Hi Fred,
If you add this line of code immediately before the try/catch block:
r.setGroupFiles(false);
...then only the selected LSM file will be opened. You will need to
update to the latest trunk build of loci_tools.jar in order for this
to work correctly.
Please let me know if that does not solve the problem for you.
Regards,
-Melissa
On Thu, Jan 7, 2010 at 4:31 AM, suendermann
<
[hidden email]> wrote:
> Dear Users,
>
> I'm writing a plugin, which uses loci-tools.jar to open lsm image files. The
> lsm files (z-stacks) belong to a timeseries, where every timepoint is stored
> in a separate file. Additionally, every series has its own mdb file. Now I
> found the following strange behavior: If I open any lsm file via the
> loci-tools (code see below) it always opens the first timepoint in the
> series. If I delete the mdb file, the file I choosed will be opened.
> Deleting the mdb file is not my method of choice, so my question is: How can
> I program a workaroud (on plugin basis)?
>
> Greetings
> Fred
>
>
> I use ImageJ 1.42k
> Java jdk 1.6.0_16
> loci-tools revision 5626
>
> code:
> private ImagePlus openWithLOCI(String fName){
> ImagePlusReader r = new ImagePlusReader(new
> ChannelSeparator(ImagePlusReader.makeImageReader()));
> try {
> r.setId(fName);
> IJ.showStatus("opening "+fName);
> int num = r.getImageCount();
> int w = r.getSizeX();
> int h = r.getSizeY();
> ImageStack stack = new ImageStack(w,h);
> IJ.showStatus("opening...");
> for (int i=0;i<num;i++){
> IJ.showProgress(i, (num-1));
> ImageProcessor lociIP = r.openProcessors(i)[0];
> stack.addSlice(""+i, lociIP);
> }
> r.close();
> IJ.showStatus("generating ImagePlus");
> ImagePlus lociImp = new ImagePlus(fName,stack);
> IJ.showStatus("");
> return lociImp;
> } catch (FormatException e){
> IJ.error(e.getMessage());
> return null;
> } catch (IOException e){
> IJ.error(e.getMessage());
> return null;
> }
> }
>
Locked
