveAs(format, outFile);
close();
}
//if it is EELS
else {
//by saving here we obtain a shitty image, just to get the icon when
//looking through the files
//saveAs(format, outFile);
close();
run("CSI DM3 Reader", "load=[&path]");
//spectrum needs to be centered and calibrated
//we get the drift of the tube, the offset energy and the dispersion
//from the values recorded on the file
drift = parseFloat(getTag("EELS.Acquisition.Spectrometer.Drift tube voltage"));
offset = parseFloat(getTag("EELS.Acquisition.Spectrometer.Prism offset"));
dispersion = parseFloat(getTag("EELS.Acquisition.Spectrometer.Dispersion"));
energy = newArray(2048);
//this is width of the profile, where it starts and where it ends.
energy_width = dispersion * 2048;
// TODO: check what is wrong with the spectra where OFFSET exist , p.e. for M4,5 lines
//when using -3500eV, sometimes you get up to 11 eV of difference
inicio = drift - offset - floor(energy_width / 10);
fin = inicio + dispersion * 2048;
run("Select All");
// evilly copied from the macro of
// Version 1.0, 24-Sep-2010 Michael Schmid
//this part gets the profile, saves it in variables x and y, and save them in
//a 2-column txt file
run("Plot Profile");
Plot.getValues(x, y);
saveAs(format, outFile);
str = "Energy(eV)\tCounts\n"; // header
for (i = 0; i < x.length; i++) {
energy[i] = inicio + dispersion * i;
str += "" + energy[i] + "\t" + y[i] + "\n";
}
File.saveString(str, outFile + ".txt");
close();
}
print (file_dm3+" READY");
}
function getFormat() {
//choose the output format
formats = newArray("TIFF", "JPEG", "GIF", "PNG",
"PGM", "BMP", "FITS", "Text Image", "ZIP", "Raw");
Dialog.create("Output format");
Dialog.addChoice("Convert to: ", formats, "TIFF");
Dialog.show();
return Dialog.getChoice();
}
function getTag(tag) {
//get the needed tag
info = getImageInfo();
index1 = indexOf(info, tag);
if (index1 == -1) return "";
index1 = indexOf(info, "=", index1);
if (index1 == -1) return "";
index2 = indexOf(info, "\n", index1);
value = substring(info, index1 + 1, index2);
return value;
}
function crea_bar(ancho) {
//function that prints the scalebar with certain width
//first calculate the ideal width
baseWidth = floor(300 * ancho);
scaleValues = newArray(1, 2, 5);
factor = 1;
j = 0;
for (t = 0; t < 20; t++) {
scaleWidth = scaleValues[j] * factor;
if (baseWidth > scaleWidth) {
j++;
if (j >= scaleValues.length) {
j = 0;
factor *= 10;
}
} else {
t = 20;
}
}
//then print it
run("Scale Bar...", "width=&scaleWidth height=8 font=50 color=White background=Black location=[Lower Right] bold");
return;
}
that´s it.
Regards,
