[ome-users] Read write large tiff

[Erwan Bocher]

Hi Melissa,

Thanks a lot for your answer.
> 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?
Below all metadata from the source image :

  BitsPerPixel = 8
  DimensionOrder = XYCZT
  IsInterleaved = false
  IsRGB = false
  LittleEndian = true
  PixelType = uint8
  Series 0 Name = Nantes_93_lambert2.tif
  SizeC = 3
  SizeT = 1
  SizeX = 4957
  SizeY = 4213
  SizeZ = 1
BitsPerSample = 8
Compression = Uncompressed
ImageLength = 4213
ImageWidth = 4957
Location = /tmp/Nantes_93_lambert2.tif
MetaDataPhotometricInterpretation = RGB
MetaMorph = no
NumberOfChannels = 3
PhotometricInterpretation = RGB
PlanarConfiguration = Planar
SampleFormat = unsigned integer
SamplesPerPixel = 3

------------------------

Title: Nantes_93_lambert2.tif
Width:  4957 pixels
Height:  4213 pixels
Depth:  1 pixels
Voxel size: 1x1x1 pixel
ID: -4
Coordinate origin:  0,0,0
Bits per pixel: 8 (grayscale LUT)
Display range: 0-255
Image: 1/3 (c:1/3 - Nantes_93_lambert2)
   Channels: 3
   Composite mode: "composite"
No Threshold
Magnification: 0.16666666666666666
Uncalibrated
Path: /tmp/Nantes_93_lambert2.tif
No Selection

>
> 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.
By the way I have tested with a single tile in x (equals to the image 
width) and a tile heigth equals to 16 in y.
The result is the same : very large image, pixels shifted...



Erwan
>
> 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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