Ignore:
Timestamp:
02/01/08 10:02:55 (12 years ago)
Author:
melissa
Message:

Tweaked reader guide to reflect changes in package structure; added note about subimages. Also updated list of files that we would like.

Location:
trunk/loci/formats/doc
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • trunk/loci/formats/doc/reader-guide.txt

    r2938 r3591  
    2424  is non-null. 
    2525 
    26 byte[] openBytes(int) throws FormatException, IOException : 
    27   Returns a byte array containing the pixel data for the specified image from 
    28   the given file.  Should throw a FormatException if the image number is invalid 
    29   (less than 0 or >= the number of images).  The ordering of the array 
    30   returned by openBytes should correspond to the values returned by 
     26byte[] openBytes(int, byte[], int, int, int, int) throws FormatException, IOException : 
     27  Returns a byte array containing the pixel data for a subimage specified 
     28  image from the given file.  The dimensions of the subimage (upper left X 
     29  coordinate, upper left Y coordinate, width, and height) are specified in the 
     30  final four int parameters.  This should throw a FormatException if the image 
     31  number is invalid (less than 0 or >= the number of images).  The ordering of 
     32  the array returned by openBytes should correspond to the values returned by 
    3133  isLittleEndian() and isInterleaved().  Also, the length of the 
    3234  byte array should be [image width * image height * bytes per pixel].  Extra 
    33   bytes will generally be truncated. It is recommended that the first line of  
    34   this method be "FormatTools.asserId(currentId, true, 1)" - this ensures that  
     35  bytes will generally be truncated. It is recommended that the first line of 
     36  this method be "FormatTools.assertId(currentId, true, 1)" - this ensures that 
    3537  the file name is non-null. 
    3638 
    37 BufferedImage openImage(int) throws FormatException, IOException : 
     39BufferedImage openImage(int, int, int, int, int) throws FormatException, IOException : 
    3840  Basically the same as openBytes, but returns a java.awt.image.BufferedImage 
    3941  instead of a byte array.  In general, the easiest way to implement this is 
     
    116118 
    117119- Several common image compression types are supported through subclasses of 
    118   loci.formats.BaseCompressor.  These include LZW, LZO, Base64, ZIP and 
     120  loci.formats.BaseCompressor.  These include JPEG, LZW, LZO, Base64, ZIP and 
    119121  RLE (PackBits). 
    120122 
     
    122124 
    123125- If you wish to convert a file's metadata to OME-XML (strongly encouraged), 
    124   loci.formats.ome.OMEXMLMetadataStore provides methods for creating OME-XML 
    125   from metadata values.  Note that OMEXMLMetadataStore is a subclass of 
    126   loci.formats.MetadataStore (every subclass of FormatReader keeps an instance 
    127   of MetadataStore by default); so to add OME-XML support is as simple as 
    128   calling getMetadataStore() on a format reader instance, and then 
    129   calling the appropriate "set" methods as documented in OMEXMLMetadataStore. 
     126  please see metadata-guide.txt further information. 
    130127 
    131128- Utility methods for reading and writing individual bits from a byte array 
    132   can be found in loci.formats.BitBuffer and loci.formats.BitWriter 
     129  can be found in loci.formats.codec.BitBuffer and loci.formats.codec.BitWriter 
    133130 
    134131- Once you have written your file format reader, add a line to the readers.txt 
     
    140137 
    141138- The easiest way to test your new reader is by calling "java 
    142   loci.formats.ImageReader <file name>".  If all goes well, you should see 
     139  loci.formats.tools.ImageInfo <file name>".  If all goes well, you should see 
    143140  all of the metadata and dimension information, along with a window showing 
    144141  the images in the file.  ImageReader can take additional parameters; a 
     
    163160    -map                Specify file on disk to which name should be mapped. 
    164161 
    165 - If you wish to test using TestNG, loci.formats.test.ReaderTest provides 15  
    166   basic tests that work with all Bio-Formats readers.  See the 
     162- If you wish to test using TestNG, loci.formats.test.ReaderTest provides 
     163  several basic tests that work with all Bio-Formats readers.  See the 
    167164  ReaderTest source code for additional information. 
    168165 
  • trunk/loci/formats/doc/samples-needed.txt

    r3524 r3591  
    33  - T series 
    44  - 16 bit data 
     5 
     6Aperio SVS: 
     7  - any 
    58 
    69AVI: 
     
    912 
    1013BioRad: 
    11   - 16 bit data  
     14  - 16 bit data 
    1215  - 2+ GB files 
    1316 
     
    4447ND2: 
    4548  - any files acquired with most recent NIS Elements 
    46   - multi-Z, multi-T 
    4749 
    48 Olympus CellR: 
     50Olympus CellR (APL): 
    4951  - any 
    5052 
     
    6264    interpretation type 
    6365  - BigTIFF files 
     66  - anything compressed with Group 3 fax, Group 4 fax, or JPEG2000 
    6467 
    6568Visitech XYS: 
     
    7679    used 
    7780 
    78 Zeiss LSM: 
    79   - anything compressed with an algorithm other than LZW 
    80  
    8181Zeiss ZVI: 
    8282  - JPEG compressed 
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