ome-files 0.1.0

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Todo List

Class ome::files::CoreMetadata
  We may want to consider refactoring the FormatReader getter methods that fill in missing CoreMetadata fields on the fly (getThumbSizeX, getThumbSizeY) to avoid doing so – one alternate approach would be to have this class use getter methods instead of public fields.
Member ome::files::createOMEXMLRoot (const std::string &document)
  Implement model transforms.
Member ome::files::detail::CopySubchannelVisitor::operator() (const T &v)
  Only call setBuffer if the shape and pixel type differ, to allow user control over storage order.
Member ome::files::detail::FormatReader::coreIndex
  Remove use of stateful API which requires use of series switching in const methods.
Member ome::files::detail::FormatReader::getBitsPerPixel () const
  : Move this logic into a CoreMetadata accessor. Why are we modifying coremetadata during an explicitly nonmodifying operation??
Member ome::files::detail::FormatReader::isUsedFile (const boost::filesystem::path &file)
  : Use a set rather than a list?
Member ome::files::detail::FormatReader::openThumbBytes (dimension_size_type plane, VariantPixelBuffer &buf) const
  Implement openThumbBytes. This requires implementing image rescaling/resampling.
Member ome::files::detail::FormatReader::plane
  Remove use of stateful API which requires use of series switching in const methods.
Member ome::files::detail::FormatReader::resolution
  Remove use of stateful API which requires use of series switching in const methods.
Member ome::files::detail::FormatReader::series
  Remove use of stateful API which requires use of series switching in const methods.
Member ome::files::detail::FormatReader::setId (const boost::filesystem::path &id)
  Implement addModuloAlong. Requires bits of MetadataTools OMEXMLServiceImpl.
Member ome::files::FileInfo::reader
  Document factory function to create reader.
Member ome::files::FormatHandler::isThisType (const boost::filesystem::path &name, bool open=true) const =0
  Could this method be static?
Member ome::files::FormatReader::getIndex (dimension_size_type z, dimension_size_type c, dimension_size_type t) const =0

  unify with the pixel buffer dimension indexes.

  Don't use separate values to match the return of getZCTCoords.

Member ome::files::FormatReader::getIndex (dimension_size_type z, dimension_size_type c, dimension_size_type t, dimension_size_type moduloZ, dimension_size_type moduloC, dimension_size_type moduloT) const =0

  unify with the pixel buffer dimension indexes.

  Don't use separate values to match the return of getZCTModuloCoords.

Member ome::files::FormatReader::getPossibleDomains (const std::string &id) const =0
  can this be a reference to static data?
Member ome::files::FormatReader::getRequiredDirectories (const std::vector< std::string > &files) const =0
  This could use a much better explanation, it's not at all clear what the return value means. Is it an index into `files`? Is it an index into the path components? Of which of the files? In which order? From the root or common parent? Is the order of `files` important?
Member ome::files::FormatReader::getZCTCoords (dimension_size_type index) const =0
  unify with the pixel buffer dimension indexes.
Member ome::files::FormatReader::getZCTModuloCoords (dimension_size_type index) const =0
  unify with the pixel buffer dimension indexes.
Member ome::files::FormatReader::isOriginalMetadataPopulated () const =0
  The name of this method is awful.
Member ome::files::FormatReader::isThisType (const uint8_t *begin, const uint8_t *end) const =0
  Could this method be static and/or const?
Member ome::files::FormatReader::isThisType (const uint8_t *begin, std::size_t length) const =0
  Could this method be static and/or const?
Member ome::files::FormatReader::isThisType (std::istream &stream) const =0
  Could this method be static and/or const?
Member ome::files::FormatReader::setCoreIndex (dimension_size_type index) const =0
  Remove use of stateful API which requires use of series switching in const methods.
Member ome::files::FormatReader::setPlane (dimension_size_type plane) const =0
  Remove use of stateful API which requires use of plane switching in const methods.
Member ome::files::FormatReader::setResolution (dimension_size_type resolution) const =0
  Remove use of stateful API which requires use of series switching in const methods.
Member ome::files::FormatReader::setSeries (dimension_size_type series) const =0
  Remove use of stateful API which requires use of series switching in const methods.
Class ome::files::FormatWriter
  Implement saveBytes methods using 2D `Region` with and/or in terms of Boost.MultiArray index ranges.
Member ome::files::FormatWriter::setPlane (dimension_size_type plane) const =0
  Remove use of stateful API which requires use of plane switching in const methods.
Member ome::files::FormatWriter::setSeries (dimension_size_type series) const =0
  Remove use of stateful API which requires use of series switching in const methods.
Member ome::files::getOriginalMetadata (ome::xml::meta::OMEXMLMetadata &omexml)
  log error
Member ome::files::in::OMETIFFReader::close (bool fileOnly=false)
Member ome::files::in::OMETIFFReader::initFile (const boost::filesystem::path &id)
  Log.
Member ome::files::Modulo::size () const
  Use proper rounding (compat function for round(3)).
Member ome::files::out::OMETIFFWriter::originalMetadataRetrieve
  Overriding getMetadataRetrieve will be a cleaner solution, but need to eliminate all direct use of metadataRetrieve in all writers first.
Class ome::files::PixelBuffer< T >
  Add support for subsetting dimensions.
Member ome::files::tiff::FieldBase::readCount () const
  : Check TIFF_VARIABLE/TIFF_VARIABLE2/TIFF_SPP and adjust the return value accordingly.
Member ome::files::tiff::FieldBase::writeCount () const
  : Check TIFF_VARIABLE/TIFF_VARIABLE2/TIFF_SPP and adjust the return value accordingly.
Member ome::files::tiff::getCoreMetadata (const IFD &ifd, CoreMetadata &core)

  EXIF IFDs

  Text stream output for Tag enums.

  Metadata type for PhotometricInterpretation.

  Image orientation (storage order and direction) from ORIENTATION; fix up width and length from orientation.

  Only set if debugging/verbose.

  Only set if debugging/verbose.

  sminsamplevalue

  smaxsamplevalue

  Only set if debugging/verbose.

  JPEG tags

  Text stream output for Tag enums.

  Metadata type for PhotometricInterpretation.

  Image orientation (storage order and direction) from ORIENTATION; fix up width and length from orientation.

  Only set if debugging/verbose.

  Only set if debugging/verbose.

  sminsamplevalue

  smaxsamplevalue

  Only set if debugging/verbose.

  JPEG tags

  Text stream output for Tag enums.

  Metadata type for PhotometricInterpretation.

  Image orientation (storage order and direction) from ORIENTATION; fix up width and length from orientation.

  Only set if debugging/verbose.

  Only set if debugging/verbose.

  sminsamplevalue

  smaxsamplevalue

  Only set if debugging/verbose.

  JPEG tags

Member ome::files::tiff::TIFF::Impl::~Impl ()
  Log the error elsewhere.
Class ome::files::VariantPixelBuffer
  Add support for subsetting dimensions.