# # ChangeLog for trunk/projects # # Generated by Trac 0.12.2 # 12/14/19 18:48:28 Wed, 21 Dec 2011 00:45:53 GMT aivar [7842] * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/AbstractBaseFittedImage.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/FittedImageManager.java (deleted) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/IFittedImage.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/InvalidDouble.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/callable/FittingEngineCallable.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/params/GlobalFitParams.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/params/IGlobalFitParams.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramDataChannel.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/SLIMProcessor.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IUserInterfacePanel.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/ui/UserInterfacePanel.java (modified) UI panel now has noise model, fitted images, and chi square target Wed, 21 Dec 2011 00:44:10 GMT aivar [7841] * trunk/projects/curve-fitter/src/main/java/loci/curvefitter/AbstractCurveFitter.java (modified) * trunk/projects/curve-fitter/src/main/java/loci/curvefitter/ICurveFitData.java (modified) * trunk/projects/curve-fitter/src/main/java/loci/curvefitter/ICurveFitter.java (modified) * trunk/projects/curve-fitter/src/main/java/loci/curvefitter/SLIMCurveFitter.java (modified) Gets the noise model to the fitter. Tue, 20 Dec 2011 00:47:04 GMT aivar [7840] * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/OutputImageParser.java (added) OutputImageParser added Tue, 20 Dec 2011 00:45:13 GMT aivar [7839] * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/FLIMFittedImageFactory.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/FLIMImageFitter.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/SLIMProcessor.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IUserInterfacePanel.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/ui/UserInterfacePanel.java (modified) UI Changes Mon, 19 Dec 2011 07:35:32 GMT aivar [7838] * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/AbstractBaseFittedImage.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/ColorBarPanel.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramData.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramPanel.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramTool.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/IHistogramDataListener.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/IHistogramPanelListener.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/UIPanel.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IUserInterfacePanel.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/ui/UserInterfacePanel.java (modified) Continued work on histogram, add fields to user interface. Thu, 15 Dec 2011 21:40:53 GMT aivar [7837] * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramPanel.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramTool.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/IHistogramPanelListener.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/MyStackWindow.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/ui/UserInterfacePanel.java (modified) Still working on fitted images, starting UI changes Thu, 15 Dec 2011 17:46:56 GMT aivar [7836] * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramPanel.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramTool.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/IHistogramPanelListener.java (added) Added cursors to histogram to change LUT ranges. Thu, 15 Dec 2011 00:14:07 GMT aivar [7835] * trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/DataColorizer2.java (modified) Fixed bug that killed Jenkins compile Thu, 15 Dec 2011 00:08:35 GMT aivar [7834] * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramData.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramDataChannel.