Posted by
Marina Franck on
URL: http://imagej.273.s1.nabble.com/Batch-opening-Volocity-files-tp5011589p5011609.html
Hi,
Thanks Curtis for your input, unfortunately it didn't solve the problem. This in now a simple example macro that would just rename the files and save them as .tif, but it doesn't do its job - only the first image in a set gets processed. I think it just thinks there is only one file to process because there is only one .mvd2 file, and I can't make it process all the images that file points to!
Any ideas how to get around this?
dir=getDirectory("Choose a Source Directory containing the .mvd2 file");
savedir=getDirectory("Choose a Storage Directory");
list = getFileList(dir);
setBatchMode(true)
for (i=0; i<list.length; i++) {
inputPath = dir + list[i];
if (endsWith(inputPath, ".mvd2")) {
run("Bio-Formats Importer", "open=[" + inputPath + "] autoscale color_mode=Grayscale view=Hyperstack stack_order=XYCZT");
title=getTitle();
title = replace(title," ","_");
title = replace(title,".","_");
savename=savedir+title+".tif";
saveAs("tiff", savename);
close();
}
}
setBatchMode(false)
Regards,
Marina
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Curtis Rueden
Sent: den 13 februari 2015 17:40
To:
[hidden email]
Subject: Re: Batch opening Volocity files
Hi Marina,
> I think I might need a completely different approach with the Volocity
> files since it's not a list of .mvd2 files.
Actually, I think your strategy should work just fine, as long as the user chooses the directory containing the .mvd2 files when prompted.
> run("Bio-Formats Importer", "open=[inputPath autoscale
color_mode=Grayscale view=Hyperstack stack_order=XYCZT");
Note that the above line of macro code will not work as written; it should rather be something like:
run("Bio-Formats Importer", "open=[" + inputPath + "] autoscale color_mode=Grayscale view=Hyperstack stack_order=XYCZT");
Regards,
Curtis
On Fri, Feb 13, 2015 at 8:38 AM, Marina Franck <
[hidden email]>
wrote:
> Hi,
>
> I'm trying to make a macro for batch processing images taken with
> Volocity. But I stumbled on the first step - I can't get the macro to
> open the files! Other imaging software save a bunch of files in a
> folder and I can direct the macro there, but Volocity creates a .mvd2
> file and a separate folder containing the data. I can manually open
> the files in imageJ using the Bio-Formats Importer and asking it to
> open the .mvd2 file, but the problem is to get this into a macro.
>
> Usually I would start the macro something like this:
>
> dir=getDirectory("Choose Source Directory");
> savedir=getDirectory("Choose a Storage Directory"); list =
> getFileList(dir);
> setBatchMode(true)
>
> for (i=0; i<list.length; i++) {
> inputPath = dir + list[i];
> if (endsWith(inputPath, ".mvd2")) {
> run("Bio-Formats Importer",
> "open=[inputPath autoscale color_mode=Grayscale view=Hyperstack
> stack_order=XYCZT");
>
>
> ...but I think I might need a completely different approach with the
> Volocity files since it's not a list of .mvd2 files. Any ideas would
> be appreciated!
>
> Thanks,
> Marina
> ______________________________________________________________________
> ___
> Marina Franck, PhD
> Department of Neuroscience
> Uppsala University
> BMC, Box 593, Husargatan 3
> 751 23 Uppsala
> Sweden
>
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
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