[ome-users] writing tif in tiles

[MEYENHOFER Felix]

Hi

I just run it with 5.1.5 and this did not fix the tile problem as described here bellow.

Felix

> On 13 Oct 2015, at 16:38 , MEYENHOFER Felix <felix.meyenhofer at unifr.ch> wrote:
> 
> Hi 
> 
> I recently bumped the bio-formats versions up to 5.1.4 And observed some weird behaviour when writing tiles in my plugins. To analyse what what happens during the writing process I took the code from
> http://www.openmicroscopy.org/site/support/bio-formats5.1/developers/export.html
> 
> public class BioFormatTest {
> 
>    public static void main(String[] args) throws DependencyException, ServiceException, IOException, FormatException {
>        MetadataStore metadata;
>        ServiceFactory factory = new ServiceFactory();
>        OMEXMLService service = factory.getInstance(OMEXMLService.class);
>        metadata = service.createOMEXMLMetadata();
> 
>        IFormatReader reader = new ImageReader();
>        reader.setMetadataStore(metadata);
>        // Take the  from File > Open Samples > Fluorescent Cells (collapse the colors or extract one and save as tif)
>        reader.setId("");
>        reader.setSeries(0);
> 
>        // create a writer that will automatically handle any supported output format
>        IFormatWriter writer = new ImageWriter();
>        writer.setMetadataRetrieve((MetadataRetrieve)reader.getMetadataStore());
>        writer.setId("/Users/turf/Desktop/mb/bftest/test.ome.tif");
> 
>        int tileWidth = reader.getSizeX() /2;
>        int tileHeight = reader.getSizeY() /2;
> 
>        int tileRows = reader.getSizeY() / tileHeight;
>        int tileColumns = reader.getSizeX() / tileWidth;
> 
>        for (int image=0; image<reader.getImageCount(); image++) {
>            for (int row=0; row<tileRows; row++) {
>                for (int col=0; col<tileColumns; col++) {
>                    int xCoordinate = col * tileWidth;
>                    int yCoordinate = row * tileHeight;
>                    byte[] tile = reader.openBytes(image, xCoordinate, yCoordinate, tileWidth, tileHeight);
>                    writer.saveBytes(image, tile, xCoordinate, yCoordinate, tileWidth, tileHeight);
>                }
>            }
>        }
> 
>        reader.close();
>        writer.close();
>    }
> }
> 
> The result looks like this
> https://drive.switch.ch/public.php?service=files&t=eb9e1fdcdd3e0d9eeeeba4ca66f941cd
> https://drive.switch.ch/public.php?service=files&t=0ae325e0327c551b8a668392c1e86f08
> 
> So it seems like only the last column is written out independent of the number of tiles I choose. Am I missing something, or is this a bug?
> 
> Best,
> 
> Felix
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