[ImageJ-builds] Build failed in Jenkins: fiji-windows-full #340

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See <https://qa.nest-initiative.org/job/fiji-windows-full/340/changes>

Changes:

[admin] Inited new repo

[admin] Started adding FFT

[admin] Small change

[admin] Removed inconsequent update of arrays in the types, it is now done by returning different types instead

[Stephan] Added BasePairTypes

[Stephan] Continued working on exponential windowing

[Stephan] Finished exponential mirrored windowing strategy

[Stephan] First version of generic FFT almost done

[Stephan] Fixed bug in ComplexFloatType

[Stephan] Working on FFT

[admin] Updated to new LOCI library, order of bytes in short inverted

[Stephan] Simple change in test class

[Stephan] Working on Canvas Image

[Stephan] Starting major test of Vectors

[Stephan] FFT and Inverse FFT are working now

[Stephan] Optimized so that no intermediate images are produced during FFT

[Stephan] Working on FFT Convolution

[Stephan] FFT convolution almost done

[Stephan] Fourier Convolution works

[Stephan] Threading fixed, uses number of assigned threads

[Stephan] Small change

[admin] Added support for little/big endian encoding

[Stephan] Added Gauss package

[Stephan] Numeric Types got getReal() and setReal()

[Stephan] Worked on PhaseCorrelation

[Stephan] Refactored Circle Strategy to Periodic Strategy

[Stephan] PhaseCorrelation seems to work, we just have to add the CrossCorrelation test

[Stephan] Wrote PhaseCorrelationTest

[Stephan] Worked on Phase Correlation

[Stephan] Renamed base package to mpicbg

[Stephan] Added RegionOfInterestCursor

[Stephan] Fixed bug for high translations

[Stephan] Removed Test Class, should be in a separate Project

[Stephan] Changed static methods to take int[] shift as input for cross correlation

[admin] Corrected error in PhaseCorrelation when one image is extended more due to fft min extension

[admin] Added computeAverage in MathLib

[Stephan] Image<T> class has now a calibration

[Stephan] Reading calibration while opening

[admin] Added close function to PhaseCorrelation

[admin] Fixed Java bug that Float.MIN_VALUE is not min value, replaced by -Float.MAX_VALUE, funnily Integer.MIN_VALUE is the min value (-2^31), so there it needs no change

[Stephan] Added Documentation

[Stephan] Added 1D/2D interpolators

[Stephan] Edited Factory to create efficient interpolators

[Stephan] Not creating untested instances of fast interpolators

[Johannes Schindelin] Turn DOS line endings in Unix line endings

[Johannes Schindelin] Work around a bug of Sun's JavaC

[Johannes Schindelin] Add a .mailmap

[Johannes Schindelin] Add missing GPLv2 license (+FFT exception) to algorithms

[Johannes Schindelin] Add a BSD license boilerplate as a file

[Johannes Schindelin] Add a script to convert the license boilerplates from GPl -> BSD

[Johannes Schindelin] Remove GPL exception from the wrong place

[Johannes Schindelin] Change authorship for a class that was really written by Stephan Preibisch

[Johannes Schindelin] Convert all the licenses from GPL -> BSD

[Johannes Schindelin] Remove the script which is no longer needed

[Stephan] Fixed bug, another RGBALegacyType has to be adressed with .get() not with the own index, stupid

[Stephan] Fixed bug that when instantiating new ImagePlusContainer with an exisiting ImagePlus it is not newly created but used

[Curtis Rueden] Documentation.

[Curtis Rueden] Add Eclipse project for imglib.

[jean-yves.tinevez] Doc: added some javadocs

[Stephan] Small doc

[Stephan] Commented the Image<T> class

[Stephan] Renamed BooleanType to BitType and gave it the capabilities of the NumericType

[Stephan] Git diff shows no differences but I played around with it and used the undo function

[Stephan] Has now a static function to create a Cursor on Fake Data for n-dimensional iterations

[Stephan] Added Dithering, works n-dimensionally on any numeric type

[Stephan] LocalNeighborhoodCursors can return their local position

[Stephan] Removed debug stuff

[Stephan] Added license

[Stephan] Fixed bug for setReal() method

[Stephan] Added static methods for computing distance and length

[Stephan] copyToImagePlus method recognizes RGBALegacyType automatically

[Stephan] Added Bandpass algorithm

[Stephan] Removed eclipse project

[Stephan] ImagePlus Container supports 1d, 2d and 3d now properly

[Stephan] Added BitContainer for ImagePlus

[Johannes Schindelin] Revert "Removed eclipse project"

[Stephan] Added a final statement

[Stephan] Corrected wrong assumption in FFT computation (moving outside of the image might fail even if no pixel is addressed)

[Stephan] ImagePlus container supports all BasicTypes now

[Stephan] Speeded up processing as suggested by Aivar

[Stephan] copyVariable() renamed to clone()

[Stephan] Added Unsigned Types

[Stephan] Added CursorLink Test, test if NullLink does not cost anything

[Stephan] Does not ignore numberOfThreads in efficient implementation anymore

[Stephan] No duplicate variable if efficient containers are used (was previously in ImageFactory and ContainerFactory, now only ContainerFactory)

[Stephan] Added median for long

[Stephan] Is final class now

[Stephan] Contain commented Null-Link for performance testing ( not active )

[Stephan] Gaussian Convolution can return the kernel size in each dimension

[Stephan] Container manages all dimension-related numbers and arrays now

[Stephan] Added dynamic container (can change size), not finished yet

[Stephan] Removed BitDynamicContainer as it does not work anyways

[acardona] ImagePlusAdapter now uses UnsignedByteType for an 8-bit ImagePlus,

[saalfeld] Removed small rarely required things from Image

[acardona] Removed one whitespace.

[acardona] Renamed UnsignedByteImagePlus back to ByteImagePlus,

[acardona] Short and Byte ImagePlus use now Unsigned types, since that

[saalfeld] Separated PixelGrid logic from the Container Interface.

[larry] Editted(*) FourierConvolution to handle changing Image *or* Kernel, but

[saalfeld] Removed fancy character

[larry] Created NormalizeImageFloat, which will take any variety of single

[Stephan] LOCI can open UnsignedByteType images

[Stephan] Inverse Fourier Transform has additional normalization factor

[saalfeld] On the way to abstract the pixel access into get and

[Stephan] Both implement Benchmark now

[Stephan] Benchmarking class added

[Stephan] Benchmarking class added

[Stephan] Both implement Benchmark now

[Stephan] Fixed the CubeContainer Structure for the changes in access to the data

[Stephan] Fixed the ImagePlusContainer Structure to match the changes done in accessing the data

[llindsey] HoughTransform - an abstract class to handle vote-type transforms

[llindsey] NormalizeImageFloat now closes the cursors its supposed to close.

[Stephan] Arrays have more constructors so that they can be used by other containers more easily

[Stephan] Fixed errors in accessing the data, not finished yet

[Stephan] Updated to remove redundancies (f. ex. ByteCubeContainer is no ByteContainer anymore but a BasicTypeContainer<ByteContainer>, so one the structure holding the data has to implement get() and set()

[Stephan] Small changes

[Stephan] Image implements Collection now, so an Image can be iterated

[Stephan] Small changes for testing

[Stephan] Finished updating all Arrays to more constructors

[Stephan] Fixed all NumericTypes

[Stephan] Finished all other Types...

[Stephan] Forget to add new constructor to Bit and Char....

[Stephan] Removed unnecessary import

[Stephan] Found error, wrong constructor in Types is called when inititalized with an Container

[Stephan] Fixed all types again

[Stephan] Removed unnecessary constructor in all Types

[Stephan] Small changes

[Stephan] Small changes

[Stephan] Complete rework of imglib succeeded, preliminary tests successful! (Running FFT on all StorageTypes)

[Stephan] Removed Dynamic Container

[Stephan] Added ImgLibException that can be thrown

[Stephan] getImagePlus() throws Exception if is does not work internally with an ImagePlus

[Stephan] Internal ImagePlus are only created if it is 1 entity per pixel

[Stephan] Fixed inconsistend license authors

[Stephan] Fixed Exception, one super() call was missing

[Stephan] Fixed huge bug in CubeCursor

[Stephan] Removed old comment

[Stephan] Whitespace changes

[Stephan] Fixed bug in ComplexFloatType to init complexI correctly

[Stephan] Added DynamicContainer which uses ArrayLists to store the data

[Curtis Rueden] Make it easier to build imglib.jar in Eclipse.

[Curtis Rueden] Fix building of imglib in Eclipse, again.

[larry] Maybe is better for the voteSpace image to also be final

[larry] Some Updates.  These should get flattened

[larry] PickImagePeaks - a class to pick peaks out of imglib Images.  Produces a peak image as well as a list of peak locations in an ArrayList<int[]>

[larry] PickImagePeaks now appears to work. Anyone else want to test it?

[larry] Removed System.out.println (oops), added final keyword to input.

[larry] HoughLineTransform now appears to function correctly.

[larry] Operates on ComparableType rather than NumericType, commented.

[larry] Fixed peak suppression problem, by adding a clone() in the correct place.

[Stephan] New NumericType structure introduced

[Stephan] Consistent Implementation Structure, supports generic implementation of math on the package level

[Stephan] Streamlined everything, NumericTypes can be much shorter now

[saalfeld] Refactored outside into outOfBounds

[saalfeld] two comments fixed

[saalfeld] Use getType() for high level access.

[saalfeld] No compiling intermediate commit of a ShapeList

[saalfeld] This is a hack to have a semi-working ShapeList container.  It

[saalfeld] Extended TestShapeList

[saalfeld] moveTo() failed for getPosition( int ) returning 0 always ...

[saalfeld] Refactored Cube to Cell as planned in Heidelberg.

[saalfeld] Commented Localizable interface to make sure where to return

[saalfeld] not yet working outofbounds cursor for shapelists

[Stephan] Added a new hierarchy level in the Container package.

[Stephan] Huge Refactoring to remove warnings in Types, using a LinkedType for this

[Stephan] Revert "Huge Refactoring to remove warnings in Types, using a LinkedType for this"

[Stephan] Removed normalizeLength from ComplexFloatType and made it a method in Phasecorrelation

[Curtis Rueden] Ignore build-eclipse folder.

[Curtis Rueden] Add a simple imglib test that squares an image.

[Stephan] Types do not have the Warning anymore, a linked type is given to the DirectAccessContainer when created by the Type, a new clone method can duplicate the

[Stephan] Fixed bug that if entitiesPerPixel > 1 (e.g. ComplexFloatType) the value was actually ignored

[Stephan] Fixed bug that if entitiesPerPixel > 1 (e.g. ComplexFloatType) the value was actually ignored

[Stephan] For creating Cursors there are no Types passed anymore

[Stephan] Fixed bug, gets 3 bits now

[Stephan] RealTypes set, add, mul, div and sub now

[Stephan] Added Unsigned12BitType for microscopic data

[Stephan] Fixed some bugs in Unsigned12BitType

[Johannes Schindelin] Ignore generated .jar

[Stephan] Finished BitType

[Stephan] RGBALegacyType is only a NumericType now

[Stephan] IntegerTypeDisplay is initialized with the Min and Max Value of the respective IntegerType

[Stephan] Fixed some issues in the Displays

[Stephan] LinearInterpolators work again with any NumericType

[Stephan] Fixed bug in NearestNeighborsInterpolator which assumed that a Cursor always returns the same type

[Stephan] Fixed problem that LinearInterpolator assumed constant Type Instance returned by Cursor

[Stephan] Factory returns efficient LinearInterpolators for 1d and 2d

[Stephan] LOCI opener can read 12Bit Data now, but the Type still has a bug

[Stephan] Showed git to David

[Stephan] Revert "Showed git to David"

[Stephan] Fixed another entitiesPerPixel bug in ImagePlusContainer

[Stephan] Fixed another entitiesPerPixel bug in ImagePlusContainer

[Stephan] LocalizableByDim(Cursors) can now move to any Localizable, not only LocalizableCursor

[Stephan] Iterable has no reset() call anymore

[Stephan] Looks nicer

[Stephan] GenericCursorLink for generic linking to a LocalizableCursor

[saalfeld] added package declaration

[saalfeld] launch an ImageJ instance

[Stephan] Fixed a bug that I put in during refactoring container system

[Stephan] Updated ShapeListTest

[Stephan] Updated CursorLinks

[Stephan] Changed ImageTransform to be able to create another Type of Container for the

[Stephan] ShapeListTest uses the ImageTransform Algorithm to rotate shapes into an pixel image

[Stephan] Removed unnecessary import

[llindsey] ROIAlgorithm is an abstract class to aid in convolution, morphological ops, etc.

[llindsey] Theoretically, this should perform direct convolution of an image against a kernel.

[llindsey] Fixed my switchup between cursors.  Perhaps I'll rename some variables to make things more obvious so this doesn't happen again.

[llindsey] Fixed some things.  This code appears to work but further testing is needed.

[llindsey] Added reset(int[] offset) and reset(int[] offset, int[] size).

[llindsey] Changed output image size back to input image size.

[llindsey] DirectConvolution now DirectConvolution<T, R, S>.

[llindsey] Fixed convolution offset problem

[llindsey] Implemented Benchmark, fixed offset proble. Minor fixes.

[llindsey] Now names output image.

[llindsey] New morphological operators.  There is still some work to be done

[Stephan] Added Cached ShapeList

[Stephan] ShapeListCached is now synchronized and working and slow

[Stephan] Updated test to containerlevel branch

[Stephan] Implemented cached ShapeList with variable Caching Strategy, Caching is on CursorLevel for non-synchronized caching

[Stephan] More reasonable naming for setting caching strategy of a container

[llindsey] Added static sobel operators

[llindsey] Added ShortType convolution, and translated peak list.

[llindsey] Added support for peak exclusion

[Stephan] Fixed ImagePlusWrapper, forgot to set the linkedType in there

[llindsey] Cross corr

[Curtis Rueden] Fix compile problem with tests package.

[Curtis Rueden] Close cursors properly.

[Stephan] Added a class that handles different precisions for computation

[Stephan] Added a more efficient Gaussian Convolution for RealTypes

[Stephan] Precision adjustment

[Stephan] Added more precisions

[Stephan] DownSampling uses GaussianConvoltionRealType

[Stephan] GaussianConvolutionRealType uses preferred precision of the RealType

[Stephan] FFT stuff can use/create any ComplexType now (ComplexFloatType, ComplexDoubleType, ... )

[Stephan] Updated AlgorithmPerformance to new FFT calls

[Stephan] Removed ComplexPrecision

[Stephan] ComplexTypes and RealType have a preferred precision now algorithms can ask for

[Johannes Schindelin] Add a base class for JUnit tests, and use it for most basic tests

[Johannes Schindelin] Add comments to the test classes

[saalfeld] ImagePlusAdapter: Set the Image's calibration from the ImagePlus's calibration

[saalfeld] ImagePlusAdapter: Set the Image's calibration from the ImagePlus's calibration

[Stephan] Fixed Generics in ImagePlusAdapter method

[Johannes Schindelin] Adjust tests to recent API change

[saalfeld] Introduced the Sampler interface that unifies pixel

[saalfeld] comments improved

[saalfeld] Split Localizable and RasterLocalizable.  Localizable can

[saalfeld] moved testshapelist to the other tests

[saalfeld] Replaced LocalizableByDim with the Positionable interface,

[llindsey] Updated code to work with changes to main

[Stephan] Added a comprehensive test for Containers and Cursors

[saalfeld] Refactored LocalizableByDim to Positionable and cleaned up

[llindsey] Fixed a pretty dumb bug, added some sparse comments.

[saalfeld] Re-added deprecated methods getPosition( int[] ) to

[llindsey] Added close(), comments.

[llindsey] Added comments

[llindsey] Changes to checkInput

[llindsey] Added comments, minor changes.

[llindsey] Added comments, minor changes.

[saalfeld] Iterable renamed to Iterator< E > which extends

[saalfeld] added comment fwd( long ) considered harmful

[saalfeld] Image is Iterable<T>, not Collection<T>

[saalfeld] removed Vectors from cursor.vector

[saalfeld] * moved Dimensionality into the top-most package

[saalfeld] * refactored fwd( long ) to jumpFwd( long )

[saalfeld] linkIterable finished (? not tested yet, tests missing)

[saalfeld] ups.   VoidIterator missed hasNextLinked()

[saalfeld] Commented Iterator

[Stephan] Removed all special 3d implementations for Containers and Cursors

[saalfeld] link RasterPositionable:

[saalfeld] link RasterPositionable:

[Stephan] NumPixels and NumEntites are held as long now, they actually are quite often

[saalfeld] link RasterPositionable:

[Stephan] Removed unnecessary import

[saalfeld] link RasterPositionable:

[saalfeld] link RasterLocalizable:

[saalfeld] link RasterLocalizable:

[saalfeld] link RasterLocalizable:

[saalfeld] * Dimensionality separated from Dimensions

[saalfeld] Adapted LinearInterpolator1D, 2D and 3D with x,y,z fields.

[saalfeld] Make TestShapeList measure time

[saalfeld] Make LinearInterpolator3D extendable and add the

[saalfeld] LinearInterpolator3DRealType adapted but does not work

[saalfeld] Linear and NearestNeighbor interpolation successfully

[Stephan] removed getStorageIndex from Cursor

[saalfeld] Terrible non-compiling commit for sharing the workload :)

[Stephan] LocalNeighborhoodCursor works again

[Stephan] Fixed LocalNeighborHoodCursor3D und Factory

[Stephan] LocalNeighborhoodCursor can go outside if wanted

[saalfeld] Array cursors compile but do not satisfy what we finally want

[saalfeld] Compiles instead PhaseCorrelation and math.

[Stephan] Fixed all algorithms

[Stephan] DirectAccessContainers and Types take only Cursor and not IterableCursor

[Stephan] Added licenses

[Stephan] Renamed ArrayLocalizableIterableCursor back to ArrayLocalizableCursor

[Stephan] Renamed all Cursors to IterableCursors

[saalfeld] image can be null (for variables)

[Stephan] Removed isActive() from Cursor

[Stephan] Cursors remove themselves from Image

[saalfeld] added coordinate printer for long coordinates to MathLib

[saalfeld] Non-compiling intermediate commit towards:

[saalfeld] ImagePlusIterableCursor should work too (not tested)

[saalfeld] DynamicIterableCursor uses the same approach as Array

[saalfeld] LocalNeighborhoodCursor localizes through its

[Stephan] Fixed CellLocalizableCursor

[Stephan] Changing dimensions from int to long

[Stephan] Fixed Array, internally works with int

[Stephan] Fixed ImagePlusContainer and some stuff in Array

[Stephan] Fixed DynamicContainer

[saalfeld] dimensions int[] to long[]

[Stephan] Added TODO for DynamicContainer

[saalfeld] dimensions int[] to long[] ShapeList fixed

[saalfeld] dimensions int[] to long[] AbstractLocalizableCursor fixed

[Stephan] Changed all types and displays

[Stephan] Fixed Array again

[Stephan] Fixed outofbounds

[saalfeld] Revert changing dimensions from int[] to long[].

[saalfeld] * CellCursors implement the recent changes in the hierarchy.

[saalfeld] * updated DynamicCursors

[saalfeld] * ImagePlusCursors adapted

[Stephan] Added test for DynamicContainer

[llindsey] Fixed setZero / setOne mixup

[Curtis Rueden] Support for NIO-backed arrays in array containers.

[saalfeld] Non-compiling intermediate commit

[saalfeld] Fixed bad casts in DynamicContianer implementations for basic types.

[saalfeld] finalized dimIsOutOfBounds[]

[saalfeld] Fixed wrong initialization of ShapeListPositionableCursor

[saalfeld] Fixed wrong initialization of ShapeListPlaneIterator (new name? not yet ;))

[saalfeld] simplified ArrayLocalizableCursor.fwd()

[saalfeld] * Cell.getPosGlobal is Cell.plobalPositionToIndex now

[saalfeld] Half way done some renaming, have to do something else now :(

[Johannes Schindelin] Fix for Bio-Formats 4.2

[Johannes Schindelin] Adjust .mailmap

[Curtis Rueden] Add method to obtain backing storage array as an Object.

[Stephan] Added function to convert into Matrix4f

[bdezonia] fixed overflow in the calculation of getMaxValue()

[preibisch] Fixed small bug in Display

[preibisch] Implemented HyperSphereIterator (n-dimensional)

[saalfeld] added a main method to HyperSphereIteratorTest

[jan.funke] ImagePlusContainer: getCorrectDimensionality considers 5D images now

[saalfeld] intermediate commit making ImagePlusContainers 5d

[saalfeld] * minimize number of dimensions and the respective array

[saalfeld] 5d-ification of ImagePlusContainer passed JUnit test

[saalfeld] As expected, the test was inappropriate and testing

[saalfeld] cosmetics

[saalfeld] Fixed dimensions not being properly reduced,

[saalfeld] fixed messed up dimension order when creating

[saalfeld] * merge master LOCI

[saalfeld] refactoring to the updated naming scheme whose main components are

[saalfeld] * comments added

[saalfeld] triaage bug, stop test at failure

[saalfeld] merged imageplus5d ContainerTest

[saalfeld] finalized some parameters that should be final

[saalfeld] Removed link-chain concept.  Instead of attaching Iterator/

[bdezonia] whitespace change - testing git works

[bdezonia] whitespace change

[bdezonia] whitespace change

[saalfeld] LinearInterpolator1D, NearestNeighborInterpolator2D and 3D

[saalfeld] Interpolators implemented but not yet tested...

[saalfeld] * DirectAccessContianer.update( ... ) takes an Object instead

[preibisch] Added some Average/Min/Max functions for java.util.List

[saalfeld] Cell.getDimensions( int[] ) -> Cell.dimensions( int[] )

[Curtis Rueden] Maven version of imglib project.

[Curtis Rueden] Fix test class package names.

[Curtis Rueden] Require Java 1.6 for imglib.

[Curtis Rueden] Add 2D planar arrays to array container.

[Curtis Rueden] Use a common interface for planar access classes.

[Curtis Rueden] Add deployment server information.

[Curtis Rueden] Adjust license layout to match text of other projects.

[Curtis Rueden] Add/update project description blurbs.

[Curtis Rueden] Tweak SCM connection strings.

[Curtis Rueden] Reorganize imglib into sub-projects.

[preibisch] Small changes in gauss kernel creation method

[saalfeld] * parameter refactor

[saalfeld] Fixed a long standing bug in CellLocalizableByDimCursor.  It

[preibisch] Fixed the same bug in CellLocalizableByDimOutOfBoundsCursor, this was a really nasty bug

[preibisch] Fixed bug that Container.compareStorageContainerCompatibility() is done by each instance of Container, for example CellContainer has to check if the cell size is the same.

[preibisch] Small changes in GaussianConvolution, shares the static FloatArray3D method now

[preibisch] Added a generic ImageCalculator

[preibisch] Fixed small bug

[preibisch] Some renamings

[Curtis Rueden] Better behavior for PlanarArray.getPlane(int).

[saalfeld] Fixed the master bug in CellPositionableRasterSampler that made

[preibisch] Small changes in naming

[preibisch] Added ImageConverter and the Converter Interface

[preibisch] Removed unnecessary cast to <T> that created a warning

[preibisch] Image.clear() clears all pixels now

[preibisch] LocalNeighborhoodCursor can return the parent cursor

[preibisch] Added GaussianConvolution2 which can convert too

[preibisch] Fixed another crazy bug in fwd(dim) and bck(dim) in the cell cursors. Oh man alter!!

[preibisch] Added AdvancedType which is able to do more math functions and exemplarily implemented it for DoubleType

[preibisch] Added means to split an Image into Chunks that can be processed multithreaded

[preibisch] ImageConverter is multithreaded now

[preibisch] Added some converters and functions

[preibisch] Implemented min(a,b) and max(a,b) for ComparableType

[preibisch] GaussianConvolution supports now various input/output types

[preibisch] SpecialPoint enum is now public

[bdezonia] fixed an issue with getUnsignedInt() failing to cast and returning negative values

[Johannes Schindelin] Work around a bug of Sun's JavaC

[bdezonia] fix calc of unsigned value from signed value

[Curtis Rueden] Ignore Eclipse metadata files.

[preibisch] small fix

[preibisch] ImageCalculator is multithreaded

[preibisch] Renamed AdvancedType to ExponentialMathType

[preibisch] Updated GaussianConvolution with unlimited precision to support ExponentialType only

[preibisch] Subpixel localization

[preibisch] Sorts now by correlation coefficient and if it is equal by size of overlapping area

[preibisch] Fixed small bugs in SubpixelLocalization

[preibisch] Removed unecessary import

[saalfeld] Introduces IterableRaster and separated imglib Iterator from java Iterator.

[preibisch] Min and Max methods do not create a new type but return one of the input types

[preibisch] Multithreaded computation of min and max value of an image

[preibisch] Normalize and image to [0...1] using the ComputeMinMax algorithm and a new norming function

[preibisch] can change input image and sigma now

[preibisch] First working and tested implementation of n-dimensional ScaleSpace (multithreaded)

[preibisch] Added gpl

[preibisch] DifferenceOfGaussian can compute Gaussian convolutions after one another or paralell

[Johannes Schindelin] Fix compile error

[preibisch] uint8 is now opened as UnsignedByteType

[preibisch] removed ambiguity in mathlib

[preibisch] Removed unnecessary imports

[preibisch] Update supresswarnings

[preibisch] Added PlanarContainer

[saalfeld] comment in Type

[saalfeld] removed unnecessary getStorageArrayAsObject method

[saalfeld] Added PlanarContainer and respective cursors, an n-d variant of how

[Curtis Rueden] Sort new classes into respective sub-projects.

[llindsey] NumericType no longer implements ComparableType

[saalfeld] Fix broken ImagePlus container.  Data mirror had to be cleared,

[saalfeld] NumericType still extends Type ;)

[saalfeld] Remove ComparableType because it was one of these empty

[saalfeld] Replace T Type<T>.clone() by T Type<T>.copy().  Sun's compiler cannot

[Curtis Rueden] Fix dependencies for imglib-io.

[Curtis Rueden] Move more algorithms into imglib-algorithms.

[Curtis Rueden] Split MathLib into two separate utility classes.

[Curtis Rueden] Remove PlanarAccess class with wrong package.

[Curtis Rueden] Rename tests to conform to Maven convention.

[Curtis Rueden] Rename tests to conform to Maven convention.

[llindsey] Basic hack test to show shear problem I'm seeing.

[llindsey] Fixed minor oops.  Discovered wierdness.

[Curtis Rueden] Fix bug Barry found in Unsigned12BitType.

