diff --git a/jar/EigenPSF_Extractor-0.0.3.jar b/jar/linux/EigenPSF_Extractor-0.0.3.jar similarity index 98% rename from jar/EigenPSF_Extractor-0.0.3.jar rename to jar/linux/EigenPSF_Extractor-0.0.3.jar index 2e4004d81f0bed41dfb0bb7e6764c980478f2a5d..7e266640617c475167ab597baf84a0b5c47cbb4c 100644 Binary files a/jar/EigenPSF_Extractor-0.0.3.jar and b/jar/linux/EigenPSF_Extractor-0.0.3.jar differ diff --git a/java code/build.xml b/src/build.xml similarity index 100% rename from java code/build.xml rename to src/build.xml diff --git a/java code/eigenpsf.epf b/src/eigenpsf.epf similarity index 100% rename from java code/eigenpsf.epf rename to src/eigenpsf.epf diff --git a/java code/lib/JTransforms-3.1-with-dependencies.jar b/src/lib/JTransforms-3.1-with-dependencies.jar similarity index 100% rename from java code/lib/JTransforms-3.1-with-dependencies.jar rename to src/lib/JTransforms-3.1-with-dependencies.jar diff --git a/java code/lib/bilib-commons.jar b/src/lib/bilib-commons.jar similarity index 100% rename from java code/lib/bilib-commons.jar rename to src/lib/bilib-commons.jar diff --git a/java code/lib/ij.jar b/src/lib/ij.jar similarity index 100% rename from java code/lib/ij.jar rename to src/lib/ij.jar diff --git a/java code/lib/jblas-1.2.5.jar b/src/lib/jblas-1.2.5.jar similarity index 100% rename from java code/lib/jblas-1.2.5.jar rename to src/lib/jblas-1.2.5.jar diff --git a/java code/listfiles.csv b/src/listfiles.csv similarity index 100% rename from java code/listfiles.csv rename to src/listfiles.csv diff --git a/java code/plugins.config b/src/plugins.config similarity index 100% rename from java code/plugins.config rename to src/plugins.config diff --git a/java code/src/EigenPSF_Manager.java b/src/src/EigenPSF_Manager.java similarity index 100% rename from java code/src/EigenPSF_Manager.java rename to src/src/EigenPSF_Manager.java diff --git a/java code/src/JBlasExample_CG.java b/src/src/JBlasExample_CG.java similarity index 100% rename from java code/src/JBlasExample_CG.java rename to src/src/JBlasExample_CG.java diff --git a/java code/src/Manual_PSF.java b/src/src/Manual_PSF.java similarity index 100% rename from java code/src/Manual_PSF.java rename to src/src/Manual_PSF.java diff --git a/java code/src/RefineCodeCpp/EigenPSF_Refine.cpp b/src/src/RefineCodeCpp/EigenPSF_Refine.cpp similarity index 100% rename from java code/src/RefineCodeCpp/EigenPSF_Refine.cpp rename to src/src/RefineCodeCpp/EigenPSF_Refine.cpp diff --git a/java code/src/RefineCodeCpp/eigenpsf_processing_CInterface.h b/src/src/RefineCodeCpp/eigenpsf_processing_CInterface.h similarity index 100% rename from java code/src/RefineCodeCpp/eigenpsf_processing_CInterface.h rename to src/src/RefineCodeCpp/eigenpsf_processing_CInterface.h diff --git a/java code/src/RefineCodeCpp/libEigenPSF_Refine.dylib b/src/src/RefineCodeCpp/libEigenPSF_Refine.dylib similarity index 100% rename from java code/src/RefineCodeCpp/libEigenPSF_Refine.dylib rename to src/src/RefineCodeCpp/libEigenPSF_Refine.dylib diff --git a/java code/src/RefineCodeCpp/libEigenPSF_Refine.so b/src/src/RefineCodeCpp/libEigenPSF_Refine.so similarity index 100% rename from java code/src/RefineCodeCpp/libEigenPSF_Refine.so rename to src/src/RefineCodeCpp/libEigenPSF_Refine.so diff --git a/java code/src/Simulator_Field_Beads.java b/src/src/Simulator_Field_Beads.java similarity index 100% rename from java code/src/Simulator_Field_Beads.java rename to src/src/Simulator_Field_Beads.java diff --git a/java code/src/Unit_Tests.java b/src/src/Unit_Tests.java similarity index 100% rename from java code/src/Unit_Tests.java rename to src/src/Unit_Tests.java diff --git a/java code/src/eigenpsf/AdvancedSettingsPanel.java b/src/src/eigenpsf/AdvancedSettingsPanel.java similarity index 100% rename from java code/src/eigenpsf/AdvancedSettingsPanel.java rename to src/src/eigenpsf/AdvancedSettingsPanel.java diff --git a/java code/src/eigenpsf/Constants.java b/src/src/eigenpsf/Constants.java similarity