[ome-users] question about Bio-Formats.

[Melissa Linkert]

Hi Qi,

> I find in the web you gave me, all the sample is begin by bfopen. Thus, I
> try the code. But it give me some errors as attachment. The warning is
> about memory, do you think the error is also because that? For memory, I
> find we could paste the java.opts file as attachment in matlab root folder
> to increase it. But we are building a GUI by matlab, we want to compile it
> and send to other people. Then other user could only install MATLAB
> Compiler Runtime to run it. I think they will have the same problem. Does
> it possible they paste the java.opts file to their MATLAB Compiler Runtime
> folder to solve the problem.

The error you see is a result of the image size exceeding 2GB; while we
suggest increasing the memory in general (as noted in the warning), this
won't resolve the error.  To resolve the warning, Mathworks has documentation
on using java.opts with MCR:

http://www.mathworks.com/matlabcentral/answers/99448-how-can-i-include-a-java-opts-file-in-my-matlab-compiler-generated-application

To resolve the error though, you will need to open the image in smaller tiles.
This can be done by starting with bfGetReader:

http://www.openmicroscopy.org/site/support/bio-formats5.0/developers/matlab-dev.html#reading-from-an-image-file

and then using bfGetPlane to retrieve a tile.  Using the variables from
above page, that would look something like:

%%%%
imageWidth = reader.getSizeX();
imageHeight = reader.getSizeY();
firstTile = bfGetPlane(reader, 1, 1, 1, 1024, 1024);
lastTile = bfGetPlane(reader, 1, imageWidth - 1023, imageHeight - 1023, 1024, 1024);
%%%%

As noted in bfGetPlane.m, the 5 integer parameters are the plane number,
X and Y coordinates of the upper-left tile corner, and width and height
of the tile.  We do not currently have a good Matlab example of working
with large images, but the corresponding Java example is (ignoring the
lines referencing "writer"):

http://www.openmicroscopy.org/site/support/bio-formats5.0/developers/export.html#converting-large-images

"reader" in this example is the same class as "reader" in the above
Matlab-specific example.

Hopefully that helps, but if you encounter any other problems please let
us know.

Regards,
-Melissa

On Mon, Mar 30, 2015 at 03:03:14PM -0400, Qi Gong wrote:
> Hello Lan,
> 
> I find in the web you gave me, all the sample is begin by bfopen. Thus, I
> try the code. But it give me some errors as attachment. The warning is
> about memory, do you think the error is also because that? For memory, I
> find we could paste the java.opts file as attachment in matlab root folder
> to increase it. But we are building a GUI by matlab, we want to compile it
> and send to other people. Then other user could only install MATLAB
> Compiler Runtime to run it. I think they will have the same problem. Does
> it possible they paste the java.opts file to their MATLAB Compiler Runtime
> folder to solve the problem. Thank you.
> 
> On Mon, Mar 30, 2015 at 11:31 AM, Munro, Ian <i.munro at imperial.ac.uk> wrote:
> 
> > My apologies for mistyping your name.
> >
> > Ian
> >
> >
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> 
> 
> 
> -- 
> mobile phone: 2024060862



> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users