[saalfeld] Fix PlanarLocalizableCursor, index decrement was 1 too large

[saalfeld] moved TestROIAlgorithm into imglib-io

[saalfeld] Fix PlanarLocalizableCursor, index decrement was 1 too large

[saalfeld] Added InverseFourierConvolution to imglib-algorithm which performs

[saalfeld] use numDimensions member field

[saalfeld] Fix NullPointer in PlanarContainer with more than 2 dimensions on

[saalfeld] use numDimensions member field

[saalfeld] Fix NullPointer in PlanarContainer with more than 2 dimensions on

[saalfeld] Added InverseFourierConvolution to imglib-algorithm which performs

[preibisch] Moved Function and Converter implementations to algorithm package

[preibisch] Corrected wrong commit of mine, added files

[preibisch] Moved general converters back to core

[preibisch] Removed dependency on Java3d

[preibisch] added supresswarnings for rawtypes

[preibisch] removed algorithm based on transform3d

[preibisch] Renamed MathLib in core to Util

[saalfeld] Replace boundary calculation by mpicbg interface

[saalfeld] Fix previous commit: Use dimensions!

[preibisch] Disabled virtual display for coordinate transforms

[saalfeld] Fix previous commit: max pixels are at dim - 1

[preibisch] Types can return the entitiesPerPixel

[preibisch] Low level access to create basictypecontainers from basic type arrays

[saalfeld] getIndex is inherited from TypeImpl already

[saalfeld] Simplify hasNext-checking in PlanarCursor for a very minor speedup.

[Curtis Rueden] Add a simple performance benchmark.

[Curtis Rueden] Add "expensive" test, for comparison.

[Curtis Rueden] Add ability to save results to a CSV file.

[acardona] ShapeList: added getShapeLists(), which returns a new list

[preibisch] DifferenceOfGaussian can keep the image

[admin] SubpixelLocalization supports maxima tolerance

[admin] Added an implementation of Localizable

[preibisch] Made some member variables protected

[Curtis Rueden] Scripts for generating benchmark data and charts.

[Curtis Rueden] Build code with Maven before running benchmark.

[Curtis Rueden] Only enable a few specific lines by default.

[preibisch] Fixed typo found by Albert

[saalfeld] Fixed broken Iterator in PlanarLocalizableCursor.  Thanks to Jan Funke

[saalfeld] Fixed broken Iterator in PlanarLocalizableCursor.  Thanks to Jan Funke

[preibisch] Started documentation

[preibisch] Changed indentation

[llindsey] Imglib Histogram

[llindsey] Added basic test for Histogram

[llindsey] HistogramTest now more unit-test-like.

[acardona] First attempt at generic math with images.

[acardona] Second round of generic image math: added numbers.

[acardona] Added a few finals.

[acardona] Fixed error in order of operations.

[acardona] Properly compose the operations.

[acardona] Minor issues and comments.

[acardona] Operations: replaced NumericType with RealType

[acardona] Operations: the math is done with floats, and with a float output.

[acardona] Operations: finally proper results.

[acardona] Operations: fixed generics with lots of hand-holding from Preibisch

[acardona] Operations: renamed to Compute, and do it all in doubles.

[acardona] Operations: moved to scripting.math package

[Curtis Rueden] Move scripting classes to imglib-scripting.

[Curtis Rueden] Add imglib-scripting to umbrella POM.

[acardona] Operations: added all from java.lang.Math,

[acardona] Operations: made Compute throw exceptions

[acardona] Operations: added future-proof message.

[acardona] Operations: cleaned up and fixed AN.asType(Number)

[acardona] Operations: getImages with a generic Image<?>.

[acardona] Operations: rgb package for RGB-related operations.

[acardona] Operations: fixes for Channel

[acardona] Scripting: added benchmark test (current ~3x slower)

[acardona] Scripting Cbrt, and fixed error in one of the constructors.

[acardona] Scripting: added benchmark for heavy operations, shows 1.1x penalty only.

[acardona] Scripting: minor fixes.

[acardona] Scripting: abstracted unary and binary operations,

[Curtis Rueden] Add Game of Death example.

[acardona] Scripting: down to 1.8x slower for light operations,

[acardona] Scripting: finished math2 package, performance is ~1x !

[acardona] Scripting: added forgotten old class rgb.op.RGBAOp -- will be deleted soon.

[acardona] Scripting: removed old math package and associated rgb package.

[acardona] Scripting: renamed math2 and rgb2 to math and rgb.

[acardona] Scripting: fixing lack of update of the test math package name.

[acardona] Scripting: added some documentation to core classes.

[acardona] Scripting: close cursors instead of image.removeAllCursors()

[saalfeld] Added simplified and thus faster 2d-cursors for Planar and ImagePlus.

[preibisch] Updated POM file to include dependencies on imglib-ij and imglib-io

[preibisch] Added convienient show method

[preibisch] Scripting is multithreaded

[preibisch] Removed unnecessary imports and added a SuppressWarnings

[acardona] Scripting: fixed errors in rgb package classes.

[acardona] Scripting: new Process class to wrap Algorithm and OutputAlgorithm

[acardona] Scripting: indicate what IFunction error in duplication prevented Compute from running multithreaded.

[acardona] Scripting: indicate what IFunction error in duplication prevented Compute from running multithreaded.

[acardona] Scripting: fixed error in Luminance

[acardona] Scripting: package algorithm

[acardona] Scripting: renamed rgb package to color, and added new algorithm package

[acardona] Fix by Preibisch on DownSample.

[acardona] Scripting: Compute got two convenience methods

[acardona] Scripting: fixes for algorithm package, added more algorithms.

[acardona] Scripting: all algorithms now extend Image,

[acardona] Scripting: proper HSB image composition from hue, saturation and brightness channels.

[acardona] Scripting: documented channel value ranges for HSB and RGBA.

[acardona] Scripting: generalized Compute to also output RGBALegacyType images,

[preibisch] can get/set new dimensions and offset for individual dimensions

[acardona] PlanarContainer: fixed typos and indentation.

[acardona] Scripting: added Scale2D, Scale3D, Affine2D and Affine3D.

[acardona] Scripting: reverse order of 2 parameters in Affine3D

[acardona] Scripting: added Resample, and some documentation,

[acardona] Scripting: added docs to Affine3D

[acardona] Added LOCI.open

[acardona] Scripting: renamed mpicbg.imglib.scripting to script.imglib

[acardona] Scripting: Resample now accepts an array of target dimensions

[acardona] Scripting: generalized inputs of Affine3D and relatives.

[acardona] Scripting: ensure that RGBA reads only 8 bits for each channel.

[acardona] Scripting: Affine3D should correct the Z dimension only if third row is 0, 0, 1

[acardona] Scripting: DoGPeaks in script.imglib.analysis package

[acardona] Scripting: renamed Normalize to NormalizeSum, and added Normalize (min and max)

[acardona] Scripting: added PickPeaks, which uses PickImagePeaks algorithm.

[acardona] Scripting: fixed Normalize compilation error with javac.

[acardona] Scripting: added math Close, Open, Dilate, Erode

[Curtis Rueden] First version of new imglib-io ImageOpener.

[acardona] Scripting: added Average and Difference to math package.

[acardona] Scripting: added another benchmark.

[acardona] Scripting: added documentation to Compute

[Johannes Schindelin] Remove bogus import

[acardona] Scripting: remove another bogus import (eclipse: !@#$%^&)

[Curtis Rueden] Add copyright notices to imglib-io sources.

[Curtis Rueden] Various improvements to ImageOpener.

[Curtis Rueden] Ignore toplevel target directory.

[Curtis Rueden] Add simple test class for ImageOpener.

[acardona] Scripting: Normalize will become an empty image if min == max.

[acardona] Scripting: remove bogus test in Normalize, and added docs

[preibisch] Added fast population of plane if not a PlanarContainer

[acardona] DifferenceOfGaussian now accepts double or double[] for the sigmas.

[acardona] Scripting: added util methods

[acardona] Scripting: PickPeaks must take a single-channel image.

[acardona] Scripting: ensure that all cursors related to the IFunction

[acardona] Scripting: DogPeaks now has more constructors and an asPoints method.

[acardona] Scripting: remove unused imports from DoGPeaks

[Curtis Rueden] Fix imglib-io and imglib-scripting dependencies.

[acardona] Scripting: removed unused imports from Normalize

[acardona] Scripting: removed unnecessary warning suppression.

[leek] Added initial implementation of labeling + connected components algorithm + tests

[acardona] Scripting: started SIO class, to ease the pain for I/O in scripting.

[unknown] Initial labeling checkin

[Johannes Schindelin] Add a simple wrapper a la IJ

[Curtis Rueden] Add JUnit dependency to imglib-algorithms test.

[leek] Added watershed algorithm + tests, added copyrights

[leek] Reset file modes back to 644 (sorry)

[acardona] Adjusted error printout of ImagePlusAdapter.

[acardona] Scripting: removed SIO, documented ImgLib and added reverse wrap method

[acardona] Scripting: all operations now implement ImageComputation,

[acardona] ImageJVirtualStack has to extend VirtualStack and not ImageStack

[acardona] Scripting: ImgLib.open has to use wrap(IJ.openImage(pathOrURL))

[acardona] Scripting: ImgLib.save must return a boolean

[preibisch] Renamed LogicType interface into BooleanType

[stephan.preibisch] ImageOpener reads calibration now

[stephan.preibisch] Fixed bug in ImageOpener, crashed

[Curtis Rueden] Remove ImageJ dependency from histogram code.

[Curtis Rueden] Convert HistogramTest to JUnit test.

[Curtis Rueden] Add performance benchmark for histograms.

[Curtis Rueden] Add Fiji_Plugins.jar dependency to imglib-algorithms.

[Johannes Schindelin] Fix compilation on MacOSX

[Curtis Rueden] Clean up and standardize POMs a bit.

[preibisch] Added KDTree to imglib-algorithm

[stephan.preibisch] Removed dependency on fiji-plugins as kdtree is in imglib-algorithms now

[stephan.preibisch] moved kdtree into a new package

[stephan.preibisch] DifferenceOfGaussian can update detection threshold now

[stephan.preibisch] Added some more statistic helper functions

[stephan.preibisch] Updated KDTree to get rid of warnings

[preibisch] Started Adaptive selection of peaks

[leek] Fixed bug in labeling type display, added Carolina Wahlby's watershed segmentation algorithm

[stephan.preibisch] DoG peak has copy method

[preibisch] Added Radius based neighbor search and added GPL licensing

[preibisch] Added adaptive non maximal suppression as possible step after DoG detector

[leek] Moved gradient watershed algorithm to an OutputAlgorithm class

[leek] Got rid of unused imports

[preibisch] Changed line endings in imglib core to unix

[preibisch] Changed line endings in gameofdeath to unix

[preibisch] Changed line endings in algorithms to unix

[preibisch] Changed line endings in io to Unix

[preibisch] Added convenience implementations of typical combinations of interfaces for algorithm development.

[saalfeld] updated outofbounds

[saalfeld] updated sampler

[saalfeld] updated location

[saalfeld] updated interpolation

[saalfeld] updated image

[saalfeld] updated algorithm

[saalfeld] testshapelist nearest neighbor

[Johannes Schindelin] Re-add /imglib*.jar to the .gitignore file

[saalfeld] fix false return to continue in

[saalfeld] fix OutOfBoundsConstantValue bug not updating

[saalfeld] fix LinearInterpolator2D/3D and

[saalfeld] fix multiplication complex with real

[Johannes Schindelin] Fix DOS line endings

[saalfeld] kdTree cosmetics

[saalfeld] rename Dimensionality into EuclideanSpace

[saalfeld] convert win line endings to unix

[saalfeld] introduced Function interface

[saalfeld] introduced Function interface

[saalfeld] added comment

[saalfeld] more comments

[saalfeld] added FiniteSpace

[acardona] Added BinaryInterpolation2D, based on Johannes' vib.BinaryInterpolator

[acardona] Added a test for BinaryInterpolator2D.

[acardona] BinaryInterpolation2D: enable setting the weight and calling process() again.

[preibisch] ImageTransform can change Interpolation without need to re-instantiate

[preibisch] Added DCT Interpolation

[preibisch] LinearInterpolation for RealType in 2d added

[preibisch] Using PeriodicFactory

[bdezonia] Fixed a bug in set() where first bit might be set inconsistently when passing negative numbers.

[Curtis Rueden] Move TestBinaryInterpolation to imglib-ij project.

[saalfeld] ImgLib2 derived from sampler-link:

[preibisch] Removed expensive arraycopy methods (they are only faster for large arrays > ~30)

[preibisch] Removed new position array which is already inherited

[preibisch] Maybe small enhancement to the "ROICursor", uses a final int for dim now when iterating

[preibisch] Small typo-fix for deprecated opener

[preibisch] Added Lanczos interpolation

[preibisch] Removed weights, sinc is normalized already

[saalfeld] updated diagram

[preibisch] Fixed override hierarchie for Differenceofgaussian

[Johannes Schindelin] ImagePlusAdapter.wrap: throw an exception when not able to wrap the image

[Curtis Rueden] Fix up ImgLib POM structure.

[acardona] Updated BinaryInterpolation2D to enable finer reuse.

[acardona] Recovering classes after mishap.

[acardona] scripting: Histogram can create a plot, a plot window, or an Image of the plot.

[acardona] scripting: ChartUtils aggregates chart-to-image methods.

[saalfeld] work in progress...

[saalfeld] started documentation

[saalfeld] added injective intervals as a contract to

[saalfeld] work in progress...

[saalfeld] more work in progress...

[saalfeld] * moving container samplers into container

[saalfeld] adapted and moved containersamplers

[Curtis Rueden] Serve Maven artifacts using Apache on port 80.

[saalfeld] more (unjustified?) changes...

[preibisch] stupid commit of the classpath before removing it

[preibisch] Try to open and display with arraycontainer

[preibisch] First ImgLib2 that can open and display using ArrayContainer

[preibisch] Fixed ImageJVirtualDisplay

[saalfeld] removed eclipse project file

[acardona] Remove unused import.

[acardona] Added jfreechart and jcommon jars as dependencies of imglib-scripting.jar

[Curtis Rueden] Fix JFreeChart versions.

[saalfeld] updated diagram

[preibisch] First successful test

[saalfeld] check diagram for changes

[saalfeld] container fixed (?)

[preibisch] Started fixing Array

[saalfeld] fixed names of some container related stuff

[preibisch] Fixed Array (?)

[preibisch] Removed unnecessary import

[saalfeld] more namefixes in containers

[saalfeld] specialize container cursor in the interface

[preibisch] Fixed openanddisplay example

[preibisch] Fixed Array, GaussianConvolution works now

[preibisch] Started fixing Interpolators

[preibisch] More Interpolator changes

[preibisch] Fixed AbstractInterpolator

[preibisch] AbstractInterpolator requires EuclideanSpace for numDimensions call

[preibisch] Removed ContainerInterpolator and ContainerInterpolatorFactory

[preibisch] Fixed NearestNeighborInterpolator

[preibisch] Fixed RoundRasterPositionable

[preibisch] NearestNeighborInterpolator should work

[preibisch] ImageTransform works again, with NearestNeighborInterpolation and OutOfBoundsValue

[preibisch] Removed test for affine

[preibisch] Nothing

[preibisch] Renamed DirectAccessContainer into NativeContainer

[preibisch] Container is now Img, NativeContainer will become Container

[preibisch] Finished renaming Img

[preibisch] Forgot one...

[preibisch] Splitted Type into Type and NativeType. Types which have a NativeType implement NativeTypeCapable

[tobias.pietzsch] added javadoc comments

[tobias.pietzsch] position to flat array index translation

[saalfeld] renamed indexer and added offset array

[preibisch] Refactored clone to copy in Types

[preibisch] Fixed Types (there are NativeTypes or Types only)

[preibisch] Started fixing DynamicContainer

[preibisch] Moved dynamic samplers to container directory

[preibisch] Continued working on DynamicContainer

[preibisch] Fixed DynamicCursor and DynamicLocalizingCursor

[preibisch] Finished DynamicContainer

[tobias.pietzsch] IntervalIndexer can use offsets

[tobias.pietzsch] Array uses IntervalIndexer now

[saalfeld] Added ARGBScreenImage and a simple not yet

[preibisch] Continued working on Types

[preibisch] Continued working on Types

[preibisch] Fixed DevUtil

[preibisch] Generics Fix in Opener

[saalfeld] * fixed alpha value in RealARGBConverter

[Curtis Rueden] Update to ImageJ 1.44.

[saalfeld] fixed missing refactorings

[preibisch] Started working on ROI

[tobias.pietzsch] use IntervalIndexer in DynamicContainer

[tobias.pietzsch] git-ignore .class files and eclipse .project

[tobias.pietzsch] starting CellContainer implementation

[saalfeld] added bytescreenimage and respective floatconverter

[preibisch] Fixed ComplexTypes

[saalfeld] updated diagram:

[preibisch] Fixed all Types...

[saalfeld] minor fixes in dynamiccontainer, uses

[Curtis Rueden] Tweak ImageJ1 version.

[saalfeld] renamed coordinate access the previously announced

[preibisch] Refactored DynamicContainer to ListContainer

[saalfeld] XYProjector didn't get the refactors...

[saalfeld] removed most non-core elements for conversion

[saalfeld] put back fixed algorithms

[preibisch] Small change in ListContainer

[saalfeld] iterator comment

[preibisch] Fixed small bug

[preibisch] Removed Image import from OrthoSliceiterator

[saalfeld] added Util methods to create dimension

[saalfeld] fixed missing refactoring in constantvaluefactory

[saalfeld] fixed missing corrections in the naming scheme

[Curtis Rueden] Merge imglib2 source into Maven project structure.

[preibisch] Added IJ_PREFS.txt to gitignore

[preibisch] Fixed DevUtil

[saalfeld] introduce LinearRange as an interface that can set and read a min and max

[preibisch] Removed all old display stuff

[preibisch] Fixed ImgCursor

[tobias.pietzsch] Img now has firstElement() instead of createVariable()

[tobias.pietzsch] removed create() from Sampler

[preibisch] Fixed OutofBoundsValue, Interpolator and the Screenimages for .firstElement()

[preibisch] Fixed warning in array

[preibisch] Started adapting PlanarContainer

[Curtis Rueden] Add a project, imglib-ui, for GUI components.

[Curtis Rueden] Regenerate ARGB Image with each call to image()

[preibisch] Added PlanarAccess, continued on PlanarContainer

[saalfeld] finished virtual IntervalIterators using the indexer

[preibisch] Contiuned working on PlanarContainer

[tobias.pietzsch] renamed some abstract classes

[saalfeld] fixed name of randomAccess method in RandomAccessInterval

[tobias.pietzsch] implemented CellCursor

[saalfeld] added constructor with dimensions only for IntervalIterator

[saalfeld] added AbstractLocalizable

[preibisch] PlanarCursors are ready, not tested yet

[saalfeld] abstractLocalizable implements EuclideanSpace

[saalfeld] added localizing version of virtual interval iterator

[preibisch] Almost done Planar

[tobias.pietzsch] numPixels() is not required because there is size()

[tobias.pietzsch] still working on CellContainer...

[saalfeld] removed numPixels in AbstractImg

[saalfeld] fix numPixels calls in planar and list

[saalfeld] added .mailmap

[saalfeld] fixed mirroring out of bounds strategies

[saalfeld] simplified out of bounds with constant value

[saalfeld] more fixes in mirror out of bounds

[preibisch] Finished PlanarContainer, not tested yet

[preibisch] Fixed OLD gaussianconvolution

[preibisch] Fixed NNeightorInterpolator

[saalfeld] restored diagram

[saalfeld] OutputAlgorithm typed after the output data, not its type

[preibisch] Removed giving Type instance to BasicTypeContainerFactory when calling createBit/Byte/Int/.../instance

[preibisch] added the good old open display gauss transform test

[saalfeld] out of bounds periodic compiles

[preibisch] Renamed test, Mirror Double Boundary fails

[preibisch] Fixed one(of more) bugs in planarcontainer

[tobias.pietzsch] small beautifications.

[tobias.pietzsch] cursors for CellContainer.

[tobias.pietzsch] git-ignore class files

[preibisch] Adapted Algorithms to new interface

[preibisch] Fixed OrthoSliceIterator so that it is not initialized with (-1,0)

[saalfeld] fixes for mirror outofbounds

[saalfeld] abstractmirroroutofbounds fixed to return offset compensated coordinates

[saalfeld] argbscreenimage fixed according to the simplified array constructors

[preibisch] Fixed devutil for new array constructor

[saalfeld] updated diagram

[preibisch] Removed <T extends Type<T>> whereever Type is not really necessary

[preibisch] Fixed bug that PlanarLocalizingCursor was not extending PlanarLocation

[preibisch] Added constructor to ListContainer where it can be instantiated with Collection<T>

[saalfeld] added svg version of diagram

[saalfeld] added generic parameter to RealARGBConverter to process all reals

[Curtis Rueden] Fix OutOfMemoryErrors when generating AWT images.

[tobias.pietzsch] fixed equalIterationOrder in ListContainer and Array

[tobias.pietzsch] CellContainer should work now (not tested though)

[tobias.pietzsch] CellContainer fixes and OpenAndDisplay test.

[preibisch] Fixed override of localize methods to use local int[] position instead of super long[] position array

[preibisch] PlanarContainer working!

[preibisch] Removed some spaces

[preibisch] Small changes

[preibisch] ImgFactory can now create a new ImgFactory of itself for a different T. This might not work and therefore throws an exception.

[preibisch] LOCI ImageOpener works again, calibration is still missing...

[Curtis Rueden] Update ImgPanel to use ImageOpener.

[preibisch] Small changes in ImageOpener to fix correct Metadata import

[preibisch] Fixed the now so-called FlatIterator and added a FlatLocalizingIterator

[preibisch] Worked on the rectangular roi, now SubImage

[preibisch] Noticed that Saalfeld did that already before, at least I found some ancient,

[preibisch] Added static methods to get min[] max[] from Interval and RealInterval

[preibisch] Our Iterator was lacking a hasNext() method, added it

[preibisch] Finished SubImage, not tested yet

[preibisch] SubImage works, tested with Gaussian convolution....

[preibisch] Added a version of GaussianConvolution that can deal with SubImages

[preibisch] Updated the inverse code from Johannes

[preibisch] put in the code

[tobias.pietzsch] bugfix in CellContainer cursors

[tobias.pietzsch] cell need not necessarily contain NativeTypes

[tobias.pietzsch] CellContainer returns it's own factory so that containers

[tobias.pietzsch] example: copy and display 2D image using CellContainer

[tobias.pietzsch] CellContainerFactory.imgFactory() returns a CellContainerFactory with the same

[tobias.pietzsch] fixed comment

[tobias.pietzsch] move new CellContainer to package mpicbg.imglib.container.cell.

[Curtis Rueden] Initial version of ImgLib operations API.

[bdezonia] eliminate backup files

[bdezonia] partial implementation of rev 3 (proof of concept) of ops code

[bdezonia] minor fix to image creation code

[bdezonia] package reorganization

[bdezonia] forgot to delete old package structure. doing so now.

[tobias.pietzsch] there was no need to use a generic type parameter in Cell

[tobias.pietzsch] CellContainerFactory creates CellContainers.

[tobias.pietzsch] some CellContainer tests

[bdezonia] note some TODOs for future reference

[bdezonia] quick implementation to outline how a Condition could be constructed with a DistanceFunction.

[saalfeld] Added final classes ExtendedRandomAccessibleInterval and

[tobias.pietzsch] ArrayContainer creates Arrays.

[tobias.pietzsch] more CellContainer tests

[bdezonia] since work is all done in doubles remove unnecessary generics

[saalfeld] * fixed mirroring outofbounds (single and double boundary)

[saalfeld] * fixed periodic outofbounds strategy, added junit test

[bdezonia] added Constraints to the imglib-ops subproject

[bdezonia] In imglib subproject only: towards eliminating compile errors in Imglib2 I replaced all references to the class mpicbg.imglib.image.Image to references to the mpicbg.imglib.container.Img interface.

[tobias.pietzsch] CellRandomAccess is much faster now.

[tobias.pietzsch] benchmark copying between cell and array containers using cursor and randomAccess

[saalfeld] updated diagram

[saalfeld] fixed AbstractImgRandomAccess using int[] instead of long[]

[saalfeld] planarcontainer and access do not work at all

[bdezonia] made many classes and class members final. also got rid of code where functions may return their last evaluation. that code would not have been threadsafe.

[bdezonia] renamed IntegralScalarFunction to IntegerIndexedScalarFunction

[bdezonia] this file belonged in previous commit

[Curtis Rueden] Add imglib-ops to toplevel build.

[bdezonia] implement ComposedImageFunction to be able to replicate rev2 ops functionality

[bdezonia] renamed the null function to the easier to handle NullFunction

[tobias.pietzsch] fixed PlanarContainer issue

[tobias.pietzsch] removed overwriting of long[] position field by int[] position.

[tobias.pietzsch] copying benchmark and unit test for planar container.

[preibisch] Updated to the Multithreading in master

[preibisch] Added constructor with long[]

[preibisch] Added getIndex() method and int[] constructor

[preibisch] Added int2long and long2int methods for arrays

[preibisch] Worked on LocalNeighborhoodCursor

[preibisch] Removed LegacyRGBType, is now ARGBType

[acardona] Updated most of script.imglib for imglib2, still some work to go.

[acardona] Tentative upgrade for NormalizeImageFloat

[acardona] Partial fixes for many script.imglib.algorithm classes.

[acardona] Proper imglib2 upgrade for NormalizeImageFloat

[acardona] Upgraded 3 more algorithms.

[acardona] More algorithms upgraded.

[acardona] More upgrades for algorithms.

[acardona] Upgraded BinaryInterpolation2D

[acardona] More fixes for algorithms.

[acardona] Added Util.getArrayFromValue(long, int)

[acardona] Upgraded FloydSteinbergDithering algorithm

[acardona] Tentative upgrade for ImagePlus wrapper classes.

[saalfeld] refactor size into dimension, minor comment corrections

[saalfeld] renamed OrthoSliceIterator to OrthoSliceCursor

[acardona] Fixed error in FloydSteinbergDithering: "moveTo" is now "setPosition", not "move".

[acardona] UnsignedByteScreenImage now generates a proper BYTE java.awt.Image

[acardona] ImgProxy: add method to grab underlying Img instance.

[acardona] Compute: proper checking of image compatibility.

[acardona] ScreenImage: updatable ARGBScreenImage and UnsignedByteScreenImage

[acardona] Proper color model for ARGBScreenImage

[acardona] Upgraded ShapeList classes.