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramPanel.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramTool.java (modified) Working on histogram Wed, 14 Dec 2011 01:17:07 GMT aivar [7833] * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/AbstractBaseFittedImage.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/FLIMImageFitter.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/IFittedImage.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramData.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramDataChannel.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramTool.java (modified) Still working on fitted images. Tue, 13 Dec 2011 06:58:58 GMT aivar [7832] * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/AbstractBaseFittedImage.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/FittedImage.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/FractionalContributionImage.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/config/Configuration.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramTool.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/SLIMProcessor.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/DataColorizer2.java (modified) Shows fitted images. Needs work & buggy. Tue, 13 Dec 2011 06:57:50 GMT aivar [7831] * trunk/projects/slim-plugin/src/main/java/ij (deleted) Shows fitted images. Needs work & buggy. Tue, 13 Dec 2011 00:18:57 GMT aivar [7830] * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/AbstractBaseFittedImage.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/FLIMFittedImageFactory.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/FLIMImageFitter.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/IFittedImage.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/SLIMProcessor.java (modified) Can now display selection of fitted images; buggy. Sat, 10 Dec 2011 00:51:19 GMT aivar [7829] * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/AbstractBaseFittedImage.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/FLIMFittedImageFactory.java (moved) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/FLIMImageFitter.java (moved) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/FittedImage.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/FractionalContributionImage.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/FractionalIntensityImage.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/IFittedImage.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/IOutputImage.java (deleted) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/OutputImage.java (deleted) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramData.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramDataChannel.java (moved) FLIMImageFitter is coming along Fri, 09 Dec 2011 20:20:48 GMT aivar [7828] * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/AbstractBaseFittedImage.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/FittedImageManager.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/IFittedImage.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramTool.java (modified) Working on the FittedImageManager that will build output fitted images. Fri, 09 Dec 2011 10:15:57 GMT avivekan [7827] * trunk/projects/flow-cytometry/src/main/java/loci/apps/flow/FlowCytometry.java (modified) Flow update. still testing... Fri, 09 Dec 2011 02:12:19 GMT aivar [7826] * trunk/projects/slim-plugin/lkjl.irf (deleted) Deleted some junk. Fri, 09 Dec 2011 02:09:38 GMT aivar [7825] * trunk/projects/slim-plugin/lkjl.irf (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/IOutputImage.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/ImageFitter.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/OutputImage.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/OutputImageFactory.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/ColorBarPanel.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramChannelData.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramData.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramPanel.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/HistogramTool.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/histogram/UIPanel.java (added) * trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/DataColorizer2.java (modified) Misc work in progress Fri, 09 Dec 2011 02:08:39 GMT aivar [7824] * trunk/projects/slim-plugin/src/main/java/imagej/histogram (deleted) * trunk/projects/slim-plugin/src/main/java/loci/slim/ui/histogram (deleted) Miscellaneous work in progress. Thu, 08 Dec 2011 16:14:35 GMT paulbarber [7823] * trunk/projects/slim-curve/src/main/c/GCI_Phasor.h (modified) Unnecessary define. Tue, 06 Dec 2011 21:19:54 GMT curtis [7822] * trunk/projects/slim-plugin/pom.xml (modified) Update to SezPoz 1.9 This matches the version we are using in ImageJ2. Sat, 03 Dec 2011 02:58:15 GMT aivar [7821] * trunk/projects/slim-plugin/src/main/java/ij (added) * trunk/projects/slim-plugin/src/main/java/ij/process (added) * trunk/projects/slim-plugin/src/main/java/ij/process/MyFloatProcessor.java (added) * trunk/projects/slim-plugin/src/main/java/loci/slim/MyStackWindow.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/SLIMProcessor.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/DataColorizer2.java (added) Experimented with MyFloatProcessor and DataColorizer2 to get IJ LUTs ... Sat, 19 Nov 2011 01:57:07 GMT aivar [7811] * trunk/projects/slim-plugin/src/main/java/imagej/slim/Test.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/callable/FittingEngineCallable.java (moved) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/callable/IFittingEngineCallable.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/config/Configuration.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/engine/IFittingEngine.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/engine/ThreadedFittingEngine.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/params/FitResults.java (moved) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/params/GlobalFitParams.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/params/IFitResults.java (moved) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/params/IGlobalFitParams.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/params/ILocalFitParams.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/params/LocalFitParams.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/CursorHelper.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/SLIMProcessor.java (modified) Got the new style fitting engine working. Bit of a hack; SLIMProcessor ... Sat, 19 Nov 2011 01:55:02 GMT aivar [7810] * trunk/projects/curve-fitter/src/main/java/loci/curvefitter/AbstractCurveFitter.java (modified) * trunk/projects/curve-fitter/src/main/java/loci/curvefitter/CurveFitData.java (modified) * trunk/projects/curve-fitter/src/main/java/loci/curvefitter/GrayCurveFitter.java (modified) * trunk/projects/curve-fitter/src/main/java/loci/curvefitter/GrayNRCurveFitter.java (modified) * trunk/projects/curve-fitter/src/main/java/loci/curvefitter/ICurveFitData.java (modified) * trunk/projects/curve-fitter/src/main/java/loci/curvefitter/ICurveFitter.java (modified) * trunk/projects/curve-fitter/src/main/java/loci/curvefitter/SLIMCurveFitter.java (modified) Got rid of the idea of creating an ICurveFitter for each fit type (i.e. ... Fri, 18 Nov 2011 15:07:43 GMT paulbarber [7809] * trunk/projects/slim-curve/src/main/c/EcfSingle.c (modified) Better comments on why the convolution is actually correct. Fixed one ... Sat, 12 Nov 2011 00:37:43 GMT aivar [7807] * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/callable/IFittingEngineCallable.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/callable/SLIMCurveCallable.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/engine/ThreadedFittingEngine.java (modified) Work in progress, refactoring fit process Sat, 12 Nov 2011 00:24:45 GMT aivar [7806] * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/callable/SLIMCurveCallable.