Ignore:
Timestamp:
12/20/07 12:43:09 (12 years ago)
Author:
melissa
Message:

Added notes on multi-series support and ChannelFiller; added OME-TIFF to list of formats that can be written.

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/loci/formats/doc/using-bioformats.txt

    r3118 r3492  
    2828 
    2929Prior to retrieving pixels or metadata, it is necessary to call setId(String) 
    30 on the reader instance, passing in the name of the file to read. 
     30on the reader instance, passing in the name of the file to read.  Some formats 
     31allow multiple series (5D image stacks) per file; in this case you may wish to 
     32call setSeries(int) to change which series is being read. 
    3133 
    3234Raw pixels are always retrieved one plane at a time.  Planes can be returned 
     
    4446- image width (getSizeX()) 
    4547- image height (getSizeY()) 
    46 - total number of images per file (getImageCount()) 
    47 - number of slices per file (getSizeZ()) 
    48 - number of timepoints per file (getSizeT()) 
    49 - number of actual channels per file (getSizeC()) 
     48- number of series per file (getSeriesCount()) 
     49- total number of images per series (getImageCount()) 
     50- number of slices in the current series (getSizeZ()) 
     51- number of timepoints in the current series (getSizeT()) 
     52- number of actual channels in the current series (getSizeC()) 
    5053- number of channels per image (getRGBChannelCount()) 
    51 - the ordering of the images within the file (getDimensionOrder()) 
     54- the ordering of the images within the current series (getDimensionOrder()) 
    5255- whether each image is RGB (isRGB()) 
    53 - whether the pixel bytes in little-endian order (isLittleEndian()) 
     56- whether the pixel bytes are in little-endian order (isLittleEndian()) 
    5457- whether the channels in an image are interleaved (isInterleaved()) 
    5558- the type of pixel data in this file (getPixelType()) 
     
    8790  + ChannelMerger extends IFormatReader, and merges grayscale 
    8891    images to RGB if the number of channels is greater than 1. 
     92  + ChannelFiller extends IFormatReader, and converts indexed color images to 
     93    RGB images. 
    8994  + MinMaxCalculator extends IFormatReader, and provides an API 
    9095    for retrieving the minimum and maximum pixel values for each channel. 
     
    102107 
    103108- TIFF (uncompressed or LZW) 
     109- OME-TIFF (uncompressed or LZW) 
    104110- JPEG 
    105111- PNG 
     
    119125file. 
    120126 
    121 A word of warning: IFormatWriter.saveImage(Image, boolean) accepts  
     127A word of warning: IFormatWriter.saveImage(Image, boolean) accepts 
    122128generic java.awt.Images, and converts them to a BufferedImage under the hood. 
    123129The problem is that not all formats support all types of data (e.g. JPEG 
Note: See TracChangeset for help on using the changeset viewer.