Changes for publication in MEE
spectralIndices()can now be customized. We made the indices available as an editable option in the RStoolbox package as suggested by a reviewer. Users now can append a custom index to it that will be then calculated via the C++ plus within spectralIndices.cpp.
mesma()now does not throw an error anymore when given no models and the default value was too high
Minor changes before major release
mesma()now better differentiates SMA and MESMA: For single endmember unmixing, each supplied endmember represents a class to unmix (row by row). For multiple endmemeber unmixing, the columnclasscan be used to group endmembers by class. If multiple endmembers per class are provided,mesma()will compute a number of SMA (determined through the new argumentn_models) for multiple endmember combinations drawn from endmembers and will select the best fit per pixel based on the lowest RMSE. See?mesmafor details (fixes #57, reported by @ytarazona)
mesma()now implements the sum to one constraint by default (argumentsum_to_one) (fixes #62, reported by @michaeldorman)- added a new example to
mesma()to reflect the changes
Rewrite of RStoolbox, migration from raster to terra and sp to sf
- RStoolbox moved on from the outdated
spandrasterpackages tosfandterrato ensure long term support of the tools. - Thrown out unnecessary libraries
rasterPCA(): Fixed a bug that caused the method and its unit tests to fail on Linux due to a corrupted covariance matrix calculated previously withterra::layerCor()superClass()unable to predict when there is NA in raster data (closes #102, reported by @bappa10085)
rasterCVA()by default no longer enforces a minimal change magnitude (can still be accomplished with thetmfargument). Also a new argumentnctallows to fix this threshold to a user selected value instead of deriving it based on the median of the observed change magnitudes.unsuperClass()has a new argumentoutputwhich allows to return the distances to all cluster centers as raster layers, instead of the class itself- added spectral index kNDVI in
spectralIndices()as suggested by Camps-Valls et al (2021) - added support for
terra::SpatRastobjects throughout RStoolbox (as alternative torasterobjects). Note: internal functionality is still based onraster.
- arguments
masterandslaveincoregisterImages()were deprecated in favor ofrefandimg, respectively (closes #63, suggested by @MatthiasSiewert)
rasterCVA()estimates median values now for entire rasters and not per chunkcloudMask()now returns NA for non-clouds instead of NaNtopCor()now works for tiny rasters as well (fixes #55, reported by @latenooker)rasterPCA()now correctly considers the number observations in face of missing values (fixes #79, reported by @andliszmmu)superClass()now accepts different geometries for trainData and valData (fixes #73, suggested by @Silviculturalist)- fix
readMeta()for MTL files delivered with Landsat collection data (fixes #71, reported by @jkoellin et al.)
- added several Sentinel-2 optimized spectral indices relying on red-edge bands:
- red-edge inflection point (REIP),
- normalized difference red-edge indices (NDREI1, NDREI2),
- green-band chlorophyll index (CLG), red-edge chlorophyll index (CLRE)
- Modified Chlorophyll Absorption Ratio Index (MCARI)
- MERIS Terrestrial Chlorophyll Index (MTCI)
readSLI()andwriteSLI()now handle endian of binary spectral libraries correctly (#47, fix contributed by @aloboa)- fix calculation of prediction probabilities in
superClass()(reported by Benson Kemboi) - adapt to raster 2.9.5 API changes
- fix order of thermal calibration coefficients for Landsat 8 L1 MTL metadata in
readMeta(reported by Xiaoma Li) - fixed an issue where
readSLI()did not find header files with dots in pathnames (#51, reported by @aloboa)
- modified readSLI label parsing. Internal white space is now converted to underscores (#52)
- function
oneHotEncode(): splits a single rasterLayer into multiple layers (one per class) with one-hot encoding, i.e. pixel value = 1 for matches, pixel value = 0 for all other classes (background). ggR()can now display more than one layer. Each layer can be plotted to a subplot in a multi-panel figure.encodeQA(),decodeQA()andclassifyQA()can now deal with the new QA format introduced with Landsat Collection data. Legacy QA designations can still be interpreted by setting thelegacyargument.- new
predict()method for unsupervised classification models (unsuperClass()).