[acardona] Fixed LUT of UnsignedByteScreenImage

[acardona] Scripting: removed obsolete import in HSB

[acardona] Scripting: fixed Histogram

[tobias.pietzsch] abstract RandomAccess classes based on int instead of long.

[tobias.pietzsch] base ArrayRandomAccess on AbstractImgRandomAccessInt.

[tobias.pietzsch] abstract Cursor classes based on int instead of long

[tobias.pietzsch] base ArrayCursors on int AbstractCursors

[tobias.pietzsch] fixed some javadoc comments.

[tobias.pietzsch] Test Array-to-array copy using compatible iteration order.

[tobias.pietzsch] container benchmarks use int[] positions.

[tobias.pietzsch] cleaned-up PlanarContainer, faster cursors and RandomAccess.

[tobias.pietzsch] added javadoc in CellContainer.

[bdezonia] added test code to average multiple images together. temporarily hacked AverageFunction to smoothly handle 3d averaging given a 2d coordinate. Must address in a general way later.

[tobias.pietzsch] ImagePlusContainer and ImagePlusAdapter. not tested yet.

[tobias.pietzsch] removed unused package.

[tobias.pietzsch] small PlanarContainer fixes

[tobias.pietzsch] fixed PerformanceBenchmark

[tobias.pietzsch] removed obsolete packages

[tobias.pietzsch] fixed ImagePlusAdapter.convertFloat()

[tobias.pietzsch] clean up imports.

[tobias.pietzsch] started fixing ImageJFunctions

[tobias.pietzsch] fixed javadoc comments.

[tobias.pietzsch] refactored "*Impl" into "Abstract*"

[tobias.pietzsch] faster n-dimensional PlanarCursors

[tobias.pietzsch] faster cell cursors.

[bdezonia] reorganize package structure in imglib-opps : break out imglib.ops.function into subcategories that delineate the number of paramaeters each function implmementation can accept

[saalfeld] * remove InjectiveInterval and RealInjectiveInterval (thanks to B.D. for spotting)

[saalfeld] updated diagram respectivly

[saalfeld] * RandomAccessibleInterval extends RandomAccessible

[tobias.pietzsch] use int[] positions to fill CellContainer in CellRandomAccessBenchmark.

[saalfeld] replace the term Container by Img in all places Eclipse did manage to...

[tobias.pietzsch] fixed some names that eclipse didn't catch.

[bdezonia] implementation of a few functions in ops for exploitation by IJ2 plugins. Use of imglib-scripting functions can replace these in the future.

[acardona] Package container -> img

[saalfeld] renaming container->img in  ImgPanel

[saalfeld] half done Round and Floor walkers and connectors...

[saalfeld] deleted half of non-working packages, added package comments

[saalfeld] moved shapelist accessors and added pakcage comment for later fixing

[saalfeld] added half implementation of a LocalizingFlatIterator---chack later

[saalfeld] moved shapelist accessors and added pakcage comment for later fixing

[tobias.pietzsch] fixed NearestNeighborInterpolator

[bdezonia] added operators to support simple IJ2 plugin capabilities

[Johannes Schindelin] Remove a few non-compiling classes for now

[Johannes Schindelin] Positionable's moveTo() method has been renamed to move()

[acardona] Added Util.computeLength(long[])

[acardona] Restored missing algorithm HoughLineTransform and HoughTransform

[acardona] Fixed scripting of HoughLineTransform

[acardona] Fixed container => img for ImageTransform algorithm

[acardona] Fixed container => img for FloydSteinbergDithering

[acardona] Tentative fix for RegionOgInterestCursor

[acardona] Starting fixes for scripting ImgLib class.

[saalfeld] Added Util.computeLength(long[])

[saalfeld] Restored missing algorithm HoughLineTransform and HoughTransform

[saalfeld] Fixed scripting of HoughLineTransform

[saalfeld] Fixed container => img for ImageTransform algorithm

[saalfeld] Fixed container => img for FloydSteinbergDithering

[saalfeld] Starting fixes for scripting ImgLib class.

[saalfeld] Tentative fix for RegionOgInterestCursor

[saalfeld] * cleaned up some rough edges in Types

[saalfeld] * cleaned up some rough edges in Types

[saalfeld] deleted remaining non-working packages from imglib core

[saalfeld] * cleaned up remaining rough edges in Types

[saalfeld] on the way to make the basic test work again...

[saalfeld] * cleaned up remaining rough edges in Types

[saalfeld] removed non-working tests

[acardona] Tentative port of Larry Lindsey's histogram and roi classes to imglib2

[acardona] Restored mpicbg.imglib.algorithm.* interfaces but in imglib-algorithm

[acardona] More container => img

[acardona] Fixes for script.imglib.algorithm.

[acardona] Removed 2 obsolete classes related to histogram.

[saalfeld] refactor dim to d in interfaces, i was tired of renaming them after eclipse

[saalfeld] fixed Floor, Round and Floor and Round linkers

[saalfeld] package move in broken interpolators, sorry for the potential merge conflict

[saalfeld] refactor dim to d in interfaces, i was tired of renaming them after eclipse

[saalfeld] fixed Floor, Round and Floor and Round linkers

[saalfeld] Fixed and tested Johannes' basic tests.

[tobias.pietzsch] fixed InterpolatorFactories

[tobias.pietzsch] renamed the move() parameter from "position" to the more appropriate "distance".

[tobias.pietzsch] added comments: Do not put specialised Interpolators into stable branch.

[tobias.pietzsch] feeding my inner nerd: Interpolators will accumulate values in a gray code

[bdezonia] add the final keyword in numerous places to aid performance

[tobias.pietzsch] LinearInterpolator seems to work.

[tobias.pietzsch] fixed bug in NearestNeighborInterpolator

[tobias.pietzsch] slight speedup of LinearInterpolator

[tobias.pietzsch] specialised versions of LinearInterpolator.

[tobias.pietzsch] this seems a bit faster (in the context of LinearInterpolator)

[tobias.pietzsch] example includes NearestNeighborInterpolator as well.

[bdezonia] implement UnaryOperator named Invert. Used by IJ2 to invert data values.

[tobias.pietzsch] fixed some warnings.

[tobias.pietzsch] removed SamplerFactory

[bdezonia] implementation of AddNoise unary function. used in IJ2.

[bdezonia] implement a number of binary operators to support an imglib-ops implementation of the Image Calculator in IJ2.

[saalfeld] fixed IntervalIterators, test not yet finished

[tobias.pietzsch] unclutter ImgSamplers. ImgSampler no longer implements EuclideanSpace and Interval.

[tobias.pietzsch] fixed errors caused by absent inherited dimension[] in LocalizingCursor implementations.

[tobias.pietzsch] cleaned up ArrayRandomAccess.

[bdezonia] create a Copy operator to be used to copy data from a source

[tobias.pietzsch] moved isOutOfBounds to separate Bounded interface.

[tobias.pietzsch] separated ImgSampler interface and abstract accessor implementation hierarchy.

[tobias.pietzsch] moved abstract accessor classes to mpicbg.imglib package

[tobias.pietzsch] OutOfBound extends Bounded

[tobias.pietzsch] fixed javadoc comments.

[tobias.pietzsch] split AbstractImgOutOfBoundsRandomAccess into Img-specific and generic part.

[tobias.pietzsch] concatenate experiments.

[tobias.pietzsch] Img is a View, too.

[tobias.pietzsch] ViewTransform concatenates permutations, translations, projections.

[tobias.pietzsch] RandomAccess using ViewTransformed position. untested.

[tobias.pietzsch] removed View from Img interface

[tobias.pietzsch] wrap a RandomAccessibleInterval in a View.

[tobias.pietzsch] View into another View via a ViewTransform.

[tobias.pietzsch] helpers to create commonly used views.

[tobias.pietzsch] cleaning up.

[tobias.pietzsch] example using views.

[saalfeld] added simplified changelog for Madison Hackathon

[tobias.pietzsch] creating "hyper-slice" views and an example.

[tobias.pietzsch] cleaning up

[tobias.pietzsch] added rotatedView and example.

[tobias.pietzsch] fixed a bug in rotatedView

[tobias.pietzsch] updated class diagram (not implemented yet):

[tobias.pietzsch] remove getImg() from ImgSampler, removed specialised OutOfBoundsRandomAccesses

[tobias.pietzsch] removed empty ImgSampler interface

[tobias.pietzsch] removed empty ImgCursor interface.

[tobias.pietzsch] removed javadoc reference to ImgCursor

[tobias.pietzsch] AbstractPlanar* base classes no longer needed.

[tobias.pietzsch] removed OutOfBounds creation from RandomAccessibleInterval interface.

[tobias.pietzsch] Only one OutOfBoundsRandomAccess needed.

[tobias.pietzsch] removed ImgRandomAccess interface.

[tobias.pietzsch] added TODOs.

[tobias.pietzsch] RandomAccessibleInterval is just RandomAccessible and Interval. (not Iterable).

[tobias.pietzsch] added randomAccess( Interval interval ) method to RandomAccessible.

[tobias.pietzsch] removed RealOutOfBounds creation from RealRandomAccessibleRealInterval interface.

[tobias.pietzsch] fixed javadoc comments.

[tobias.pietzsch] fixed OrthoSliceCursor

[tobias.pietzsch] passing Intervals through ViewTransform

[tobias.pietzsch] Pair and Triple utility classes

[tobias.pietzsch] * View.untransformedRandomAccess provides untransformed efficient

[tobias.pietzsch] interval containment test helper methods.

[tobias.pietzsch] fixed View implementations.

[tobias.pietzsch] fixed view factory and examples

[tobias.pietzsch] ExtendedRandomAccessibleInterval is not an Interval itself, because

[tobias.pietzsch] added javadoc explaining randomAccess() semantics.

[tobias.pietzsch] removed obsolete classes.

[tobias.pietzsch] added View.untransformedRandomAccessible(Interval). This returns

[saalfeld] added IterableIntervalSubset being an IterableInterval over another

[saalfeld] added IterableIntervalSubset being an IterableInterval over another

[tobias.pietzsch] Interfaces for integer and real transformations.

[tobias.pietzsch] - renamed *View to *RandomAccessibleView.

[tobias.pietzsch] Fixed wrong package name, renamed IntegerTransform to simply Transform.

[leek] Merged transform from imglib2-dirty and implemented interfaces for ROI

[tobias.pietzsch] * changed variable: the underlying RandomAccessible is now called source instead of target

[Curtis Rueden] Add version number to maven-javadoc-plugin.

[llindsey] Fixed up Histogram to work with imglib2. No longer requires T

[tobias.pietzsch] fixed ViewTransformView

[Curtis Rueden] Add explicit casts to avoid javac compiler errors.

[tobias.pietzsch] added int version of applyInverse()

[tobias.pietzsch] final classes to represent the inverse of InvertibleTransforms

[tobias.pietzsch] Transform n-dimensional to m-dimensional coordinates (m<n) by flattening dimensions > m

[tobias.pietzsch] added BoundingBox and BoundingBoxTransform interface.

[tobias.pietzsch] * creation of RandomAccess on views is now handled by TransformBuilder.

[tobias.pietzsch] fixed Views factory

[tobias.pietzsch] fixed view examples

[leek] Greatly modified ROI defs. Added an AbstractROI class to act as a base and wrote tests for it.

[tobias.pietzsch] Concatenable and PreConcatenable interfaces

[tobias.pietzsch] dummy interface hierarchy and implementations for RealTransforms

[tobias.pietzsch] reduce a list of Concatenable/PreConcatenable objects.

[tobias.pietzsch] MixedTransform and TranslationTransform implement Concatenable interfaces.

[tobias.pietzsch] fixed views to work with updated MixedTransform.

[tobias.pietzsch] BoundingBox is not an Interval. It is defined by any two opposite corners.

[tobias.pietzsch] * moved transforms from view package to transforms.integer package

[tobias.pietzsch] added new transform for dimension permutation.

[jaensch] added cursor that iterates over pixels ordered by their intensities

[jaensch] added unit test for SortedGrayLevelIterator

[saalfeld] added transform example into diagram

[tobias.pietzsch] added javadoc for Mixed transform

[tobias.pietzsch] revised MixedRandomAccess, added special-case implementation for Mixed transforms without down-projection.

[tobias.pietzsch] base class for ImageJVirtualStacks

[tobias.pietzsch] VirtualStack for images that are convertible to float, and an example.

[tobias.pietzsch] VirtualStack for images that are convertible to unsigned byte.

[tobias.pietzsch] revised RealUnsignedByteConverter

[leek] I hate GIT

[saalfeld] Moved interpolators according to the revised understanding:

[leek] Got labeling to compile, test. Refactored AbstractROIs somewhat

[saalfeld] removed evil TypeConverter

[saalfeld] update svg from dia

[leek] LabelingOutOfBoundsRandomAccessFactory + partial AllConnectedComponents

[leek] Got AllConnectedComponents and Watershed to compile and pass tests

[preibisch] Removed old opener, new opener still needs to report pixel sizes

[preibisch] Updated ImgOpener, reads properly all types

[preibisch] Removed warnings

[preibisch] Removed old Gaussian Convolution that did not work

[preibisch] Added GaussianConvolution from ImgLib1

[Johannes Schindelin] Fernando found a bug...

[tobias.pietzsch] ImagePlusAdapter returns specialised Img types specific wrap* methods

[tobias.pietzsch] ImagePlusImg must not close it's ImagePlus on finalisation because it might still be displayed by IJ.

[tobias.pietzsch] added ImageJVirtualStack for GRAY16 images.

[tobias.pietzsch] moved BoundingBox to imglib.transform.integer package

[tobias.pietzsch] bug fix.

[tobias.pietzsch] TransformBuilder creates special RandomAccess if the Mixed transform has full source component mapping.

[tobias.pietzsch] Some tests for moving/localizing RandomAccesses.

[tobias.pietzsch] added javadoc for TransformBuilder

[tobias.pietzsch] For ComponentMapping transformations, I decided that mapping a source

[tobias.pietzsch] view and randomaccess for generic integer transforms.

[tobias.pietzsch] TranslationTransformed RandomAccess.

[tobias.pietzsch] TransformBuilder checks for special cases of MixedTransform and simplifies.

[tobias.pietzsch] fixed some examples to work with new ImgOpener.

[preibisch] Working on Gaussian Convolution

[preibisch] Added new Gauss Framework

[leek] Stub of PolygonRegionOfInterest

[leek] Added point classes

[leek] Added localizable constructors + tests

[leek] Continuing work on PolygonRegionOfInterest + invalidate cache on AbstractROI classes

[leek] Added point classes

[leek] Added localizable constructors + tests

[leek] added toString() to Point and RealPoint

[leek] Buggy PolygonRegionOfInterest + tests

[leek] added toString() to Point and RealPoint

[leek] Trap door opened, but I was prepared. Resurrection\!

[saalfeld] Added point classes

[saalfeld] Added localizable constructors + tests

[saalfeld] added toString() to Point and RealPoint

[saalfeld] Point and RealPoint:

[saalfeld] Point and RealPoint:

[tobias.pietzsch] QuickSelect utility functions and unit tests.

[Curtis Rueden] Add missing OrthoSliceCursor needed for imglib-io.

[Curtis Rueden] Reduce test array size to avoid OutOfMemoryError.

[Curtis Rueden] Fix name of imglib-ui project.

[saalfeld] added copy method to Sampler interface

[saalfeld] * complete Cell Cursors and RandomAccess copy

[saalfeld] copy in OutOfBoundsConstantValue

[saalfeld] copy in OutOfBoundsConstantValue and Mirror double and single boundary

[saalfeld] copy in OutOfBoundsPeriodic

[saalfeld] copy in NLinearInterpolators

[tobias.pietzsch] added copy() to View RandomAccesses

[saalfeld] working on k-nearest-neighbor search...

[tobias.pietzsch] removed Jama dependency from Transform classes

[saalfeld] removed deprecated getType() method from Sampler interface

[leek] intermediate PolygonRegionOfInterest

[saalfeld] update KNearestNeighborSearch interface, it is expected to store the

[leek] Changed LabelingType.duplicateTypeOnSameNativeContainer to LabelingType.duplicateTypeOnSameNativeImg

[saalfeld] * added RealPointSampleList, a list of arbitrary samples at real

[saalfeld] removed unused AbstractLocalizable and its personal package

[saalfeld] added k-nearest-neighbor-search for iterables with real coordinates as

[saalfeld] fixed stupid typo from previous commit

[Curtis Rueden] Update ImgLib2 POMs to use net.imglib2 groupId.

[Curtis Rueden] Fix build to include only compiling projects.

[Curtis Rueden] Eliminate Maven warnings when using Maven 3.x.

[Curtis Rueden] Make ImageOpener return an Img container object.

[Curtis Rueden] Move some non-compiling tests to separate project.

[saalfeld] fixed bug in KNearestNeighborSearchOnRealInterval, added test and

[Curtis Rueden] Merge imglib-ops project to imglib2 branch.

[saalfeld] added NearestNeighborSearch and a linear implementation on

[leek] Polygon rasterization test passes. Points on line are in

[saalfeld] ExtendedRandomAccessible(Real)Interval return OutOfBounds versions

[saalfeld] fixed tests for OutOfBoundsStrategies periodic and mirror with single and

[saalfeld] fixed ContainerTest, renamed to ImgTest and moved to appropriate package

[tobias.pietzsch] added copy() to OrthoSliceCursor

[saalfeld] fixed missing copy in rois

[tobias.pietzsch] moved tests requiring Jama to the imglib-tests project

[gharris] Initial working version of Composite Image Projector and Converter using LUTs

[Curtis Rueden] Fix compile errors in imglib-io tests.

[Curtis Rueden] Fix compile errors in imglib-ui project.

[Curtis Rueden] Rename internal cursor class to avoid confusion.

[Curtis Rueden] Remove redundant interface declarations.

[Curtis Rueden] Work around a really unfortunate bug in Javac.

[Curtis Rueden] Fix some warnings.

[Curtis Rueden] Move ImgLib1 code into dedicated subtree.

[Curtis Rueden] Simplify ImgLib1 directory names.

[Curtis Rueden] Move ImgLib2 projects into dedicated subtree.

[Curtis Rueden] Change ImgLib2 package prefix to net.imglib2.

[Curtis Rueden] Temporarily comment out broken tests.

[Curtis Rueden] Remove obsolete TestBase class.

[Curtis Rueden] Fix a few warnings.

[tobias.pietzsch] just copied the incomplete KDTree implementation from my old

[acardona] Fixes for imglib2 scripting

[acardona] imglib2 scripting: new class CursorFunction.

[tobias.pietzsch] It should be possible to construct a KDTree with two lists,

[tobias.pietzsch] partitionSubList() variant that takes an int[]-array to mirror the list permutation.

[Curtis Rueden] Fix some Javadoc warnings.

[Curtis Rueden] Move ImgPlus container class from io to core.

[Curtis Rueden] Fix references to ImgPlus class.

[Curtis Rueden] Update ImgOpener and dependent classes:

[bdezonia] port OPS to imglib2.

[bdezonia] add OPS back into base POM.xml

[Curtis Rueden] Fix bug introduced by method refactoring.

[Curtis Rueden] Add utility method for reading Imgs from URLs.

[gharris] Underconstruction...

[gharris] Fixed imports to allow build.

[bdezonia] remove debugging print statements

[bdezonia] fix syntax error in code

[gharris] Fixed filename case of Lut

[bdezonia] improve implementation of RegionCursor::hasNext()

[Curtis Rueden] Tweak Javadoc.

[Curtis Rueden] Remove LUT class with wrong capitalization.

[acardona] Scripting: more fixes, getting close to working again.

[acardona] Return type of ExtendedRandomAccessibleInterval is F, not only RandomAccessible.

[acardona] Fixes for ImageTransform: takes an ExtendedRandomAccessibleInterval that wraps an Img.

[acardona] Scripting: fixes for Resample and AbstractAffine3D.

[acardona] Fixed ImagePlusAdapter. Needed a new convertToFloat.

[acardona] ImageJVirtualStack: added missing GRAY16

[acardona] Makes no sense that InverseTransformDescription had the factory

[acardona] ImgLib2Display: update int[] to long[]

[acardona] Updated cursor methods for SliceTransformableExtraction

[acardona] Fixed methods for the cursors of ImageJVirtualDisplay.

[Curtis Rueden] Better dimensional axis code for ImgPlus metadata.

[Curtis Rueden] Fix some warnings.

[gharris] Changes to Composite display components...

[Curtis Rueden] Add "unknown" axis type.

[Curtis Rueden] Fix some compile errors and warnings in imglib-ij.

[Curtis Rueden] More compile error fixes, possibly pointless.

[gharris] More on composite display...

[Curtis Rueden] Change net.imglib2 image to img in more places.

[Curtis Rueden] Create default axes if invalid axes are passed.

[tobias.pietzsch] Changed return type for Views.extend() to the more specific ExtendedRandomAccessibleInterval.

[Curtis Rueden] Use List instead of array for AssignOperation.

[Curtis Rueden] Enrich ImgPlus a bit:

[Curtis Rueden] Add getBitsPerPixel method to RealType interface.

[Curtis Rueden] Fix test to match changes to AssignOperation.

[gharris] Moved most of this to imagej.display

[bdezonia] change implementation of AssignOperation, MultiImageIterator, and RegionCursor so

[Curtis Rueden] Improve Metadata interface:

[bdezonia] fix a bug in next(). reorganize order of method declarations.

[Curtis Rueden] Add more ImgPlus metadata, for ImgOpener to use.

[Curtis Rueden] Add support for 16-bit color tables.

[Curtis Rueden] Disallow null calibration arrays.

[tobias.pietzsch] kthElement() variant that takes an int[]-array to mirror the list permutation.

[tobias.pietzsch] construct the KDTree with a list of values and a list of corresponding positions.

[tobias.pietzsch] NearestNeighborSearchOnKDTree implements NearestNeighborSearch interface

[tobias.pietzsch] Instead of Node<T>, there is now ValueNode<T> to represent nodes which hold a T.

[tobias.pietzsch] KDTree and nearest neighbor searches are now based on AbstractNode.

[tobias.pietzsch] illustrating KDTree on IterableRealInterval.

[saalfeld] enriched nearest neighbor search behavior test,

[tobias.pietzsch] renamed AbstractNode KDTreeNode and made specialisations thereof inner classes of KDTree.

[Curtis Rueden] Fix copyright for color table classes.

[Curtis Rueden] Add Tobias, Barry and Grant to developers list.

[Curtis Rueden] Revert to working version of imglib2-ui.

[Curtis Rueden] Create common superclass for ColorTables.

[Curtis Rueden] Add XY projector for compositing along one axis.

[Curtis Rueden] Add ARGB converter that uses a color table.

[tobias.pietzsch] * renamed nearestneighbor package to neighborsearch

[tobias.pietzsch] RadiusNeighborSearch interface and implementation for KDTrees.

[tobias.pietzsch] fixed typo.

[tobias.pietzsch] renamed getNumResults() to numNeighbors().

[tobias.pietzsch] added copyright comments

[bdezonia] minor performance considerations

[leek] Updated PolygonRegionOfInterest + tests: now works. RectangleRegionOfInterest + tests.

[leek] Added methods to set rectangle origin & extent + tests

[leek] EllipseRegionOfInterest + tests

[bdezonia] fix RegionCursor::next() to not set the underlying RandomAccess' position if it is out of bounds.

[Curtis Rueden] Allow unspecified composite index (-1).

[Curtis Rueden] Fix fatal bug in color table population.

[Curtis Rueden] Reenable channel filling.

[bdezonia] add another wrap() utility method that preserves metadata

[tobias.pietzsch] ExtendedRandomAccessibleInterval on F requires an  for a super-type of F (instead of an OutOfBoundsFactory eexplicitly for F)

[tobias.pietzsch] added convenience methods for creating extended intervals with standard OutOfBounds strategies.

[tobias.pietzsch] ExtendedRealRandomAccessibleRealInterval on F requires a RealOutOfBoundsFactory for a super-type of F (instead of a RealOutOfBoundsFactory explicitly for F)

[leek] Added binary mask region of interest + tests

[leek] Updated AllConnectedComponents + Watershed to compile and pass tests

[bdezonia] begin definition of TransformOperation - a class for more performant transformation of data in place.

[tobias.pietzsch] javadoc for Cursor and RealCursor interfaces.

[bdezonia] replace calls to RandomAccess::setPosition() with specific calls to RandomAccess::move(delta,dimAxis) as needed. This should make RegionCursor more performant.

[bdezonia] added main() which can do a speed test. confirmed new version of next() is at least 15% faster.

[preibisch] Added comments for the copy() method

[preibisch] Fixed errors in the gauss implementation

[preibisch] Fixed the LocalizabePoint

[bdezonia] minor refactoring

[bdezonia] documentation change

[bdezonia] documentation change

[bdezonia] fix typo

[preibisch] Added Location and RealLocation classes which implement Localizable and RealLocalizable (but not Positionable as Point and RealPoint do)

[preibisch] Updated Gauss, still not finished

[preibisch] Added toString methods

[preibisch] Updated FinalInterval to support instantiation with size and added comments and final statements where appropriate

[preibisch] Added constructor for another Interval

[preibisch] Gauss is almost done...

[preibisch] Added comment

[bdezonia] strengthen the code that checks that each defined subregion is compatible in all dimensions and yet allows a 2d image and a 2d plane in a 5d image to be iterated together.

[stephan.preibisch] Working on FFT...

[preibisch] Working on Gauss...

[preibisch] Finished adapting the FFT functions to imglib2

[preibisch] ImgFactory can now create an Img also with an int[] array as size

[preibisch] All virtual iterators support now int[] sizes, min and max

[preibisch] Added methods to get an instance of T from a RandomAccess and a RandomAccessible

[preibisch] Corrected a comment which is important for understanding

[preibisch] Continued with FourierTransform object to work with the adapted FFTFunctions

[preibisch] Added OutOfBounds with Exponential intensity decay on top of mirroring outside of the interval

[preibisch] Made convience method for getting Type instance from RandomAccessible & Interval more generic

[preibisch] Fixed FourierTransform, not tested yet

[preibisch] Fixed (Inverse)FourierTransform, not tested yet.

[preibisch] Fixed the Fourier Convolution, not tested yet

[preibisch] Fixed the InverseFourierTransform

[preibisch] Fixed FFT to include possible offset in the input data

[preibisch] Fixed that InverseFFT works with offset

[preibisch] Started working on PhaseCorrelation

[preibisch] Added the functionality that an Img can copy itself

[preibisch] Added final statements and removed unnecessary "hiding" statements

[preibisch] Small fix for offsets in FFTFunctions

[bdezonia] pull the allocation of a temporary object out of the inner loop to improve performance and memory management.