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/params/GlobalFitParams.java (modified) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/params/IGlobalFitParams.java (modified) Working on calling the curvefitter Fri, 11 Nov 2011 21:25:50 GMT aivar [7805] * trunk/projects/slim-plugin/src/main/java/imagej (added) * trunk/projects/slim-plugin/src/main/java/imagej/histogram (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/Test.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/TestFittingEngineConcepts.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/callable (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/callable/IFittingEngineCallable.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/callable/SLIMCurveCallable.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/config (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/config/Configuration.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/config/ConfigurationHelper.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/cursor (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/cursor/Cursor.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/cursor/ICursor.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/cursor/ICursorEstimator.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/cursor/LameCursorEstimator.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/engine (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/engine/IFittingEngine.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/engine/ThreadedFittingEngine.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/params (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/params/GlobalFitParams.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/params/IGlobalFitParams.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/params/ILocalFitParams.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/params/ILocalFitResults.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/params/LocalFitParams.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/slim/fitting/params/LocalFitResult.java (added) * trunk/projects/slim-plugin/src/main/java/imagej/thread (added) * trunk/projects/slim-plugin/src/main/java/imagej/thread/ThreadPool.java (added) Added 'imagej.slim' package files from my local ... Fri, 11 Nov 2011 21:21:12 GMT aivar [7804] * trunk/projects/slim-plugin/src/main/java/loci/slim/SLIMProcessor.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/refactor/ui/charts/DecayGraph.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/refactor/ui/charts/IDecayGraph.java (added) * trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IUserInterfacePanel.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IUserInterfacePanelListener.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/ui/UserInterfacePanel.java (modified) * trunk/projects/slim-plugin/src/main/java/loci/slim/ui/histogram (added) * trunk/projects/slim-plugin/src/main/java/loci/slim/ui/histogram/HistogramData.java (added) Don't pop up multiple DecayGraphs Tue, 08 Nov 2011 16:47:14 GMT paulbarber [7803] * trunk/projects/slim-curve/src/main/c/EcfGlobal.c (modified) * trunk/projects/slim-curve/src/main/c/EcfSingle.c (modified) * trunk/projects/slim-curve/src/main/c/EcfUtil.c (modified) * trunk/projects/slim-curve/src/main/c/GCI_Phasor.c (modified) Fixed some memory leaks and some compile warnings. Tue, 08 Nov 2011 16:10:49 GMT fong [7802] * trunk/projects/misc-plugins/src/main/java/loci/plugins/IntensityMacro_Squirrell_Ogle.ijm (added) Mon, 31 Oct 2011 18:34:06 GMT curtis [7799] * trunk/projects/visbio-plugins/src/main/java/loci/visbio/OrthoStack.java (modified) Standardize order of exception handling. Mon, 31 Oct 2011 18:34:02 GMT curtis [7798] * trunk/projects/visbio-plugins/src/main/java/loci/visbio/OrthoStack.java (modified) Add checkbox for toggling parallel projection. Sat, 29 Oct 