Create customized sidebar block with Downloads & Licensing links #242
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setSeries and getSeries work by using coreIndex to compute the correct value (replaces series), while getCoreIndex and setCoreIndex use the coreIndex directly. Readers using series directly have been fixed to use getSeries. toSeries and toCoreIndex methods convert between series and core index numbers, and handle resolution flattening. All functions dealing with series numbering use these to handle conversion.
Allow use of both the http://www.leica-microsystems.com/scn/2010/03/10 and http://www.leica-microsystems.com/scn/2010/10/01 schemas. - In order to handle both schemas identically, the pixels element sizeR/sizeZ/sizeC/firstIFD attributes are no longer parsed; instead the sizes for R, Z and C are computed from the dimensions elements. We do require that the dimensions are a non-sparse array. - Fix data order as XYCZT (this matches the existing test cases). - Thumbnails: + Correct IFD mapping for thumbnails + Get thumbnail size from correct image + Use flattened resolutions when getting thumbnails
Warn if the schema is unsupported, but otherwise try to read it.
This required adding toSeries and toCoreIndex to IFormatReader (and hence ImageReader).
Subresolutions are not supported. This removes the need for series ↔ coreIndex conversion, since they are always the same.
These override the ReaderWrapper implementation, and return their argument (since subresolutions are not supported).
This enables getSeries to be O(1) in addition to coreIndex. seriesToCoreIndex and coreIndexToSeries are also O(1) when the current series/coreIndex matches their arguments. FileStitcher also has a series member, but this is currently unused; it was added purely to match the FormatReader behaviour.
The existing constructor using a reader and series number has two problems: - it's unsuitable when using non-flattened resolutions since one can't directly specify the subresolution - getSeriesCount will fail if the core[] array is not yet fully initialised, making this unusable when using during initialisation and strictly validating core[] Here, a new (simple) copy contructor that does a simple copy of the CoreMetadata is provided, and this is used directly in all readers. This is safe since they are copying their own metadata, so avoiding the reader interface is not a problem here. We also update the existing constructor to use a core index instead of series, so that it will work for all readers, whether flat or nonflat, and internally we use setCoreIndex and getCoreIndex.
Fixes #9627. See also: http://www.libpng.org/pub/mng/spec/jng.html
Noticed while looking for a dataset that contains masks.
Fixes Fiji ome#518.
Reported by Olivier Burri.
This is a continuation of what 5e5e99b was trying to accomplish.
Conflicts: ant/toplevel.xml components/legacy/ome-editor/build.properties components/legacy/ome-editor/pom.xml components/legacy/ome-notes/build.properties components/legacy/ome-notes/pom.xml
Conflicts: components/scifio/src/loci/formats/UpgradeChecker.java
The test expects the next-to-last defined URL to be invalid.
…develop Yet another build fix (develop)
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Temporarily closing since final layout is still undecide (see comments of #236 vs ome/omero-documentation#150) |
Hiding header and menu when printing
Improve OMEXMLMetadata
CoreMetadata: Simplify copying and cloning
Zeiss CZI: parse Z positions from XML
Fixes for pyramid TIFF reading
Broken links
Remove legacy ome-editor and ome-notes
Convert README to Markdown
A couple of minor documentation tweaks
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Oct 11, 2013
Begin improving DSL section
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Same as #236 rebased onto
origin/develop