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Batch opening Volocity files

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Marina Franck
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Batch opening Volocity files

Marina Franck
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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ctrueden
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Re: Batch opening Volocity files

ctrueden
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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Marina Franck
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Re: Batch opening Volocity files

Marina Franck
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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ctrueden
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Re: Batch opening Volocity files

ctrueden
Hi Marina,

> 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!

Ah, I think I understand now. It is probably a multi-series dataset. When
you select the .mvd2 with the Bio-Formats Importer command, does it bring
up a second dialog box with thumbnails so that you can choose the "image
series" you want to import? If so, the macro becomes more complicated:

https://gist.github.com/ctrueden/bb0c51bc8e93f7197143

Regards,
Curtis


On Mon, Feb 16, 2015 at 5:37 AM, Marina Franck <[hidden email]>
wrote:

> 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
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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