problems with Batch Converter

[Lars Damgaard]

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

[ctrueden]

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
>

... [show rest of quote]

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

[Lars Damgaard]

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
>

... [show rest of quote]

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

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

[ctrueden]

Hi Lars,

> Only thing now seems to be that my JPGs come in B/W instead of color
> like the source ZVIs.

Probably your source ZVIs store channels as separate planes, so they open
as a composite color image, rather than an RGB color one.

> Any suggestions to solve that also (present code is below)?

Sure, you can try adjusting the opening step to do something like:

    run("Bio-Formats Importer", "open='" + inBase + path + "'
        color_mode=Composite view=[Hyperstack] stack_order=Default");
    run("RGB Color");

That will open the file as a hyperstack in composite color mode, then
convert to RGB color before exporting as JPEG.

> PS.  I read about ImageJ2 now and then - when is it due?

It is in beta now, meaning lots of stuff works but there are technical
aspects that are still subject to change. You can download and try it from
http://developer.imagej.net/downloads. That page also has the release
schedule.

> PPS. Is there a way to halt processes and macros in ImageJ (like
> Ctrl-Break in some programs)?

Not that I know of, other than quitting ImageJ. However, if you control the
macro code, you could always build in a way to cancel it mid-execution.

Regards,
Curtis


On Fri, Apr 19, 2013 at 9:06 AM, Lars Riis Damgaard <[hidden email]>wrote:

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

... [show rest of quote]

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

[Lars Damgaard]

Thanks Curtis, that did brought colors. Only thing now is that the brightness of the resulting JPG's is lower than if I view the original in AxioVision. I wonder which is 'correct'?
Lars

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis Rueden
Sent: 19. april 2013 16:48
To: [hidden email]
Subject: Re: problems with Batch Converter

Hi Lars,

> Only thing now seems to be that my JPGs come in B/W instead of color
> like the source ZVIs.

Probably your source ZVIs store channels as separate planes, so they open as a composite color image, rather than an RGB color one.

> Any suggestions to solve that also (present code is below)?

Sure, you can try adjusting the opening step to do something like:

    run("Bio-Formats Importer", "open='" + inBase + path + "'
        color_mode=Composite view=[Hyperstack] stack_order=Default");
    run("RGB Color");

That will open the file as a hyperstack in composite color mode, then convert to RGB color before exporting as JPEG.

> PS.  I read about ImageJ2 now and then - when is it due?

It is in beta now, meaning lots of stuff works but there are technical aspects that are still subject to change. You can download and try it from http://developer.imagej.net/downloads. That page also has the release schedule.

> PPS. Is there a way to halt processes and macros in ImageJ (like
> Ctrl-Break in some programs)?

Not that I know of, other than quitting ImageJ. However, if you control the macro code, you could always build in a way to cancel it mid-execution.

Regards,
Curtis


On Fri, Apr 19, 2013 at 9:06 AM, Lars Riis Damgaard <[hidden email]>wrote:

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

... [show rest of quote]

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

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

[ctrueden]

Hi Lars,

> Only thing now is that the brightness of the resulting JPG's is lower
> than if I view the original in AxioVision.

Perhaps AxioVision is autoscaling your display range. You could try adding
the "autoscale" flag to the "Bio-Formats Importer" command in your ImageJ
macro:

    run("Bio-Formats Importer", "open='" + inBase + path + "'
        color_mode=Composite view=[Hyperstack] stack_order=Default
autoscale");

The above sets the displayed minimum and maximum values to match those of
the data itself.

Alternately, you could do something like:

    run("Enhance Contrast", "saturated=0.35");

Which gives you more control over what percentage of pixels fall outside
the bounds of the displayed min/max.

Regards,
Curtis


On Mon, Apr 22, 2013 at 7:57 AM, Lars Riis Damgaard <[hidden email]>wrote:

> Thanks Curtis, that did brought colors. Only thing now is that the
> brightness of the resulting JPG's is lower than if I view the original in
> AxioVision. I wonder which is 'correct'?
> Lars
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Curtis Rueden
> Sent: 19. april 2013 16:48
> To: [hidden email]
> Subject: Re: problems with Batch Converter
>
> Hi Lars,
>
> > Only thing now seems to be that my JPGs come in B/W instead of color
> > like the source ZVIs.
>
> Probably your source ZVIs store channels as separate planes, so they open
> as a composite color image, rather than an RGB color one.
>
> > Any suggestions to solve that also (present code is below)?
>
> Sure, you can try adjusting the opening step to do something like:
>
>     run("Bio-Formats Importer", "open='" + inBase + path + "'
>         color_mode=Composite view=[Hyperstack] stack_order=Default");
>     run("RGB Color");
>
> That will open the file as a hyperstack in composite color mode, then
> convert to RGB color before exporting as JPEG.
>
> > PS.  I read about ImageJ2 now and then - when is it due?
>
> It is in beta now, meaning lots of stuff works but there are technical
> aspects that are still subject to change. You can download and try it from
> http://developer.imagej.net/downloads. That page also has the release
> schedule.
>
> > PPS. Is there a way to halt processes and macros in ImageJ (like
> > Ctrl-Break in some programs)?
>
> Not that I know of, other than quitting ImageJ. However, if you control
> the macro code, you could always build in a way to cancel it mid-execution.
>
> Regards,
> Curtis
>
>
> On Fri, Apr 19, 2013 at 9:06 AM, Lars Riis Damgaard <[hidden email]
> >wrote:
>
> > 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/lo
> > ci-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
> > >
> >
> > --
> > 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
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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

