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Timestamp:
02/22/07 16:56:17 (13 years ago)
Author:
curtis
Message:

Some documentation updates.

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  • trunk/loci/formats/reader-guide.txt

    r2292 r2319  
    1               Bio-Formats Getting Started Guide by Melissa Linkert 
     1            Bio-Formats File Format Reader Guide by Melissa Linkert 
    22 
    33This document is a brief guide to writing new Bio-Formats file format readers. 
     
    88---=== Methods to override ===--- 
    99 
    10 boolean isThisType(byte[]) :  
     10boolean isThisType(byte[]) : 
    1111  Check the first few bytes of a file to determine if the file can be read by 
    1212  this reader.  You can assume that the first byte of the array corresponds to 
     
    2929  is different from the file's native ordering.  If the pixel data is 
    3030  guaranteed to have 8 bits per pixel, then isLittleEndian can return 
    31   anything. This method should begin by checking if the given argument is equal  
     31  anything. This method should begin by checking if the given argument is equal 
    3232  to the current file; if not, initFile(String) should be called (see below). 
    3333 
     
    3737  planes are RGB, and the pixel data is stored as "RRR...GGG...BBB", then 
    3838  return false.  Otherwise, if the pixel data is stored as "RGBRGBRGB..." 
    39   return true.  This method should begin by checking if the given argument  
    40   is equal to the current file; if not, initFile(String) should be called  
     39  return true.  This method should begin by checking if the given argument 
     40  is equal to the current file; if not, initFile(String) should be called 
    4141  (see below). 
    4242 
     
    105105    int sizeT[0] : number of planes along T axis (set to 1 if there are none) 
    106106    String currentOrder[0] : the dimension ordering of the planes 
    107     int pixelType[0] : corresponds to the number of bytes per pixel; see  
     107    int pixelType[0] : corresponds to the number of bytes per pixel; see 
    108108                       constant values in FormatReader for a list of valid 
    109109                       values 
     
    133133  protected void initFile(String id) throws FormatException, IOException { 
    134134    super.initFile(id); 
    135      
     135 
    136136    RandomAccessStream in = new RandomAccessStream(id); 
    137137    // alternatively, 
     
    153153  It is recommended that you use this for reading binary files. 
    154154 
    155 - loci.formats.Location provides an API similar to java.io.File, and supports  
    156   File-like operations on URLs.  It is highly recommended that you use this  
     155- loci.formats.Location provides an API similar to java.io.File, and supports 
     156  File-like operations on URLs.  It is highly recommended that you use this 
    157157  instead of File.  See the javadoc for additional information. 
    158158 
     
    167167  information. 
    168168 
    169 - If your reader relies on third-party code which may not be available to all  
     169- If your reader relies on third-party code which may not be available to all 
    170170  users, it is strongly suggested that you access this code only through a 
    171171  loci.formats.ReflectedUniverse object.  For an example of how this works, 
     
    173173 
    174174- Several common image compression types are supported through subclasses of 
    175   loci.formats.BaseCompressor.  These include LZW, LZO, Base64, ZIP and  
     175  loci.formats.BaseCompressor.  These include LZW, LZO, Base64, ZIP and 
    176176  RLE (PackBits). 
    177177 
     
    180180- If you wish to convert a file's metadata to OME-XML (strongly encouraged), 
    181181  loci.formats.OMEXMLMetadataStore provides methods for creating OME-XML from 
    182   metadata values.  Note that OMEXMLMetadataStore is a subclass of  
     182  metadata values.  Note that OMEXMLMetadataStore is a subclass of 
    183183  loci.formats.MetadataStore (every subclass of FormatReader keeps an instance 
    184184  of MetadataStore by default); so to add OME-XML support is as simple as 
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