index 100% rename from java code/src/eigenpsf/Constants.java rename to src/src/eigenpsf/Constants.java diff --git a/java code/src/eigenpsf/Log.java b/src/src/eigenpsf/Log.java similarity index 100% rename from java code/src/eigenpsf/Log.java rename to src/src/eigenpsf/Log.java diff --git a/java code/src/eigenpsf/LogScheduler.java b/src/src/eigenpsf/LogScheduler.java similarity index 100% rename from java code/src/eigenpsf/LogScheduler.java rename to src/src/eigenpsf/LogScheduler.java diff --git a/java code/src/eigenpsf/MaskDialog.java b/src/src/eigenpsf/MaskDialog.java similarity index 100% rename from java code/src/eigenpsf/MaskDialog.java rename to src/src/eigenpsf/MaskDialog.java diff --git a/java code/src/eigenpsf/Params.java b/src/src/eigenpsf/Params.java similarity index 100% rename from java code/src/eigenpsf/Params.java rename to src/src/eigenpsf/Params.java diff --git a/java code/src/eigenpsf/SettingsDialog.java b/src/src/eigenpsf/SettingsDialog.java similarity index 100% rename from java code/src/eigenpsf/SettingsDialog.java rename to src/src/eigenpsf/SettingsDialog.java diff --git a/java code/src/eigenpsf/data/Convolution.java b/src/src/eigenpsf/data/Convolution.java similarity index 100% rename from java code/src/eigenpsf/data/Convolution.java rename to src/src/eigenpsf/data/Convolution.java diff --git a/java code/src/eigenpsf/data/Dict.java b/src/src/eigenpsf/data/Dict.java similarity index 100% rename from java code/src/eigenpsf/data/Dict.java rename to src/src/eigenpsf/data/Dict.java diff --git a/java code/src/eigenpsf/data/EigenElements.java b/src/src/eigenpsf/data/EigenElements.java similarity index 100% rename from java code/src/eigenpsf/data/EigenElements.java rename to src/src/eigenpsf/data/EigenElements.java diff --git a/java code/src/eigenpsf/data/HyperMatrix.java b/src/src/eigenpsf/data/HyperMatrix.java similarity index 100% rename from java code/src/eigenpsf/data/HyperMatrix.java rename to src/src/eigenpsf/data/HyperMatrix.java diff --git a/java code/src/eigenpsf/display/ColorName.java b/src/src/eigenpsf/display/ColorName.java similarity index 100% rename from java code/src/eigenpsf/display/ColorName.java rename to src/src/eigenpsf/display/ColorName.java diff --git a/java code/src/eigenpsf/display/Display.java b/src/src/eigenpsf/display/Display.java similarity index 100% rename from java code/src/eigenpsf/display/Display.java rename to src/src/eigenpsf/display/Display.java diff --git a/java code/src/eigenpsf/display/DisplayDialog.java b/src/src/eigenpsf/display/DisplayDialog.java similarity index 100% rename from java code/src/eigenpsf/display/DisplayDialog.java rename to src/src/eigenpsf/display/DisplayDialog.java diff --git a/java code/src/eigenpsf/display/DisplayElement.java b/src/src/eigenpsf/display/DisplayElement.java similarity index 100% rename from java code/src/eigenpsf/display/DisplayElement.java rename to src/src/eigenpsf/display/DisplayElement.java diff --git a/java code/src/eigenpsf/display/ProgressStatusBar.java b/src/src/eigenpsf/display/ProgressStatusBar.java similarity index 100% rename from java code/src/eigenpsf/display/ProgressStatusBar.java rename to src/src/eigenpsf/display/ProgressStatusBar.java diff --git a/java code/src/eigenpsf/filemanager/IO.java b/src/src/eigenpsf/filemanager/IO.java similarity index 100% rename from java code/src/eigenpsf/filemanager/IO.java rename to src/src/eigenpsf/filemanager/IO.java diff --git a/java code/src/eigenpsf/gui/ButtonIcon.java b/src/src/eigenpsf/gui/ButtonIcon.java similarity index 100% rename from java code/src/eigenpsf/gui/ButtonIcon.java rename to src/src/eigenpsf/gui/ButtonIcon.java diff --git a/java code/src/eigenpsf/gui/SpinnerInfoRangeDouble.java b/src/src/eigenpsf/gui/SpinnerInfoRangeDouble.java similarity index 100% rename from java code/src/eigenpsf/gui/SpinnerInfoRangeDouble.java rename to src/src/eigenpsf/gui/SpinnerInfoRangeDouble.java diff --git a/java code/src/eigenpsf/gui/SpinnerInfoRangeInteger.java