[bdezonia] Renamed RegionCursor to RegionIterator. Made RegionIterator conform to the Iterator

[preibisch] Implemented main convolution method for all Gauss variants

[bdezonia] minor refactor

[leek] Added copy function to NativeImgLabeling

[stephan.preibisch] The old LOCI opener can now open directories with 2d images as 3d image, need that for SPIM registration

[preibisch] Finished convolution of line for the case that the input is smaller than the kernel

[acardona] Minor fixes for imglib2 scripting.

[acardona] ListImg must override size() of AbstractImg.

[leek] Added some getters for origin and extent to RectangleRegionOfInterest + tests

[saalfeld] added behavior test for nearest neighbor search to draw

[tobias.pietzsch] fixed View examples and added CopyViews example.

[preibisch] Played with GameOfDeath

[Curtis Rueden] Readd ij1 compile-time dependency for ImgLib1 I/O.

[Curtis Rueden] Fix ImgPlus.copy(), and fix constructor bugs.

[acardona] Updated scripting to use IterableRealInterval instead of Img.

[acardona] Created new Identity IFunction for scripting.

[acardona] Updated Benchmark for scripting.

[acardona] Fix scripting Benchmark for imglib1

[acardona] Fixed scripting Benchmark for imglib2.

[preibisch] Added new min(Positionable), max(Positionable), realMin(RealPositionable) and realMax(RealPositonable) to

[preibisch] Continued working on Gauss

[preibisch] No change...

[preibisch] Added another outofboundsstrategy

[Curtis Rueden] Fix return types of openImg methods.

[preibisch] Gauss implemented, now testing

[preibisch] Fixed ImgOpener calibration

[preibisch] Fixed importer for imglib1

[preibisch] ImageJFunctions.show() is working again for 2d, 3d

[preibisch] ImageJFunctions.show() is working again for 2d, 3d, 4d, 5d

[preibisch] ImageJFunctions.show() should display all types of Img<RealType> and Img<ARGBType> properly

[preibisch] Continued working on algorithms

[bdezonia] added a TODO

[saalfeld] Fixed ImageJFunctions:

[saalfeld] Fixed Sampler docs, thanks to Albert Cardona for notice.

[preibisch] Added missing files

[preibisch] Debugging Gauss

[preibisch] Added missing RGB Virtual stack

[preibisch] added those IJ_Prefs.txt files to gitignore

[preibisch] More fixes in Gauss...

[preibisch] Convolution in x works

[Curtis Rueden] Allow comma-separated argument lists.

[preibisch] First working version of new Gauss

[preibisch] Gauss has now efficient implementations for NativeType and float

[preibisch] Implemented the optimized case for if kernel is bigger than image

[Curtis Rueden] Add support for channel min/max metadata.

[Curtis Rueden] Make ImgOpener populate min/max metadata.

[gharris] Corrected references to channelMax/Min (copy/paste error)

[leek] Added ConstantRandomAccessible, ConstantRealRandomAccessible, supporting abstract base classes + tests

[Curtis Rueden] Fix bugs in min/max population.

[Curtis Rueden] Add accessor methods for composite color.

[leek] Added ImgTranslationAdapter + tests, fixed bug in TransformBuilder where bounding box is null and a translation transform is applied

[leek] ImgLib #300 - fixed tests and broken, untested things

[acardona] ImageJFunctions has now both wrap* and show* methods

[acardona] Fixed error in ImagePlusAdapter: use NumericType instead of RealType,

[acardona] Fixed ImageJVirtualStackARGB ImagePlus' type to COLOR_RGB.

[acardona] Added test for ImageJFunctions, all pass after last fixes.

[Curtis Rueden] Make min/max population optional.

[Curtis Rueden] Add more convenience method signatures.

[Curtis Rueden] Do not use MinMaxCalculator if computeMinMax=false.

[leek] Made RegionOfInterest extend RealRandomAccessibleRealInterval and all of the sudden life is a bowl of cherries.

[leek] Fixed bug when querying membership for pixel outside of bitmap

[preibisch] Fixed bug in 1d gaussian convolution

[leek] Moved Metadata interface to net.imglib2.meta and split into 3 pieces in anticipation of reusing them for overlays

[leek] cosmetic: removed unused imports

[bdezonia] make initialize() public

[leek] Added K-D tree-based volumetric search: find all RealIntervals that contain a given point (+ tests)

[leek] Added composite region of interest + test. Some copyright notices added. Made VolumetricSearch implement RealRandomAccessible<List<I>> to find all intervals containing the random access's current location

[bdezonia] fixed typo in error message

[bdezonia] initial changes to change MultiImageIterator accept ImgPluses rather than Imgs

[Curtis Rueden] Fix problems with PlanarCursor.localize().

[preibisch] Fixed more bugs in the PlanarImg and PlanarCursor1d

[bdezonia] added documentation

[bdezonia] relax unnecessary generic type constraints in OPS

[bdezonia] improve TransformOperation and define tests

[tobias.pietzsch] added javadoc for KDTree.

[tobias.pietzsch] KDTree now is an IterableRealInterval.

[tobias.pietzsch] bug fixed in TransformBuilder

[tobias.pietzsch] moved basic Interval implementation to AbstractInterval.

[tobias.pietzsch] using ImageJFunctions.show() in View tests now and moved them to imglib2-tests project.

[tobias.pietzsch] added IntervalView, which puts a bonudary interval to a RandomAccessible

[tobias.pietzsch] added RandomAccessibleIntervalCursor to iterate through (non-zero-mean) intervals.

[tobias.pietzsch] MixedTransformView no longer is an Interval

[tobias.pietzsch] started to adapt static Views methods

[tobias.pietzsch] extended and renamed static Views methods. deprecated old flippedView, rotatedView, superIntervalView methods.

[tobias.pietzsch] View using the SequentializeTransform.

[stephan.preibisch] Added mirroring algorithm (n-dimensional)

[stephan.preibisch] Fixed error in toString method of UnsignedByteType

[Curtis Rueden] Limit CompositeXYProjector to ARGBType.

[Curtis Rueden] Add hack to handle embedded ImageJ color modes.

[stephan.preibisch] Updated DoG to support individual sigmas for the dimensions

[bdezonia] default compositeChannelCount to 1

[leek] Tests + bug fix to LabelingMapping. Thanks Christian Dietz

[stephan.preibisch] Added some comments

[stephan.preibisch] Added more comments and removed some windows line endings (sorry!)

[bdezonia] deletion of rev2 ops

[bdezonia] initial implementation of rev6 ops

[bdezonia] add copyright headers and author tags to all files

[bdezonia] initial implementation of a ConditionalFunction

[bdezonia] add a CachingFunction class. extend the basic types so that they can be used by the CachingFunction. add some documentation to various files.

[bdezonia] added initial implementation of ComplexImageAssignment class

[bdezonia] unknown changes. file only contains notes.

[bdezonia] update all copyright notices

[bdezonia] initial implementation of RealPowerConstant operation

[bdezonia] unknown changes

[bdezonia] Big changes. All related to the ability to pass the current neighborhood and a point within that neighborhood as input to the evaluate() function. This allows the Condition code to reason spatially if needed. An example is fleshed out (Example4).

[bdezonia] fixed inefficiency in example code

[bdezonia] migrate classes out of Example4 and into public class hierarchy

[bdezonia] OPS - add a few more functions and operations

[bdezonia] minor tweak

[bdezonia] implementation of a convolution function

[bdezonia] example implementation of a impulse function

[bdezonia] add a convolution example

[bdezonia] Make a naive 2d interpolator example

[bdezonia] create a complicated assignment example

[bdezonia] fix oversight in definition of neighborhood

[bdezonia] fix oversight in circle condition

[bdezonia] code reorganization of Example6

[bdezonia] - add size() to neighborhood implementations

[bdezonia] Partial implmentation of a method for nesting neighborhoods. Example

[bdezonia] add last commit message to internal documentation of Example8

[tobias.pietzsch] sort filenames when opening a directory as 3D stack.

[tobias.pietzsch] remove leftover println from previous commit...

[bdezonia] - fix NeighborhoodAdapterFunction to locate local neighborhood correctly

[bdezonia] Make Complex definitions and implementations more standard

[bdezonia] fix intitialization of r & theta when necessary

[bdezonia] minimize some computations when figuring r and theta

[bdezonia] remove warnings

[Curtis Rueden] Simplify gitignore rules.

[bdezonia] add getPrincipleArgument() to the Complex class

[bdezonia] large changes to accomodate further generalization of GeneralUnaryFunction  and

[bdezonia] fix bug with RealMedianFunction. improve performance of other Real neighborhood

[bdezonia] remove warnings

[bdezonia] fix Example7 so that it verifies it's calculated values

[bdezonia] fix Example8 to test it's values

[bdezonia] generalize functions that convert one input type into another

[leek] Added ImgUtil and tests - utilities for copying data from flat arrays to Img to support image transfer via JNI / JVM

[tobias.pietzsch] started implementing linear time MSER detection.

[tobias.pietzsch] finding extremal regions works.

[tobias.pietzsch] extracted Component interface and made Component type a generic parameter of ComponentTree.

[tobias.pietzsch] extracted ComponentHandler interface.

[bdezonia] make some methods of ImgOpener public and static for reuse by forthcoming virtual Img classes.

[bdezonia] initial untested implementations of classes that allow planar virtual access to image data that is backed by a BioFormats IFormatReader.

[bdezonia] simplify VirtualImg constructor to calculate it's type from the IFormatReader

[bdezonia] improve the construction of VirtualImg's. now they are only constructed via a public static factory method that relies on filename only.

[bdezonia] minor cleanup and documentation

[bdezonia] make the return type of the create() method more powerful

[bdezonia] various improvements after writing some tests

[bdezonia] In the VirtualImg classes of imglib-io: fixed bug with cursors/accessors where

[bdezonia] documentation changes

[bdezonia] OPS - add a few more Real and Complex operations. Pave way for ComplexLog.

[bdezonia] OPS - add more Complex and Real operations

[bdezonia] OPS - declare some variables final in some Complex operations

[bdezonia] OPS - minor code naming edit

[bdezonia] OPS - make more variables final in some Complex operations

[bdezonia] OPS - add a few Real operations

[bdezonia] OPS - add more Complex operations

[bdezonia] OPS - create a ComplexLog operation (of the principal branch)

[bdezonia] OPS - fix bug in ComplexDifference and document ComplexLog

[bdezonia] OPS - make operations "final"

[bdezonia] OPS - test code and notes

[bdezonia] OPS = add hyperbolic trig functions (real and complex) and ComplexPower

[bdezonia] OPS - add the arc* functions for reals (arcsin, arccoth, etc.)

[bdezonia] OPS - added the missing arcsec and arccsc definitions

[bdezonia] OPS - improve some variable names

[bdezonia] OPS - add arc* function for complex type (arccos, arctanh, etc.) and some refactoring

[bdezonia] OPS - add a couple of basic operations

[bdezonia] OPS - rename ComplexSetConstant to ComplexConstant

[bdezonia] OPS - rename RealSetConstant to RealConstant

[bdezonia] IO - add VirtualImgTest and associated TestImage.tif

[bdezonia] IO - temporarily remove test class until I can edit pom dependencies to add JUnit

[tobias.pietzsch] build up component-size history tree using MserEvaluationNodes.

[leek] Corrected max extent of labeling to be inclusive (thx Christian Dietz), modified and added tests, added copy of bit Img to/from boolean array in ImgUtils

[bdezonia] IO - add the ability to maintain virtual planes as byte[]'s always

[Curtis Rueden] Fix javadoc.

[bdezonia] IO - fix some return types in VirtualCursor

[bdezonia] IO - code formatting changes

[bdezonia] IO - add VirtualImgTest and modify pom to reference JUnit

[bdezonia] IO - some serious refactoring to streamline design of Cursors and RandomAccesses

[bdezonia] IO - code formatting and warning removal changes

[bdezonia] IO - make plane loader set little endian flag based on IFormatReader's value

[bdezonia] IO - bypass hack and fix bug where setting a plane did not update existing cursors

[bdezonia] IO - simplify responsibilities for initialization of VirtualPlaneLoader

[bdezonia] IO - documentation possible issue in test code

[bdezonia] OPS - check and update some operation definitions

[bdezonia] OPS - style edits, documentation, and small fixes to some operations

[stephan.preibisch] Fixed a lot of bugs in the UnsignedTypes

[stephan.preibisch] Added more comments

[stephan.preibisch] old LOCI opener can open directories with 2d images as 3d

[bdezonia] OPS - verify some operation defintions and fix where needed

[bdezonia] OPS - document which real functions have been verified externally

[bdezonia] OPS - document complex functions that have been verified externally

[bdezonia] OPS - document verification of more complex formulas

[bdezonia] OPS - document more verified complex operations

[bdezonia] OPS - rewrite real versions of asec and acsc and document formula source

[bdezonia] OPS - document more functions from external sources and add some err checking

[bdezonia] OPS

[bdezonia] OPS - make more complex operation code more consistent

[bdezonia] OPS - style changes for real binary operations

[bdezonia] OPS - make style changes to some real operations

[bdezonia] OPS - more style changes for real functions

[Johannes Schindelin] Update .mailmap

[leek] Fixed bug in AllConnectedComponents.PositionStack. Thanks Jean-Yves Tinevez for reporting and suggested fix.

[bdezonia] OPS - style change

[bdezonia] OPS - make a Sobel filter example

[bdezonia] OPS - add some notes to RealConvolutionFunction

[bdezonia] OPS - make a very simple ComposedFunction implementation

[bdezonia] OPS - improve ComposedFunction to work along any axis

[bdezonia] OPS - proof of concept implementation of an alternating function

[bdezonia] OPS - fix a bug in ComposedFunction and do some code reorganization

[bdezonia] OPS - add a TODO item to ComposedFunction

[bdezonia] OPS - note an issue in AlternatingFunction

[tobias.pietzsch] MSER detection works for building the component tree starting from intensity minima.

[bdezonia] OPS - add a note on a limitation of current implementation

[saalfeld] removed obsolete self referential generic parameter from

[saalfeld] remove unused import in ImagePlusAdapter

[saalfeld] added junit dependency to imglib2/tests/pom.xml

[tobias.pietzsch] added RealLocation construction from RealLocalizable.

[bdezonia] OPS - make ComplexAdapterFunction adapt one or two Real functions

[bdezonia] OPS - improve some generic type naming

[bdezonia] OPS - make constant functions a little more general and use "final" more

[bdezonia] OPS - make most instance variables final

[tobias.pietzsch] added RealLocation construction from RealLocalizable.

[bdezonia] OPS - lay groundwork for parallel computation

[bdezonia] OPS - parallelize RealImageAssignment and redefine it's constructor

[bdezonia] OPS - make RealImageAssignment abortable and improve JavaDoc

[bdezonia] OPS - extend multithreaded capabilities to ComplexImageAssignment via refactor

[bdezonia] OPS - improved abort() logic and added JavaDoc

[bdezonia] OPS - added some JavaDoc

[bdezonia] OPS - add some convenience constructors and related JavaDoc

[tobias.pietzsch] fixed bugs in MixedRandomAccesses and view transformation chaining.

[bdezonia] OPS - more example functions : sinc()

[bdezonia] OPS - document formula reference for sinc() functions

[saalfeld] Sun javac fails to infer return types, so make it explicit

[saalfeld] Convince javac to compile ImageJFunctions by silly casting

[Johannes Schindelin] Fix ticket 800

[bdezonia] OPS - remove some warnings in the image assignment classes

[bdezonia] OPS - a simple DFT/IDFT example

[saalfeld] moved non-compiling tests and experiments form imglib2/ij to

[stephan.preibisch] I guess Tobias added that ...

[stephan.preibisch] Fixed bug in ImagePlusContainers that hold and ImagePlus instance when setting planes, it has to be set in the mirror and the ImagePlus!

[stephan.preibisch] Fixed same setPlane bug in imglib2

[acardona] Potential fix for imglib2's FloydSteinbergDithering.

[acardona] Scripting: new function Utils.extractDimensions

[acardona] Scripting: fixing ImgProxy to newer imglib2 API.

[acardona] Scripting: ImgLib services class compiles with newest imglib2.

[acardona] Scripting: new class Slice to extract X,Y slices from stacks.

[saalfeld] default implementation of an Iterable on RandomAccessibleInterval

[acardona] ComputeMinMax compiles.

[acardona] Scripting: ImgLib.open and openVirtual use ImgOpener methods.

[acardona] Scripting: Compute.checkContainers does nothing if there's only one image.

[acardona] Scripting: created OrthoSlice and SliceXY, SliceXZ and SliceYZ.

[Curtis Rueden] Update Bio-Formats version to the actual latest.

[bdezonia] OPS - make two types of complex adapter functions: caartesian and polar

[bdezonia] OPS - extend Real and Complex image functions to work out of bounds if desired

[bdezonia] OPS - simplify real and complex image functions

[Curtis Rueden] Add accessor for current LUT.

[tobias.pietzsch] simpler stability criterion looks only at ancestor EvaluationNodes. keep value as long.

[tobias.pietzsch] compute and visualise ellipsoids for MSER regions. filter MSER candidates.

[bdezonia] ImgPlus: default calibration values to 1.0 rather NaN

[bdezonia] OPS - a couple more functions added

[bdezonia] OPS - add a discrete version of an integral function

[tobias.pietzsch] refactoring and cleaning up.

[tobias.pietzsch] remove old mser classes

[tobias.pietzsch] Modified PixelListComponent to use Img<Long> to store component locations in a single linked list.

[tobias.pietzsch] factored out PixelList

[tobias.pietzsch] use PixelList in SimpleMserComponemnt

[Curtis Rueden] Update ImageJ groupId to match latest.

[Curtis Rueden] Update ImageJ version to use a range.

[tobias.pietzsch] build mser tree

[tobias.pietzsch] prune duplicated MSERs using min_diversity check.

[bdezonia] OPS - fix an apparent bug in ComplexIntegerPower for negative exponents

[acardona] imglib-algorithms: LocalNeighborhoodCursor, with a test.

[acardona] Util.computeDistance for long[]

[acardona] imglib-algorithm: PhaseCorrelation compiles and works well.

[acardona] imglib-algorithm: Bandpass compiles (not tested).

[acardona] imglib2-algorithm: fixed PhaseCorrelation, the checking

[acardona] imglib2-algorithm: removed debugging code from PhaseCorrelation.

[bdezonia] OPS - finally fix ComplexIntegerPower and simplify it considerably

[acardona] imglib2-algorithms: minor fix for a test.

[acardona] imglib2-algorithm: remove unused import

[acardona] imglib2-scripting: fixed InverseFFT

[acardona] imglib2-scripting: created Img wrappers for RandomAccessible and RandomAccessibleInterval.

[acardona] imglib2-scripting: ROI and RectangleROI fns.

[acardona] imglib2-scripting: test for RectangleROI

[acardona] imglib2-scripting: docs for OrthoSliceCursor constructor.

[acardona] imglib2-scripting: test for *.script.slice.* classes

[acardona] imglib2-scripting: fixes to ImgLib utility class,

[acardona] imglib2-scripting: OrthoSlice and the Slice* classes are now Img themselves,

[acardona] imglib2-scripting: Insert function to insert one image into another with some offset.

[acardona] imglib2-algorithm: use GaussFloat from the gauss2 package.

[acardona] imglib2: InvervalIndexer.indexToPositionWithOffset has to add the

[acardona] imglib2-scripting: fixed error, second IFunction was never asked

[acardona] imglib2-scripting: RectangleROI also accepts a List for the 4 numeric entries.

[acardona] imglib2-scripting: test for RectangleROI and for Insert.

[acardona] imglib2-scripting: clearer code for Insert.

[acardona] imglib2-scripting: new fns Copy and Clear.

[acardona] imglib2-scripting: more AlgorithmUtil methods

[acardona] imglib2-scripting: new FloatImage(long[]) class to create an array float image.

[acardona] imglib2-scripting: simplified test, also tests for FloatImage.

[acardona] imglib2-scripting: new UnsignedByteImage, UnsignedShortImage and Dimensions,

[saalfeld] Complete inversion of offset handling in IntervalIndexer from last

[acardona] imglib2-scripting: better docs for Clear and Insert.

[tobias.pietzsch] added UnsignedShortType to FloatType conversion in TypeConverter.

[stephan.preibisch] Added same support for UnsignedByteType

[stephan.preibisch] Fixed a bug in the TypeConverter for ShortType, has to be 0xffff instead of 0xff

[stephan.preibisch] Removed a stupid System.out.println( "ja" ); in the LinearInterpolator2DRealType

[bdezonia] ImgOpener - fix decodeWord() cases for UINT32 and DOUBLE

[bdezonia] ImageOpener: fix decodeWord() cases for UINT32 and DOUBLE

[bdezonia] AbstractIntegerType: fix implementations of setZero() and setOne()

[bdezonia] IntegerTypeImpl: fix setZero() and setOne() implementations

[bdezonia] UnsignedIntType: clean up definitions a bit and remove unreachable code

[bdezonia] UnsignedIntType: restore some bounds checking code

[bdezonia] UnsignedIntType: minor code format changes

[acardona] imglib2-scripting: Affine2D, less boxing

[acardona] imglib2-scripting: ARGBImage to create a new ARGB Img

[acardona] imglib2-scripting: allow new images from native arrays.

[acardona] imglib2-scripting: a base class for filters,

[acardona] imglib2-scripting: Gamma and CorrectFlatField as filters.

[jean-yves.tinevez] imglib1: DevUtil: added function to generate Image from arrays

[jean-yves.tinevez] imglib1: DevUtil: added function to generate Image from arrays

[bdezonia] OPS - define a couple relations for supporting "near" testing

[bdezonia] OPS - add relations that can combine via and/or/not

[tobias.pietzsch] changed score computation such that we don't need to create an intermediate node for every single level.

[tobias.pietzsch] benchmarking

[tobias.pietzsch] use RealType<T> instead of IntegerType<T>. use T instead of long for evaluation.

[Curtis Rueden] Remove tests manifest's incorrect package prefix

[Curtis Rueden] Refactor non-compiling classes to separate subtree

[Curtis Rueden] Avoid two javac typing issues

[Curtis Rueden] Rename non-unit test, to avoid Jenkins failure

[Curtis Rueden] Rename another non-unit-test class, for Jenkins

[Curtis Rueden] Update to latest Bio-Formats dev version (4.4)

[Curtis Rueden] Tweak ImageJ version (1.45s or later)

[Curtis Rueden] Fix various dependency problems

[Curtis Rueden] Tweak javadoc

[acardona] imglib2-scripting: fix ImgLib.openVirtual

[tobias.pietzsch] move T-Comparison and T-subtraction to Comparator and ComputeDeltaValue interfaces in preparation for implementing the bright-to-dark pass.

[acardona] imglib2-scripting: moved new images from edit to img package.

[tobias.pietzsch] inlined createIntermediateNodes (which did only forward to constructor anyway).

[Curtis Rueden] Fix javadoc in a few places

[tobias.pietzsch] cleaning up.

[tobias.pietzsch] removed unused example

[tobias.pietzsch] implement Comparators for DarkToBright and BrightToDark passes as inner classes of ComponentTree.

[tobias.pietzsch] ComponentTree constructor is now private. Use static buildComponentTree() methods.

[tobias.pietzsch] Build up tree of PixelListComponents using PixelListComponentTree.buildComponentTree().

[tobias.pietzsch] moved generic ComponentTree and PixelListComponentTree to separate packages.

[tobias.pietzsch] remove unused example.

[tobias.pietzsch] added documentation. renamed "ancestors" to "children" and "successor" to "parent" to fit usual tree nomenclature.

[stephan.preibisch] Added an n-dimensional max-projection

[stephan.preibisch] Added license to Gauss package

[tobias.pietzsch] more javadoc

[Curtis Rueden] Rename LabeledAxes to CalibratedSpace

[Curtis Rueden] Make Axes.get method thread-safe

[Curtis Rueden] Tweak javadoc

[Curtis Rueden] Make CalibratedSpace extend EuclideanSpace

[Curtis Rueden] Tweak Named javadoc

[Curtis Rueden] Move axis classes into net.imglib2.meta package

[Curtis Rueden] Rename CustomAxis to CustomAxisType

[tobias.pietzsch] more javadoc and restricted access modifiers for helper classes.

[tobias.pietzsch] rename "SimpleMser..." to "Mser..."

[tobias.pietzsch] rename MserComponent to MserComponentIntermediate.

[tobias.pietzsch] added javadoc.

[tobias.pietzsch] With comparison and subtraction factored out, we only require Type<T>, not RealType<T>.

[tobias.pietzsch] split MserComponentHandler into MserComponentHandler and MserComponentGenerator.

[tobias.pietzsch] made MserTree.Mser a static class.

[tobias.pietzsch] extracted MserTree.Mser class to new file.

[acardona] imglib2-scripting: supress boxing warnings

[tobias.pietzsch] can iterate through all Mser in MserTree.

[acardona] imglib2-scripting: naive region operations.

[acardona] imglib2-scripting: avoid class name collisions.

[tobias.pietzsch] factor ComputeDelta implementation out of MserTreeTest class

[tobias.pietzsch] moved MserFilter candidate checks to MserTree.

[tobias.pietzsch] removed SimpleMserProcessor interface

[tobias.pietzsch] removed MserComponentHandler (emitted components are now processed by MserTree).

[tobias.pietzsch] removed unused Iterable implementation. javadoc.

[tobias.pietzsch] made ComputeDeltaValue implementations final.

[tobias.pietzsch] restrict access modifiers. renamed ancestors to children, successor to parent. javadoc.

[tobias.pietzsch] testing and visualising bright-to-dark pass.

[acardona] imglib2-scripting: n-dimensional integral image

[acardona] imglib2-scripting: fixed error in ImgProxy

[acardona] imglib2-scripting: integral images now of any target type.

[acardona] imglib2-scripting: docs

[acardona] imglib2-scripting: test performance of integral image.

[acardona] imglib2-scripting: DoubleImage and LongImage

[acardona] imglib2-scripting: add data to the test array.

[acardona] imglib2-scripting: UnsignedIntImage

[tobias.pietzsch] static methods to build PixelListComponentTree for Type<T>.

[acardona] imglib2-scripting: properly test Saalfeld's mpicbg.integral.DoubleIntegralImage

[tobias.pietzsch] static methods to build MSER tree. documentation.

[acardona] imglib2-scripting: AlgorithmUtil method to get a Type from a number.

