Adding format/reader documentation pages

Documentation pages for the supported formats and readers are auto-generated during the build. This page explains how to amend/extend this part of the Bio-Formats documentation.

Formats

The supported formats pages are generated as part of the documentation build using maven. The metadata for each format is contained in format-pages.txt and the build generates a reStructuredText file for each format as well as an index page for all supported formats using Velocity.

The format-pages.txt is an INI file where each section corresponds to a particular format given by the section header. Multiple key/values should be defined for each section:

pagename
The name of the output reStructuredText file. If unspecified, the section header will be used to generate the filename.
extensions
The list of extensions supported for the format
owner
The owner of the file format
developer
The developer of the file format
bsd
A yes/no flag specifying whether the format readers/writers are under the BSD license
versions
A comma-separated list of all versions supported for this format
weHave
A bullet-point list describing the supporting material we have for this format including specification and sample datasets
weWant
A bullet-point list describing the supporting material we would like to have for this format
pixelRating
metadataRating
opennessRating
presenceRating
utilityRating

See Ratings legend and definitions. Available choices are: Poor, Fair, Good, Very Good, Outstanding. The metadataRating should be set as follows:

  • base metadataRating is the smaller of opennessRating and pixelsRating
  • increment metadataRating by 1 if any combination of Instrument.ID plus Image.InstrumentRef, or Channel.EmissionWavelength, or Channel.ExcitationWavelength are supported
  • increment metadataRating by 1 if any SPW metadata is supported or pyramid is yes
reader
A string or a comma-separated list of all readers for this format
mif
set to true if the format can store multiple Images (in OME-XML terminology) or series (in Bio-Formats API terminology)
pyramid
set to yes if the format can store a single image at multiple resolutions
notes
Additional relevant information e.g. that we cannot distribute specification documents to third parties
options
A link to additional reader and writer options documentation where they are available for the format

Dataset structure table

The summary table listing the extensions for each reader is generated by the build process reading their extensions and descriptions from all Bio-Formats readers (BSD and GPL). A reStructuredText file with a table summary of all file extensions is created.

Readers

The metadata pages for each reader are generated by the build process parsing their metadata support from all Bio-Formats readers (BSD and GPL). An intermediate meta-support.txt file is created which is then converted into one reStructuredText page for each reader as well as a metadata summary reStructuredText file using Velocity.