b/src/src/eigenpsf/gui/SpinnerInfoRangeInteger.java similarity index 100% rename from java code/src/eigenpsf/gui/SpinnerInfoRangeInteger.java rename to src/src/eigenpsf/gui/SpinnerInfoRangeInteger.java diff --git a/java code/src/eigenpsf/gui/WalkBar.java b/src/src/eigenpsf/gui/WalkBar.java similarity index 100% rename from java code/src/eigenpsf/gui/WalkBar.java rename to src/src/eigenpsf/gui/WalkBar.java diff --git a/java code/src/eigenpsf/lib/Loader.java b/src/src/eigenpsf/lib/Loader.java similarity index 100% rename from java code/src/eigenpsf/lib/Loader.java rename to src/src/eigenpsf/lib/Loader.java diff --git a/java code/src/eigenpsf/processing/AbstractBackground.java b/src/src/eigenpsf/processing/AbstractBackground.java similarity index 100% rename from java code/src/eigenpsf/processing/AbstractBackground.java rename to src/src/eigenpsf/processing/AbstractBackground.java diff --git a/java code/src/eigenpsf/processing/AbstractDetection.java b/src/src/eigenpsf/processing/AbstractDetection.java similarity index 100% rename from java code/src/eigenpsf/processing/AbstractDetection.java rename to src/src/eigenpsf/processing/AbstractDetection.java diff --git a/java code/src/eigenpsf/processing/AbstractRegistration.java b/src/src/eigenpsf/processing/AbstractRegistration.java similarity index 100% rename from java code/src/eigenpsf/processing/AbstractRegistration.java rename to src/src/eigenpsf/processing/AbstractRegistration.java diff --git a/java code/src/eigenpsf/processing/CInterface.class b/src/src/eigenpsf/processing/CInterface.class similarity index 100% rename from java code/src/eigenpsf/processing/CInterface.class rename to src/src/eigenpsf/processing/CInterface.class diff --git a/java code/src/eigenpsf/processing/CInterface.java b/src/src/eigenpsf/processing/CInterface.java similarity index 100% rename from java code/src/eigenpsf/processing/CInterface.java rename to src/src/eigenpsf/processing/CInterface.java diff --git a/java code/src/eigenpsf/processing/CoGRegistration.java b/src/src/eigenpsf/processing/CoGRegistration.java similarity index 100% rename from java code/src/eigenpsf/processing/CoGRegistration.java rename to src/src/eigenpsf/processing/CoGRegistration.java diff --git a/java code/src/eigenpsf/processing/DoGDetection.java b/src/src/eigenpsf/processing/DoGDetection.java similarity index 100% rename from java code/src/eigenpsf/processing/DoGDetection.java rename to src/src/eigenpsf/processing/DoGDetection.java diff --git a/java code/src/eigenpsf/processing/PolynomialFitBackground.java b/src/src/eigenpsf/processing/PolynomialFitBackground.java similarity index 100% rename from java code/src/eigenpsf/processing/PolynomialFitBackground.java rename to src/src/eigenpsf/processing/PolynomialFitBackground.java diff --git a/java code/src/eigenpsf/processing/Processing.java b/src/src/eigenpsf/processing/Processing.java similarity index 100% rename from java code/src/eigenpsf/processing/Processing.java rename to src/src/eigenpsf/processing/Processing.java diff --git a/java code/src/eigenpsf/processing/ProcessingPanel.java b/src/src/eigenpsf/processing/ProcessingPanel.java similarity index 100% rename from java code/src/eigenpsf/processing/ProcessingPanel.java rename to src/src/eigenpsf/processing/ProcessingPanel.java diff --git a/java code/src/eigenpsf/processing/Refinement.java b/src/src/eigenpsf/processing/Refinement.java similarity index 100% rename from java code/src/eigenpsf/processing/Refinement.java rename to src/src/eigenpsf/processing/Refinement.java diff --git a/java code/src/eigenpsf/processing/SIFTDetection.java b/src/src/eigenpsf/processing/SIFTDetection.java similarity index 100% rename from java code/src/eigenpsf/processing/SIFTDetection.java rename to src/src/eigenpsf/processing/SIFTDetection.java diff --git a/java code/src/eigenpsf/processing/ScaleSpaceRegistration.java b/src/src/eigenpsf/processing/ScaleSpaceRegistration.java similarity index 100% rename from java