[acardona] imglib2-scripting: Extend, ExtendMirroringSingle and *Double and ExtendPeriodic.

[tobias.pietzsch] added TODOs.

[tobias.pietzsch] fixed slice ordering bug in ImagePlus Imgs.

[tobias.pietzsch] fixed slice ordering bug in ImagePlus Imgs.

[tobias.pietzsch] add imglib2-algorithms as a dependency of imglib2-tests.

[acardona] imglib2-scripting: minor fix

[acardona] imglib2-scripting: generics, that dark art

[acardona] imglib2-scripting: fix equalIterationOrder value for RandomAccessible proxies.

[acardona] imglib2-scripting: minor fixes.

[acardona] imglib2-scripting: Duplicate to make a copy of an image or IterableInterval.

[acardona] imglib2-scripting: fixes to Extend.

[acardona] imglib2-scripting: new IterableIntervalProxy

[acardona] imglib2-scripting: reworked Insert to insert in the target in place.

[acardona] imglib2-scripting: Paste, an IFunction to paste an image into an other with an offset.

[acardona] imglib2-scripting: Flip and Rotate classes.

[acardona] imglib2-scripting: rotations need a zeroMin!

[acardona] imglib2-scripting: RandomAccessible*Proxy now have methods to get the underlying RandomAccessible

[acardona] imglib2-scripting: simplified Extend* and ROI,

[acardona] imglib2-scripting: proper Paste IFunction.

[acardona] imglib2-scripting: minor fixes to Util

[acardona] imglib2-core: fixed typo in doc of Type

[acardona] imglib2-scripting: fixed order of parameters in Affine2D

[acardona] imglib2-scripting: fixed docs

[acardona] imglib2-scripting: ImageFunction is now typed and

[acardona] imglib2-scripting: fixed docs.

[acardona] imglib2-scripting: ROI and RectangleROI are views smaller or larger than the images.

[acardona] imglib2-scripting: TestTransformations to test Paste, ROI, Extend*, Rotate*

[acardona] imglib2-scripting: fixes to equalIterationOrder of two proxies.

[tobias.pietzsch] fixed Views javadoc

[tobias.pietzsch] rename ComputeDeltaValue to ComputeDelta. add javadoc.

[tobias.pietzsch] made MserTree constructor private.

[tobias.pietzsch] move package mser to componenttree.mser. MserTreeTest example now uses imagej sample image.

[Curtis Rueden] Label tests project POMs with test scope

[Curtis Rueden] Clean up POM dependency order

[Curtis Rueden] Clean up and update dependency on mpicbg

[acardona] imglib2-scripting: removed bogus doc

[acardona] imglib2-scripting: removed imports

[acardona] imglib2-scripting: added Flip* functions to TestTransformations

[acardona] imglib2-scripting: silenced warnings.

[acardona] imglib2-scripting: moved Paste to filters, since that's what it is.

[acardona] imglib2-scripting: LazyConvert and derivatives: ConvertToFloat, etc.

[tobias.pietzsch] add test scope to imglib2-algorithms dependency.

[Curtis Rueden] Move core algorithm interface to imglib2-core

[Curtis Rueden] Move histogram logic to imglib2-core

[ipatron] whitespace change

[bdezonia] whitespace change

[Curtis Rueden] Add missing javadoc

[Curtis Rueden] Fix javadoc author tags

[Curtis Rueden] Add algorithms dependency on commons-math 3.0

[Curtis Rueden] Remove empty math utility class

[Curtis Rueden] Move ComputeMinMax into new stats package in core

[Curtis Rueden] Move Function interface into function package

[Curtis Rueden] Move Histogram code to net.imglib2.stats package

[tobias.pietzsch] MSER: MserTree.size() returns number of found MSERs.

[tobias.pietzsch] MSER: EvaluationNode do not keeps list of children (so that they can be garbage collected)

[tobias.pietzsch] MSER: prune MserTree after every prunAfterNMinima added nodes.

[tobias.pietzsch] remove debug chatter

[tobias.pietzsch] renamed *TreeTest to *TreeExample to prevent JUnit from running it.

[acardona] imglib2-scripting: ImgMin, ImgMax, ImgMean, ImgStdDev, ImgIterativeMean

[acardona] imglib2-scripting: new method Util.intervalDimensions for IterableRealInterval.

[acardona] imglib2-scripting: minor edits to Benchmark

[acardona] imglib2-scripting: more flexible Reduction of images.

[acardona] imglib2-scripting: better Reduce* functions.

[acardona] imglib2-scripting: fixes for Random IFunction.

[acardona] imglib2-scripting: cleaned up BinaryOperation javadocs.

[acardona] imglib2-scripting: Util.flatIterable to return or wrap an image as flat-iterable or fail.

[acardona] imglib2-scripting: ImageFunction wraps RandomAccessibleInterval as IterableRandomAccessibleInterval.

[acardona] imglib2-scripting: adjust Compute class to new changes in ImageFunction.

[acardona] imglib2-scripting: TestReduce

[acardona] imglib1-algorithm: IntegralImage

[tobias.pietzsch] MSER: fixed bug in ComponentTree.

[tobias.pietzsch] make RealRandomAccessible from RandomAccessible using interpolation.

[tobias.pietzsch] add static create method to let the compiler figure out T.

[tobias.pietzsch] fixed bug with out-of-bounds checking in OutOfBoundsConstantValue.

[stephan.preibisch] Corrected a "documentation bug"

[stephan.preibisch] The ImgOpener calls where the type is defined by the file, now

[stephan.preibisch] Fixed a bug in the Orthoslice cursor, it failed when the size of the

[stephan.preibisch] ImgOpener now opens files where the size in x or y is only 1

[stephan.preibisch] just some documentation change and testing

[acardona] imglib2-scripting: another test for Rois

[bdezonia] KnimeInterfce initial work

[bdezonia] more work towards using imglib types.

[bdezonia] more changes towards using Imglib types

[christian.dietz] Changed duplicate() to copy().

[stephan.preibisch] Fixed gauss for float when kernel is bigger than image with Tobias

[stephan.preibisch] Fixed gauss so that it also works with images where one dimension

[stephan.preibisch] GaussFloat has also static methods now

[stephan.preibisch] GaussNativeType is now not abstract any more

[stephan.preibisch] Added a gauss version with double precision

[stephan.preibisch] Added a completely generic Gauss that will compute on any numeric type

[tobias.pietzsch] Removed try-catch because, with p=dimension*2, divide-by-zero will never happen for the DoubleBoundary case.

[tobias.pietzsch] fixed javadoc.

[tobias.pietzsch] fixed bug with out-of-bounds checking in OutOfBoundsMirror.

[tobias.pietzsch] renamed AbstractOutOfBoundsMirror's position field to zeroMinPos to avoid confusion with the external position (setPosition/localize).

[tobias.pietzsch] fixed bug with out-of-bounds checking in OutOfBoundsMirrorExpWindowing and OutOfBoundsPeriodic.

[tobias.pietzsch] fixed bug introduced by previous fix.

[stephan.preibisch] Finished all Gauss implementations, multithreading still need to be implemented

[stephan.preibisch] ImgLib2 gauss works multithreaded

[bdezonia] more translation of real operators

[stephan.preibisch] fixed alberts code because of new return type from gauss

[stephan.preibisch] Removed unnecessary import

[bdezonia] make binary real operations use RealType

[bdezonia] make Real conditions use RealType

[bdezonia] rename Relation::duplciate() to copy()

[bdezonia] continue migrating real functions to use RealType. also delete old test classes.

[tobias.pietzsch] renamed the RandomAccess "cursorOnCells" to "randomAccessOnCells".

[bdezonia] make BinaryRelation take two type parameters rather than one

[tobias.pietzsch] extracted Cells interface

[bdezonia] add a couple binary boolean operations

[bdezonia] add a RealConvert operation that can do type scaling and conversion

[stephan.preibisch] Added frames per second counter so that it can compare with ImgLib2

[stephan.preibisch] Added the new imglib2 game of death

[tobias.pietzsch] extracted Cell interface.

[christian.dietz] Added new UnaryRelations

[bdezonia] change all uses of duplicate() to copy() - more conventional

[bdezonia] fix ImageAssignment classes. genericize base and deprecate others.

[acardona] imglib2-scripting: renamed a method

[acardona] imglib2-scripting: doc edit

[acardona] imglib2-scripting: fixed two tests.

[acardona] imglib2-scripting: ImgLib show and wrap methods do not need to require a NativeType

[stephan.preibisch] Refactored Gauss2 -> Gauss in imglib2 as it is finished now

[tobias.pietzsch] IterableRandomAccessibleInterval wrapper implements RandomAccessible.

[tobias.pietzsch] experimental knime SubImg clone using Views.

[tobias.pietzsch] SamplerConverter interface and RealType-to-FloatType implementation.

[tobias.pietzsch] Accessors and Accessibles for on-the-fly type conversion.

[stephan.preibisch] Started with a proper calling of Gauss

[stephan.preibisch] implements now randomaccessibleinterval instead of randomaccessible

[stephan.preibisch] added double converter support

[bdezonia] multiple refactroing changes re: porting for Knime

[stephan.preibisch] Gauss class can deal with float images, also in-place

[stephan.preibisch] Removed unnecesarry commit

[bdezonia] fix complex and real unary adapter functions

[bdezonia] fix complex exp operation

[tobias.pietzsch] modified ListImg< T > so that it does not require T to implement Type< T >

[bdezonia] unary mixed complex/real adapters and some broken complex operations

[tobias.pietzsch] removed Cell interface, created AbstractCell instead, renamed ListImgCell to DefaultCell.

[bdezonia] fix operations binary complex and partially edit unary ones too

[bdezonia] update some complex operations to use types and make more generic

[tobias.pietzsch] more concrete accessor types

[tobias.pietzsch] fixed compile error.

[Curtis Rueden] Fix compile error in Gauss

[bdezonia] update a couple more complex operations

[bdezonia] port a few more complex operations

[bdezonia] port a few more complex operations

[bdezonia] ported a couple more complex operations

[bdezonia] port a couple more complex operations

[bdezonia] port a few more complex operations

[bdezonia] port a couple more complex operations

[bdezonia] finish porting complex unary operations

[bdezonia] finish a complex helper/utils class.

[bdezonia] port some real functions that refer to complex types

[bdezonia] port some more complex functions

[bdezonia] port the DFT & IDFT example functions

[bdezonia] some cleanup and work on examples

[bdezonia] commiting experimental ops code in a sandbox

[bdezonia] commiting additional experimental code

[bdezonia] commiting additional experimental code

[bdezonia] continue porting examples

[bdezonia] fix issues of initialization of DFT and IDFT function classes

[bdezonia] fix bug in ComplexAdd

[tobias.pietzsch] IterableRandomAccessibleInterval wrapper implements RandomAccessible.

[bdezonia] Add some test code and UnaryOutputOperation and BinaryOutputOperation

[bdezonia] update UnaryOperation to return output type

[bdezonia] retry commit and update BinaryOperation output type

[bdezonia] whitespace

[bdezonia] undo the changes to AbstractROI::isMember()

[christian.dietz] Refactoring of unaryoperations, binaryoperations

[tobias.pietzsch] views: replaced MixedTransform by Mixed interface where it made sense.

[bdezonia] fix bug in ComplexSubtract. fix ComplexAddTest code.

[bdezonia] provide outputs for some general functions

[bdezonia] fix a couple examples

[bdezonia] implement some unit tests for complex binary operations

[bdezonia] try to optimize ComplexMultiply. flesh out ComplexPowerTest.

[Curtis Rueden] Fix parent for broken imglib2 projects

[Curtis Rueden] Add ImgLib2 examples to main build

[Curtis Rueden] Update repository URLs to new domain name

[christian.dietz] Added new Assignment classes

[christian.dietz] Deleted Constant operation

[Curtis Rueden] Fix distribution repository

[bdezonia] fix a bug in ComplexHelper angle calc method and improve ComplexPowerTest

[bdezonia] create tests for ComplexLog

[bdezonia] eliminate warnings

[bdezonia] fix bugs in a couple complex unary operations

[tobias.pietzsch] added Type contructors with dataAccess.

[tobias.pietzsch] added javadoc for conatenation interfaces.

[tobias.pietzsch] views: SlicingTransform and Slicing-concatenation unit test.

[tobias.pietzsch] views: optimized RandomAccess for Slicing transform.

[tobias.pietzsch] views: TransformBuilder checks for pure Slicing transforms. (plus some minor changes)

[bdezonia] write tests for ComplexExp

[bdezonia] add ComplexIntegerPowerTest and cleanup ComplexPowerTest

[stephan.preibisch] Finished all static methods for static gauss calls via Gauss.java

[bdezonia] test reciprocal operation

[stephan.preibisch] Gaussian convolution finished, has all static methods in Gauss.java,

[stephan.preibisch] Added toFloat() and toDouble() methods where the output of Gauss

[stephan.preibisch] Fixed the Gauss package so that the cursors never go outside of the defined area

[stephan.preibisch] Fixed a bug, gauss was never called

[stephan.preibisch] Fixed another bug, forgot the OutOfBounds in some cases

[stephan.preibisch] Fixed a bug in the FourierConvolution so that it preserves by default the fft of the input image

[bdezonia] fix type declaration errors in many real unary ops

[bdezonia] fix complex relation defs. also make two kinds of "complex near" testers.

[bdezonia] tag files with copyright and author info

[bdezonia] restore operations used by IJ2 that were deleted by Christian

[bdezonia] restore RealInverts ability to invert around a range.

[bdezonia] cleanup sandbox to get code compiling

[bdezonia] make a few functions more general (NumericType rather than ComplexType)

[bdezonia] minor formatting changes in test code

[bdezonia] restore double based function code and homogenize style

[jean-yves.tinevez] Perona & Malik Anisotropic diffusion

[jean-yves.tinevez] Test for Anisotropic diffusion

[jean-yves.tinevez] Special cursors using physical coordinates as bounds

[jean-yves.tinevez] Regional finder

[jean-yves.tinevez] Special cursors: remove tests from java file to allow compiling

[bdezonia] major changes towards simplifying RealType generics

[bdezonia] remove generic typing from ImageAssignment

[stephan.preibisch] Fixed bug pointed out by Barry that ComplexDoubleTypes should take doubles

[bdezonia] simplify generics for Complex operations

[bdezonia] update code to reflect changes to ComplexDoubleType

[bdezonia] convert example code into JUnit tests

[bdezonia] simplify generics in the operation.unary.mixed package

[bdezonia] eliminate warning

[tobias.pietzsch] MSER: added buildMserTree method for RealType which takes delta parameter as double.

[bdezonia] expand ImageAssignement so it handles real and complex images

[bdezonia] inconsequential edits

[bdezonia] some minor reorganization

[bdezonia] improve SpeedCalc output

[bdezonia] Change all real operations to be based upon ComplexType

[bdezonia] flesh out some investigative redefinitions for functions

[bdezonia] cleanup some experimental sandbox classes

[saalfeld] do not copy double[] coordinates in RealPoint constructor

[saalfeld] finalize parameters

[saalfeld] NearestNeighborSearch is EuclideanSpace and got a copy method

[saalfeld] adjusted tests to RealPoint not copying position arrays

[saalfeld] Revert "adjusted tests to RealPoint not copying position arrays"

[saalfeld] Revert "do not copy double[] coordinates in RealPoint constructor"

[saalfeld] added wrap( double[] ) method to RealPoint

[saalfeld] protected package public methods in Round

[saalfeld] added NearestNeighborInterpolator for NearestNeighborSearch

[saalfeld] added copyright notice to transforms

[saalfeld] created imglib2-realtransform maven module

[saalfeld] moved real transform interfaces into new module

[saalfeld] added affine interfaces and classes

[saalfeld] Deleted RealLocation since it is redundant with RealPoint and

[saalfeld] cosmetics: removing Eclipse complaints about name-clashes

[saalfeld] added interface method to RealRandomAccessible

[saalfeld] recover the original (k)nearestneighbortests

[bdezonia] add some TODOs

[saalfeld] fixed AbstractRealRandomAccess setPosition calls with Localizable

[saalfeld] intermediate commit of RealTransformRealRandomAccessible while

[bdezonia] cleanup sandbox some

[bdezonia] fix getArgument() to match textbook definitions when dx & dy == 0

[bdezonia] ComplexHelper: documentation cleanup

[Johannes Schindelin] Undo (most) of the changes in KnimeInterface outside ops

[bdezonia] Temp workaround: use floats instead of doubles w/ ComplexDoubleTypes

[bdezonia] Revert "Temp workaround: use floats instead of doubles w/ ComplexDoubleTypes"

[bdezonia] Update test to match recent changes to ComplexHelper

[saalfeld] Fixed serious bug in AbstractRealLocalizableSampler, localize methods

[saalfeld] RealTransformRealRandomAccess finished

[saalfeld] added RealTransformRealRandomAccessible

[bdezonia] OPS: add JUnit dependency to pom

[saalfeld] added RandomAccessibleOnRealRandomAccessible

[saalfeld] add dependency to imglib2-realtransform to imglib2-tests

[saalfeld] fix apply methods in AbstractAffineTransform

[saalfeld] Let XYProjector use a single setPosition() call instead of two per

[saalfeld] added a behavior test for affine transformed real views into

[saalfeld] added AffineTransform3D from mpicbg just to test if the performance

[saalfeld] provide Point with a wrapper for existing long[] coordinates

[saalfeld] make RealTransformRealRandomAccess and inner class of

[saalfeld] add RealTransformRandomAccessible, providing a RandomAccess directly

[saalfeld] variants in the behavior test

[saalfeld] RealTransform(Real)RandomAccessible executes coordinate transfer

[saalfeld] Revert "Let XYProjector use a single setPosition() call instead of two per"

[saalfeld] make ARGBScreenImage implement RandomAccessibleInterval

[saalfeld] added XYRandomAccessibleProjector that maps by scanline instead

[saalfeld] specialize return type of ArrayImg.randomAccess( Interval )

[saalfeld] behavior test of XYRandomAccessibleProjector

[saalfeld] * removed Affine interface and relpaced it by AffineReadable and

[Curtis Rueden] Add missing version numbers for some Maven plugins

[Curtis Rueden] Build source JARs by default

[bdezonia] added some javadoc

[bdezonia] add javadoc

[bdezonia] documentation note added

[bdezonia] javadoc improvements

[bdezonia] more javadoc tweaks

[saalfeld] affinereadable gets getRowPackedCopy method analogous to Jama

[saalfeld] ConstantAffineRandomAccess stores and works on a copy of the

[saalfeld] test considers linear calibration relative to x

[saalfeld] added Interactive3DRotationTest, an implementation of Stack_Rotate

[bdezonia] improve test to handle higher powers

[saalfeld] * fixed scaling bug in visualization

[saalfeld] more fancy rotating box, rendering anti-aliased and axes labeled

[saalfeld] fixed help text

[stephan.preibisch] Added Lanczos interpolation

[saalfeld] * refactored AffineReadable to AffineGet and AffineWritable to

[saalfeld] LanczosInterpolator generates sinc from linearly interpolated

[stephan.preibisch] Fixed a bug in the FFT rearrangment if the size of images is odd ...

[stephan.preibisch] Removed unnecessary import

[stephan.preibisch] Fixed the same FFT-rearrangement bug in imglib2, works now fine if the FFT has an odd size for dimensions > 0.

[saalfeld] LanczosInterpolator uses double instead float, speed is the same

[saalfeld] protect private members in LanczosInterpolator

[tobias.pietzsch] bug fix. thanks to Christian Dietz for noticing.

[saalfeld] coordinates for Point constructor can be varargs

[saalfeld] * added real2integer transforming RealRandomAccess FloorOffset,

[saalfeld] * simplifyed LanczosInterpolator by extending FloorOffset

[jean-yves.tinevez] Anisotropic diffusion: move test to test folder

[jean-yves.tinevez] Gaussian peak fitter: fit n-D gaussians on peaks

[Johannes Schindelin] Add the ImgLib1 examples from Stephan Preibisch

[Johannes Schindelin] Add a stupid reimplementation of RealSum

[Johannes Schindelin] ij2-examples: Remove DOS-line endings

[Johannes Schindelin] ij2-examples: Fix whitespace

[Johannes Schindelin] ij2-examples: Rename and move the sandbox Example

[Johannes Schindelin] ij2-examples: Big move

[Johannes Schindelin] ij2-examples: fix javadoc

[Johannes Schindelin] Force the IJ2 examples' dependency to be ImgLib2

[Johannes Schindelin] ij2-examples: remove obsolete imports

[Johannes Schindelin] ij2-examples: RealType is now in net.imglib2.type.numeric

[Johannes Schindelin] ij2-examples: ImagePlusAdapter now lives in net.imglib2.img

[Johannes Schindelin] ij2-examples: ImageJFunctions moved to net.imglib2.img.display.imagej

[Johannes Schindelin] ij2-examples: displayAsVirtualStack() is now show()

[Johannes Schindelin] ij2-examples: Image is now Img

[Johannes Schindelin] ij2-examples: LOCI is now ImgOpener

[Johannes Schindelin] ij2-examples: openLOCI() is now openImg()

[Johannes Schindelin] ij2-examples: openImg() is no longer static

[Johannes Schindelin] ij2-examples: ArrayContainerFactory is now ArrayImgFactory<T>

[Johannes Schindelin] ij2-examples: Img lacks the getDisplay() method

[Johannes Schindelin] ij2-examples: what happened to openLOCIFloatType?

[Johannes Schindelin] ij2-examples: openImg() now returns an Img<RealType & NativeType>

[Johannes Schindelin] ij2-examples: openImg() can create its own ArrayImgFactory

[Johannes Schindelin] ij2-examples: openImg() now throws ImgIOException and IncompatibleTypeException

[Johannes Schindelin] ij2-examples: Example2a no longer needs to implement the copy() method

[stephan.preibisch] Fixed example2 for imglib2

[stephan.preibisch] removed an imp.show() as ImageJFunctions.show() shows it already....

[stephan.preibisch] Added two more explanations for the opener

[stephan.preibisch] removed show commands that are not necessary...

[stephan.preibisch] removed some unnecessary imports

[stephan.preibisch] Converter example1c

[stephan.preibisch] Fixed example2b

[stephan.preibisch] Removed the show methods

[stephan.preibisch] Added the code for creating another image with same size

[stephan.preibisch] Finished example2c

[stephan.preibisch] Made example3 almost ready

[stephan.preibisch] Added computePercentile for float

[acardona] imglib2-algorithm: New class IntegralImage, ripped from imglib2-scripting TypedIntegralImage.

[acardona] imglib2-scripting: use imglib2-algorithm new IntegralImage.

[stephan.preibisch] Added a generic IntegerTypeConverter

[stephan.preibisch] Added a generic version of the IntegralImage that can also works on NumericTypes and uses the same logic

[stephan.preibisch] Added possibility to return images to FFTconvolution

[acardona] Preliminary ScaleAreaAveraging2d based on IntegralImage

[stephan.preibisch] Added a direct implementation of the summing of each line for long and double basic type.

[acardona] imglib1-algorithm: work around javac compilation error.

[stephan.preibisch] Added an implementation of a constant image to imglib1&imglib2. It has only one value at each position but

[stephan.preibisch] Fixed a bug in the ListLocalizingCursor, dimensions were set wrongly.

[stephan.preibisch] Added Cross Correlation

[bdezonia] OPS - make operations more generic

[bdezonia] OPS - change generic declarations of operations

[bdezonia] OPS - update documentation for real unary operations

[bdezonia] OPS - minor code formatting changes

[jean-yves.tinevez] PickImagePeaks: add a flag to allow border peaks to be found

[Curtis Rueden] Update performance benchmark to ImgLib2

[Curtis Rueden] Skip unit tests when running the benchmark

[Curtis Rueden] Update PixLib to version 0.7.6

[Curtis Rueden] Revert to older PixLib, to avoid compile errors

[acardona] SimpleMultiThreading: when  1 == nThreads, call the run()

[Curtis Rueden] Use new maven.imagej.net subdomain

[tobias.pietzsch] fixed bug in size calulation of IterableRandomAccessibleInterval (thanks to Christian Dietz)

[tobias.pietzsch] KDTree: implemented VolumetricSearch using new KDTree. tests run ok.

[tobias.pietzsch] KDTree: fixed javadoc

[tobias.pietzsch] KDTree: use KDTreeNode.getSplitDimension() instead of keeping track of split dimensions ourselves.

[tobias.pietzsch] KDTree: use a RealLocalizable wrapper instead of creating a RealPoint for every interval.

[tobias.pietzsch] Removed old KDTree implementation.

[saalfeld] 3d rotation test centers at the original mouse click

[saalfeld] added broken 2d rotation test

[saalfeld] abstracted common test implementations

[saalfeld] added 2d affine transformation

[saalfeld] added a beanshell to visualize the difference between the interpolated

[acardona] ImgLib1: minor simplification in IntegralImage

[acardona] ImgLib1: added ScaleAreaAveraging.setOutputDimensions

[acardona] Removed old IntegralImage class and renamed IntegralImage2

[tobias.pietzsch] started to implement access to ntree node structure.

[tobias.pietzsch] moved Ntree to separate class. added junit tests.

[tobias.pietzsch] starting with NativeType and IntAccess (this will be enough to make the Labeling work).

[tobias.pietzsch] NtreeImg implementation that supports every NativeType< T > based on IntAccess and with numEntities == 1.

[tobias.pietzsch] NtreeImg Example, where a 2D IntType image is loaded, copied to a NtreeImg, and displayed.

[tobias.pietzsch] testing sparse labeling. This is a copy of LabelingTest. I just replaced the ArrayImgFactory with a NtreeImgFactory.

[tobias.pietzsch] Moved the algorithm and stats packages from imglib2-core to imglib2-algorithms.

[Curtis Rueden] Fix parent POM reference

[Curtis Rueden] Split algorithms into BSD and GPL portions

[Curtis Rueden] Use better names for POM projects

[acardona] imglib2-algorithms: imported integral package from imglib1-algorithms.

[acardona] imglib2-scripting: fix IntegralImage to work with the new IntegralImg in imglib2-algorithms.

[acardona] imglib2-scripting: fix the ackward situation of enum values in AbstractAffine3D.

[acardona] imglib2-scripting: decorative changes and fixes to documentation.

[acardona] imglib2-scripting: ConstantImg and its cursors.

