Re: Filename problem leading to exception in latest Bioformat ?

Posted by lechristophe on Dec 17, 2010; 11:40pm
URL: http://imagej.273.s1.nabble.com/Filename-problem-leading-to-exception-in-latest-Bioformat-tp3686158p3686160.html

That fixed the problem, thank you Melissa. Do you have a link to
documentation about the file grouping and its logic ?

Thanks,

Christophe

On Fri, Dec 17, 2010 at 17:30, Melissa Linkert
<[hidden email]>wrote:

> Hi Christophe,
>
> You can solve this problem by adding this line:
>
> Ext.setGroupFiles("false");
>
> right before Ext.setId(FILE_PATH).  That will disable the file grouping
> logic, and so each file should be read individually.   If you still see
> an error message after adding that line, please let us know.
>
> Regards,
> -Melissa
>
> On Fri, Dec 17, 2010 at 06:09:14AM +0100, Christophe Leterrier wrote:
> > Hi,
> >
> > My macros that use the BioFormat macro extensions stopped working lately.
> I
> > finally got some time to try to narrow the problem and it was actually
> quite
> > puzzling. I finally isolated a minimal set of images and a test macro
> that
> > reproduce the problem. I'm using the latest (updated) Fiji with its
> current
> > BioFormats version, which is dev 4.2 rev 7334 (6 dec. 2010), under OSX
> > 10.6.5 Java 1.6.0_22 (64bits).
> >
> > The files necessary to reproduce the bug are available in this archive
> zip:
> > http://www.cleterrier.net/up/BioFormats_Filename.zip
> >
> > Just run the Test.ijm macro, point it to the "Test Images" folder. It
> will
> > get the file name for the three images inside the folder and open it
> using
> > BioFormats through the macro extensions interface. It will progress
> through
> > the images but will throw an error message that I captured in Error.png
> (it
> > is a non-text window where you cannot copy and paste the text,
> > unfortunately).
> >
> > Here is the text of the macro :
> >
> > DIR_PATH=getDirectory("Select a directory");
> > ALL_NAMES=getFileList(DIR_PATH);
> > for (i=0; i<ALL_NAMES.length; i++) {
> >  run("Bio-Formats Macro Extensions");
> > FILE_PATH=DIR_PATH+ALL_NAMES[i];
> >  Ext.setId(FILE_PATH);
> > run("Bio-Formats Importer", "open=["+ FILE_PATH + "] " + "view=[Standard
> > ImageJ]" + " stack_order=Default split_channels ");
> > }
> >
> >
> > What I understand is that the three images are named 16.tif, 17.tif and
> > 26.tif in the folder. For some reason BioFormats interprets that as a
> > logical serie of names and throws an error at the Ext.setId() instruction
> > because it expects for a fourth image called 27.tif that doesn't exist.
> In
> > fact the error appears for any combination of numbered images that have
> N,
> > N+1 and N+10 as indexes.
> >
> > Is there something wrong in the code or some new option that I've missed
> and
> > that has to be taken care of when using Ext.setId() ? Thanks for your
> help
> > in solving this.
> >
> > Christophe
>