source: trunk @ 7634

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Diff Rev Age Author Log Message
(edit) @7634   9 years curtis Clean up wiscscan-java package a bit.
(edit) @7633   9 years curtis Rename wiscscan-utils to wiscscan-java in base POM.
(edit) @7632   9 years curtis Remove renamed wiscscan-utils project.
(edit) @7631   9 years curtis Collect needed WiscScan Java code into a single aggregator project.
(edit) @7630   9 years curtis Add ability to specify additional JARs to wrap.
(edit) @7629   9 years curtis Add separate settings for library vs. classpath JARs. Library JARs are …
(edit) @7628   9 years curtis Enable cppwrap for flow-cytometry project.
(edit) @7627   9 years curtis Add all dependencies to the library path. This is not a longterm …
(edit) @7626   9 years curtis Ostensibly working version of cppwrap-maven-plugin.
(edit) @7625   9 years curtis Fix minor issues with cppwrap project.
(edit) @7624   9 years curtis Update target Java platform to 1.6.
(edit) @7623   9 years curtis Add new projects to toplevel build.
(edit) @7622   9 years curtis Initial skeleton for jar2lib-based cppwrap Maven plugin.
(edit) @7621   9 years curtis Use Jace r39, since nothing newer works yet.
(edit) @7620   9 years curtis Clean up KerberosAuth, fix compile errors.
(edit) @7619   9 years hanly Added the source code for the kerberos login module.
(edit) @7618   9 years curtis Initial skeleton for WiscScan utilities project. This project is intended …
(edit) @7617   9 years curtis Ignore Eclipse metadata.
(edit) @7616   9 years curtis Update slim-plugin dependencies to match latest ImageJ2 project structure.
(edit) @7615   9 years curtis Tweak ImageJ1 version.
(edit) @7614   9 years curtis Update to ImageJ v1.44.
(edit) @7613   9 years rlentz Progress on OpenCL iterative 3D deconvolution.
(edit) @7612   9 years curtis Serve Maven artifacts using Apache on port 80. Previously it was done via …
(edit) @7611   9 years aivar Added float chisq_delta parameter to …
(edit) @7610   9 years curtis Remove unnecessary include folder.
(edit) @7609   9 years curtis Initial CMakeLists build file for slim-curve.
(edit) @7608   9 years paulbarber Utility.h not needed.
(edit) @7607   9 years paulbarber Added single frequency phasor routine for lifetime. Added Non-negative …
(edit) @7606   9 years paulbarber To compile in TRI2, moved declarations to top of relevant block. Added …
(edit) @7605   9 years aivar I had inverted the image to correspond with SLIMPlotter, but the natural …
(edit) @7604   9 years aivar I had inverted the image to correspond with SLIMPlotter, but the natural …
(edit) @7603   9 years aivar Thought there might be a bug here, so made the display table more flexible …
(edit) @7602   9 years aivar Added TODO comment.
(edit) @7601   9 years aivar Needed an out of bounds strategy.
(edit) @7600   9 years aivar New 7x7 binner.
(edit) @7599   9 years aivar Deleted some vestigial files.
(edit) @7598   9 years aivar Parameter ordering problems. GrayNRCurveFitter was out of date.
(edit) @7597   9 years aivar Fixed null pointer exception when library not found.
(edit) @7596   9 years aivar Fixed null pointer exception when library not found.
(edit) @7595   9 years curtis Fix up LOCI Software POM structure.
(edit) @7594   9 years aivar Commented out unused #include <ansi.h>
(edit) @7593   9 years aivar Nar plugin dependency added (temporarily)
(edit) @7592   9 years curtis Remove obsolete svn:ignore property.
(edit) @7591   9 years curtis Remove obsolete class.
(edit) @7590   9 years curtis Add Deep Zoom plugin to umbrella POM.
(edit) @7589   9 years curtis Remove Bio-Formats ITK project. Bio-Formats has moved to its own …
(edit) @7588   9 years curtis Remove old JRE bundles.
(edit) @7587   9 years curtis Remove Bio-Formats projects, and merge Maven branch. Bio-Formats has …
(edit) @7584   9 years melissa One more pixel data offset fix.
(edit) @7583   9 years melissa Deprecated superfluous getHexString(byte[]) method.
(edit) @7582   9 years melissa Prevent StringIndexOutOfBoundsException when file names start with "_".
(edit) @7581   9 years melissa Prevent extra Plane(Timing).ExposureTime attributes from being populated.
