source: trunk @ 4775

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Diff Rev Age Author Log Message
(edit) @4775   11 years melissa LIFReader now populates more metadata; closes #340.
(edit) @4774   11 years melissa Fixed InCellReader's timestamps and element references.
(edit) @4773   11 years curtis Fix compile errors.
(edit) @4772   11 years melissa Changed package names of POI fork from org.apache.poi.* to loci.poi.* to …
(edit) @4771   11 years melissa Fixed how exposure times and ND filter settings are parsed from …
(edit) @4770   11 years melissa Added preliminary support for iVision files - most pixel data can be read, …
(edit) @4769   11 years melissa Fixed a couple of metadata population bugs; closes #340.
(edit) @4768   11 years melissa Updated metadata support documentation for MetamorphReader. Also added a …
(edit) @4767   11 years curtis Update to latest Jace snapshot; hopefully fix class version issue.
(edit) @4766   11 years curtis Move Bio-Formats includes into separate header file.
(edit) @4765   11 years melissa Lots of improvements to Metamorph metadata support (see #339).
(edit) @4764   11 years melissa Moved docs out of src/loci/formats.
(edit) @4763   11 years curtis Tweak documentation.
(edit) @4762   11 years melissa Populate Pixels.ID before Image.DefaultPixels.
(edit) @4761   11 years curtis Progress on bfjace. Working on Linux!
(edit) @4760   11 years curtis Progress on Bio-Formats Jace C++ wrapper.
(edit) @4759   11 years melissa Do not adjust pixel values for signed images when a BufferedImage is …
(edit) @4758   11 years melissa Fixed NPE if LogicalChannel.SamplesPerPixel is not populated.
(edit) @4757   11 years melissa Better metadata support for ND2, including correct timestamps.
(edit) @4756   11 years melissa Fixed some MetadataStore population bugs.
(edit) @4755   11 years melissa Catch NumberFormatException when parsing Objective data.
(edit) @4754   11 years melissa Better Objective population.
(edit) @4753   11 years melissa Fixed how rows per strip/strip byte counts mismatch is handled.
(edit) @4752   11 years melissa Fixed Objective IDs.
(edit) @4751   11 years melissa Fixed ArrayIndexOutOfBoundsException.
(edit) @4750   11 years melissa Fixed some OME-XML validation errors.
(edit) @4749   11 years melissa Fixed TiffData population and multi-series OME-TIFF import bug.
(edit) @4748   11 years melissa Fixed some OME-XML validation issues - Image.DefaultPixels is now …
(edit) @4747   11 years melissa Updated metadata documentation.
(edit) @4746   11 years melissa Fixed dimension calculation bugs; closes #346.
(edit) @4745   11 years curtis Some tweaks for Steve: * Output probe details to the log, but only on …
(edit) @4744   11 years melissa Fixed NPE when assigning a custom color to single channel data.
(edit) @4743   11 years melissa Fixed default stack order for the Data Browser.
(edit) @4742   11 years melissa Adjust the number of rows per strip if the original value is greater than …
(edit) @4741   11 years curtis Tweak error message.
(edit) @4740   11 years melissa Fixed plane index bug.
(edit) @4739   11 years melissa Improved metadata population for Leica LEI files; see #340.
(edit) @4738   11 years curtis Add -valid flag for xmlindent to preserve CDATA whitespace.
(edit) @4737   11 years curtis Tweak some out-of-date/misleading documentation.
(edit) @4736   11 years melissa FluoviewReader now expresses multifield data as multiple series; see #332.
(edit) @4735   11 years melissa * Instead of rearranging channels in a LIF file to be in RGB order, apply …
(edit) @4734   11 years curtis Fix dependencies for editor, notes and ijview command line tools.
(edit) @4733   11 years curtis More robust parsing of command line flags.
(edit) @4732   11 years melissa Moved EditTiffG to and added an option to tiffcomment …
(edit) @4731   11 years melissa Minor metadata updates.
(edit) @4730   11 years melissa Added option to specify which colors are used when colorizing; closes …
(edit) @4729   11 years melissa Several additions to the MetadataStore API, including the new ROI model …
(edit) @4728   11 years melissa Added majority of upgrade checking functionality (see #327). Does not yet …
(edit) @4727   11 years melissa Improved OME-XML population for MicroManager; closes #334.
(edit) @4726   11 years melissa Parse the XML comment from TIFF files that are part of a Metamorph .nd …
(edit) @4706   11 years melissa Updated what's new for today's release.
