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Cardinal 3.8.0

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@kuwisdelu kuwisdelu released this 04 Dec 23:02
· 6 commits to RELEASE_3_20 since this release
v3.8.0
8db2b5b

CHANGES IN VERSION 3.7.8 [2024-10-26]

SIGNIFICANT USER-VISIBLE CHANGES

o Deprecate 'slice()' in factor of 'sliceImage()'
    to avoid conflicts with users attaching dplyr

CHANGES IN VERSION 3.7.7 [2024-10-24]

SIGNIFICANT USER-VISIBLE CHANGES

o Update 'peakAlign()' with 'binratio' parameter

CHANGES IN VERSION 3.7.6 [2024-10-16]

NEW FEATURES

o Reading/writing imzML now preserves 'metadata' slot
o Reading/writing imzML now supports parallel processing

SIGNIFICANT USER-VISIBLE CHANGES

o Update 'estimateDomain()' to select resolution
    based on 'median', 'min', 'max', or 'mean'
o Update 'peakAlign()' to build domain bins based on
    the minimum of peak gaps (instead of the median)
o Write log file when writing imzML/Analyze files

BUG FIXES

o Fix bug in 'process()' resulting in output matrix
    with 'list' elements under certain conditions

CHANGES IN VERSION 3.7.5 [2024-9-3]

NEW FEATURES

o Add 'setCardinalParallel()' for setting a parallelization
    backend with reasonably-selected defaults

SIGNIFICANT USER-VISIBLE CHANGES

o Add 'SAR=FALSE' option to 'simulateImage()' for faster
    simulation if spatial autoregressive model is not needed
o Change default array order for 'MSImagingArrays' so that
    'intensity' is first array and 'mz' is second array
o Improved logging with pre-processing functions

BUG FIXES

o Fix leaky 'meansTest()' closures

CHANGES IN VERSION 3.7.4 [2024-8-28]

NEW FEATURES

o Add 'saveCardinalLog()' for saving log file
o Add 'getCardinalLogger()' + 'setCardinalLogger()'
o Add 'fetch()' and 'flash()' methods for moving
    spectra between shared memory and temporary files

SIGNIFICANT USER-VISIBLE CHANGES

o Update compatibility with matter 2.7.6
o Changes to 'simulateSpectra()' and 'simulateImage()'
    in parallelization and spectral noise generation
o RNG in 'simulateSpectra()' and 'simulateImage()'
    now warn if 'RNGkind()' is not "L'Ecuyer-CMRG"

BUG FIXES

o Fix calculation of "adaptive" spatial weights
    in 'spatialWeights()' for accuracy and stability

CHANGES IN VERSION 3.7.3 [2024-7-29]

SIGNIFICANT USER-VISIBLE CHANGES

o Add 'setCardinalChunksize()' + 'getCardinalChunksize()'
o Update vignettes due to spectral processing updates

BUG FIXES

o Fix plot() and image() not always respecting dimnames
o Fix plot() and image() not plotting multiple columns
o Fix plot() and image() failing for non-syntactic names

CHANGES IN VERSION 3.7.2 [2024-7-13]

BUG FIXES

o Merge bug fix from 3.6.4.

CHANGES IN VERSION 3.7.1 [2024-5-18]

NEW FEATURES

o Update 'spectrapply()' so index array is optional
o Update 'plot()' to support 2 domains (e.g., for ion mobility)
o Add plotting methods for 'XDataFrame' and 'PositionDataFrame'

BUG FIXES

o Fix default 'tolerance' in 'pixels()'
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