10/19/06 14:23:32 (13 years ago)

A few minor edits.

1 edited


  • trunk/loci/formats/getting-started.txt

    r1647 r1653  
    1 Some notes on writing a new file format reader for LOCI Bio-Formats: 
     1              Bio-Formats Getting Started Guide by Melissa Linkert 
     3This document is a brief guide to writing new Bio-Formats file format readers. 
    35All format readers should extend either loci.formats.FormatReader or a reader 
    46in loci.formats.in. 
    6 The following methods must be overridden: 
     8---=== Methods to override ===--- 
    810boolean isThisType(byte[]) :  
    9698usually sufficient to override initFile(String) and isThisType(byte[]). 
    98 A few other useful things: 
     100---=== Other useful things ===--- 
    100102- loci.formats.RandomAccessStream is a hybrid RandomAccessFile/InputStream 
    101103  class that is generally more efficient than either RandomAccessFile or 
    102   InputStream.  It is recommended that you use this for reading binary files. 
     104  InputStream, and implements the DataInput interface. 
     105  It is recommended that you use this for reading binary files. 
    104107- loci.formats.DataTools provides a number of methods for converting bytes to 
    105108  shorts, ints, longs, etc.  It also supports reading most primitive types 
    106   directly from a RandomAccessStream. 
     109  directly from a RandomAccessStream (or other DataInput implementation). 
    108111- loci.formats.ImageTools provides several methods for manipulating 
    133136- Once you have written your file format reader, add a line to the readers.txt 
    134   file with the fully name of the reader, followed by a '#' and the file 
    135   extensions associated with the file format. 
     137  file with the fully qualified name of the reader, followed by a '#' and the 
     138  file extensions associated with the file format. Note that ImageReader, 
     139  the master file format reader, tries to identify which format reader to use 
     140  according to the order given in readers.txt, so be sure to place your reader 
     141  in an appropriate position within the list. 
    137143- The easiest way to test your new reader is by calling "java 
    151157    -stitch             Open all files with a similar name. 
    152158    -separate           Force RGB images to be split into separate channels. 
    153     -ignore             Intepret indexed color images as grayscale. 
     159    -nocolors           Intepret indexed color images as grayscale. 
    154160    -omexml             Output the OME-XML for the file. 
    155161    -range              Specify a range of images to open. 
    161167  straightforward one).  loci.formats.in.LIFReader and ZeissZVIReader are also 
    162168  good references that show off some of the nicer features of Bio-Formats. 
     170If you have questions about Bio-Formats, please contact: 
     171  Curtis Rueden <ctrueden@wisc.edu> 
     172  Melissa Linkert <linkert@wisc.edu> 
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