2011 23:11:54 GMT paulbarber [7797] * trunk/projects/slim-curve/src/main/c/EcfInternal.h (modified) Increased MAXBINS for a test. Really should check that bins does not ... Sat, 29 Oct 2011 01:05:38 GMT aivar [7796] * trunk/projects/slim-plugin/src/main/java/loci/slim/refactor (added) * trunk/projects/slim-plugin/src/main/java/loci/slim/refactor/ui (added) * trunk/projects/slim-plugin/src/main/java/loci/slim/refactor/ui/charts (added) * trunk/projects/slim-plugin/src/main/java/loci/slim/refactor/ui/charts/DecayGraph.java (added) * trunk/projects/slim-plugin/src/main/java/loci/slim/refactor/ui/intensity (added) Added "refactor" package to avoid conflicts. Tidy up DecayGraph and ... Fri, 28 Oct 2011 19:08:36 GMT aivar [7795] * trunk/projects/slim-plugin/src/main/java/loci/slim/CursorHelper.java (modified) Emulate TRI2 parameter estimation. Fri, 14 Oct 2011 18:29:34 GMT aivar [7794] * trunk/projects/slim-plugin/src/main/java/loci/slim/ExcitationFileHandler.java (modified) Better handle ICS excitation files. Thu, 13 Oct 2011 21:45:40 GMT curtis [7793] * trunk/projects/visbio-plugins (modified) Add SVN ignore rules for visbio-plugins project. Thu, 13 Oct 2011 21:43:04 GMT curtis [7792] * trunk/projects/visbio-plugins/src/main/java/loci/visbio/OrthoStack.java (modified) Eliminate hardcoded reference to MouseBehaviorJ3D. This fixes a ... Thu, 13 Oct 2011 20:54:04 GMT curtis [7791] * trunk/projects/visbio-plugins/src/main/java/loci/visbio/OrthoStack.java (modified) Fix snapshot feature to actually work. VisAD snapshots can only be done ... Thu, 13 Oct 2011 20:54:03 GMT curtis [7790] * trunk/projects/visbio-plugins/src/main/java/loci/visbio/OrthoStack.java (modified) Normalize color scale ranges. Thu, 13 Oct 2011 20:54:01 GMT curtis [7789] * trunk/projects/visbio-plugins/src/main/java/loci/visbio/OrthoStack.java (modified) Add bounding box toggle and snapshot features. Thu, 13 Oct 2011 20:54:00 GMT curtis [7788] * trunk/projects/visbio-plugins/src/main/java/loci/visbio/OrthoStack.java (modified) Use a finer grained stretch step. Thu, 13 Oct 2011 20:53:56 GMT curtis [7786] * trunk/projects/visbio-plugins/src/main/java/loci/visbio/OrthoStack.java (modified) Remove obsolete TODO. Thu, 13 Oct 2011 20:53:55 GMT curtis [7785] * trunk/projects/visbio-plugins/src/main/java/loci/visbio/OrthoStack.java (modified) Better handling of hyperstacks. Thu, 13 Oct 2011 20:53:53 GMT curtis [7784] * trunk/projects/visbio-plugins/src/main/java/loci/visbio/OrthoStack.java (modified) Start window as tall as reasonably possible. Thu, 13 Oct 2011 20:53:52 GMT curtis [7783] * trunk/projects/visbio-plugins/src/main/java/loci/visbio/OrthoStack.java (modified) Expand stretch range. Thu, 13 Oct 2011 20:53:50 GMT curtis [7782] * trunk/pom.xml (modified) * trunk/projects/visbio-plugins (added) * trunk/projects/visbio-plugins/LICENSE.txt (added) * trunk/projects/visbio-plugins/pom.xml (added) * trunk/projects/visbio-plugins/src (added) * trunk/projects/visbio-plugins/src/main (added) * trunk/projects/visbio-plugins/src/main/java (added) * trunk/projects/visbio-plugins/src/main/java/loci (added) * trunk/projects/visbio-plugins/src/main/java/loci/visbio (added) * trunk/projects/visbio-plugins/src/main/java/loci/visbio/DoubleSlider.java (added) * trunk/projects/visbio-plugins/src/main/java/loci/visbio/OrthoStack.java (added) * trunk/projects/visbio-plugins/src/main/resources (added) * trunk/projects/visbio-plugins/src/main/resources/plugins.config (added) First version of Ortho Stack VisBio plugin. Fri, 07 Oct 2011 12:51:51 GMT paulbarber [7781] * trunk/projects/slim-curve/LICENSE.txt (modified) * trunk/projects/slim-curve/src/main/c/Ecf.h (modified) * trunk/projects/slim-curve/src/main/c/EcfGlobal.c (modified) * trunk/projects/slim-curve/src/main/c/EcfInternal.h (modified) * trunk/projects/slim-curve/src/main/c/EcfSPA.c (modified) * trunk/projects/slim-curve/src/main/c/EcfSingle.c (modified) * trunk/projects/slim-curve/src/main/c/EcfUtil.c (modified) * trunk/projects/slim-curve/src/main/c/EcfWrapper.c (modified) * trunk/projects/slim-curve/src/main/c/EcfWrapper.h (modified) * trunk/projects/slim-curve/src/main/c/GCI_Lsqnonneg.c (modified) * trunk/projects/slim-curve/src/main/c/GCI_Lsqnonneg.h (modified) * trunk/projects/slim-curve/src/main/c/GCI_Phasor.c (modified) * trunk/projects/slim-curve/src/main/c/GCI_Phasor.h (modified) * trunk/projects/slim-curve/src/main/c/loci_curvefitter_SLIMCurveFitter.c (modified) Added GPL license to all source code. Fri, 30 Sep 2011 23:29:18 GMT aivar [7780] * trunk/projects/slim-curve/src/main/c/EcfUtil.c (modified) Tidied up. Fri, 30 Sep 2011 23:05:02 GMT aivar [7779] * trunk/projects/slim-curve/src/main/c/EcfUtil.c (modified) Go back to using Gaussian method to solve and invert matrices. Fri, 30 Sep 2011 23:03:43 GMT aivar [7778] * trunk/projects/slim-curve/src/main/c/EcfSingle.c (modified) Fixed bug in NOISE_MLE case. Tue, 20 Sep 2011 17:57:36 GMT hinerm [7777] * trunk/projects/jar2lib/src/main/resources/project-files/jtools/source/javaTools.cxx (modified) Fixed append in Windows directory search Previously was appending ".*" ... Tue, 20 Sep 2011 14:56:33 GMT hinerm [7776] * trunk/projects/jar2lib/src/main/resources/CMakeLists.vm (modified) Fixed jace-runtime.jar copy path The previous path to copy ... Mon, 19 Sep 2011 20:22:18 GMT hinerm [7775] * trunk/projects/jar2lib/src/main/resources/CMakeLists.vm (modified) Added Build path consideration to EXE files The templated code for exe ... Fri, 16 Sep 2011 17:58:55 GMT hinerm [7774] * trunk/projects/jar2lib/pom.xml (modified) * trunk/projects/jar2lib/src/main/java/loci/jar2lib/Jar2Lib.java (modified) Removed StringEscapeUtils reference It was found that erroneous string ... Fri, 16 Sep 2011 17:14:28 GMT hinerm [7773] * trunk/projects/jar2lib/src/main/java/loci/jar2lib/VelocityAutogen.java (modified) * trunk/projects/jar2lib/src/main/resources/CMakeLists.vm (modified) Removed File usage from automation of CMakeLists.txt The use of a File ... Fri, 16 Sep 2011 14:09:16 GMT hinerm [7772] * trunk/projects/jar2lib/pom.xml (modified) * trunk/projects/jar2lib/src/main/java/loci/jar2lib/Jar2Lib.java (modified) Added StringEscapeUtils to Jar2Lib Added a new dependency from the ... Thu, 15 Sep 2011 21:38:40 GMT curtis [7771] * trunk/projects/misc-plugins/src/main/java/loci/plugins/StitchPrairieTiff.java (modified) Normalize Z coordinates as well. Thu, 15 Sep 2011 21:38:39 GMT curtis [7770] * trunk/projects/slim-plugin/pom.xml (modified) * trunk/projects/slim-plugin/src/main/assembly (added) * trunk/projects/slim-plugin/src/main/assembly/with-dependencies.xml (moved) Move assembly descriptor into src/main/assembly. Thu, 15 Sep 2011 20:20:13 GMT hinerm [7769] * trunk/projects/jar2lib/src/main/java/loci/jar2lib/Jar2Lib.java (modified) updated fixLibraryPath J2L method Attempting to use replaceAll method ... Thu, 15 Sep 2011 20:01:33 GMT hinerm [7768] * trunk/projects/jar2lib/src/main/java/loci/jar2lib/Jar2Lib.java (modified) Updated J2L jar path conversion method The J2L method for conversion ... Thu, 15 Sep 2011 19:56:14 GMT hinerm [7767] * trunk/projects/jar2lib/src/main/java/loci/jar2lib/Jar2Lib.java (modified) Added new method to J2L to fix jar paths A new method was added as part ... Thu, 15 Sep 2011 19:53:33 GMT curtis [7766] * trunk/projects/slim-plugin/pom.xml (modified) Move JAR plugin config out of default profile. Thu, 15 Sep 2011 19:53:30 GMT curtis [7765] * trunk/projects/slim-plugin/pom.xml (modified) Remove superfluous slim-curve dependency. Thu, 15 Sep 2011 19:40:43 GMT hinerm [7764] * trunk/projects/jar2lib/src/main/java/loci/jar2lib/Jar2Lib.java (modified) Added extra level of escape ('\') for jar file conversions A single ... Thu, 15 Sep 2011 19:26:44 GMT hinerm [7763] * trunk/projects/jar2lib/src/main/resources/CMakeLists.vm (modified) Bug fix in CMakeLists: empty variable The CMakeLists.vm included ... Thu, 15 Sep 2011 19:20:04 GMT curtis [7762] * trunk/projects/curve-fitter/src/main/assembly/with-libs.xml (modified) Fix with-libs profile to include Java class files. Still doesn't ... Thu, 15 Sep 2011 18:54:52 GMT curtis [7761] * trunk/projects/curve-fitter/pom.xml (modified) * trunk/projects/curve-fitter/src/main/assembly (added) * trunk/projects/curve-fitter/src/main/assembly/with-libs.xml (moved) Move assembly descriptor into src/main/assembly. Thu, 15 Sep 2011 18:48:53 GMT curtis [7760] * trunk/projects/curve-fitter/pom.xml (modified) Move JAR plugin config out of default profile. Thu, 15 Sep 2011 18:48:51 GMT curtis [7759] * trunk/pom.xml (modified) * trunk/projects/curve-fitter/pom.xml (modified) * trunk/projects/slim-curve/pom.xml (modified) * trunk/projects/slim-plugin/pom.xml (modified) Add maven-nar-plugin version to avoid warnings. Thu, 15 Sep 2011 18:48:13 GMT hinerm [7757] * trunk/projects/jar2lib/src/main/java/loci/jar2lib/Jar2Lib.java (modified) * trunk/projects/jar2lib/src/main/resources/CMakeLists.vm (modified) Moved jar name fixing back to Java side of processing With CMake doing ... Thu, 15 Sep 2011 18:39:16 GMT hinerm [7756] * trunk/projects/jar2lib/src/main/resources/CMakeLists.vm (modified) Fix for CMakeLists.vm - slash correction The code to convert ... Thu, 15 Sep 2011 15:28:56 GMT hinerm [7755] * trunk/projects/jar2lib/src/main/java/loci/jar2lib/Jar2Lib.java (modified) * trunk/projects/jar2lib/src/main/resources/CMakeLists.vm (modified) Moved String conversion code to CMake Instead of the Jar2Lib trying to ... Thu, 15 Sep 2011 14:11:28 GMT hinerm [7754] * trunk/projects/jar2lib/src/main/java/loci/jar2lib/Jar2Lib.java (modified) Adjusted correction of jar paths The previous fix to correct '\' to '/' ... Thu, 15 Sep 2011 13:47:23 GMT hinerm [7753] * trunk/projects/jar2lib/src/main/resources/project-files/jtools/include/javaTools.h (modified) Removed Jtools reference to dirent.h JTools source was previously ... Wed, 14 Sep 2011 20:48:45 GMT hinerm [7752] * trunk/projects/jar2lib/src/main/java/loci/jar2lib/Jar2Lib.java (modified) Jar2Lib now converts "\" to "/" in discovered jar paths On Windows, the ... Wed, 14 Sep 2011 20:45:50 GMT hinerm [7751] * trunk/projects/jar2lib/src/main/resources/project-files/jtools/include/javaTools.h (modified) * trunk/projects/jar2lib/src/main/resources/project-files/jtools/source/javaTools.cxx (modified) Modified javaTools library for Windows functionality JTools was ... Wed, 14 Sep 2011 20:43:24 GMT hinerm [7750] * trunk/projects/jar2lib/src/main/resources/CMakeLists.vm (modified) Added support for building on Windows platforms The CMakeLists.txt ... Tue, 13 Sep 2011 20:33:40 GMT curtis [7748] * trunk/projects/misc-plugins/src/main/java/loci/plugins/StitchPrairieTiff.java (modified) Progress on Prairie TIFF stitching. Seems to work. Single-image TIFFs ... Fri, 02 Sep 2011 16:38:54 GMT curtis [7747] * trunk/projects/misc-plugins/src/main/java/loci/plugins/StitchPrairieTiff.java (modified) Convert stage coords from microns to pixels. Wed, 31 Aug 2011 23:30:52 GMT curtis [7746] * trunk/projects/misc-plugins/src/main/java/loci/plugins/StitchOmeTiff.java (modified) Tweak documentation. Wed, 31 Aug 2011 23:30:50 GMT curtis [7745] * trunk/projects/misc-plugins/src/main/java/loci/plugins/StitchPrairieTiff.java (added) * trunk/projects/misc-plugins/src/main/resources/plugins.config (modified) Initial version of Prairie TIFF stitching plugin. Wed, 31 Aug 2011 21:18:18 GMT curtis [7744] * trunk/projects/misc-plugins/src/main/java/loci/plugins/StitchOmeTiff.java (modified) Improvements to Stitch OME-TIFFs plugin: * Write tile configuration ... Wed, 31 Aug 2011 15:34:02 GMT hinerm [7743] * trunk/projects/jar2lib/src/main/resources/CMakeLists.vm (modified) Improved control flow of platform specific installation Previously, ... Tue, 30 Aug 2011 19:15:07 GMT curtis [7742] * trunk/projects/misc-plugins/src/main/java/loci/plugins/VisualizeTiles.java (added) * trunk/projects/misc-plugins/src/main/resources/plugins.config (modified) Simple