[ome-users] Read write large tiff

[Melissa Linkert]

Hi Erwan,

> 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).

What are the dimensions of the original file (X, Y, and number of
planes)?  Is the original image data compressed?

I would guess that the tile dimensions in the code need to be adjusted
(as alluded to on the wiki page), but without knowing the specifics of
the input file it's a little tricky to say for sure.

Regards,
-Melissa

On Tue, May 29, 2012 at 01:30:34PM +0200, Erwan Bocher wrote:
> 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();
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