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PrairieView 5.2 fixes and improvements #1365

Merged
merged 10 commits into from
Dec 6, 2014
Merged

PrairieView 5.2 fixes and improvements #1365

merged 10 commits into from
Dec 6, 2014

Commits on Dec 3, 2014

  1. PrairieReader: remove unused import

    @ctrueden
    ctrueden committed Dec 3, 2014
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  2. PrairieMetadata: fix critical errors 

    This change fixes several metadata parsing bugs:

1) The relevant XML element is called "SubindexedValue", not
   "SubindexValue". Without this change, subindexed values are never
   read correctly, so e.g. X/Y/Z stage positions are not parsed.

2) The loop variable for subindexed values is "s", not "i".
   Without this change, an NPE is typically thrown during the
   SubindexedValues parsing loop.

3) Subindexed value table should be indexed on subindex, not index.

4) Parsing of subindexed values from old-style XML (<Key> elements)
   did not add the parsed subindexed value table to the data structure.
    @ctrueden
    ctrueden committed Dec 3, 2014
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  3. Add unit tests for PrairieMetadata 

    These tests are by no means complete, but do provide regression tests
for the bugs fixed in the previous commit.
    @ctrueden
    ctrueden committed Dec 3, 2014
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  4. OMETiffReader: remove unused import

    @ctrueden
    ctrueden committed Dec 3, 2014
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  5. OMETiffReader: support BinaryOnly OME-TIFF refs 

    This commit changes the behavior of the OME-TIFF reader to support
extraction of OME-XML metadata from an OME-TIFF reference via the
BinaryOnly MetadataFile attribute.

According to a38bd07, the BinaryOnly
MetadataFile is only supposed to reference an OME-XML document, not an
OME-TIFF file containing an embedded OME-XML document.

But according to the OME-TIFF specification [1], it is valid to
reference such an OME-TIFF.

Since supporting it is easy and very useful and already documented,
let's go ahead and do it!

[1] https://www.openmicroscopy.org/site/support/ome-model/ome-tiff/specification.html#storing-partial-metadata-blocks
    @ctrueden
    ctrueden committed Dec 3, 2014
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  6. PrairieMetadata: clarify method purpose in javadoc

    @ctrueden
    ctrueden committed Dec 3, 2014
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  7. PrairieMetadata: add API to access wavelengths

    @ctrueden
    ctrueden committed Dec 3, 2014
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  8. PrairieReader: populate emission wavelengths 

    The Prairie XML records the channel emission wavelengths, so
let's populate the OME-XML with that information as appropriate.
    @ctrueden
    ctrueden committed Dec 3, 2014
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  9. PrairieMetadata: activate all used channels 

    This makes spectral PrairieView datasets work as expected.

Previously, the reader only activated channels specifically flagged as
active in the Prairie configuration metadata. This was fragile for two
reasons:

1) The Prairie configuration metadata is subject to change
   (and in fact did change once already, from CFG to ENV).

2) PrairieView 5.2 added support for spectral datasets, where the active
   channels metadata no longer accurately reflects the actually active
   channels. Instead, the active channels are meant to be gleaned from
   the "channel" attribute of each <File> element present in the XML
   metadata.

With this change, all channels that are actually used (i.e., which
actually have one or more associated <File> elements) will affect the
final dimensional structure of each Image.
    @ctrueden
    ctrueden committed Dec 3, 2014
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  10. PrairieMetadata: add API to query spectral mode

    @ctrueden
    ctrueden committed Dec 3, 2014
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