http://imagej.273.s1.nabble.com/Open-multiple-images-in-a-sequence-batch-tp5015419p5015425.html
Thanks for pointing out the errors, Volker. After I submitted my original
And for 3, I did get that error but not all the time. When I ran my macro
third one. It said that it needs a stack to "convert images to stack". But
thanks for your tip. I used wait(1000) between those two commands and that
> That is because Process>Batch>Macro will try to save an image as a
> result and then close it. You can get around this by removing the last
> close command in your macro.
>
> However there are some more problems:
>
> 1. There is an error in line 82, there is a quote (") too much. It
> should be:
> run("Duplicate...", "title=[for mask]");
>
> 2. Since you keep all rois in the roi manager it will select the wrong
> roi in subsequent iterations (always 0 and 1). Maybe you could reset the
> roi manager at the start of the macro to solve this.
>
> 3. After that it still does not work for me. It complains that it needs
> a stack for the command run("HSB Stack"). And the run("Convert to
> Mask"); does not have its input either.
> Maybe this will not happen in your version? I can work around it by
> putting in waitForUser() commands before the to commands.
>
> Volker
>
> ram prasad:
> > Thanks Volker! That seems to have solved my problem atleast partially.
> When
> > I include that line and run the macro as a batch process it opens the
> image
> > for me to make a selection but then after processing the first image it
> > throws the following message instead of opening the next one.
> >
> > ImageJ 1.48v; Java 1.6.0_24 [64-bit]; Linux 3.13.0-48-generic; 36MB of
> > 2257MB (1%)
> >
> > java.lang.NullPointerException
> > at ij.process.ColorProcessor.<init>(ColorProcessor.java:30)
> > at ij.ImagePlus.setupProcessor(ImagePlus.java:715)
> > at ij.ImagePlus.getFileInfo(ImagePlus.java:1780)
> > at ij.io.FileSaver.<init>(FileSaver.java:34)
> > at ij.IJ.saveAsTiff(IJ.java:1736)
> > at ij.IJ.saveAs(IJ.java:1665)
> > at ij.plugin.BatchProcessor.processFolder(BatchProcessor.java:200)
> > at ij.plugin.BatchProcessor.run(BatchProcessor.java:91)
> > at ij.IJ.runPlugIn(IJ.java:169)
> > at ij.Executer.runCommand(Executer.java:131)
> > at ij.Executer.run(Executer.java:64)
> > at java.lang.Thread.run(Thread.java:662)
> >
> > How should I go about this?
> >
> > Cheers,
> > Ram
> >
> > On Thu, Jan 21, 2016 at 11:37 AM, Volker Baecker <
>
[hidden email]
> >> wrote:
> >
> >> Hello,
> >> if you add
> >>
> >> setBatchMode(false);
> >>
> >> as the first command in your macro, you might be able to run it with
> >> Process>Batch>Macro...
> >>
> >> Volker
> >>
> >> ram prasad:
> >>> Dear All,
> >>>
> >>> I have a macro that I would like to run as a batch process. I
> >>> expect it to open the file, let me draw a line and then do a few
> >>> operations based on that line. The macro works well on individual
> >>> files. however, when I try to run it as a batch process, instead of
> >>> opening the file it seems to proceed straight to the selection
> >>> step.
> >>>
> >>> I think this is happening because the macro isn't waiting until the
> >>> image is open to proceed to next step. I tried "wait" command but
> >>> had no luck. Also, when I googled about it, I found examples on
> >>> opening image sequence but that is not what I'm looking for. I want
> >>> it to work on all the image files in my directory, sequentially
> >>> without me having to select my file through the open dialog box.
> >>>
> >>> Please, find the macro attached. Any help would be appreciated.
> >>>
> >>> Regards, Ram
> >>>
> >>> -- ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >>>
> >>
> >> --
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> >
> > --
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>
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