Changes in version 4.22.0
BUG FIXES
o fixed compilation errors on Solaris
Changes in version 4.20.0
NEW FEATURES
o 'abind()' method for combining Image arrays
o 'floodFill()' has been vectorized over its arguments 'pt' and
'col' allowing to specify multiple start points and different
fill colors
SIGNIFICANT USER-VISIBLE CHANGES
o 'display()' "browser" mode has been updated to use the
htmlwidgets infrastructure
o 'filter2()' does not require filter dimensions to be odd
numbers when filter size equals image size
BUG FIXES
o fixed issues with 'normalize()'
(https://github.com/aoles/EBImage/issues/25)
o various improvements to the 'clahe()' function
Changes in version 4.18.0
NEW FEATURES
o new arguments to 'display()' enabling control over layout and
appearance of image grid in "raster" mode: 'nx' (number of
frames in a row), 'drawGrid' (draw lines between frames),
'spacing' (separation between frames) and 'margin' (outer
margin around the image)
o new function 'clahe()' for improving local contrast in images
by performing Contrast Limited Adaptive Histogram Equalization
o re-introduced 'output.origin' argument to 'rotate()'
SIGNIFICANT USER-VISIBLE CHANGES
o object masks returned by `bwlabel()`, `propagate()`, and
`watershed()`, as well as the result of thresh() are now of
storage mode integer rather than double
o binary kernels constructed by 'makeBrush()' have storage mode
integer (previously double)
o 'rmObjects()' and 'reenumerate()' now require input of storage
mode integer
o 'untile()' and morphology operations preserve data storage mode
o modified boundary behaviour of 'thresh()' to reduce artifacts
at image borders and to match the output of a corresponding
call to 'filter2()'
o added the ability for different boundary values for different
frames in 'filter2()' linear mode
(https://github.com/aoles/EBImage/pull/11)
o removed defunct '...GreyScale' family morphological functions
PERFORMANCE IMPROVEMENTS
o significantly improved performance of 'transpose()',
'getFrame()' and 'getFrames()' by using C implementation
o numerous small improvements to execution time and memory
consumption across the whole package, mostly by avoiding
storage mode conversion and object duplication in C
BUG FIXES
o proper origin handling in 'resize()'
o import 'methods::slot' (fixes
https://github.com/rstudio/blogdown/issues/17)
o fixed a bug in 'filter2()'
(https://github.com/aoles/EBImage/issues/8)
o proper check of filter size in 'thresh()' and rectified
behavior when filter dimensions are equal to image dimensions
o correct computation of 'selfComplementaryTopHat()'
o address PROTECT errors reported by Tomas Kalibera's 'maacheck'
tool
(https://stat.ethz.ch/pipermail/bioc-devel/2017-April/010771.html)
o fixed class retention in 'colorLabels()', 'colormap()',
'rgbImage()', 'stackObjects()', 'tile() and untile()'
Changes in version 4.16.0
SIGNIFICANT USER-VISIBLE CHANGES
o made defunct deprecated '...GreyScale' family morphological
functions; use common functions 'dilate', 'erode', 'opening',
'closing', 'whiteTopHat', 'blackTopHat' and
'selfComplementaryTopHat' for filtering both binary and
grayscale images
o removed defunct 'getNumberOfFrames' function
PERFORMANCE IMPROVEMENTS
o 'readImage': use 'vapply' instead of 'abind' to reduce memory
footprint
Changes in version 4.14.0
NEW FEATURES
o 'boundary' argument to 'filter2()' for specifying behaviour at
image boundaries
o the 'hist' method now returns a (list of) "histogram""
object(s) (http://stackoverflow.com/q/33831331/2792099 and
http://stackoverflow.com/a/35838861/2792099)
o 'colormap()' function for mapping a greyscale image to color
using a color palette
PERFORMANCE IMPROVEMENTS
o 'as.raster.Image': increased performance by not transposing the
image twice and improved support for Color images with less
than 3 channels
BUG FIXES
o fixed the 'log' method for Image objects
(https://support.bioconductor.org/p/74236/)
o 'affine': fixed handling of images containing an alpha channel
(https://support.bioconductor.org/p/74876/)
o retain NA's in morphological operations: 'dilate', 'erode',
'opening', 'closing', 'whiteTopHat', 'blackTopHat',
'selfComplementaryTopHat'
(https://support.bioconductor.org/p/77295/)
o fix to potential unsafe code in C function 'affine()' (thanks
Tomas Kalibera)
