[ome-users] writing tif in tiles

[David Gault (Staff)]

Hi Felix,

I just wanted to follow and provide some feedback regarding the issue you had reported.
We have been able to reproduce the issue as reported and are currently working towards a solution.
My aim is to have a proposed fix within the next few days.

Thanks again for proving feedback, I will follow up again with you once I have submitted my changes..

With Thanks,
David Gault

> On 15 Oct 2015, at 14:58, MEYENHOFER Felix <felix.meyenhofer at unifr.ch> wrote:
>
> 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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>
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