[ome-users] Read write large tiff

[Erwan Bocher]

Dear,

I want to read, process and write a big tiff with the bioformats lib. I 
use the code proposed on the official wiki that permits to read data 
block by block. The code runs without any errors but the result image
is wrong. Pixel values are shifted and the total size of the image is 
huge (original image 93 mo :  result image more than 600 mo).

Thanks for any advice you could give!

Greetings.


                // create a reader that will automatically handle any 
supported format
                 IFormatReader reader = new ImageReader();
                 // tell the reader where to store the metadata from the 
dataset
                 
reader.setMetadataStore(MetadataTools.createOMEXMLMetadata());
                 // initialize the dataset
                 reader.setId(path);

                 // create a writer that will automatically handle any 
supported output format
                 IFormatWriter writer = new ImageWriter();
                 // give the writer a MetadataRetrieve object, which 
encapsulates all of the
                 // dimension information for the dataset (among many 
other things)
                 
writer.setMetadataRetrieve(MetadataTools.asRetrieve(reader.getMetadataStore()));
                 // initialize the writer
                 writer.setId("/tmp/test.tif");


                 int tileWidth = 1024;
                 int tileHeight = 1024;

                 System.out.println("Series " + reader.getSeriesCount());
                 for (int series = 0; series < reader.getSeriesCount(); 
series++) {
                         reader.setSeries(series);
                         writer.setSeries(series);
                         // determine how many tiles are in each image 
plane
                         // for simplicity, we'll assume that the image 
width and height are multiples of 1024
                         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++) {
                                                 // open a tile - in 
addition to the image index, we need to specify
                                                 // the (x, y) 
coordinate of the upper left corner of the tile, along with the
                                                 // width and height of 
the tile
                                                 byte[] tile = 
reader.openBytes(image, col * tileWidth, row * tileHeight, tileWidth, 
tileHeight);
                                                 writer.saveBytes(image, 
tile, col * tileWidth, row * tileHeight, tileWidth, tileHeight);
                                         }
                                 }
                         }
                 }

                 reader.close();
                 writer.close();