12/03/09 09:24:43 (10 years ago)

Updated documentation and what's new for today's release.

1 edited


  • branches/4.1/components/bio-formats/doc/reader-guide.txt

    r5059 r5727  
    1515  not (or if there is no way of checking). 
    17 String[] getUsedFiles() throws FormatException, IOException : 
     17String[] getSeriesUsedFiles() throws FormatException, IOException : 
    1818  You only need to override this if your format uses multiple files in a single 
    1919  dataset.  This method should return a list of all the files associated with 
    20   the given file name (i.e. every file needed to display the current dataset). 
     20  the given file name and the current series (i.e. every file needed to display 
     21  the current series). 
    2122  For an example of how this works, see loci.formats.in.PerkinElmerReader. 
    2223  It is recommended that the first line of this method be 
    3637  this method be "FormatTools.assertId(currentId, true, 1)" - this ensures that 
    3738  the file name is non-null. 
    39 BufferedImage openImage(int, int, int, int, int) throws FormatException, IOException : 
    40   Basically the same as openBytes, but returns a java.awt.image.BufferedImage 
    41   instead of a byte array.  In general, the easiest way to implement this is 
    42   by getting the corresponding byte array from openBytes, then returning 
    43   loci.formats.ImageTools.makeImage(byte[], int width, int height, int 
    44   numberOfChannels, boolean isInterleaved, int bytesPerPixel, boolean 
    45   isLittleEndian). It is recommended that the first line of this method be 
    46   "FormatTools.assertId(currentId, true, 1)" - this ensures that the file name 
    47   is non-null. 
    4940protected void initFile(String) throws FormatException, IOException : 
    10293  instead of File.  See the javadoc for additional information. 
    104 - loci.formats.DataTools provides a number of methods for converting bytes to 
     95- loci.common.DataTools provides a number of methods for converting bytes to 
    10596  shorts, ints, longs, etc.  It also supports reading most primitive types 
    10697  directly from a RandomAccessInputStream (or other DataInput implementation). 
    10899- loci.formats.ImageTools provides several methods for manipulating 
    109   java.awt.image.BufferedImage objects.  In particular, it can create 
    110   BufferedImages from primitive type arrays, resize images, split RGB images 
    111   into 3 grayscale images, and so on.  Consult the source or javadoc for more 
    112   information. 
     100  primitive type arrays that represent images. Consult the source or javadoc 
     101  for more information. 
    114103- If your reader relies on third-party code which may not be available to all 
    115104  users, it is strongly suggested that you access this code only through a 
    116   loci.formats.ReflectedUniverse object.  For an example of how this works, 
    117   see loci.formats.in.ZeissZVIReader. 
     105  loci.common.ReflectedUniverse object.  For an example of how this works, 
     106  see loci.formats.POITools. 
    119108- Several common image compression types are supported through subclasses of 
    120   loci.formats.BaseCompressor.  These include JPEG, LZW, LZO, Base64, ZIP and 
     109  loci.formats.codec.BaseCodec.  These include JPEG, LZW, LZO, Base64, ZIP and 
    121110  RLE (PackBits). 
    160149    -map                Specify file on disk to which name should be mapped. 
    162 - If you wish to test using TestNG, loci.formats.test.ReaderTest provides 
     151- If you wish to test using TestNG, loci.tests.testng.FormatReaderTest provides 
    163152  several basic tests that work with all Bio-Formats readers.  See the 
    164   ReaderTest source code for additional information. 
     153  FormatReaderTest source code for additional information. 
    166155- For more details, please look at the source code and javadocs.  Studying 
    167156  existing readers is probably the best way to get a feel for the API; I would 
    168157  recommend first looking at loci.formats.in.ImarisReader (this is the most 
    169   straightforward one).  loci.formats.in.LIFReader and ZeissZVIReader are also 
     158  straightforward one).  loci.formats.in.LIFReader and InCellReader are also 
    170159  good references that show off some of the nicer features of Bio-Formats. 
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