(edit) @7580   9 years melissa The JPEG-2000 writer can now use lossy or lossless compression. Closes …
(edit) @7579   9 years melissa Prevent potential AIOOB.
(edit) @7571   9 years melissa Populate all of the wells, even if no image data is associated with them.
(edit) @7570   9 years melissa Sanitize the XML before we parse it.
(edit) @7568   9 years melissa Initial version of Metamorph TIFF HCS support.
(edit) @7564   9 years hinerm Added a "dist" target to the bf-cpp project. Functionally identical to …
(edit) @7562   9 years hinerm Modified the dist target for BF-ITK to no longer copy unnecessary files on …
(edit) @7561   9 years melissa Tweaked MetamorphReader's isThisType to prevent it from picking up files …
(edit) @7560   9 years melissa Tweaked well name detection so that column indexes can only contain at …
(edit) @7559   9 years melissa Clarified CLASSPATH requirements.
(edit) @7558   9 years melissa Added some documentation on file export/conversion.
(edit) @7557   9 years hinerm Forward port from branch 4.2 changes - mistakenly committed to a branch …
(edit) @7554   9 years curtis Add variable for controlling number of channels.
(edit) @7553   9 years melissa Prevent an NPE when attempting to stitch datasets that aren't stitchable. …
(edit) @7552   9 years melissa Group together separate blocks of pixels that belong to the same stack. …
(edit) @7551   9 years melissa Fixed various metadata population problems when working with multi-file …
(edit) @7544   9 years melissa Fixed channel name and wavelength population. See  omero:#3865.
(edit) @7543   9 years melissa One more adjustment to SizeX/SizeY calculations. See #643.
(edit) @7541   9 years melissa Parse valid bits per pixel from Slidebook files. Closes #626.
(edit) @7538   9 years melissa Set 'falseColor' to true, so that lookup tables are not improperly …
(edit) @7535   9 years melissa Fixed plane index in status bar. Closes #637.
(edit) @7528   9 years melissa Corrected pixel type for 32-bit images, as Andor/Fluoview assumes that all …
(edit) @7522   9 years melissa Make primitive type static variables volatile.
(edit) @7514   9 years melissa Fixed indexed flag and LUT parsing. Closes #633.
(edit) @7513   9 years hinerm Enhanced ant dist script to copy BioFormatsIO.dll to the dist directory.
(edit) @7508   9 years melissa Fixed NPE.
(edit) @7502   9 years melissa Don't overwrite existing image names.
(edit) @7500   9 years melissa Search more thoroughly for image descriptions. Image descriptions are no …
(edit) @7496   9 years curtis Fix signedness averaging problem with convertTo8Bit method.
(edit) @7494   9 years curtis Fix problem where custom LUTs override grayscale mode. This happened …
(edit) @7493   9 years melissa Slightly more robust well name checking.
(edit) @7489   9 years melissa Prevent potential NPE if the "Info" property is not set on the ImagePlus …
(edit) @7488   9 years melissa Sanitize OME-XML before attempting to create a MetadataStore.
(edit) @7487   9 years melissa Use a ConcurrentHashMap instead of a HashMap.
(edit) @7486   9 years melissa Added optional cacheing of directory listings, courtesy of Lee Kamentsky.
(edit) @7485   9 years melissa Escape backslashes when finding a pattern. Closes #634.
(edit) @7484   9 years melissa Various fixes to allow retrieval of pixel data from truncated TIFFs.
(edit) @7483   9 years melissa Fixed a handful of bugs introduced in r7481.
(edit) @7482   9 years melissa Moved 'void setWriteSequentially(boolean)' from TiffWriter to …
(edit) @7481   9 years melissa Expanded special strip unpacking case to allow multiple strips.
(edit) @7480   9 years melissa Set a more reasonable timeout when checking for updates.
(edit) @7478   9 years melissa Added tests for screen detection. Closes #619.
(edit) @7477   9 years melissa Allow sparse plates.
(edit) @7476   9 years melissa Prevent a NPE when calling isThisType on a file with no parent directory.
(edit) @7475   9 years melissa Attach non-well files as companion metadata files.
(edit) @7474   9 years melissa Allow multi-series files to be stitched if the file pattern contains only …
(edit) @7473   9 years melissa Make type detection slightly more restrictive; this should allow the tests …
(edit) @7472   9 years melissa Added more flexible plate/well detection, so that InCell 3000 datasets are …
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