http://imagej.273.s1.nabble.com/problems-with-Batch-Converter-tp5002705p5002720.html
> PS. I read about ImageJ2 now and then - when is it due?
aspects that are still subject to change. You can download and try it from
. That page also has the release
> PPS. Is there a way to halt processes and macros in ImageJ (like
Not that I know of, other than quitting ImageJ. However, if you control the
> Hi Curtis,
>
> Thanks a lot. I played a bit with it, and I seem to be doing some
> progress. In addition to changing file extensions, I had to remove the
> uppercasing of the path before it gave results. Only thing now seems to be
> that my JPGs come in B/W instead of color like the source ZVIs. Any
> suggestions to solve that also (present code is below)?
>
> Lars
>
> PS. I read about ImageJ2 now and then - when is it due?
> PPS. Is there a way to halt processes and macros in ImageJ (like
> Ctrl-Break in some programs)?
>
> CODE:
> ____________________________________________________________
>
> ext = "zvi"; // this variable controls the extension of source files
>
> requires("1.39u");
> inDir = getDirectory("Choose Directory Containing " + ext + " Files ");
> outDir = getDirectory("Choose Directory for JPG Output ");
> setBatchMode(true);
> processFiles(inDir, outDir, "");
> print("-- Done --");
>
> function processFiles(inBase, outBase, sub) {
> flattenFolders = true; // this flag controls output directory structure
> print("-- Processing folder: " + sub + " --");
> list = getFileList(inBase + sub);
> if (!flattenFolders) File.makeDirectory(outBase + sub);
> for (i=0; i<list.length; i++) {
> path = sub + list[i];
> //upath = toUpperCase(path);
> upath = path; // should not be upper-cased as line above does
> if (endsWith(path, "/")) {
> // recurse into subdirectories
> processFiles(inBase, outBase, path);
> }
> else if (endsWith(upath, "." + ext)) {
> print("-- Processing file: " + path + " --");
> run("Bio-Formats Importer", "open='" + inBase + path + "'
> color_mode=Default view=[Standard ImageJ] stack_order=Default
> use_virtual_stack");
> outFile = outBase + path + ".jpg";
> if (flattenFolders) outFile = replace(outFile, "/", "_");
> run("Bio-Formats Exporter", "save=[" + outFile + "]
> compression=Uncompressed");
> close();
> run("Collect Garbage");
> }
> }
> }
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of
> Curtis Rueden
> Sent: 18. april 2013 21:49
> To:
[hidden email]
> Subject: Re: problems with Batch Converter
>
> Hi Lars,
>
> > In the end, no matter if I OK or cancel any of the dialogs, some open
> > files are created in ImageJ, but my output folder is empty.
>
> You have run into a limitation of the way ImageJ's image I/O works. In
> this case, the symptom is that Batch Converter will not work when reading
> files using Bio-Formats.
>
> ImageJ2 will make image I/O more extensible, but in the meantime, the
> easiest solution is to convert your files using a macro.
>
> Here is a template you can adapt to do what you want:
>
>
https://github.com/openmicroscopy/bioformats/blob/v4.4.6/components/loci-plugins/utils/macros/recursiveTiffConvert.txt>
> Change the "DM3" extension to "ZVI" and then change the ".ome.tif"
> extension on line 38 to ".jpg" instead.
>
> Let us know if you have any trouble with it!
>
> Regards,
> Curtis
>
>
> On Thu, Apr 18, 2013 at 3:17 AM, Lars Damgaard <
[hidden email]> wrote:
>
> > Hi all,
> >
> > I hope someone can help me understand this:
> > I have a folder with 40 zvi files that I want to convert to jpg files.
> > I figure from searching documentation that I should use Batch
> > Converter. When I select Batch Converter, I get a Batch Convert dialog
> > as expected that allows me to select input and output folder, Output
> > format, Interpolation, and Scale factor.
> > However, when I press the Convert button, I get a Bio-Formats Import
> > Options dialog, which has a lot of options.
> > If I try to choose options and press OK, this dialog is followed by a
> > Bio-Formats File Stitching dialog.
> > If I OK this File Stitching dialog, I can see in the status bar that
> > ImageJ apparently is working its way through all files, but then the
> > Bio-Format Import Options dialog re-appears, followed by the
> > Bio-Formats File Stitching dialog. Depending on my choices I also get
> > an Import Data dialog. For each file, I get a log window that writes:
> > IJ.openImage() returned null:
> > C:\Users\lrd\Desktop\zvi-files\Position(1).zvi
> > IJ.openImage() returned null:
> > C:\Users\lrd\Desktop\zvi-files\Position(10).zvi
> > ...
> > etc.
> > In the end, no matter if I OK or cancel any of the dialogs, some open
> > files are created in ImageJ, but my output folder is empty. I have not
> > managed to make my selections so that the open created files are the
> > simple jpg files I want, rather they are separated out in color
> > channels or other advanced views, but in any case I was expecting that
> > the zvi files were batch converted and the resulting jpgs would go to
> the output folder.
> > Any suggestions as to how to achieve this?
> >
> > Lars
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
>
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