source: trunk @ 6687

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Diff Rev Age Author Log Message
(edit) @6687   10 years melissa Fixed channel data is parsed from Leica LIF files that have had one or …
(edit) @6686   10 years curtis Fix up test targets in Ant build scripts.
(edit) @6684   10 years melissa Updated what's new and switch trunk component version numbers to 5.0-DEV.
(edit) @6682   10 years curtis Add a flag to disable tests with special requirements. All tests now pass.
(edit) @6681   10 years melissa Only populate Objective.NominalMagnification if the magnification is …
(edit) @6679   10 years curtis Better handling of 5+ channel data.
(edit) @6676   10 years curtis Fix bug with dimensional extents between multiple series.
(edit) @6675   10 years curtis Fix some Eclipse warnings.
(edit) @6674   10 years melissa Fixed how Images are removed from a MetadataStore when exporting one …
(edit) @6673   10 years curtis Better error handling when constructing base reader object.
(edit) @6672   10 years curtis Fix typo.
(edit) @6671   10 years curtis Define some constants for FakeReader defaults.
(edit) @6670   10 years curtis Use native line endings for Bio-Formats C++ source code.
(edit) @6668   10 years curtis Fix autoscaling bugs, and rework autoscaling tests.
(edit) @6667   10 years melissa * Updated undeclared namespace stripping logic to look for namespaces in …
(edit) @6666   10 years melissa Catch NullPointerException when attempting to parse OME-XML comments.
(edit) @6665   10 years melissa Only overwrite the dimensions if the new values are sane.
(edit) @6664   10 years melissa OMETiffReader.isThisType now checks whether or not the OME-XML block can …
(edit) @6662   10 years melissa Removed some obsolete hacks that prevented physical sizes from being …
(edit) @6661   10 years melissa Better physical X/Y size parsing.
(edit) @6660   10 years curtis Remove unnecessary thumbnail autoscaling logic.
(edit) @6659   10 years curtis Disable 'Record modifications to virtual stack' option (broken anyway).
(edit) @6658   10 years curtis Fix problem with virtual stack pixel types.
(edit) @6657   10 years curtis Use 'uncalibrated' values for CompositeImage min/max.
(edit) @6656   10 years curtis If TimeIncrement is missing, average DeltaT values for ImageJ time …
(edit) @6655   10 years melissa Added MetadataLevel.NO_OVERLAYS, and updated readers accordingly.
(edit) @6654   10 years curtis Progress on Bio-Formats Importer: * Readd support for Ext.openImage and …
(edit) @6653   10 years callan Move reference handling until after attribute population for FilterSet …
(edit) @6652   10 years callan Re-run of code generation. ( ome-xml:r649)
(edit) @6651   10 years callan Handle class cast exceptions in ROI shape transformation.
(edit) @6650   10 years callan Handle namespace prefixes on nodes during parsing of the DOM.
(edit) @6649   10 years callan Re-run of code generation; laser pumps can be any light source. …
(edit) @6648   10 years melissa Remove any BinData elements from the OME-XML before it is written to the …
(edit) @6647   10 years callan Messed up logging by having an old version of the enum handler template, …
(edit) @6646   10 years melissa Updated schema location to 2010-06.
(edit) @6645   10 years melissa Fixed Objective parsing when Immersion and Correction are reversed.
(edit) @6644   10 years callan Re-run of code generation; DRY as a possible value for AIR immersion. …
(edit) @6643   10 years curtis Fix Jace paths to work pre-r46, with commented out code for r46+. Add …
(edit) @6642   10 years curtis Update ome-xml.h to reflect r6631.
(edit) @6641   10 years curtis Update paths to work with new Jace path structure (r52+).
(edit) @6640   10 years bdezonia minor edits. did change maxPixel calc for UINT32.
(edit) @6639   10 years curtis Update autoscale test to check CompositeImage LUT ranges.
(edit) @6638   10 years curtis Enable toggling of debug print statements using DEBUG flag.
(edit) @6637   10 years bdezonia minor edits
(edit) @6636   10 years bdezonia added UINT16 support to all colorTests. added back all virtual modes to …
(edit) @6635   10 years melissa Be more thorough when searching for the .dv file that matches a .log or …
(edit) @6634   10 years bdezonia datasetGroupFiles() improved. Constants fixed for correct style.
(edit) @6633   10 years bdezonia fixed lut testing in testColorCustom. enhanced testColorComposite to …
(edit) @6632   10 years melissa Re-run of code generation ( ome-xml:r646), closes #512.
(edit) @6631   10 years melissa Removed obsolete OME-XML model objects.