code/src/eigenpsf/processing/ScaleSpaceRegistration.java rename to src/src/eigenpsf/processing/ScaleSpaceRegistration.java diff --git a/java code/src/eigenpsf/project/DragAndDropPanel.java b/src/src/eigenpsf/project/DragAndDropPanel.java similarity index 100% rename from java code/src/eigenpsf/project/DragAndDropPanel.java rename to src/src/eigenpsf/project/DragAndDropPanel.java diff --git a/java code/src/eigenpsf/project/MainDialog.java b/src/src/eigenpsf/project/MainDialog.java similarity index 100% rename from java code/src/eigenpsf/project/MainDialog.java rename to src/src/eigenpsf/project/MainDialog.java diff --git a/java code/src/eigenpsf/project/Project.java b/src/src/eigenpsf/project/Project.java similarity index 100% rename from java code/src/eigenpsf/project/Project.java rename to src/src/eigenpsf/project/Project.java diff --git a/java code/src/eigenpsf/project/ProjectTable.java b/src/src/eigenpsf/project/ProjectTable.java similarity index 100% rename from java code/src/eigenpsf/project/ProjectTable.java rename to src/src/eigenpsf/project/ProjectTable.java diff --git a/java code/src/eigenpsf/project/StatusBar.java b/src/src/eigenpsf/project/StatusBar.java similarity index 100% rename from java code/src/eigenpsf/project/StatusBar.java rename to src/src/eigenpsf/project/StatusBar.java diff --git a/java code/src/eigenpsf/project/Toolbar.java b/src/src/eigenpsf/project/Toolbar.java similarity index 100% rename from java code/src/eigenpsf/project/Toolbar.java rename to src/src/eigenpsf/project/Toolbar.java diff --git a/java code/src/eigenpsf/stack/Patch.java b/src/src/eigenpsf/stack/Patch.java similarity index 100% rename from java code/src/eigenpsf/stack/Patch.java rename to src/src/eigenpsf/stack/Patch.java diff --git a/java code/src/eigenpsf/stack/Patches.java b/src/src/eigenpsf/stack/Patches.java similarity index 100% rename from java code/src/eigenpsf/stack/Patches.java rename to src/src/eigenpsf/stack/Patches.java diff --git a/java code/src/eigenpsf/stack/PatchesTable.java b/src/src/eigenpsf/stack/PatchesTable.java similarity index 100% rename from java code/src/eigenpsf/stack/PatchesTable.java rename to src/src/eigenpsf/stack/PatchesTable.java diff --git a/java code/src/eigenpsf/stack/PopupMenu.java b/src/src/eigenpsf/stack/PopupMenu.java similarity index 100% rename from java code/src/eigenpsf/stack/PopupMenu.java rename to src/src/eigenpsf/stack/PopupMenu.java diff --git a/java code/src/eigenpsf/stack/ShowPatchDialog.java b/src/src/eigenpsf/stack/ShowPatchDialog.java similarity index 100% rename from java code/src/eigenpsf/stack/ShowPatchDialog.java rename to src/src/eigenpsf/stack/ShowPatchDialog.java diff --git a/java code/src/eigenpsf/stack/StackCanvas.java b/src/src/eigenpsf/stack/StackCanvas.java similarity index 100% rename from java code/src/eigenpsf/stack/StackCanvas.java rename to src/src/eigenpsf/stack/StackCanvas.java diff --git a/java code/src/eigenpsf/stack/ZStack.java b/src/src/eigenpsf/stack/ZStack.java similarity index 100% rename from java code/src/eigenpsf/stack/ZStack.java rename to src/src/eigenpsf/stack/ZStack.java diff --git a/java code/src/manualpsf/ManualPSF.java b/src/src/manualpsf/ManualPSF.java similarity index 100% rename from java code/src/manualpsf/ManualPSF.java rename to src/src/manualpsf/ManualPSF.java diff --git a/java code/src/manualpsf/PSFCanvas.java b/src/src/manualpsf/PSFCanvas.java similarity index 100% rename from java code/src/manualpsf/PSFCanvas.java rename to src/src/manualpsf/PSFCanvas.java diff --git a/java code/src/resources/IconLoader.java b/src/src/resources/IconLoader.java similarity index 100% rename from java code/src/resources/IconLoader.java rename to src/src/resources/IconLoader.java diff --git a/java code/src/resources/about.png b/src/src/resources/about.png similarity index 100% rename from java code/src/resources/about.png rename to src/src/resources/about.png diff --git a/java code/src/resources/close.png b/src/src/resources/close.png similarity index 