(edit) @4705   11 years melissa Fixed various conversion bugs.
(edit) @4704   11 years curtis Tweak JRE runtime location.
(edit) @4703   11 years melissa Fixed minor metadata parsing bugs.
(edit) @4702   11 years melissa Fix for 16-bit grayscale AVIs; closes #335.
(edit) @4701   11 years curtis Remove redundant -fPIC flag.
(edit) @4700   11 years curtis Link JVM library properly, and add a couple stock Jace examples.
(edit) @4699   11 years curtis Fix some problems with the build script. Still doesn't work 100% though.
(edit) @4698   11 years melissa Link Image and Instrument in MicroManager datasets.
(edit) @4697   11 years curtis * Improve chi2 error only for selected region, if any. * Fix units for …
(edit) @4696   11 years curtis Some initial code for Bio-Formats C++ bindings using Jace. Not yet …
(edit) @4695   11 years gbonamy Fixed populating the metadata for DimensionsPhysicalSizeX, …
(edit) @4694   11 years gbonamy Modification of formating of the error messages
(edit) @4693   11 years curtis Add macro functions for querying plane timings, and add an example macro.
(edit) @4692   11 years melissa Only apply the rescaling function to signed data.
(edit) @4691   11 years melissa Prevent isThisType from throwing a NPE if the file doesn't have a parent …
(edit) @4690   11 years melissa If the .nd file contains a creation date, use it to populate …
(edit) @4689   11 years curtis Increase javadoc memory to 512MB, and fail on error.
(edit) @4688   11 years melissa Fixed problems with displaying signed data.
(edit) @4687   11 years melissa Fixed bug in plane size detection.
(edit) @4686   11 years melissa * Fixed SignedColorModel to better handle two-channel data. * Don't pad …
(edit) @4685   11 years melissa Explicitly close the writer.
(edit) @4684   11 years melissa Parse timestamps.
(edit) @4683   11 years melissa Some improvements to MicroManager metadata support. Still need to parse …
(edit) @4682   11 years melissa * Fixed bug with 16-bit RLE-compressed DICOM files. * Fixed JPEG-2000 …
(edit) @4681   11 years melissa Modified Codec API to be a little more intuitive. The compress and …
(edit) @4680   11 years melissa Fix for > 4 GB LSM files.
(edit) @4679   11 years curtis A little GUI for testing Java memory behavior.
(edit) @4678   11 years melissa Don't close the stream if it is null.
(edit) @4677   12 years melissa Fixed exception when scaling MNG images.
(edit) @4676   12 years curtis Add a second, simpler signature for ImageInfo.testRead().
(edit) @4675   12 years curtis Remove obsolete constant.
(edit) @4674   12 years melissa Instead of assuming that all TIFF files are present in the metadata file, …
(edit) @4673   12 years melissa Fixed a few more bugs exposed by the test suite.
(edit) @4672   12 years melissa If Objective data is present, populate the Iris property.
(edit) @4671   12 years melissa Added the Iris property of Objective to the MetadataStore and …
(edit) @4670   12 years melissa If zlib data is truncated, return what can be decompressed instead of …
(edit) @4669   12 years melissa Fixed IndexOutOfBounds if objective string is set to "unknown".
(edit) @4668   12 years melissa Improved Objective/LightSource population.
(edit) @4667   12 years melissa Fixed image count reported by PrairieReader when the base file is a TIFF.
(edit) @4666   12 years melissa Fixed a handful of bugs exposed by the test suite.
(edit) @4665   12 years curtis Fix tools targets to play nicely with new copy-jars logic.
(edit) @4664   12 years curtis * Add copy-jars target to fix runtime classpath dependencies. * Remove …
(edit) @4663   12 years melissa Stop decoding once the output buffer has been filled.
(edit) @4662   12 years melissa Fixed tiling bug.
(edit) @4661   12 years melissa Initialize CoreMetadata objects before attempting to populate them.
(edit) @4660   12 years melissa * Fixed a couple of metadata parsing bugs. * Added FV1000 version 2 …
(edit) @4659   12 years melissa Fixed ArrayIndexOutOfBounds when determining if a series is indexed color.
(edit) @4658   12 years melissa Use ImagePlus.getImageStack() to retrieve the stack to be exported. This …
(edit) @4657   12 years melissa Be smarter about how LogicalChannel data is set.
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