(edit) @6630   10 years callan Set fill color as well as stroke color for mask ROI.
(edit) @6629   10 years callan Fix shape indexes for ellipse X and Y radii.
(edit) @6628   10 years callan Utilize the shape label rather than a seperate text shape for MIAS ROI.
(edit) @6627   10 years melissa Switched TiffParser logging from 'debug' to 'trace'; see #512.
(edit) @6625   10 years curtis Fix autoscaling problem with >8-bit CompositeImages.
(edit) @6624   10 years curtis Remove obsolete constant from bf-cpp conflicts list.
(edit) @6623   10 years bdezonia make flesh for the color tests. remove unfinished tests. comment out some …
(edit) @6622   10 years melissa Ensure that xmlns:ome elements are preserved during transformation.
(edit) @6621   10 years melissa Merged r6614 and r6615 into trunk.
(edit) @6620   10 years bdezonia some work on composite testing and some code on dimension swapping tests. …
(edit) @6619   10 years melissa Updated stylesheets to  ome-xml:r645.
(edit) @6618   10 years callan Restoring MIAS reader overlay support.
(edit) @6617   10 years callan Support for TagAnnotation and TermAnnotation conversion.
(edit) @6616   10 years callan Re-run of code generation; support for mask bin data. ( ome-xml:r644)
(edit) @6612   10 years melissa Fixed parsing of large OME-XML files and pre-2010-04 files with …
(edit) @6610   10 years curtis Change default stack order to XYCZT, to match Hyperstack view option.
(edit) @6609   10 years curtis Fix bug in 'Metadata only' stack view option.
(edit) @6607   10 years curtis Fix plane ordering bug with channel separator when effectiveSizeC>1, …
(edit) @6606   10 years curtis Fix bug with fake data generation when rgbChannelCount>1.
(edit) @6604   10 years curtis Readd "Standard ImageJ" stack view option. Note that non-hyperstacks …
(edit) @6603   10 years curtis Cosmetic tweaks.
(edit) @6602   10 years melissa Throw a nicer exception if LuraWaveServiceImpl is instantiated with …
(edit) @6601   10 years melissa Added 'unknown' domain and updated various readers to use the unknown …
(edit) @6600   10 years melissa Fixed and uncommented most of the AnnotationRef conversion logic (and a …
(edit) @6598   10 years curtis Preserve channel-specific LUTs. Fixes #495 (again).
(edit) @6597   10 years melissa Better XZ/XT scan detection; see  omero:2321.
(edit) @6595   10 years curtis Better error handling when reading thumbnails.
(edit) @6594   10 years bdezonia put most all virtual subcases in place
(edit) @6592   10 years curtis Update required ImageJ version to 1.42+, due to CompositeImage.setLUTs …
(edit) @6591   10 years bdezonia more virtual test code
(edit) @6590   10 years bdezonia Added some virtual testing methods
(edit) @6588   10 years curtis Update copyright notice for LOCI plugins.
(edit) @6587   10 years bdezonia modified comboConcatSplit methods to work with BF's latest changes
(edit) @6585   10 years curtis Update component version numbers from 4.1.1 to 4.2-DEV.
(edit) @6583   10 years curtis Populate version information from Git, where applicable.
(edit) @6582   10 years callan Re-run of code generation; fixes UUID population in OMEXMLMetadataImpl. …
(edit) @6581   10 years curtis Preserve dimensional extents on concatenation.
(edit) @6580   10 years curtis Update color mode documentation a bit.
(edit) @6579   10 years bdezonia more options.setVirtual() support
(edit) @6578   10 years bdezonia started adding code to test everything with VirtualStacks also
(edit) @6576   10 years melissa Added experimental support for an alternate JPEG-2000 compression code.
(edit) @6575   10 years curtis Disable calibration function for INT32, since FloatProcessor is used. Also …
(edit) @6574   10 years bdezonia minor edits. enabled openAllSeries with concatenate in the combo tests.
(edit) @6573   10 years melissa Fixed GZIP pixel data detection for ICS files.
(edit) @6572   10 years bdezonia Fixed the two split timepoints tests to match against modified CZT order
(edit) @6571   10 years curtis Fix indexing bug when reading only a subset of planes.
(edit) @6570   10 years curtis Minor tweaks.
(edit) @6569   10 years melissa Updated C++ headers to reflect changes to ome.xml.* in r6531.
(edit) @6568   10 years melissa Various fixes to OME-XML/OME-TIFF handling, including support for …
(edit) @6567   10 years melissa Fixed how pixels files are found, so that having multiple *.vws files in …
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