plugin to visualize tile configuration. This is quicker than ... Mon, 29 Aug 2011 17:11:42 GMT aivar [7741] * trunk/projects/slim-plugin/src/main/java/loci/slim/GrayScaleImage.java (modified) Uses ComplexType vs UnsignedShort previously. Added "@Override" where ... Mon, 29 Aug 2011 17:02:07 GMT aivar [7740] * trunk/projects/slim-plugin/src/main/java/loci/slim/SLIMProcessor.java (modified) Misc. changes; took out fakeData and some debugging print outs. Fri, 26 Aug 2011 19:08:23 GMT curtis [7739] * trunk/projects/misc-plugins/pom.xml (modified) * trunk/projects/misc-plugins/src/main/java/loci/plugins/StitchOmeTiff.java (added) * trunk/projects/misc-plugins/src/main/resources/plugins.config (modified) First version of OME-TIFF stitching plugin. Calls Bio-Formats to get ... Fri, 26 Aug 2011 19:08:21 GMT curtis [7738] * trunk/projects/misc-plugins/pom.xml (modified) * trunk/projects/misc-plugins/src/main/java/loci (added) * trunk/projects/misc-plugins/src/main/java/loci/plugins (added) * trunk/projects/misc-plugins/src/main/java/loci/plugins/ExportAsText.java (moved) * trunk/projects/misc-plugins/src/main/java/loci/plugins/RoiMap.java (moved) * trunk/projects/misc-plugins/src/main/resources (added) * trunk/projects/misc-plugins/src/main/resources/plugins.config (added) Fix up misc_plugins into JAR with plugins.config. Thu, 25 Aug 2011 20:55:18 GMT aivar [7737] * trunk/projects/slim-curve/src/main/c/EcfUtil.c (modified) Removed code that requires C99 extensions to allow compilation in Visual ... Tue, 16 Aug 2011 20:26:42 GMT hinerm [7734] * trunk/projects/jar2lib/src/main/resources/project-files/jtools/include/javaTools.h (modified) * trunk/projects/jar2lib/src/main/resources/project-files/jtools/source/javaTools.cxx (modified) More control allowed in JavaTools The following options were added to ... Tue, 16 Aug 2011 20:22:09 GMT hinerm [7733] * trunk/projects/jar2lib/src/main/resources/CMakeLists.vm (modified) * trunk/projects/jar2lib/src/main/resources/project-files/jace/CMakeLists.txt (modified) Updated CMakeLists for OSX + Linux Changes include: *Removed redundant ... Wed, 03 Aug 2011 20:09:05 GMT hinerm [7732] * trunk/projects/jar2lib/src/main/resources/project-files/jace/Prerequisites.cmake (modified) Unix builds now default to .so Boost libraries For reasons unknown, ... Wed, 03 Aug 2011 16:13:58 GMT hinerm [7731] * trunk/projects/jar2lib/src/main/resources/CMakeLists.vm (modified) * trunk/projects/jar2lib/src/main/resources/project-files/jtools/include/javaTools.h (modified) * trunk/projects/jar2lib/src/main/resources/project-files/jtools/source/javaTools.cxx (modified) Fixes for ticket #298 and #654 Ticket #298 fixes: * search for a ... Sat, 18 Jun 2011 09:11:18 GMT curtis [7730] * trunk/projects/cppwrap-maven-plugin/pom.xml (modified) * trunk/projects/curve-fitter/pom.xml (modified) * trunk/projects/deep-zoom-plugin/pom.xml (modified) * trunk/projects/flow-cytometry/pom.xml (modified) * trunk/projects/jar2lib/pom.xml (modified) * trunk/projects/loci-checks/pom.xml (modified) * trunk/projects/misc-plugins/pom.xml (modified) * trunk/projects/slim-curve/pom.xml (modified) * trunk/projects/slim-plugin/pom.xml (modified) * trunk/projects/utils/pom.xml (modified) * trunk/projects/wiscscan-java/pom.xml (modified) Fix SVN path to license files. Wed, 15 Jun 2011 14:39:48 GMT curtis [7729] * trunk/projects/jar2lib/src/main/resources/project-files/jace/Prerequisites.cmake (modified) Add Boost versions up to 1.60. Wed, 15 Jun 2011 08:47:46 GMT curtis [7728] * trunk/projects/jar2lib/bf-cpp (deleted) * trunk/projects/jar2lib/deploy_jar.sh (deleted) Remove obsolete files. The Bio-Formats C++ bindings build process is ... Sat, 11 Jun 2011 20:13:46 GMT curtis [7727] * trunk/projects/jar2lib/src/main/resources/CMakeLists.vm (modified) Link executables to jtools. Tue, 07 Jun 2011 16:55:15 GMT ealexand [7726] * trunk/projects/ForwardCronJob/README.TXT (added) This readme should explain the configuration of the cron job on ...