Posted by
ctrueden on
Feb 13, 2015; 4:40pm
URL: http://imagej.273.s1.nabble.com/Batch-opening-Volocity-files-tp5011589p5011591.html
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
>
>
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> ImageJ mailing list:
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