[Lars Damgaard]

Hi Curtis,

Thanks, I got all my files converted now and could enhance brightness - great!
(I commented out outBase=inBase; to get the files out in a separate folder tree).
Only problem was that the macro crashed windows completely, probably by running memory down. Is the line
run("Collect Garbage")
not supposed to avoid this? The code looks as shown below.

Thanks, Lars

-----------CODE START ---------------
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 = false; // 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
      //outBase=inBase;
      processFiles(inBase, outBase, path);
    }
   else if (endsWith(upath, "." + ext)) {
      print("-- Processing file: " + path + " --");
      run("Bio-Formats Importer", "open='" + inBase + path + "' color_mode=Composite view=[Hyperstack] stack_order=Default");
      run("RGB Color");
      run("Enhance Contrast", "saturated=0.935");
      outFile = outBase + path + ".jpg";
      if (flattenFolders) outFile = replace(outFile, "/", "_");
      run("Bio-Formats Exporter", "save=[" + outFile + "] compression=Uncompressed");
      print("Outfile: " + outFile);
      close();
      run("Collect Garbage");
    }
  }
}
-----------CODE END -------------------

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis Rueden
Sent: 23. april 2013 17:02
To: [hidden email]
Subject: Re: problems with Batch Converter

Hi Lars,

> Only thing now is that the brightness of the resulting JPG's is lower
> than if I view the original in AxioVision.

Perhaps AxioVision is autoscaling your display range. You could try adding the "autoscale" flag to the "Bio-Formats Importer" command in your ImageJ
macro:

    run("Bio-Formats Importer", "open='" + inBase + path + "'
        color_mode=Composite view=[Hyperstack] stack_order=Default autoscale");

The above sets the displayed minimum and maximum values to match those of the data itself.

Alternately, you could do something like:

    run("Enhance Contrast", "saturated=0.35");

Which gives you more control over what percentage of pixels fall outside the bounds of the displayed min/max.

Regards,
Curtis


On Mon, Apr 22, 2013 at 7:57 AM, Lars Riis Damgaard <[hidden email]>wrote:

> Thanks Curtis, that did brought colors. Only thing now is that the
> brightness of the resulting JPG's is lower than if I view the original
> in AxioVision. I wonder which is 'correct'?
> Lars
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Curtis Rueden
> Sent: 19. april 2013 16:48
> To: [hidden email]
> Subject: Re: problems with Batch Converter
>
> Hi Lars,
>
> > Only thing now seems to be that my JPGs come in B/W instead of color
> > like the source ZVIs.
>
> Probably your source ZVIs store channels as separate planes, so they
> open as a composite color image, rather than an RGB color one.
>
> > Any suggestions to solve that also (present code is below)?
>
> Sure, you can try adjusting the opening step to do something like:
>
>     run("Bio-Formats Importer", "open='" + inBase + path + "'
>         color_mode=Composite view=[Hyperstack] stack_order=Default");
>     run("RGB Color");
>
> That will open the file as a hyperstack in composite color mode, then
> convert to RGB color before exporting as JPEG.
>
> > PS.  I read about ImageJ2 now and then - when is it due?
>
> It is in beta now, meaning lots of stuff works but there are technical
> aspects that are still subject to change. You can download and try it
> from http://developer.imagej.net/downloads. That page also has the
> release schedule.
>
> > PPS. Is there a way to halt processes and macros in ImageJ (like
> > Ctrl-Break in some programs)?
>
> Not that I know of, other than quitting ImageJ. However, if you
> control the macro code, you could always build in a way to cancel it mid-execution.
>
> Regards,
> Curtis
>
>
> On Fri, Apr 19, 2013 at 9:06 AM, Lars Riis Damgaard <[hidden email]
> >wrote:
>
> > 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/
> > lo ci-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
> > >
> >
> > --
> > 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
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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

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

[ctrueden]

Hi Lars,

> Only problem was that the macro crashed windows completely, probably
> by running memory down.