[jeanyves.tinevez] Perona & Malik Anisotropic diffusion

[jeanyves.tinevez] Test for Anisotropic diffusion

[jeanyves.tinevez] Special cursors using physical coordinates as bounds

[jeanyves.tinevez] Regional finder

[jeanyves.tinevez] Special cursors: remove tests from java file to allow compiling

[jeanyves.tinevez] Anisotropic diffusion: move test to test folder

[jeanyves.tinevez] Gaussian peak fitter: fit n-D gaussians on peaks

[jeanyves.tinevez] PickImagePeaks: add a flag to allow border peaks to be found

[bdezonia] Add an older experiment to the sandbox

[Curtis Rueden] Fix order of dependencies to be consistent

[Curtis Rueden] Move certain ImgLib1 tests into dedicated package

[Curtis Rueden] Use consistent version number for base POM

[Curtis Rueden] Update some URLs and mailing list details

[stephan.preibisch] Game of death can record movie

[stephan.preibisch] Added the HyperSphereCursor for ImgLib2

[stephan.preibisch] HyperspherCursor does not need Type, but only T as generic parameter

[stephan.preibisch] IntervalIndexer can now also return their current index on demand

[stephan.preibisch] Added the LocalneighborhoodCursor that iterates over the local 3x3x3...x3 environemnt

[stephan.preibisch] Added a static constructor that might return a better implemented version

[stephan.preibisch] Added a static constructor that might return a better implemented version

[tobias.pietzsch] added/fixed javadoc.

[tobias.pietzsch] ImageJVirtualStack can display intervals that do not start at the origin now.

[stephan.preibisch] Added convienience function to test if an interval is zero-bounded

[stephan.preibisch] Fixed bug that for float images min/max was not computed in the right area

[bdezonia] Add a new interface: Sourced

[bdezonia] Fix bug in ComplexPolarNear

[bdezonia] Test theta <= tolerance rather than < tolerance

[tobias.pietzsch] completed javadoc.

[saalfeld] fixed a few comments

[stephan.preibisch] Moved HyperSphere to algorithms

[Curtis Rueden] Change Jama dependency to compile scope

[Curtis Rueden] Fix parent POM reference

[Curtis Rueden] Rename files to avoid test errors with Maven 2.x

[Curtis Rueden] Add a simple README

[Curtis Rueden] Use scijava parent POM

[tobias.pietzsch] add javadoc

[stephan.preibisch] Finished the HyperSphere

[stephan.preibisch] Small adjustments of equalIterationOrder test (includes ListImg now)

[stephan.preibisch] Finished the LocalNeighborhood

[stephan.preibisch] Small addition so that 1-bit and 12-bit are displayed correctly

[saalfeld] Added Views.iterable() that creates an IterableInterval from a

[stephan.preibisch] Now created via Views.iterable()

[stephan.preibisch] Fixed the ConstantImg

[tobias.pietzsch] removed unused classes:

[tobias.pietzsch] remodeling of abstract class hierarchy for Real samplers:

[tobias.pietzsch] created pom

[tobias.pietzsch] examples from "Getting Started" tutorial.

[tobias.pietzsch] graffiti.tif for getting started tutorial.

[tobias.pietzsch] examples for RandomAccess tutorial.

[tobias.pietzsch] added examples for Cursor tutorial.

[tobias.pietzsch] procedural generated Mandelbrot RealRandomAccessible.

[tobias.pietzsch] adapted to modified abstract class hierarchy.

[tobias.pietzsch] added javadoc and cleaned up

[stephan.preibisch] Created a new OutOfBoundsRandomValue which returns random numbers outside of the Interval

[stephan.preibisch] Added a static method to Views to instantiate a OutOfBoundsRandomValue

[tobias.pietzsch] removed unused abstract classes.

[tobias.pietzsch] AbstractLocalizableSampler<T> is now AbstractLocalizable (not a Sampler anymore).

[tobias.pietzsch] made Point extend AbstractLocalizable.

[tobias.pietzsch] Location will be replaced by Point eventually.

[stephan.preibisch] Fixed the AbstractXYProjector so that he can cope with one-dimensional data

[stephan.preibisch] Fixed the XYProjector so that he can deal with one-dimensional data

[stephan.preibisch] Fixed the ImageJVirtualStack so that he can deal with one-dimensional data

[stephan.preibisch] Added static call methods to Fourier Convolution

[tobias.pietzsch] fixed CellCursor generic parameters in PerformanceTest

[tobias.pietzsch] add javadoc

[tobias.pietzsch] ListImg unit test

[tobias.pietzsch] simplify Img copy() loops and use concrete Cursor types.

[tobias.pietzsch] added ListImg javadoc, removed unused fields, added set() method to ListRandomAccess.

[tobias.pietzsch] AbstractLocalizableSamplerInt<T> is now AbstractLocalizableInt (not a Sampler anymore).

[tobias.pietzsch] ListRandomAccess extends AbstractLocalizableInt.

[tobias.pietzsch] made several RandomAccesses extend Point.

[tobias.pietzsch] ConverterImgProxy should extend neither AbstractRandomAccess nor Point,

[tobias.pietzsch] made View RandomAccesses extend AbstractLocalizable and implemented the few missing methods.

[tobias.pietzsch] made CellRandomAccess extend AbstractLocalizable and implemented missing methods.

[tobias.pietzsch] removed AbstractRandomAccess

[tobias.pietzsch] Array- and PlanarRandomAccess extend AbstractLocalizableInt.

[tobias.pietzsch] removed AbstractRandomAccessInt

[stephan.preibisch] Fixed AbstractComplexType to return the power instead of the glog of the power

[stephan.preibisch] Added the functionality to display complex images

[tobias.pietzsch] fixed javadoc.

[tobias.pietzsch] In setPosition(Localizable) implementations use Localizable.localize() instead of iterating Localizable.getPosition() for every dimensions.

[tobias.pietzsch] removed unused methods.

[Curtis Rueden] Update parent POM reference to latest version

[saalfeld] 2DRotationExample can rotate, scale, and shift waiting for

[saalfeld] added MandelbrotViewer, dragging the mouse with Shift pans the canvas,

[saalfeld] added scale method to AffineTransform3D

[tobias.pietzsch] made AbstractInterval extend EuclideanSpace

[tobias.pietzsch] scripting: use FinalInterval instead of AbstractInterval

[saalfeld] renamed viewer examples

[saalfeld] extended 3d rotation example by scaling and shifting using the mouse

[saalfeld] added scale method to AffineTransform3D

[saalfeld] extended 3d rotation example by scaling and shifting using the mouse

[tobias.pietzsch] made IntervalIterator extend AbstractInterval

[Curtis Rueden] Update developer and contributor lists

[stephan.preibisch] Added static method for interpolation to views

[Curtis Rueden] Fix POM validation error (sorry!)

[stephan.preibisch] Added implementation of the RealInterval

[tobias.pietzsch] added unit test and benchmark for RandomAccessibleIntervalCursor.

[tobias.pietzsch] RandomAccessibleIntervalCursor extends AbstractInterval, and move()s RandomAccess instead of setPosition() with array.

[tobias.pietzsch] removed RandomAccessibleZeoMinIntervalCursor. It's not faster than RandomAccessibleIntervalCursor, so it's not worth keeping both.

[tobias.pietzsch] deprecated Location

[tobias.pietzsch] made ListCursor and ListLocalizingCursor extend the abstract int[] variants. added javadoc.

[tobias.pietzsch] classes from the position.transform package extend AbstractEuclideanSpace

[tobias.pietzsch] made round() and floor() static methods public so that they can be re-used.

[tobias.pietzsch] changed setPosition( Localizable ) implementation. renamed container to img

[tobias.pietzsch] only print median in CellRandomAccessBenchmark

[tobias.pietzsch] harmonize handling of cell min / max.

[tobias.pietzsch] CellRandomAccess can now be positioned outside of the img without throwing an exception (unless you get() the value)

[tobias.pietzsch] fix unit test: was trying to wrap a null long[] array.

[tobias.pietzsch] Added javadoc and license blurbs.

[tobias.pietzsch] fixed PlanarRandomAccess1D.

[christian.dietz] Bugfixes in Wrapping Operations.

[christian.dietz] Added copyright information to files

[tobias.pietzsch] fix compilation error

[christian.dietz] Modified NtreeImg, NtreeRndAccess and Cursor.

[christian.dietz] Added new NtreeImg types

[christian.dietz] Added new ConcatenatedBufferedUnaryOperation

[christian.dietz] Fixed two bugs in BinaryOperationAssigment and BinaryRelationAssigment

[Curtis Rueden] Flesh out list of developers and contributors

[tobias.pietzsch] reformatted using eclipse.

[tobias.pietzsch] changes from labeling-revised branch

[tobias.pietzsch] changed equalIterationOrder() mechanism.

[tobias.pietzsch] forgot this in the previous commit...

[stephan.preibisch] Added printCoordinates( double[] )

[tobias.pietzsch] create IterationOrder objects when iterationOrder() is called.

[tobias.pietzsch] made AbstractRealInterval extend EuclideanSpace.

[stephan.preibisch] Fixed the IterableRandomAccessibleInterval to only return a FlatIterationOrder on demand

[stephan.preibisch] All Img return their specific type of IterationOrder

[stephan.preibisch] Added the comment that 'n' in the constructor refers to the

[stephan.preibisch] RadiusNeighborSearch now also implements EuclideanSpace so that it

[bdezonia] Fix bug in comparing angles near TWO PI.

[Curtis Rueden] Add license-maven-plugin configuration

[christian.dietz] Added performance test to LabelingTest.

[christian.dietz] Added performance Test to LabelingTest

[christian.dietz] Added labeling performance test

[bdezonia] Add copyright notice and correct @author tag

[bdezonia] Update copyrights and add correct @author tags

[tobias.pietzsch] added Views.raster() method that turns a RealRandomAccessible into a RandomAccessible

[tobias.pietzsch] fixed copy() of RandomAccessOnRealRandomAccessible: the copy must have the same location.

[tobias.pietzsch] made RandomAccessibleOnRealRandomAccessible extend AbstractEuclideanSpace.

[stephan.preibisch] Seperated NearestNeighborSearch and KNearestNeighborsearch

[stephan.preibisch] Fixed bug in test due to sepraration of interfaces

[stephan.preibisch] KNearestNeighborSearch extends NearestNeighborSearch

[stephan.preibisch] Added interpolation for sparse data based on inverse distance weighting of k nearest neighbors

[saalfeld] InverseDistanceWeightingInterpolator: check for the query point being

[stephan.preibisch] Renamed numNeighbors() by getK()

[stephan.preibisch] Fixed bug that the interpolator recognizes if not more neighbors are available, i.e.

[tobias.pietzsch] fixed bug in OutOfBoundsMirror.

[tobias.pietzsch] fixed bug in TranslationRandomAccess (thanks to Stephan Preibisch for finding it).

[stephan.preibisch] Updated DevUtil to support float, too

[jean-yves.tinevez] imglib2/algo: Test performance of various iteration methods

[jean-yves.tinevez] imglib1: edit or remove interactive dummy tests that fail to compile

[jean-yves.tinevez] imglib2: move interactive test to inglib2 test package

[Curtis Rueden] Update POMs with license plugin configuration

[Curtis Rueden] Add missing EOF newlines

[Curtis Rueden] Clean up and standardize copyright headers

[Curtis Rueden] Update LICENSE.txt files

[christian.dietz] Updated SubImg. Added SubImgTest.

[christian.dietz] Adapted NtreeImg/RandomAcess to new RandomAccess hierarchy.

[christian.dietz] Fixed bugs in AllConnectedComponents and Watershed due to merge.

[Curtis Rueden] Update to scijava POM 1.8

[Curtis Rueden] Add missing file headers

[Curtis Rueden] Update scijava POM to 1.9

[Curtis Rueden] Eliminate Windows-style newlines

[tobias.pietzsch] [Views] add a version of offsetInterval taking an Interval.

[tobias.pietzsch] [Views] add a version of offsetInterval taking an Interval.

[tobias.pietzsch] fixed yet another bug in SubImg (thanks to Christian Dietz)

[jeanyves.tinevez] WIP: pde package: filters based on partial differential equations

[jeanyves.tinevez] A simple test for anisotropic diffusion

[Curtis Rueden] Target Java 1.5 for imglib2 core

[Curtis Rueden] Add dependency on imglib2-algorithms-gpl to tests

[Curtis Rueden] Update imglib2-tests license to GPLv2 from BSD-2

[jean-yves.tinevez] DomainCursor: a neighborhood cursor that iterates over arbitrary nD rectangle

[jean-yves.tinevez] A simple example for the Domain cursor

[jean-yves.tinevez] Non-linear anisotropic diffusion: 2x2 methods for 2D

[jean-yves.tinevez] Revamp the example for non-linear anisotropic diffusion

[tobias.pietzsch] Added new methods to Jean-Yves iteration performance test:

[jean-yves.tinevez] Perona & Malik Anisotropic diffusion Algorithm

[jean-yves.tinevez] An example for Perona&Malik anisotropic diffusion scheme

[Curtis Rueden] Fix compile errors with OpenJDK version of javac

[Curtis Rueden] Clean up and unify ImgLib2 I/O sources

[Curtis Rueden] Fix import statements

[Curtis Rueden] Fix unit test error with VirtualImg

[acardona] imglib2-scripting: now that imglib2-core has ConstantImg,

[Curtis Rueden] Move Java5 configuration to a profile

[jeanyves.tinevez] WIP: Non-linear anisotropic diffusion: fundations for 3D version

[jean-yves.tinevez] n-dimensional Bresenham line

[jean-yves.tinevez] An example for BresenhamLine

[stephan.preibisch] Fixed a multi-threaded bug

[jean-yves.tinevez] Anisotropic Diffusion: almost done with 3D framework

[jean-yves.tinevez] Example for 3D anisotropic diffusion

[jeanyves.tinevez] Fix compilation error in Jenkis for the anisotropic diffusion example

[Curtis Rueden] Fix up imglib2-tests dependencies

[Curtis Rueden] Fix SCM information

[Curtis Rueden] Fix compile errors

[Curtis Rueden] Release version 2.0.0-beta1

[Curtis Rueden] Reset version number to 2.0.0-SNAPSHOT

[Curtis Rueden] Update version number for imglib2 broken projects

[christian.dietz] Adapted imglib.xml style to EllipseRegionOfInterest

[christian.dietz] Fixed bug in ellipse region of interest

[stephan.preibisch] PhaseCorrelation can keep the inversePhaseSpectrum

[stephan.preibisch] The FourierConvolution can keep the fft of the image

[jean-yves.tinevez] algoirthm.pds: fix anisotropic diffusion commit: 3D framework

[christian.dietz] getView is now public and takes RandomAccessibleInterval

[stephan.preibisch] Added Tobias's ImgLib2 benchmark

[tobias.pietzsch] [realtransform] bugfix: AffineTransform2D had numDimensions==3 in some places.

[tobias.pietzsch] [realtransform] added translate() method to AffineTransform2D.

[stephan.preibisch] Added output of min avg max

[stephan.preibisch] ListImg is supported, too - but can be disabled by a boolean (it needs a LOT of ram)

[jean-yves.tinevez] algorithms.pde: fix bugs in moment of inertia computation

[jean-yves.tinevez] Examples for 2D/3D anisotropic diffusion

[stephan.preibisch] one can specify the clipping range for the lanczos interpolator

[tobias.pietzsch] modified ImglibBenchmark to allow images with different size in each dimension.

[stephan.preibisch] Changed default size to 500x500x500

[stephan.preibisch] Benchmark computes median

[Curtis Rueden] Add missing @Override tags

[Curtis Rueden] Fix compile errors with latest version of SCIFIO

[jean-yves.tinevez] algorithm.pde: WIP - routines to compuet EV of 3x3 matrix quicler

[bdezonia] Lay the groundwork for a major refactor

[bdezonia] Eliminate the obsolete Neighborhood references

[bdezonia] Update implementers of the Condition interfaces

[bdezonia] Update some functions

[bdezonia] Update some functions to new Function definition

[bdezonia] Many changes related to Function redefinition

[bdezonia] Remove neighborhood code from ImageAssignment

[bdezonia] Make misc. function adhere to new Function definition

[bdezonia] Remove warnings

[bdezonia] Update tests to use new interfaces

[bdezonia] Delete obsolete classes

[bdezonia] Improve code organization

[bdezonia] Improve code clarity with some renaming

[bdezonia] Add some documentation

[bdezonia] Add some documentation.

[jeanyves.tinevez] Efficient numerical diagonalization of hermitian 3x3 matrices

[bdezonia] Added documentation

[saalfeld] auto finalize method parameters in AbstractNativeImg

[saalfeld] the T returned by ImageJFuncitons and ImagePlusAdapter is always

[tobias.pietzsch] fixed bug in IntervalIndexer (thanks to Steffi for noticing).

[stephan.preibisch] small changes to benchmark sizes

[stephan.preibisch] Better formatting

[bdezonia] Add copy() method to PointSet interface

[bdezonia] DFT/IDFT constructors now take an ImgFactory

[bdezonia] Make copy() return values more specific

[christian.dietz] Fixed bug in LabelingMapping

[christian.dietz] Reverted bugfix in EllipseRegionOfInterest

[bdezonia] Implement functionality for UniversalPointSet

[leek] Fixed ellipse ROI bug reported by Christian Dietz

[leek] Fixed ellipse ROI bug reported by Christian Dietz + other esoteric corner cases

[stephan.preibisch] Fixed bug when creating new image

[stephan.preibisch] support gaussian kernel with different sigma as cutoff

[jeanyves.tinevez] algorithm.pds: trying to fix thie moment of intertia

[jeanyves.tinevez] Trying to debug 3D anisotropic diffusion

[christian.dietz] Layouting of SparseLabelingTest

[christian.dietz] Added Test to SparseLabelingTest which breaks NtreeImg

[bdezonia] Fix up definitions of broken functions

[bdezonia] Minor code renaming changes

[tobias.pietzsch] fixed bug in mergeUpwards (thanks to Christian Dietz for finding bug and solution)

[tobias.pietzsch] added NtreeImg iterationOrder(). For now, the NtreeImg Cursor is stupid and uses FlatIterationOrder.

[bdezonia] Homogenize createIterator() return types

[bdezonia] Add the explode() method

[jeanyves.tinevez] algorithm.pde: Gave up on optimizing 3D M.O.I.

[jeanyves.tinevez] Revamp demo for Anisotropic diffusion

[stephan.preibisch] Added update function

[christian.dietz] Fixed bug in ConcatenatedBufferedUnaryOperation (thanks to felix schoenenberger)

[saalfeld] added julia set example

[saalfeld] moved RealSum from mpicbg into net.imglib2.util

[bdezonia] TextSpecifiedPointSet: partial implementation

[saalfeld] Replaced arraylists by arrays in RealSum by which the

[saalfeld] removed commented code from RealSum

[saalfeld] added ImgLib2 logo and QR code SVG sources

[bdezonia] Minor refactoring

[christian.dietz] Fixed copy() method in UnaryOutputOperation and added comments.

[saalfeld] weird 5-10% speedup for ArrayLocalizingCursor by re-arranging code.  It

[bdezonia] Change lexer: from "or" to "||"

[saalfeld] fixed carriage return width in XYRandomAccessibleProjector, now the first

[saalfeld] Added a first 2d CATMAIDRandomAccessible trial and a preliminary example

[saalfeld] made CATMAIDRandomAccessible 3D and an Interval

[tobias.pietzsch] Modified and commented BenchmarkHelper.

[christian.dietz] Minor speedup of internImpl in LabelingMapping.

[christian.dietz] Formatted code in imglib2 style

[bdezonia] Minor renaming changes

[saalfeld] Created a simple cache using a HashMap on SoftReferences for

[tobias.pietzsch] fixed compilation error.

[tobias.pietzsch] removed un-used code.

[tobias.pietzsch] Removed re-implementation of Positionable and Localizable interfaces from XYRandomAccessibleProjector.

[leek] Fixed bugs reported by Martin Horn in watershed

[tobias.pietzsch] Fixed copy() methods of real-view RandomAccesses (copies must be at the same position) and replaces sourcePosition by "this".

[tobias.pietzsch] fixed Positionable implementation of AffineRandomAccess (added missing methods) and fixed copy() (the copy must be at the same position).

[tobias.pietzsch] fixed bug caused by the previous commit. RealTransformRandomAccess copy constructor must be protected so that it can be called from derived AffineRandomAccess.

[tobias.pietzsch] speed-up XYProjector.

[Curtis Rueden] Eliminate "Object x" dummy constructor parameters

[tobias.pietzsch] add ImgLib2-logo overlay for interactive examples.

[tobias.pietzsch] added logo pngs

[saalfeld] Added example image for Img2DViewerExample.

[tobias.pietzsch] added ChannelARGBConverter that converts UnsignedByteType into one channel of ARGBType.

[tobias.pietzsch] speed-up of CompositeXYProjector.

[tobias.pietzsch] CompositeXYProjector: added interval for source RandomAccess (adapted from CompositeXYProjector)

[tobias.pietzsch] added CompositeXYRandomAccessibleProjector.

[bdezonia] Implement a better parser

[bdezonia] Add predefined functions to Lexer

[bdezonia] Improve support of logical operations

[tobias.pietzsch] handle the case that there is no ImageJ instance.

[tobias.pietzsch] RandomAccessibleViewer2D should do something similar to Image2DViewerExample.

[tobias.pietzsch] copied over AbstractInteractiveExample etc from test package, will be modified step by step.

[tobias.pietzsch] factored out LogoPainter. move toggleInterpolation() out of MappingThread.

[tobias.pietzsch] removed extension of PlugIn interface.

[tobias.pietzsch] re-ordered fields and added some comments.

[tobias.pietzsch] removed un-used member "img"

[tobias.pietzsch] move key-released handling to AbstractIntervactive2DViewer.

[tobias.pietzsch] removed nonsense SHIFT and CTRL handling

[tobias.pietzsch] removed un-used constructor

[tobias.pietzsch] make keyModifiedSpeed static and added javadoc

[tobias.pietzsch] move ColorProcessor to Img2DViewerExample

[tobias.pietzsch] initialize rotationList in AbstractInteractive2DViewer

[tobias.pietzsch] move GUI to separate class (maybe this will be reverted later)

[tobias.pietzsch] Moved event handling to separate class TransformEventHandler2D.

[bdezonia] Fix parsing bug with conditionals (AND, OR, XOR)

[tobias.pietzsch] move construction of gui, painter, and imp into AbstractInteractive2DViewer.

[tobias.pietzsch] AbstractInteractive2DViewer is no longer abstract. Img2DViewerExample doesn't extend it but instantiates it.

[saalfeld] re-added toggleInterpolation() as interface method of TransformListener

[tobias.pietzsch] made ARGBScreenImage extend ArrayImg instead of keeping one.

[tobias.pietzsch] moved most of the functionality into AbstractInteractive2DViewer.

[Curtis Rueden] Ignore JARs in toplevel directory

[tobias.pietzsch] renamed AbstractInteractive2DViewer to Interactive2DViewer.

[saalfeld] use smaller logo

[bdezonia] Add RealEquationFunction (a text specified function)

[tobias.pietzsch] added benchmarks to compare XYProjector and XYRandomAccessibleProjector.

[tobias.pietzsch] added benchmarks to compare XYProjector and XYRandomAccessibleProjector.

[saalfeld] added mandelbulb and mandelbox fractal variants, non of them completely

[saalfeld] use smaller logo

[saalfeld] catmaid loading from localhost based server

[saalfeld] Refactored converters.

[tobias.pietzsch] show projector rendering time.

[tobias.pietzsch] clean up TransformEventHandler2D.

[tobias.pietzsch] Interactive3DViewer and example.

[tobias.pietzsch] moved interactive viewers to gui package.

[acardona] Add binary files *class and *jar to .gitignore

[christian.dietz] Set linktype in copy method of NtreeImg

[christian.dietz] Added copy method to NtreeImg. Can be done more effcient.

[tobias.pietzsch] added two static convenience methods to create Intervals.

[tobias.pietzsch] cleaning up.

[tobias.pietzsch] removed unused parameter in AbstractOutOfBoundsValue constructor

[tobias.pietzsch] fixed a bug in OutOfBoundsValue.

[tobias.pietzsch] replaced looping move() implementations in AbstractOutOfBounds by a setPosition.

[tobias.pietzsch] some convenience methods similar to ImageJFunctions.show() using Interactive2DViewer.

[tobias.pietzsch] made ARGBScreenImage extend ArrayImg instead of keeping one.

[tobias.pietzsch] added two static convenience methods to create Intervals.

[tobias.pietzsch] removed unused parameter in AbstractOutOfBoundsValue constructor

[tobias.pietzsch] fixed a bug in OutOfBoundsValue.

[tobias.pietzsch] replaced looping move() implementations in AbstractOutOfBounds by a setPosition.

[tobias.pietzsch] convenience methods to create read/write-converted Accessibles. fixed/added javadoc.

[tobias.pietzsch] temp

[tobias.pietzsch] fixed bugs introduced by my previous "fix" (setPosition and move did recursively call themselves)

[Curtis Rueden] Release version 2.0.0-beta2

[Curtis Rueden] Reset version number to 2.0.0-SNAPSHOT

[tobias.pietzsch] added static flatIterable() method to Views.

[tobias.pietzsch] start() the painter thread instead of execute run() in our own thread.

[tobias.pietzsch] use NumericType<T> instead RealType<T> & NativeType<T>.

[tobias.pietzsch] creating/loading imgs. using accessors.

[tobias.pietzsch] adapted Stephan Saalfelds Bee example.

[tobias.pietzsch] System.exit() when viewer closes.

[saalfeld] juliasets got their own accessible

[saalfeld] julia examples use the accessible

[saalfeld] start thread instead of running it

[saalfeld] GUI takes a Colleciton of Event Handlers

[bdezonia] Create UVInsideRoiCondition

[bdezonia] Add copyright notices

[tobias.pietzsch] added read/write converter to the Bee example.

[tobias.pietzsch] clean up Mandelbrot example

[saalfeld] added NNSearch2DViewerExample

[tobias.pietzsch] added constructor without handler Collection

[tobias.pietzsch] added sparse data interpolation examples

[tobias.pietzsch] temporary changes for the demonstration

[bdezonia] Improve error checking code

[bdezonia] Add "img" syntax to equations

[bdezonia] Add new ImgReference token

[bdezonia] Fix function call parsing bug

[bdezonia] Make input syntax more flexible

[bdezonia] Add a couple more predefined functions

[bdezonia] Allow names to consist of letters and digits

[bdezonia] Fix bug on copy() method

[bdezonia] Add a few new predefined functions

[bdezonia] Make function more flexible

[christian.dietz] Fixed bug in LabelingType copy method.

[christian.dietz] Moved SubImg to new package.