o medianFilter.c: use proper rounding rather than truncation
during float to int coercion
Changes in version 4.12.0
NEW FEATURES
o 'antialias' argument to the function 'affine' allowing to
switch off bilinear filtering around image borders
SIGNIFICANT USER-VISIBLE CHANGES
o deprecated '...GreyScale' morphological functions; use common
functions 'dilate', 'erode', 'opening', 'closing',
'whiteTopHat', 'blackTopHat' and 'selfComplementaryTopHat' for
filtering both binary and grayscale images
o 'resize' doesn't perform bilinear filtering at image borders
anymore in order to prevent the blending of image edges with
the background when the image is upscaled; to switch on
bilinear sampling at image borders use the function argument
'antialias = TRUE'
o 'floodFill' and 'fillHull' preserve storage mode
PERFORMANCE IMPROVEMENTS
o all morphological operations use the efficient Urbach-Wilkinson
algorithm (up to 3x faster compared to the previous
implementation)
o 'rotate': perform lossless 90/180/270 degree rotations by
disabling bilinear filtering
BUG FIXES
o reimplemented the Urbach-Wilkinson algorithm used to perform
grayscale morphological transformations
o improved pixel-level accuracy of spatial linear
transformations: 'affine', 'resize', 'rotate' and 'translate'
o 'display(..., method = "raster")': displaying of single-channel
color images
o 'drawCircle': corrected x-y offset
o 'equalize': in case of a single-valued histogram issue a
warning and return its argument
o 'hist': accept images with 'colorMode = Color' containing less
than three color channels
o 'image': corrected handling of image frames
o 'medianFilter': filter size check
o 'normalize': normalization of a flat image when the argument
'separate' is set to 'FALSE'
o 'reenumerate': corrected handling of images without background
o 'stackObjects': corrected handling of blank images without any
objects
o 'tile': reset dimnames
Changes in version 4.10.1
SIGNIFICANT USER-VISIBLE CHANGES
o 'rgbImage' and 'combine' use dimnames if present
o 'makeBrush(..., shape = "line")': the line is drawn
symmetrically around the center of the kernel, and the argument
'size' sets the maximum x-y dimension of kernel rather than the
line length
BUG FIXES
o 'drawCircle' and 'stackObjects': corrected handling of color
channels
o 'ocontour': doubled the size of the temporary buffer to
accommodate longer contours and fixed indexing issue
Changes in version 4.10.0
NEW FEATURES
o 'paintObjects' allows control over behavior at image edges
o 'getFrames' function returning a list of Image objects
o default 'display' method can be set by
options("EBImage.display")
o 'short' argument to the Image 'print' method
o 'equalize' function performing histogram equalization
SIGNIFICANT USER-VISIBLE CHANGES
o 'translate' moves the image in the opposite direction as before
o 'rotate' returns an image centered in a recalculated bounding
box
o 'as.Image' coerces subclasses to Image objects
o 'getFrame' returns individual channels of a Color image as
Grayscale frames
o 'display' method defaults to 'raster' unless used interactively
o 'combine' allows to combine images of the same color mode only
PERFORMANCE IMPROVEMENTS
o 'filter2': calculate FFT using methods from the 'fftwtools'
package
o 'as.nativeRaster': now implemented in C
o 'medianFilter': double to integer conversion moved to C code
o 'hist': fixed binning issues and improved performance
BUG FIXES
o 'medianFilter': fixed multi-channel image handling; preserve
original object class
o 'as.nativeRaster': allow for an arbitrary number of color
channels
o 'display': set missing color channels to blank
Changes in version 4.8.3
BUG FIXES
o 'paintObjects': the body of an object with ID=1 was not
highlighted when option thick was set
Changes in version 4.8.2
BUG FIXES
o Clip images in 'as.nativeRaster'
Changes in version 4.8.1
SIGNIFICANT USER-VISIBLE CHANGES
o New sample PNG images
Changes in version 4.8.0
NEW FEATURES
o 'otsu' thresholding method (contributed by Philip A. Marais,
University of Pretoria, South Africa)
o Support for dimnames in Image objects
o 'bg.col' argument to 'affine' transformations
o 'reenumerate' argument to 'rmObjects'
o 'names' argument to 'readImage'
o 'as.array' method for Image objects
o 'as.nativeRaster' function
SIGNIFICANT USER-VISIBLE CHANGES