100% rename from java code/src/resources/close.png rename to src/src/resources/close.png diff --git a/java code/src/resources/contrast.png b/src/src/resources/contrast.png similarity index 100% rename from java code/src/resources/contrast.png rename to src/src/resources/contrast.png diff --git a/java code/src/resources/drawing.png b/src/src/resources/drawing.png similarity index 100% rename from java code/src/resources/drawing.png rename to src/src/resources/drawing.png diff --git a/java code/src/resources/edit.png b/src/src/resources/edit.png similarity index 100% rename from java code/src/resources/edit.png rename to src/src/resources/edit.png diff --git a/java code/src/resources/edit_off.png b/src/src/resources/edit_off.png similarity index 100% rename from java code/src/resources/edit_off.png rename to src/src/resources/edit_off.png diff --git a/java code/src/resources/github.png b/src/src/resources/github.png similarity index 100% rename from java code/src/resources/github.png rename to src/src/resources/github.png diff --git a/java code/src/resources/help.png b/src/src/resources/help.png similarity index 100% rename from java code/src/resources/help.png rename to src/src/resources/help.png diff --git a/java code/src/resources/imagej.png b/src/src/resources/imagej.png similarity index 100% rename from java code/src/resources/imagej.png rename to src/src/resources/imagej.png diff --git a/java code/src/resources/imagej_off.png b/src/src/resources/imagej_off.png similarity index 100% rename from java code/src/resources/imagej_off.png rename to src/src/resources/imagej_off.png diff --git a/java code/src/resources/mask.png b/src/src/resources/mask.png similarity index 100% rename from java code/src/resources/mask.png rename to src/src/resources/mask.png diff --git a/java code/src/resources/new.png b/src/src/resources/new.png similarity index 100% rename from java code/src/resources/new.png rename to src/src/resources/new.png diff --git a/java code/src/resources/open.png b/src/src/resources/open.png similarity index 100% rename from java code/src/resources/open.png rename to src/src/resources/open.png diff --git a/java code/src/resources/reset.png b/src/src/resources/reset.png similarity index 100% rename from java code/src/resources/reset.png rename to src/src/resources/reset.png diff --git a/java code/src/resources/save.png b/src/src/resources/save.png similarity index 100% rename from java code/src/resources/save.png rename to src/src/resources/save.png diff --git a/java code/src/resources/select.png b/src/src/resources/select.png similarity index 100% rename from java code/src/resources/select.png rename to src/src/resources/select.png diff --git a/java code/src/resources/settings.png b/src/src/resources/settings.png similarity index 100% rename from java code/src/resources/settings.png rename to src/src/resources/settings.png diff --git a/java code/src/resources/show.png b/src/src/resources/show.png similarity index 100% rename from java code/src/resources/show.png rename to src/src/resources/show.png diff --git a/java code/src/resources/stop.png b/src/src/resources/stop.png similarity index 100% rename from java code/src/resources/stop.png rename to src/src/resources/stop.png diff --git a/java code/src/resources/target.png b/src/src/resources/target.png similarity index 100% rename from java code/src/resources/target.png rename to src/src/resources/target.png diff --git a/java code/src/resources/time.png b/src/src/resources/time.png similarity index 100% rename from java code/src/resources/time.png rename to src/src/resources/time.png diff --git a/java code/src/resources/unselect.png b/src/src/resources/unselect.png similarity index 100% rename from java code/src/resources/unselect.png rename to src/src/resources/unselect.png diff --git a/java code/src/resources/update.png b/src/src/resources/update.png similarity index 100% rename from java code/src/resources/update.png rename to src/src/resources/update.png