Changeset 2568

04/06/07 13:26:13 (13 years ago)

Updated docs to reflect recent changes.

2 edited


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

    r2445 r2568  
    4747  the given file name (i.e. every file needed to display the current dataset). 
    4848  For an example of how this works, see 
    50 Double getChannelGlobalMinimum(String, int) throws FormatException, IOException: 
    51   You only need to override this if your format specifies the minimum value 
    52   for each channel in the metadata.  The int parameter specifies the channel 
    53   for which to return the minimum value. 
    55 Double getChannelGlobalMaximum(String, int) throws FormatException, IOException: 
    56   You only need to override this if your format specifies the maximum value 
    57   for each channel in the metadata.  The int parameter specifies the channel 
    58   for which to return the maximum value. 
    60 boolean isMinMaxPopulated(String) throws FormatException, IOException: 
    61   Only override this if you are also overriding getChannelGlobalMinimum and 
    62   getChannelGlobalMaximum.  In general, return true. 
    6450byte[] openBytes(String, int) throws FormatException, IOException : 
    117103  you should store any relevant metadata. 
    119 static void main(String[]) throws FormatException, IOException : 
    120   Consists of the following line: 
    121     "new <class name>().testRead(args);" 
    123105Note that if the new format is a variant of a format currently supported by 
    124106Bio-Formats, it is more efficient to make the new reader a subclass of the 
    214196    -stitch             Open all files with a similar name. 
    215197    -separate           Force RGB images to be split into separate channels. 
    216     -nocolors           Intepret indexed color images as grayscale. 
    217198    -omexml             Output the OME-XML for the file. 
    218199    -normalize          Normalize floating point images. 
  • trunk/loci/formats/using-bioformats.txt

    r2337 r2568  
    7575  all planes are grayscale - RGB images are split into 3 separate grayscale 
    7676  images. 
    77 - loci.formats.ChannelSeparator extends IFormatReader, and merges grayscale 
     77- loci.formats.ChannelMerger extends IFormatReader, and merges grayscale 
    7878  images to RGB if the number of channels is greater than 1. 
     79- loci.formats.MinMaxCalculator extends IFormatReader, and provides an API 
     80  for retrieving the minimum and maximum pixel values for each channel. 
     81- loci.formats.DimensionSwapper extends IFormatReader, and provides an API 
     82  for changing the dimension order of a file. 
    7983- ImageTools provides a number of methods for manipulating BufferedImages and 
    8084  primitive type arrays.  In particular, there are methods to split and merge 
    130134o IFormatWriter accepts Image objects, and not BufferedImages; yet all writers 
    131135  convert the Image to a BufferedImage.  You can still pass in a 
    132   BufferedImage, but you are free to pass in any Image object (this is mainly 
    133   for compatibility with ImageJ). 
     136  BufferedImage, but you are free to pass in any Image object. 
    135138o All readers have another openBytes method that takes a pre-allocated byte 
    141144  implement, and no one has cared so far.  If you want this method, we can work 
    142145  towards adding it. 
    144 o Leica LEI files sometimes (actually, frequently) don't look right. 
    145   However, there is a sneaky way of getting Bio-Formats to read them correctly: 
    146   call setColorTableIgnored(true) on the reader object.  Why?  Well, the LEI 
    147   file format consists of a "header" file (.lei extension), and a set of TIFF 
    148   files (which contain the actual pixel data).  The LEI acquisition software 
    149   allows the user to specify an "acquisition channel" - in fact, multiple 
    150   acquisition channels can be specified for each dataset.  Then for each 
    151   acquisition channel, a color lookup table is applied to the grayscale data. 
    152   This doesn't sound so bad, but it gets really ugly if half of the TIFF files 
    153   in a dataset had an acquisition channel specified, and half didn't - you get 
    154   alternating RGB and grayscale planes.  Forcing Bio-Formats to ignore the 
    155   color tables means you get all grayscale planes, but the number of channels 
    156   is preserved (so channel merging still works). 
    158147o Importing multi-file formats (Leica LEI, PerkinElmer, FV1000 OIF, ICS, and 
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