[christian.dietz] Added comment to SubImgTest

[christian.dietz] Fixed SparseLabelingTest to work on revised Labeling

[bdezonia] Add a few new predefined functions

[bdezonia] Add a few new predefined functions

[saalfeld] first preliminary version of convenience constructors for Imgs

[christian.dietz] Added Copyright header to files.

[bdezonia] Fix grammar errors in EquationParser

[saalfeld] specialized generic type in ArrayImg from DataAccess to ArrayDataAccess

[christian.dietz] Fixed bug in ConcatenatedBufferedUnaryOperation

[bdezonia] Fix minor grammar error

[tobias.pietzsch] implementation and usage example for sub-pixel edgel detection

[tobias.pietzsch] Convenience methods for manipulating Intervals: creating, expanding (grow/shrink), translating.

[saalfeld] moved convenience factory methods into img specific factory collections

[tobias.pietzsch] added algorithm to normalize values of an IterableInterval to a specified range.

[tobias.pietzsch] update javadoc

[tobias.pietzsch] Removed DataAccess interface.

[Curtis Rueden] Add list of benefits to using ImgLib2

[tobias.pietzsch] fix comments in ComponentTree and make some method parameters final

[tobias.pietzsch] fix a bug in PlanarImg that caused ArrayIndexOutOfBoundsException when moving a RandomAccess out of the image (without get()-ing the value).

[tobias.pietzsch] fix comments in ComponentTree and make some method parameters final

[tobias.pietzsch] fix a bug in PlanarImg that caused ArrayIndexOutOfBoundsException when moving a RandomAccess out of the image (without get()-ing the value).

[tobias.pietzsch] modified GUI so that handlers can be added at any time

[tobias.pietzsch] use addHandler() method in interactive viewers instead of passing collection of handlers in the constructor.

[christian.dietz] Resolved bug in UnaryOperationAssigment

[tobias.pietzsch] added keys to TransformEventHandler3D: R - reset transformation, UP/DOWN - zoom in/out.

[tobias.pietzsch] bugfix: forgot to add to a PixelListComponent's children the one last emitted by the same PixelListComponentIntermediate.

[saalfeld] added factory methods for ArrayImg that re-use a pre-allocated

[albert] An Img that wraps a BufferedImage, for a subset of supported types.

[albert] Revert "An Img that wraps a BufferedImage, for a subset of supported types."

[albert] imglib2-scripting: make BufferedImageImg compile with javac.

[albert] imglib2-scripting: fix error, wasn't referencing the Img but the DataAccess only from the linked type.

[albert] imglib2-scripting: test for BufferedImageImg

[albert] imglib2-scripting: test BufferedImageImg for actual changes in the BufferedImage,

[albert] imglib2-core: added unit test for ARGBScreenImage.

[albert] imglib2-core: more tests for ARGBScreenImage

[albert] imglib2-core: refined test for ARGBScreenImage

[albert] imglib2-scripting: moved BufferedImageImg to net.imglib2 where it was intended to be.

[albert] imglib2-core: make ARGBScreenImageTest suitable for junit/jenkins.

[albert] imglib2-core: make ARGBScreenImageTest suitable for mere mortals.

[albert] imglib2-core test: rename ARGBScreenImageTest to ARGBScreenImageExpectactionChecking,

[saalfeld] despecialize ArrayImg again (I cannot track where that came from!)

[saalfeld] casting madness workaround for Oracle javac bug

[saalfeld] specify type explicitly, now Fiji's javac can deal with it...

[Curtis Rueden] Tweak SCM information

[Curtis Rueden] Remove picUrl elements

[Curtis Rueden] Use tabs for whitespace in pom.xml files

[Curtis Rueden] Use GitHub names for developer IDs

[Curtis Rueden] Update issue management information

[Curtis Rueden] Add SCM revision number to manifest

[Curtis Rueden] Clean up style

[tobias.pietzsch] remove useless OutOfBoundsRandomAccess. Use OutOfBounds directly instead.

[tobias.pietzsch] added OUtOfBoundsBorder strategy which repeats border pixels.

[tobias.pietzsch] make several OutOfBounds implementations extend AbstractLocalizable to avoid re-implementations of Localizable.

[tobias.pietzsch] replace occurences of OutOfBoundsRandomAccess by OutOfBounds (fix compilation errors).

[tobias.pietzsch] TripleIterableInterval is a wrapper around three RandomAccessibles and allows to iterate them simultaneously.

[tobias.pietzsch] add version of partial-derivative implementation using TripleIterableInterval and a benchmark.

[bdezonia] Fix documentation

[bdezonia] Extend ROI definitions to allow move()'s

[bdezonia] Change origin of BinaryMaskRegionOfInterest

[bdezonia] Make handling of double/long mix as consistent as possible

[bdezonia] Remove redundant code

[leek] Fix for bug 434 + tests - added nextRaster(long[],long[],Interval) which skips rasters wholly outside of the interval). If iterating over a RandomAccessibleInterval, constrain min and max of the IterableInterval to the more conservative of the RandomAccessibleInterval and ROI

[Curtis Rueden] Update PixLib to latest version

[Curtis Rueden] Fix script to work regardless of project version

[bdezonia] Add new RegionsOfInterest: Angle and Line

[bdezonia] Documentation change

[bdezonia] Add contains(point) to RegionOfInterest classes

[Johannes Schindelin] Add a unit test for FFT

[bdezonia] Implement LineRegionOfInterest::contains(pt)

[tobias.pietzsch] added convenience methods to check for interval containment.

[tobias.pietzsch] moved BenchmarkHelper to package net.imglib2.util

[tobias.pietzsch] Revert "add version of partial-derivative implementation using TripleIterableInterval and a benchmark."

[tobias.pietzsch] Revert "TripleIterableInterval is a wrapper around three RandomAccessibles and allows to iterate them simultaneously."

[Curtis Rueden] Remove Bio-Formats dependency from imglib2-io

[Curtis Rueden] Remove Bio-Formats dependency from imglib-io

[tobias.pietzsch] bug fix.

[stephan.preibisch] Added new basic FFT implementation for imglib2, not tested yet

[stephan.preibisch] removed unnecessary method

[stephan.preibisch] added the corresponding class for inverse FFT

[stephan.preibisch] Removed unnecessary class again

[stephan.preibisch] complex-to-complex transform can now do forward and reverse transform

[stephan.preibisch] working version of FFT, bug in complex-to-complex transform

[stephan.preibisch] bug fixed in complex-to-complex transform

[stephan.preibisch] fixed some comments and give some feedback if failed

[bdezonia] Add additional accessors to some RegionOfInterest classes

[bdezonia] Remove print statement

[stephan.preibisch] Added scaling support and documentation

[stephan.preibisch] Renamed FFT to FFTMethods

[stephan.preibisch] Added functionality to print out attributes of an Interval

[stephan.preibisch] Added helper methods to verify if padding is necessary

[stephan.preibisch] started implementing the partial fft to avoid unnecessary inverse FFT computation if padding was applied

[stephan.preibisch] Allow to cut of padding directly on the real-to-complex and complex-to-real transforms

[stephan.preibisch] Fixed bug in partly fft

[stephan.preibisch] Added static user methods

[stephan.preibisch] Added high-level calls for FFT

[stephan.preibisch] Fixed documentation

[stephan.preibisch] Fixed formatting

[stephan.preibisch] Started with FourierConvolution ... needs to be a class as it has states (re-use previous FFT of kernel or previous FFT of image)

[stephan.preibisch] Commented the LifeForm class in GameOfDeath

[stephan.preibisch] More documentation, split Arena into an easier version that does not support recording

[stephan.preibisch] Replaced Location by Point in all calls

[stephan.preibisch] Supports up to 7 races

[stephan.preibisch] Added epidemic to make it more interesting in the long run

[stephan.preibisch] Finished documentation for GameOfDeath

[stephan.preibisch] Fixed parameters

[stephan.preibisch] Fourier convolution seems to work ...

[stephan.preibisch] fourier convolution works, error of around 10^-5 per pixel when comparing gauss against gauss with fft

[stephan.preibisch] Added the dimensions interface

[stephan.preibisch] Added an implementation of the Dimensions interface

[stephan.preibisch] Converting FFTConvolution into a class

[stephan.preibisch] Updated fft code to make use of Dimensions interface

[bdezonia] Make sure all cached state invalidated on data change

[stephan.preibisch] Finished fft package

[Curtis Rueden] Move ImgPanel into imglib2-tests project

[Curtis Rueden] Remove empty imglib2-ui project

[tobias.pietzsch] Gauss: state the interval in the input image that the RandomAccess will use.

[stephan.preibisch] Fixed bug found by Christian Dietz. When kernel or img are set as RandomAccessibleInterval, they were not extended

[tobias.pietzsch] deprecated DevUtil.createImageFromArray methods. These are available through ArrayImgs convenience methods now.

[tobias.pietzsch] Fixed several bugs in MixedRandomAccess. Thanks to Martin Horn for finding.

[stephan.preibisch] Optimizations in IntegralImage

[stephan.preibisch] Added workaround for javac bug

[stephan.preibisch] Added another workaround for another javac bug

[tobias.pietzsch] fixed 2 bugs in realtransform:

[tobias.pietzsch] added simple methods to find minimum/maximum (value and location) in an IterableInterval.

[stephan.preibisch] Updated the Game of death and added better documentation

[stephan.preibisch] Added the game of death movie recoder

[stephan.preibisch] Another workaround for the javac

[sapristi] imglib2-algorithms-gpl: work around another javac bug

[stephan.preibisch] Fixed a bug in the bugfixes, would have failed on runtime

[Curtis Rueden] Add stub project for imglib2-algorithms-legacy

[Curtis Rueden] Add imglib2-algorithms-legacy to toplevel build

[stephan.preibisch] LocalNeighborhood can be placed at a localizable

[stephan.preibisch] Img can be also created using the new Dimensions interface

[stephan.preibisch] Added a few legacy algorithms from imglib1 -> they are very badly

[bdezonia] OPS - bugfix: add missing "mod" token to Lexer

[jean-yves.tinevez] Replace DomainCursor by proper neighborhood, a la Stephan

[stephan.preibisch] Added Downsampling

[stephan.preibisch] moved downsampling into correct directory

[stephan.preibisch] Added more setCalibration and calibration methods

[stephan.preibisch] fixed comment

[stephan.preibisch] Removed deprecated Location class (it it now net.imglib2.Point)

[stephan.preibisch] Added class to compute min and max

[stephan.preibisch] Joined old and new implementation

[Curtis Rueden] Readd ComputeMinMax(Img) constructor

[stephan.preibisch] Fixed follow-up bug in scripting

[stephan.preibisch] Removed unnecessary converter

[stephan.preibisch] removed unnecessary import

[stephan.preibisch] added Jama as dependency

[stephan.preibisch] added long[] setter method

[stephan.preibisch] added legacy subpixel localization

[jeanyves.tinevez] neighborhood: prepare hierarchy for re-use

[stephan.preibisch] Added ImageTransform

[Curtis Rueden] Fix version number in ImgLib1 benchmark script

[jean-yves.tinevez] Cursor iterating over a 3D ellipsoid

[stephan.preibisch] moved phasecorrelation to deprecated package

[stephan.preibisch] finished moving it to legacy

[stephan.preibisch] added missing setting of coordinate

[stephan.preibisch] Added method to return an ImgPlus when wrapping

[stephan.preibisch] fixed bug in static method of ComputeMinMAx

[stephan.preibisch] Reverted hack's since johannes fixed the bug in the javac

[stephan.preibisch] Removed unnecessary imports and deprecated classes

[jeanyves.tinevez] ImagePlusAdapter: set correct calibration and Axis types from source ImagePlus

[stephan.preibisch] Added 3 static opener methods for convinience

[stephan.preibisch] forgot a "static" comment

[jean-yves.tinevez] HyperSliceImgPlus: an hpuerslice view of an ImgPlus as an ImgPlus

[stephan.preibisch] Significant speed-up of ImgOpener by optimized iteration when populating plane

[stephan.preibisch] Removed unnecessary import and some lines

[stephan.preibisch] Every Gauss method can be called with a single double sigma value for all dimensions

[stephan.preibisch] Removed import

[tobias.pietzsch] small formatting change

[tobias.pietzsch] added Util method to compute distance between two RealLocalizables.

[tobias.pietzsch] removed algorithms-legacy KDTree implementation.

[jean-yves.tinevez] ImageJFunctions: copy spatial calibration if we can

[jean-yves.tinevez] Local neighborhoods to iterate over a disc/sphere taking into account the source image sptial calibration

[jeanyves.tinevez] Make some local neighborhoods RealPositionable

[jean-yves.tinevez] Port Larry Lindsey PickImagePeaks to imglib2

[jean-yves.tinevez] Local neighborhoods: WIP: fix thinko

[jeanyves.tinevez] RealPositionable Local neighborhoods: solve Dissociative identity disorder

[jean-yves.tinevez] LocalNeighborhoods: brown paper bag test removal

[tobias.pietzsch] fixed Bug in RandomAccessibleIntervalCursor: jumpFwd() calculated maxIndexOnLine wrong (thanks to Christian Dietz for finding).

[jeanyves.tinevez] Local neighborhoods: really add  Dissociative identity disorder

[tobias.pietzsch] fixed the RandomAccessibleIntervalCursor jumpFwd() bug (again, thanks to Christian Dietz)

[bdezonia] Make a number of parser related changes

[bdezonia] Allow image dimensions to be specified in equations

[bdezonia] Allow equation language to support "dctr"

[bdezonia] Give poorly named function a more general name

[bdezonia] Allow equation language to specify measured "angle"'s

[bdezonia] Rename a couple classes

[christian.dietz] Init of localneighborhood-revised

[christian.dietz] Fixed tests

[jean-yves.tinevez] LocalNeighborhoods: remove real positionable stuff

[jean-yves.tinevez] LocalNeighborhoods: drafted the mother interface

[Curtis Rueden] Enable generation of source JARs

[tobias.pietzsch] removed ImgFactory.create( Interval ) because it just duplicates ImgFactory.create( Dimensions ), and Interval extends Dimensions.

[tobias.pietzsch] make Util method a bit shorter (RandomAccess is Positionable).

[tobias.pietzsch] attempt at making Gaussian convolution faster.

[christian.dietz] Added several new operations

[christian.dietz] Added subsetviews to ops

[christian.dietz] Removed SubImg (will be replaced in the future)

[christian.dietz] Removed SubImgTest

[christian.dietz] Added comments to subset

[christian.dietz] Added comments

[christian.dietz] Removed BinaryOperationAssigment (duplicate in ops.image)

[christian.dietz] Fixed bug in localize long[] in Bresenham

[stephan.preibisch] Multiplication done multihreaded now

[stephan.preibisch] Open directory full of files ignores hidden files now

[tobias.pietzsch] make Util method a bit shorter (RealRandomAccess is RealPositionable)

[tobias.pietzsch] generalization: gauss() source and target can be different types if they both extend RealType

[tobias.pietzsch] fix Gauss3Example: catch IncompatibleTypeException

[christian.dietz] Fixed casting bug in IterationOperations

[tobias.pietzsch] fix javadoc

[stephan.preibisch] Added option to not extend image during Fourierconvolution

[tobias.pietzsch] LocalNeighborhood2 from "localneighborhoodcursor" branch, for comparison...

[tobias.pietzsch] bugfix: make RandomAccessibleIntervalCursor.jumpFwd() work for non-zero-min Intervals

[tobias.pietzsch] little speed-up for ComponentTree

[tobias.pietzsch] playing with rectangular neighborhood implementations.

[tobias.pietzsch] helpers for debugging neighborhoods: a type that can hold its own coordinates.

[tobias.pietzsch] benchmarking different LocalNeighborhood implementations.

[tobias.pietzsch] small re-arrangements

[tobias.pietzsch] added a NeighborhoodRandomAccess. Can be iterated using Views.iterable().

[tobias.pietzsch] Using RectangleNeighborhoodFactory to switch to between Neighborhood that re-uses a single cursor and one that doesn't.

[tobias.pietzsch] * added RectangleNeighborhoods that do not skip the center pixel.

[tobias.pietzsch] refactoring and adding javadoc, added MinFilterExample

[tobias.pietzsch] moved old LocalNeighborhood stuff into "old" sub-package

[tobias.pietzsch] minor changes

[tobias.pietzsch] INCOMPLETE and rudimentary implementation of HyperSphereShape (works for MinFilterExample at least).

[tobias.pietzsch] fix javadoc

[tobias.pietzsch] bugfix: make RandomAccessibleIntervalCursor.jumpFwd() work for non-zero-min Intervals

[tobias.pietzsch] little speed-up for ComponentTree

[tobias.pietzsch] fix javadoc

[tobias.pietzsch] MinFilterExample: use the faster shape.neighborhoods() instead of shape.neighborhoodsSafe().

[tobias.pietzsch] LocalMaximaBenchmark: clean up old test-cases.

[bdezonia] Make BjectiveFunction's API more similar to Function's API

[grislis] Added Binning class with static methods to assign values to a bin, and associated BinningTest test class.

[grislis] Added extra comment

[tobias.pietzsch] fixed compilation errors (when compiling with maven)

[christian.dietz] Fixed bug in RectangleNeighborhood ( removed -1 at size).

[christian.dietz] removed examples from prev. implementation of neigh.

[christian.dietz] Removed test of prev. local-neighborhood

[tobias.pietzsch] State the interval in which the neighborhood will use the source RandomAccess.

[grislis] Added methods to Binning to get arrays of edge and center values for each bin.

[tobias.pietzsch] NeighborhoodsAccessible needs to be public if we return it.

[tobias.pietzsch] fixed compilation errors (when compiling with maven)

[bdezonia] Renames some generic types for clarity

[bdezonia] Add an ImageCreator class in the OPS package

[bdezonia] Minor code tweak in ImageCreator

[bdezonia] New API for accepting an output Img to fill

[bdezonia] OPS - major package restructuring

[bdezonia] OPS - more package restructuring

[grislis] Finish up Binnning class

[bdezonia] OPS - more package restructuring

[bdezonia] Make ImageCreator operations more type flexible

[bdezonia] OPS - Rename ImageCreator to ImageCombiner

[christian.dietz] Implementations of HyperSphere

[christian.dietz] Formatting packages with imglib.xml format

[christian.dietz] More moving and formatting

[christian.dietz] Added region-growing (voronoi/cca) ops

[christian.dietz] Added some new operations

[christian.dietz] Fixed compilation error in ExtractLabelingOutlien.java

[christian.dietz] Fixed compiliation errors

[christian.dietz] Formatting

[christian.dietz] Renamed ImageCreator to ImageCombiner

[christian.dietz] Changed package structure

[christian.dietz] Added copyright, formatting and moved classes

[bdezonia] Add another constructor to HyperVolumePointSet

[christian.dietz] StrucutringElementBoundsBox of Hypersphere centered around 0

[bdezonia] Make convenience methods static and format code for standard display widths

[bdezonia] Avoid rounding errors in AbstractIntegerType::getRealFloat()

[bdezonia] OPS - add binary operation ImgCombine

[bdezonia] Minor performance improvement

[bdezonia] Avoid data truncation errors in IntegerTypeImpl::getRealFloat()

[bdezonia] Provide missing cast

[tobias.pietzsch] remove strange file probably added by accident earlier...

[tobias.pietzsch] several performance tweaks for ComponentTree:

[tobias.pietzsch] ComponentTree speedup: move visitedRandomAccess when moving neighbor access.

[bdezonia] Adaptive median func: improve algorithm readability

[tobias.pietzsch] several performance tweaks for ComponentTree:

[tobias.pietzsch] ComponentTree speedup: move visitedRandomAccess when moving neighbor access.

[tobias.pietzsch] renamed "container" variable to "img" in ArrayImg Accessors.

[tobias.pietzsch] helper method to compute intersection of two intervals.

[tobias.pietzsch] [Views] take translation parameter as long... instead of long[]

[tobias.pietzsch] [ComponentTree] add clear() method to PixelList (allows to reuse PixelList).

[tobias.pietzsch] add DifferenceOfGaussianPeak constructor from Localizable.

[stephan.preibisch] added float[] instantiation

[tobias.pietzsch] Modified DifferenceOfGaussian (legacy algorithm) using Gauss3 and RectangleShape neighborhood. Added a benchmark to compare to the old one.

[christian.dietz] MetadataUtil, LabelingOperators, SubsetView fix

[christian.dietz] Some renamings of LabelingTypeOps

[Johannes Schindelin] Introduce GeneralPathRegionOfInterest

[Johannes Schindelin] Deprecate the CompositeRegionOfInterest class

[Curtis Rueden] Refactor ColorTable code

[Curtis Rueden] benchmark.sh: generalize version number

[Curtis Rueden] Add a script for tagging releases

[Curtis Rueden] Add profile for broken projects

[Curtis Rueden] tag-release.sh: update broken project POM versions

[Johannes Schindelin] tag-release: test the output of the grep

[Johannes Schindelin] tag-release: fix -i argument for GNU sed

[Johannes Schindelin] tag-release: always output to stderr

[Johannes Schindelin] tag-release: avoid extra call to grep

[Johannes Schindelin] tag-release: fetch before checking whether the tag exists

[Johannes Schindelin] tag-release: wrap lines a bit nicer

[Johannes Schindelin] tag-release: exit if there are still old version references

[tobias.pietzsch] make HyperSphere.NeighborhoodsAccessible class public

[bdezonia] OPS: add a nonparallel image assignment class

[Curtis Rueden] Merge ImgLib2 examples with Game of Death example

[Curtis Rueden] Bring examples in sync with wiki page

[Curtis Rueden] imglib2-examples: fix compile errors

[Curtis Rueden] imglib2-example: clean up imports

[Curtis Rueden] imglib2-examples: do not throw unneeded exceptions

[Curtis Rueden] imglib2-examples: fix javadoc warnings

[Curtis Rueden] imglib2-examples: use an existing kernel image

[Curtis Rueden] imglib2-examples: add template for Example6c

[christian.dietz] Fixed bug in CopyCalibratedSpace

[Curtis Rueden] imglib2-examples: fix typo

[Curtis Rueden] imglib2-examples: add needed GPL header

[Curtis Rueden] imglib2-examples: add incorrect code to Example2b

[Curtis Rueden] imglib2-examples: fix another typo

[tobias.pietzsch] use new Gauss3 in GameOfDeath2

[tobias.pietzsch] use new local neighborhoods in Example4b

[tobias.pietzsch] Use Gauss3 in Example6a2-6a4. It is less code, except for Example6a1 where

[tobias.pietzsch] Example4b: use Intervals utility method to shrink the source interval by a 1-pixel border.

[tobias.pietzsch] moved tutorial into examples package

[tobias.pietzsch] make AbstractXYProjector extend Point to avoid reimplementing Localizable and Positionable.

[tobias.pietzsch] speed up XYRandomAccessibleProjector.

[tobias.pietzsch] implemented Concatenable<AffineGet> and PreConcatenable<AffineGet> for AffineTransform and AffineTransform3D.

[tobias.pietzsch] added method to reset AffineTransform3D to identity.

[bdezonia] OPS: Implement a threshold condition

[tobias.pietzsch] Be more specific in RGBAScreenImage: use BufferedImage instead of Image

[tobias.pietzsch] create new subproject "imglib2-ui" for basic interactive image viewers.

[tobias.pietzsch] ui: add MouseWheelListeners to the canvas instead of the window

[tobias.pietzsch] Revised interactive viewers and put them into imglib2-ui.

[tobias.pietzsch] Converted all the interactive examples to use imglib2-ui viewers.

[tobias.pietzsch] update Bee example to use imglib2-ui viewers

[tobias.pietzsch] CATMAIDRandomAccessibleInterval: clear cache by finalize instead of

[tobias.pietzsch] moved interactive examples to imglib2-examples project, added README.txt and imglib2 logo.

[tobias.pietzsch] removed some unfinished example stuff that should not go into master...

[tobias.pietzsch] cleaning up and trying to fix build error.

[bdezonia] OPS: rename ThresholdCondition to WithinRangeCondition

[bdezonia] OPS: document RangeCondition

[bdezonia] Fix some javadoc

[tobias.pietzsch] Utility functions for basic linear algebra, where vectors and matrices are represented as double[] and double[][], respectively.

[bdezonia] Add minimal documentation to TestSpecifiedPointSet

[bdezonia] A little more documentation for TextSpecifiedPointSet

[jeanyves.tinevez] Put back the Sphere & Disc neighborhood after Tobias major move

[tobias.pietzsch] LinAlgHelpers (linear algebra utilities): add matrix copy method.

[jean-yves.tinevez] Remove DiscNeighbohood and SphereNeighborhood

[jean-yves.tinevez] Fix bug in EllipseCursor

[bdezonia] OPS: big change in PointSet API (handling origins)

[bdezonia] Fix coding error in  GeneralPointSet::calcBounds()

[bdezonia] Minor performance improvements to HyperVolumePointSet

[bdezonia] Add a point counting function

[bdezonia] Add a RegionOfInterest adapter class

[bdezonia] GneralPointSet improvewments

[bdezonia] HyperVolumePointSet improvements

[bdezonia] Minor code cleanup and documentation

[bdezonia] Add some documentation to PointSet classes

[bdezonia] PointSetUnion - simplify bounds calculation

[tobias.pietzsch] Change the behaviour of Views.translate() such that the translation vector acts on source.

[stephan.preibisch] Added wrapReal function

[sapristi] imglib2-core: simplified and fixed AbstractComplexType.getPhaseDouble.

[sapristi] imglib2-core: simplified AbstractComplexType.getPhaseFloat.

[sapristi] imglib2-core: fixed AbstractComplexType.getPowerFloat to avoid losing precision.

[stephan.preibisch] added wrapRealNative, wrapNumeric and wrapNumericNative to cover all possibilities

[jean-yves.tinevez] Minor fix in EllipseCursor

[bdezonia] OPS: add min() and max() to equation language

[bdezonia] OPS: add some statistical functions

[bdezonia] OPS StatCalculator - fix overflow bugs

[stephan.preibisch] changed a potential bug that the HyperSphereCursor does not clone the center from the HyperSphere,

[bdezonia] OPS: major refactor of the statistics functions

[bdezonia] OPS: document StatCalculator

[Johannes Schindelin] Add a real double converter

[tobias.pietzsch] cosmetics: fix javadoc typo, remove unused code, add serialVersionUID.

[tobias.pietzsch] move permute() method from SubsetViews to Views.

[tobias.pietzsch] move addDimension() method from SubsetViews to Views.

[tobias.pietzsch] Views: add javadoc, very minor refactoring in TransformBuilder

[tobias.pietzsch] add Intervals convenience method to compute number of elements in an integer interval

[tobias.pietzsch] Abstract convenience classes that forward Interval and RealInterval interfaces to a wrapped interval.

