source: trunk @ 6720

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Diff Rev Age Author Log Message
(edit) @6720   10 years melissa Populate physical pixel sizes, if present. Closes #515.
(edit) @6719   10 years melissa Set BinData.Length to "0" to prevent validation errors.
(edit) @6718   10 years bdezonia no change except whitespace - hudson test
(edit) @6717   10 years curtis Eliminate excessive xmlvalid output.
(edit) @6716   10 years curtis More fixes to LWF license code handling.
(edit) @6715   10 years melissa Close open files to prevent "too many open files" error when exporting …
(edit) @6714   10 years curtis Fix up support for LWF license codes.
(edit) @6713   10 years melissa Prevent ArithmeticException if stage coordinates are not present.
(edit) @6712   10 years melissa Allow sane used file test to be run separately; useful for testing #273.
(edit) @6711   10 years melissa Speed up plane access by using one reader for each constituent file.
(edit) @6710   10 years melissa * Fixed how ICS files with > 4 channels are read. * Fixed Channel …
(edit) @6709   10 years melissa Added utility that prints out all of the files in a directory that are …
(edit) @6708   10 years melissa Added one more date format to the list of acceptable TIFF date formats.
(edit) @6707   10 years melissa Fixed problems with exporting multi-channel data.
(edit) @6706   10 years melissa Tweaked isThisType to automatically return false if the TIFF comment is an …
(edit) @6705   10 years melissa Fixed bytes per pixel calculation for RGB data.
(edit) @6704   10 years melissa * Reverted r6703 stupidity. * Fixed Image5D display mode to work with …
(edit) @6703   10 years melissa Disable the "concatenate series" option when displaying with Image5D. See …
(edit) @6702   10 years melissa * Fixed ROI retrieval logic in ImageJ import plugin. * Updated FV1000 …
(edit) @6701   10 years melissa Fixed View5D instantiation; see #514.
(edit) @6700   10 years melissa More robust Z position parsing. The value of 'absoluteZ' is now taken …
(edit) @6699   10 years melissa Fixed pixel data offset.
(edit) @6698   10 years curtis Fix problem with GUI locking when using LOCI Plugins Shortcut Window.
(edit) @6697   10 years melissa First attempt at parsing stage coordinates from LSM files.
(edit) @6696   10 years curtis Add toString method to StatusEvent, for debugging.
(edit) @6695   10 years melissa Fixed problems with unaligned RLE-compressed images. Closes #511.
(edit) @6694   10 years melissa Adjust SizeC internally when writing RGB OME-TIFF files. Closes #513.
(edit) @6693   10 years melissa Fixed ArrayIndexOutOfBoundsException when opening sub-images from 16- and …
(edit) @6692   10 years melissa * Updated CellWorXReader to delegate to DeltavisionReader when reading …
(edit) @6690   10 years melissa Initial version of CellWorX .pnl reader.
(edit) @6689   10 years melissa Fixed emission wavelength parsing.
(edit) @6688   10 years curtis Whitespace.
(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, …
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