o Performance improvements to 'Image', 'selectChannel', 'combine
' and 'reenumerate'
o Use a more efficient 'nativeRaster' representation in
'displayRaster'
o Cleaner output of the 'show-Image' method; print true object
class name and dimorder (if set)
o 'readImage' sets Image dimnames to corresponding file names
o 'filter2' and 'affine' return object of the same class as input
o Renamed 'getNumberOfFrames' to 'numberOfFrames'
BUG FIXES
o Handling of dimensions of character arrays
o Drawing of grid lines in 'displayRaster'
o Passing of '...' arguments in 'readImage'
Changes in version 4.6.0
NEW FEATURES
o 'toRGB' function for convenient grayscale to RGB conversion
o 'luminance' mode in 'channel' for luminance-preserving RGB to
grayscale conversion
SIGNIFICANT USER-VISIBLE CHANGES
o Performance improvements to: 'Image', 'is.Image', 'readImage',
'writeImage', 'show', 'normalize', 'getFrame', 'selectChannel',
'rgbImage', 'colorLabels', 'flip'/'flop'
o Reduced memory footprint of 'readImage'
o When called on an 'Image' object, 'as.Image' returns its
argument rather than the Grayscale-coerced copy
o 'displayRaster' sets 'par$usr' coordinates to image pixel
coordinates easing up plot annotation
BUG FIXES
o 'getFrame', 'getNumberOfFrames' and 'colorLabels' support
multi-dimensional images
o Proper handling of multi-dimensional character arrays by the
'Image' constructor
o Fixed 'getFrame' and 'combine' in case of single-channel Color
Images
o Fixed color mode check in 'validImageObject'
o Proper 'fg.col' and 'bg.col' color handling in 'tile'
o Updates to documentation
Changes in version 4.4.0
NEW FEATURES
o New 'colorLabels' function for color-coding labels of object
masks by a random permutation (Bernd Fisher)
o Additional 'inputRange' argument to 'normalize' allowing for
presetting a limited input intensity range
o Additional 'thick' argument to 'paintObjects' controlling the
thickness of boundary contours
SIGNIFICANT USER-VISIBLE CHANGES
o 'normalize' and 'combine' use the generics from BiocGenerics
o Removed the 'along' argument from 'combine'
o Re-introduced calculation of 's.radius.sd' (standard deviation
of the mean radius) in cell features
BUG FIXES
o XY dimensions equal 1 were dropped by 'getFrame'
Changes in version 4.2.0
NEW FEATURES
o 'localCurvature' function for computing local curvature along a
line (J. Barry)
SIGNIFICANT USER-VISIBLE CHANGES
o The range of pixel coordinates displayed in the JavaScript
viewer is now (1,1):(w,h) rather than (0,0):(w-1,h-1) and
matches the indices of the corresponding Image array
BUG FIXES
o 'erode'/'dilate': fixed a bug introduced in the previous
version (4.0.0)
o 'resize': new image width was calculated incorrectly when only
height was provided (reported by B. Fischer)
o 'medianFilter': incorrect [0:1] <-> integer range conversion
(thanks to K. Johnson)
Changes in version 4.0.0
NEW FEATURES
o 'transpose' function for transposing an image by swapping its
spatial dimensions
o Grayscale functions for computing the self-complementary
top-hat (I. Kats)
o Median filter based on Perreault's constant time median filter
(J. Barry)
SIGNIFICANT USER-VISIBLE CHANGES
o Removed all dependencies towards GTK+ and ImageMagick
o Replaced the former GTK+ based 'display' function by a new one
displaying images using either a JavaScript image viewer, or
R's built-in raster graphics
o 'readImage' and 'writeImage' now rely on 'jpeg', 'png' and
'tiff' packages and do not depend on ImageMagick any more
o Added support for images containing an alpha channel; both
grayscale and color images with an alpha channel are stored as
an Image with 'colormode = Color'
o Re-factored the functions, not using ImageMagick any longer:
'translate', 'affine', 'rotate', 'resize'
o Deprecated: 'blur', 'equalize', 'drawtext', 'drawfont',
'getFeatures', 'hullFeatures', 'zernikeMoments', 'edgeProfile',
'edgeFeatures', 'haralickFeatures', 'haralickMatrix',
'moments', 'smoments', 'rmoments', 'cmoments', 'animate',
o Improved 'getFrame': better performance by reassigning array
dimension only when needed
o Modified 'as.raster'
o 'inst/images/lena.gif' is now 'inst/images/lena.png'
o Overhauled the testing procedure in 'tests/test.R'
o Added 'NEWS.Rd'
BUG FIXES
o 'erode'/'dilate': incorrect range of loop indices caused memory
reads from outside the kernel vector