Sorry to hear that. There are many different potential causes there.
Normally, a Java program cannot crash Windows by running out of memory --
you would typically just see a message containing the word
"OutOfMemoryError".

> Is the line run("Collect Garbage") not supposed to avoid this?

See this FAQ entry:
http://developer.imagej.net/how-do-i-avoid-outofmemoryerrors

Regards,
Curtis


On Wed, May 1, 2013 at 2:09 AM, Lars Riis Damgaard <[hidden email]>wrote:

> Hi Curtis,
>
> Thanks, I got all my files converted now and could enhance brightness -
> great!
> (I commented out outBase=inBase; to get the files out in a separate folder
> tree).
> Only problem was that the macro crashed windows completely, probably by
> running memory down. Is the line
> run("Collect Garbage")
> not supposed to avoid this? The code looks as shown below.
>
> Thanks, Lars
>
> -----------CODE START ---------------
> 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 = false; // 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
>       //outBase=inBase;
>       processFiles(inBase, outBase, path);
>     }
>    else if (endsWith(upath, "." + ext)) {
>       print("-- Processing file: " + path + " --");
>       run("Bio-Formats Importer", "open='" + inBase + path + "'
> color_mode=Composite view=[Hyperstack] stack_order=Default");
>       run("RGB Color");
>       run("Enhance Contrast", "saturated=0.935");
>       outFile = outBase + path + ".jpg";
>       if (flattenFolders) outFile = replace(outFile, "/", "_");
>       run("Bio-Formats Exporter", "save=[" + outFile + "]
> compression=Uncompressed");
>       print("Outfile: " + outFile);
>       close();
>       run("Collect Garbage");
>     }
>   }
> }
> -----------CODE END -------------------
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Curtis Rueden
> Sent: 23. april 2013 17:02
> To: [hidden email]
> Subject: Re: problems with Batch Converter
>
> Hi Lars,
>
> > Only thing now is that the brightness of the resulting JPG's is lower
> > than if I view the original in AxioVision.
>
> Perhaps AxioVision is autoscaling your display range. You could try adding
> the "autoscale" flag to the "Bio-Formats Importer" command in your ImageJ
> macro:
>
>     run("Bio-Formats Importer", "open='" + inBase + path + "'
>         color_mode=Composite view=[Hyperstack] stack_order=Default
> autoscale");
>
> The above sets the displayed minimum and maximum values to match those of
> the data itself.
>
> Alternately, you could do something like:
>
>     run("Enhance Contrast", "saturated=0.35");
>
> Which gives you more control over what percentage of pixels fall outside
> the bounds of the displayed min/max.
>
> Regards,
> Curtis
>
>
> On Mon, Apr 22, 2013 at 7:57 AM, Lars Riis Damgaard <[hidden email]
> >wrote:
>
> > Thanks Curtis, that did brought colors. Only thing now is that the
> > brightness of the resulting JPG's is lower than if I view the original
> > in AxioVision. I wonder which is 'correct'?
> > Lars
> >
> > -----Original Message-----
> > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> > Curtis Rueden
> > Sent: 19. april 2013 16:48
> > To: [hidden email]
> > Subject: Re: problems with Batch Converter
> >
> > Hi Lars,
> >
> > > Only thing now seems to be that my JPGs come in B/W instead of color
> > > like the source ZVIs.
> >
> > Probably your source ZVIs store channels as separate planes, so they
> > open as a composite color image, rather than an RGB color one.
> >
> > > Any suggestions to solve that also (present code is below)?
> >
> > Sure, you can try adjusting the opening step to do something like:
> >
> >     run("Bio-Formats Importer", "open='" + inBase + path + "'
> >         color_mode=Composite view=[Hyperstack] stack_order=Default");
> >     run("RGB Color");
> >
> > That will open the file as a hyperstack in composite color mode, then
> > convert to RGB color before exporting as JPEG.
> >
> > > PS.  I read about ImageJ2 now and then - when is it due?
> >
> > It is in beta now, meaning lots of stuff works but there are technical
> > aspects that are still subject to change. You can download and try it
> > from http://developer.imagej.net/downloads. That page also has the
> > release schedule.
> >
> > > PPS. Is there a way to halt processes and macros in ImageJ (like
> > > Ctrl-Break in some programs)?
> >
> > Not that I know of, other than quitting ImageJ. However, if you
> > control the macro code, you could always build in a way to cancel it
> mid-execution.
> >
> > Regards,
> > Curtis
> >
> >
> > On Fri, Apr 19, 2013 at 9:06 AM, Lars Riis Damgaard <[hidden email]
> > >wrote:
> >
> > > 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/
> > > lo ci-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
> > > >
> > >
> > > --
> > > 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
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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