[tobias.pietzsch] Removed SequentializeView.

[tobias.pietzsch] added javadoc

[bdezonia] OPS: rename the statistical functions

[christian.dietz] Added new adapters to ops

[christian.dietz] Added Examples to ops

[bdezonia] OPS: rename methods in StatCalculator

[bdezonia] Views: fix bug in bck() (was calling fwd())

[bdezonia] OPS: remove some broken functions

[bdezonia] OPS: make NullNumericFunction return NaN values

[bdezonia] OPS: RoiPointSet - change definition of bounds

[bdezonia] OPS: update RealConvolutionFunction

[bdezonia] OPS: document some of the Function classes

[bdezonia] OPS: document some functions

[bdezonia] OPS: improve documentation of ConverterFunction

[bdezonia] OPS: document more classes and eliminate redundant code

[bdezonia] OPS: rename a couple Condition classes

[christian.dietz] Added liscenses and authors to classes

[christian.dietz] Added license and author information to classes

[bdezonia] OPS: make RealImageFunction more general

[bdezonia] OPS: update example code to reflect RealImageFunc changes

[bdezonia] OPS: treat any IterableInterval as a PointSet

[tobias.pietzsch] bugfix: When converting packed ARGB to luminance, alpha was treated as signed byte.

[tobias.pietzsch] Use AbstractWrappedInterval as base class for several classes that wrap an Interval.

[tobias.pietzsch] clean up javadoc.

[bdezonia] OPS: update some javadoc

[bdezonia] IterableSubsetView: fix compile error

[bdezonia] OPS: PointSets now implement EuclideanSpace

[bdezonia] OPS: make PointSetIterator extend Iterator<long[]>

[bdezonia] OPS: make PointSet extend Iterable<long[]>

[christian.dietz] Moved Normalize/Convert. Added license/author information

[christian.dietz] Added Convert / Normalize again

[christian.dietz] ExtendedLabeling revisted

[bdezonia] OPS: make PointSetIterators implement Cursor<long[]>

[bdezonia] OPS: PointSet - fix javadoc

[bdezonia] OPS: PointSet - more javadoc changes

[bdezonia] OPS: eliminate some unnecessary inheritance

[bdezonia] OPS: add author and license info as needed

[tobias.pietzsch] moved contains(Interval, Interval) static method from Util to Intervals.

[bdezonia] OPS: make PointSet implement IterableInterval<long[]>

[bdezonia] OPS: finish PointSet changes from calcSize() to size()

[bdezonia] OPS: PointSets - add test code and fix related bugs

[bdezonia] OPS: eliminate public findBoundMin/Max methods from interface

[bdezonia] OPS: add coordinate adapter functions (double[] / long[])

[bdezonia] OPS: change real coord adaptation (now do rounding)

[bdezonia] OPS: minor updates to example code

[bdezonia] OPS: PrimtiveDoubleArray - change memory allocation

[bdezonia] OPS: StatCalculator - add TODO notes

[bdezonia] OPS: RealEquationFunction - add convenience constructor

[christian.dietz] Added two helper methods

[tobias.pietzsch] Displaying 4D/5D images with ImageJFunctions.show().

[hinerm] Added header to net.imglib2.display.ColorTable

[bdezonia] OPS: pull class out of example code

[Curtis Rueden] Remove duplicate Neighborhood interface

[Curtis Rueden] Rename clashing RectangleNeighborhood class

[tobias.pietzsch] bugfix: copying a SlicingRandomAccess didn't work correctly. Thanks to Florian Jug for noticing.

[Curtis Rueden] Update pom-scijava parent to the latest

[christian.dietz] Made ConvexHull2D thread safe

[tobias.pietzsch] PointSampleList<T> is a list of samples of type T at integer coordinates.

[tobias.pietzsch] ListImgFactory can be created for any T (not just T extends Type<T>)

[martin.horn] Fixed bug in CCA.

[christian.dietz] Fixed several bugs in Normalize/Equalize

[christian.dietz] Fixed compilation error in EqualizeHistogram

[christian.dietz] fixed bug in ImgConvert

[christian.dietz] Fixed bug in MinMax (num bins for long)

[christian.dietz] Fixed another bug in MinMax

[christian.dietz] Fixed formatting of Intervals and Utils

[christian.dietz] Formatted Util and Interval accoring to imglib style

[christian.dietz] Fixed java doc for Util

[tobias.pietzsch] split AbstractListImg part of ListImg (this will be shared by cached-to-disk cellimg).

[tobias.pietzsch] The data access type A does not need to extend ArrayDataAccess<A> in most parts of the CellImg.

[tobias.pietzsch] Factored AbstractCells abstract class out of ListImgCells.

[tobias.pietzsch] formatted cellimg package to imglib style, added some finals, fix javadoc.

[tobias.pietzsch] added eclipse code formatter profile for imglib2 code style.

[Curtis Rueden] Created ArrayColorTable interface

[Curtis Rueden] Reorganized AbstractColorTable

[Curtis Rueden] AbstractColorTable implements ArrayColorTable

[Curtis Rueden] Push AbstractColorTable API into ArrayColorTable

[Curtis Rueden] Add missing @Override tags

[Curtis Rueden] Clean up javadoc

[hinerm] Renamed AbstractColorTable

[tobias.pietzsch] bugfix: synchronized NTree methods to make NTreeImg thread-safe.

[bdezonia] OPS: remove 2d limitation from interpolating function

[Curtis Rueden] Organize imports

[Curtis Rueden] Fix a bunch of Eclipse warnings

[Curtis Rueden] Avoid a javac compiler bug

[stephan.preibisch] Florian Jug found a bug in the setKeepImg

[Johannes Schindelin] Follow the SNAPSHOT version of mpicbg.jar

[Curtis Rueden] imglib2-io: use new SCIFIO API

[Curtis Rueden] imglib2-io: add explicit scifio-devel dependency

[Curtis Rueden] imglib2-tests: use new SCIFIO API

[michael.zinsmaier] synchronized set value to make planewise multithreading secure.

[michael.zinsmaier] makes compute method robust against empty images

[bdezonia] OPS: derive statistical functions from abstract base class

[bdezonia] OPS: undo commit of .factorypath

[bdezonia] OPS: add license header to a file

[bdezonia] OPS: Enhance statistical function support

[jeanyves.tinevez] A package for spot localization with gaussian fitting algorithm

[jeanyves.tinevez] An interactive test for gaussian peak fitting

[christian.dietz] Changed out of bounds strategy for MorphOps

[jeanyves.tinevez] Gaussian peak fitting: add a JUnit test case to ensure behavior

[martin.horn] EqualizeHistogram-operation now works for all real types.

[martin.horn] EqualizeHistogram: fixed compilation problems

[tobias.pietzsch] Renamed getPixel/setPixel in ListImg implementation to get/set.

[tobias.pietzsch] created Pair interface and renamed old Pair class to ValuePair (implements the Pair interface).

[tobias.pietzsch] fix compilation error (forgot to replace Pair by ValuePair in ImgConvert).

[bdezonia] StatCalculator: add center of mass and centroid code

[Curtis Rueden] tag-release: use better fetch command

[stephan.preibisch] Supports specialized out of bounds strategies

[tobias] added quaternion power operation.

[tobias] added LabelingTests that fail for copyCursor() and copyRandomAccess() on LabelingType accessors.

[tobias] changed Util.printCoordinates to take RealLocalizable instead of Localizable.

[tobias] bugfix: copy() methods for NativeImgLabeling accessors fixed

[tobias] added SparseLabelingTests for copyCursor() and copyRandomAccess() and fixed a bug in NtreeCursor copy constructor.

[tobias] Hypersphere logic fix. Current radius for each dimension has to be stored

[bdezonia] OPS: Make the constant functions easier to use

[jean-yves.tinevez] Orthogonal Gaussian peak fitter: specify the fitter parameters

[jean-yves.tinevez] An example of gaussian peak fitting, for M. El Beheiry

[Curtis Rueden] GaussianFitTestDrive2: fix javac compile error

[tobias] toArray() methods of AffineTransform2D/3D write values in row-major order.

[Curtis Rueden] Update mailmap

[Curtis Rueden] Clean up package-info.java

[Curtis Rueden] Update copyrights and licenses for 2013

[Curtis Rueden] Add copyright headers *before* package statement

[Curtis Rueden] Remove duplicate blank lines

[Curtis Rueden] Update licenses & copyrights for broken projects

[Curtis Rueden] Fix misplaced package statements

[Curtis Rueden] Move license-maven-plugin config off the server

[Curtis Rueden] Add project.rootdir that always points to toplevel

[Curtis Rueden] Fix GPL copyright blurbs in broken projects

[bdezonia] Allow condition's range to be configurable

[bdezonia] Add adapter class to treat a PointSet as a RegionOfInterest

[bdezonia] OPS: make ConditionalPointSets configurable

[bdezonia] OPS: make PointSetRegionOfInterest::move() more functional

[bdezonia] Provide setters/getters for some classes

[bdezonia] Provide simple conditions for testing values of functions

[bdezonia] ImageAssignment now uses RandomAccessibleIntervals

[christian.dietz] fixed iterationorder of imgview and labelingview

[tobias.pietzsch] minor changes to TransformEventHandler3D:

[bdezonia] OPS: distinguish correlation from convolution

[tobias.pietzsch] fix javadoc

[jeanyves.tinevez] Fix a bug in Astigmatic Gaussian peak localizer

[jeanyves.tinevez] Minor javadoc typos in HyperSliceImgPlus

[jeanyves.tinevez] Localization: renamed elliptic orthogoanl gaussian

[jeanyves.tinevez] Localization: plain symmetric gaussian function

[jean-yves.tinevez] Localization: fix the gaussian Gradient and Hessian calculation

[jeanyves.tinevez] Localization: extend FitFunction interface for other solvers

[jeanyves.tinevez] Localization: WIP: embryonic generic peak localizer

[jean-yves.tinevez] Localization: utils to collect data for subsequent fitting

[jean-yves.tinevez] Localization: interface and class to initialize fitter and provide estimates

[jean-yves.tinevez] Localization: ML estimator for symetric gaussian peaks

[jean-yves.tinevez] Localization: renamed ML estimator for elliptic gaussian

[jean-yves.tinevez] Localization: javadoc and field names edit

[jean-yves.tinevez] Localization: cleanup interactive tests

[jean-yves.tinevez] Localization: Update mother class in charge of localization process

------------------------------------------
[...truncated 246 lines...]
+ CWD=/c/jenkins/workspace/fiji-windows-full
+ PATHSEP=';'
+ case "$PROCESSOR_ARCHITEW6432" in
+ platform=win64
+ java_submodule=win64
+ exe=.exe
+ LAUNCHER=ImageJ-win64.exe
+ FIJILAUNCHER=fiji-win64.exe
+ test -n win64
+ test -z ''
++ get_java_home
++ test -d ''
++ test -n win64
++ test -d /c/jenkins/workspace/fiji-windows-full/java/win64
+++ ls -t /c/jenkins/workspace/fiji-windows-full/java/win64
+++ head -n 1
++ echo /c/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre
+ JAVA_HOME=/c/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre
+ test -z win64
+ test -f /c/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre/lib/tools.jar
+ test -f /c/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre/../lib/tools.jar
+ case "$JAVA_HOME" in
+ test -n /c/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre
+ test -d /c/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre
+ test -d /c/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre
+ test -d /c/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre/jre
+ export PATH=/c/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre/bin:/bin:/mingw/bin:/c/Windows/system32:/c/Windows:/c/Windows/System32/Wbem:/c/Windows/System32/WindowsPowerShell/v1.0/:/usr/bin:/usr/mingw/bin
+ PATH=/c/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre/bin:/bin:/mingw/bin:/c/Windows/system32:/c/Windows:/c/Windows/System32/Wbem:/c/Windows/System32/WindowsPowerShell/v1.0/:/usr/bin:/usr/mingw/bin
++ get_java_home
++ test -d /c/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre
++ echo /c/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre
++ get_java_home
++ test -d /c/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre
++ echo /c/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre
+ PATH=/c/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre/bin:/bin:/mingw/bin:/c/Windows/system32:/c/Windows:/c/Windows/System32/Wbem:/c/Windows/System32/WindowsPowerShell/v1.0/:/usr/bin:/usr/mingw/bin:/c/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre/bin:/c/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre/../bin
+ export PATH
+ case "$UNAME_S" in
++ cd /c/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre
++ pwd -W
+ export JAVA_HOME=c:/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre
+ JAVA_HOME=c:/jenkins/workspace/fiji-windows-full/java/win64/jdk1.6.0_24/jre
++ uname -s
+ test Darwin = MINGW32_NT-6.1
+ case "$CWD" in
+ ARGV0=/c/jenkins/workspace/fiji-windows-full/./Build.sh
+ SCIJAVA_COMMON=/c/jenkins/workspace/fiji-windows-full/modules/scijava-common
+ MAVEN_DOWNLOAD=/c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh
+ VERSION=2.0.0-SNAPSHOT
+ SCIJAVA_COMMON_VERSION=1.0.0-SNAPSHOT
+ maven_update sc.fiji:javac:2.0.0-SNAPSHOT
+ uptodate /c/jenkins/workspace/fiji-windows-full/./Build.sh /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh
+ test -f /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh
+ test -d /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/.git
+ git clone git://github.com/scijava/scijava-common /c/jenkins/workspace/fiji-windows-full/modules/scijava-common
Cloning into 'c:/jenkins/workspace/fiji-windows-full/modules/scijava-common'...
+ test '!' -f /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh
+ touch /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh
+ for gav in '"$@"'
+ artifactId=javac:2.0.0-SNAPSHOT
+ version=2.0.0-SNAPSHOT
+ artifactId=javac
+ path=jars/javac-2.0.0-SNAPSHOT.jar
+ cd /c/jenkins/workspace/fiji-windows-full
+ test -f jars/javac.jar
+ for file in 'jars/"$artifactId"-[0-9]*.jar'
+ test 'ajars/javac-[0-9]*.jar' = ajars/javac-2.0.0-SNAPSHOT.jar
+ test -f 'jars/javac-[0-9]*.jar'
+ continue
+ uptodate /c/jenkins/workspace/fiji-windows-full/./Build.sh jars/javac-2.0.0-SNAPSHOT.jar
+ test -f jars/javac-2.0.0-SNAPSHOT.jar
+ echo 'Downloading sc.fiji:javac:2.0.0-SNAPSHOT'
Downloading sc.fiji:javac:2.0.0-SNAPSHOT
+ cd jars/
+ sh /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh install sc.fiji:javac:2.0.0-SNAPSHOT
+ test '!' -f jars/javac-2.0.0-SNAPSHOT.jar
+ touch jars/javac-2.0.0-SNAPSHOT.jar
+ maven_update org.scijava:scijava-common:1.0.0-SNAPSHOT
+ uptodate /c/jenkins/workspace/fiji-windows-full/./Build.sh /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh
+ test -f /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh
+ test /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh -nt /c/jenkins/workspace/fiji-windows-full/./Build.sh
+ case "$2" in
+ for gav in '"$@"'
+ artifactId=scijava-common:1.0.0-SNAPSHOT
+ version=1.0.0-SNAPSHOT
+ artifactId=scijava-common
+ path=jars/scijava-common-1.0.0-SNAPSHOT.jar
+ cd /c/jenkins/workspace/fiji-windows-full
+ test -f jars/scijava-common.jar
+ for file in 'jars/"$artifactId"-[0-9]*.jar'
+ test 'ajars/scijava-common-[0-9]*.jar' = ajars/scijava-common-1.0.0-SNAPSHOT.jar
+ test -f 'jars/scijava-common-[0-9]*.jar'
+ continue
+ uptodate /c/jenkins/workspace/fiji-windows-full/./Build.sh jars/scijava-common-1.0.0-SNAPSHOT.jar
+ test -f jars/scijava-common-1.0.0-SNAPSHOT.jar
+ echo 'Downloading org.scijava:scijava-common:1.0.0-SNAPSHOT'
Downloading org.scijava:scijava-common:1.0.0-SNAPSHOT
+ cd jars/
+ sh /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh install org.scijava:scijava-common:1.0.0-SNAPSHOT
+ test '!' -f jars/scijava-common-1.0.0-SNAPSHOT.jar
+ touch jars/scijava-common-1.0.0-SNAPSHOT.jar
+ maven_update net.imagej:ij-core:2.0.0-SNAPSHOT
+ uptodate /c/jenkins/workspace/fiji-windows-full/./Build.sh /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh
+ test -f /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh
+ test /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh -nt /c/jenkins/workspace/fiji-windows-full/./Build.sh
+ case "$2" in
+ for gav in '"$@"'
+ artifactId=ij-core:2.0.0-SNAPSHOT
+ version=2.0.0-SNAPSHOT
+ artifactId=ij-core
+ path=jars/ij-core-2.0.0-SNAPSHOT.jar
+ cd /c/jenkins/workspace/fiji-windows-full
+ test -f jars/ij-core.jar
+ for file in 'jars/"$artifactId"-[0-9]*.jar'
+ test 'ajars/ij-core-[0-9]*.jar' = ajars/ij-core-2.0.0-SNAPSHOT.jar
+ test -f 'jars/ij-core-[0-9]*.jar'
+ continue
+ uptodate /c/jenkins/workspace/fiji-windows-full/./Build.sh jars/ij-core-2.0.0-SNAPSHOT.jar
+ test -f jars/ij-core-2.0.0-SNAPSHOT.jar
+ echo 'Downloading net.imagej:ij-core:2.0.0-SNAPSHOT'
Downloading net.imagej:ij-core:2.0.0-SNAPSHOT
+ cd jars/
+ sh /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh install net.imagej:ij-core:2.0.0-SNAPSHOT
+ test '!' -f jars/ij-core-2.0.0-SNAPSHOT.jar
+ touch jars/ij-core-2.0.0-SNAPSHOT.jar
+ maven_update net.imagej:ij-minimaven:2.0.0-SNAPSHOT
+ uptodate /c/jenkins/workspace/fiji-windows-full/./Build.sh /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh
+ test -f /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh
+ test /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh -nt /c/jenkins/workspace/fiji-windows-full/./Build.sh
+ case "$2" in
+ for gav in '"$@"'
+ artifactId=ij-minimaven:2.0.0-SNAPSHOT
+ version=2.0.0-SNAPSHOT
+ artifactId=ij-minimaven
+ path=jars/ij-minimaven-2.0.0-SNAPSHOT.jar
+ cd /c/jenkins/workspace/fiji-windows-full
+ test -f jars/ij-minimaven.jar
+ for file in 'jars/"$artifactId"-[0-9]*.jar'
+ test 'ajars/ij-minimaven-[0-9]*.jar' = ajars/ij-minimaven-2.0.0-SNAPSHOT.jar
+ test -f 'jars/ij-minimaven-[0-9]*.jar'
+ continue
+ uptodate /c/jenkins/workspace/fiji-windows-full/./Build.sh jars/ij-minimaven-2.0.0-SNAPSHOT.jar
+ test -f jars/ij-minimaven-2.0.0-SNAPSHOT.jar
+ echo 'Downloading net.imagej:ij-minimaven:2.0.0-SNAPSHOT'
Downloading net.imagej:ij-minimaven:2.0.0-SNAPSHOT
+ cd jars/
+ sh /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh install net.imagej:ij-minimaven:2.0.0-SNAPSHOT
+ test '!' -f jars/ij-minimaven-2.0.0-SNAPSHOT.jar
+ touch jars/ij-minimaven-2.0.0-SNAPSHOT.jar
+ maven_update net.imagej:ij-updater-ssh:2.0.0-SNAPSHOT
+ uptodate /c/jenkins/workspace/fiji-windows-full/./Build.sh /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh
+ test -f /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh
+ test /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh -nt /c/jenkins/workspace/fiji-windows-full/./Build.sh
+ case "$2" in
+ for gav in '"$@"'
+ artifactId=ij-updater-ssh:2.0.0-SNAPSHOT
+ version=2.0.0-SNAPSHOT
+ artifactId=ij-updater-ssh
+ path=jars/ij-updater-ssh-2.0.0-SNAPSHOT.jar
+ cd /c/jenkins/workspace/fiji-windows-full
+ test -f jars/ij-updater-ssh.jar
+ for file in 'jars/"$artifactId"-[0-9]*.jar'
+ test 'ajars/ij-updater-ssh-[0-9]*.jar' = ajars/ij-updater-ssh-2.0.0-SNAPSHOT.jar
+ test -f 'jars/ij-updater-ssh-[0-9]*.jar'
+ continue
+ uptodate /c/jenkins/workspace/fiji-windows-full/./Build.sh jars/ij-updater-ssh-2.0.0-SNAPSHOT.jar
+ test -f jars/ij-updater-ssh-2.0.0-SNAPSHOT.jar
+ echo 'Downloading net.imagej:ij-updater-ssh:2.0.0-SNAPSHOT'
Downloading net.imagej:ij-updater-ssh:2.0.0-SNAPSHOT
+ cd jars/
+ sh /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh install net.imagej:ij-updater-ssh:2.0.0-SNAPSHOT
+ test '!' -f jars/ij-updater-ssh-2.0.0-SNAPSHOT.jar
+ touch jars/ij-updater-ssh-2.0.0-SNAPSHOT.jar
+ maven_update net.imagej:ij-ui-swing-updater:2.0.0-SNAPSHOT
+ uptodate /c/jenkins/workspace/fiji-windows-full/./Build.sh /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh
+ test -f /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh
+ test /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh -nt /c/jenkins/workspace/fiji-windows-full/./Build.sh
+ case "$2" in
+ for gav in '"$@"'
+ artifactId=ij-ui-swing-updater:2.0.0-SNAPSHOT
+ version=2.0.0-SNAPSHOT
+ artifactId=ij-ui-swing-updater
+ path=jars/ij-ui-swing-updater-2.0.0-SNAPSHOT.jar
+ cd /c/jenkins/workspace/fiji-windows-full
+ test -f jars/ij-ui-swing-updater.jar
+ for file in 'jars/"$artifactId"-[0-9]*.jar'
+ test 'ajars/ij-ui-swing-updater-[0-9]*.jar' = ajars/ij-ui-swing-updater-2.0.0-SNAPSHOT.jar
+ test -f 'jars/ij-ui-swing-updater-[0-9]*.jar'
+ continue
+ uptodate /c/jenkins/workspace/fiji-windows-full/./Build.sh jars/ij-ui-swing-updater-2.0.0-SNAPSHOT.jar
+ test -f jars/ij-ui-swing-updater-2.0.0-SNAPSHOT.jar
+ echo 'Downloading net.imagej:ij-ui-swing-updater:2.0.0-SNAPSHOT'
Downloading net.imagej:ij-ui-swing-updater:2.0.0-SNAPSHOT
+ cd jars/
+ sh /c/jenkins/workspace/fiji-windows-full/modules/scijava-common/bin/maven-helper.sh install net.imagej:ij-ui-swing-updater:2.0.0-SNAPSHOT
+ test '!' -f jars/ij-ui-swing-updater-2.0.0-SNAPSHOT.jar
+ touch jars/ij-ui-swing-updater-2.0.0-SNAPSHOT.jar
+ OPTIONS='-Dimagej.app.directory="/c/jenkins/workspace/fiji-windows-full"'
+ test 3 -gt 0
+ case "$1" in
+ OPTIONS='-Dimagej.app.directory="/c/jenkins/workspace/fiji-windows-full" -Dminimaven.updateinterval=1'
+ shift
+ test 2 -gt 0
+ case "$1" in
+ break
+ test 2 = 0
+ for name in '"$@"'
+ case "$name" in
+ artifactId=--
+ artifactId=--
+ artifactId=--
+ case "$name" in
+ eval sh /c/jenkins/workspace/fiji-windows-full/bin/ImageJ.sh --mini-maven '-Dimagej.app.directory="/c/jenkins/workspace/fiji-windows-full" -Dminimaven.updateinterval=1' -DartifactId=-- install
++ sh /c/jenkins/workspace/fiji-windows-full/bin/ImageJ.sh --mini-maven -Dimagej.app.directory=/c/jenkins/workspace/fiji-windows-full -Dminimaven.updateinterval=1 -DartifactId=-- install
Looking at children of pom-imglib
Looking at children of pom-imglib1
Compiling 251 files in C:\jenkins\workspace\fiji-windows-full\imglib1\core
Compiling 87 files in C:\jenkins\workspace\fiji-windows-full\imglib1\algorithms
Compiling 21 files in C:\jenkins\workspace\fiji-windows-full\imglib1\ij
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Compiling 3 files in C:\jenkins\workspace\fiji-windows-full\imglib1\GameOfDeath
Compiling 2 files in C:\jenkins\workspace\fiji-windows-full\imglib1\io
Compiling 53 files in C:\jenkins\workspace\fiji-windows-full\imglib1\ops
Compiling 94 files in C:\jenkins\workspace\fiji-windows-full\imglib1\scripting
Exception in thread "main" java.io.IOException: Artifact does not exist: C:\jenkins\workspace\fiji-windows-full\imglib1\tests\target\imglib-tests-2.0.0-SNAPSHOT.jar
	at imagej.build.minimaven.MavenProject.copyToImageJAppDirectory(MavenProject.java:613)
	at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:336)
	at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:326)
	at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:326)
	at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:288)
	at imagej.build.MiniMaven.main(MiniMaven.java:133)
+ for name in '"$@"'
+ case "$name" in
+ artifactId=verbose=true
+ artifactId=verbose=true
+ artifactId=verbose=true
+ case "$name" in
+ eval sh /c/jenkins/workspace/fiji-windows-full/bin/ImageJ.sh --mini-maven '-Dimagej.app.directory="/c/jenkins/workspace/fiji-windows-full" -Dminimaven.updateinterval=1' -DartifactId=verbose=true install
++ sh /c/jenkins/workspace/fiji-windows-full/bin/ImageJ.sh --mini-maven -Dimagej.app.directory=/c/jenkins/workspace/fiji-windows-full -Dminimaven.updateinterval=1 -DartifactId=verbose=true install
Looking at children of pom-imglib
Looking at children of pom-imglib1
Exception in thread "main" java.io.IOException: Artifact does not exist: C:\jenkins\workspace\fiji-windows-full\imglib1\tests\target\imglib-tests-2.0.0-SNAPSHOT.jar
	at imagej.build.minimaven.MavenProject.copyToImageJAppDirectory(MavenProject.java:613)
	at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:336)
	at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:326)
	at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:326)
	at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:288)
	at imagej.build.MiniMaven.main(MiniMaven.java:133)
Build step 'Execute shell' marked build as failure