- all
radCor()DOS methods now work for Landsat 8 OLI
- fix
unsuperClass()for algorithms other than Hartigan-Wong (reported by Alex Ilich)
- added
tasseledCap()coefficients for Quickbird, Spot5 and RapidEye
readEE()'Date' column is now returned as POSIXct instead of POSIXlt
- corrected
tasseledCap()coefficient for Landsat 5 TM (#40, reported by @philipperufin)
- fixed non-portable c++ headers
- function
mesma()for spectral unmixing (#33, provided by Jakob Schwalb-Willmann)
- improved NA handling and faster implementation of mlc classifier (#32, pull request by Neal Fultz)
- adapt to upcoming caret version (new constraint caret >= 6.0-79)
- fix tests for upcoming raster version
- adapt to new caret version
- fix
readEE()for new EarthExplorer formats - corrected sign of greenness
tasseledCap()coefficient for Landsat5 TM band 1 (reported by Thomas Day) - adapt
readMeta()andstackMeta()to new Landsat collection 1 metadata
spectralIndices()can now apply a mask internally, e.g. to exclude cloud pixels. New arguments are:maskLayerandmaskValue(suggested by Andrea Hess).- added spectral index GNDWI
- update
readEE()to deal with new EarthExplorer export columns (reported by Christian Bauer)
spectralIndices()has a new argument skipRefCheck, which skips the heuristic check for reflectance-like values [0,1] which is run if EVI/EVI2 are requested. This can be usefull if clouds with reflectance > 1.5 are part of the image.superClass()now returns the geometries which were used for validation, e.g. polygons (under $validation$geometry) and also the exact samples taken for validation including cell number and coordinates ($validation$validationSamples)- added example data-set for spectral library see ?readSLI
- increased overall test coverage
- ESUN lookup tables for
radCor()are adjusted to match current USGS recommendations from: https://landsat.usgs.gov/esun spectralIndices()swir wavelength ranges are now defined consistently and correctly. Bands formerly provided as swir1 (version <1.7.0) should now (>=1.7.0) be provided as swir2 and former swir2 as swir3 respectively (see docu). The actual calculations were correct, but the naming was off.
- fix
ggR()andggRGB()in annotation mode (default). No image was drawn and excessive memory allocation requested (= RStudio crash) (reported by Christian Walther) - fix
spectralIndices()documentation for NDWI. Formula was based on McFeeters1996 but attributed to Gao1996. Now there is NDWI (McFeeters) and NDWI2 (Gao) (reported by Christian Bauer) estimateHaze()now ensures correct histogram order, which could be off when raster had to read from disk (reported by Xavier Bailleau).readMeta()now makes concise bandnames also for Landsat Collection MTL files.- fix
radCor()for Landsat 4 TM (reported by Thomas Day) classifyQA()confidence layer for type='water' now correctly returns only confidence levels in [1,3]- enable reading ENVI plot files in ASCII mode with
readSLI()
Deprecated:
spectralIndices()indexLSWIhas been deprecated, as it is identical with the now available NDWI2.
- fix import issue: replace deprecated export from caret
- If the bandSet argument in
radCor()is used to process only a subset of bands it will no longer return unprocessed bands along with processed bands. Instead only processed bands are returned. - By default
superClass()will now use dataType = 'INT2S' for classification maps to avoid issues with raster NA handling in INT1U - Allow reading and importing from Landsat MSS MTL files with
readMeta()andstackMeta()(@aszeitz, #7)
- fix readMeta time-stamp conversion now correctly set to GMT time (@mraraju, #12)
- radCor caused R to crash if bandSet was a single band
- fix single RasterLayer capability for superClass
- spectralIndices now calculates all documented indices if specified to do so (@mej1d1, #6)
- unsuperClass predicted map now handles NAs properly
- pifMatch did not return adjusted image (@tmb3006, #13)
Deprecated:
- argument
normwas dropped from rasterPCA, because it was effectively a duplicate of the standardized pca (spca) argument in the same function.
- new function
validateMap()for assessing map accuracy separately from model fitting, e.g. after majority or MMU filtering - new function
getValidation()to extract specific validation results of superClass objects (proposed by James Duffy) - new spectral index NDVIc (proposed by Jeff Evans)
- new argument scaleFactor for
spectralIndices()for calculation of EVI/EVI2 based on scaled reflectance values. - implemented dark object subtraction radCor(..,method='sdos') for Landsat 8 data (@BayAludra, #4)
- superClass based on polygons now considers only pixels which have their center coordinate within a polygon
- rasterCVA now returns angles from 0 to 360° instead of 0:45 by quadrant (reported by Martin Wegmann)
- improved dark object DN estimation based on maximum slope of the histogram in
estimateHaze()(@BayAludra, #4)
- superClass failed when neither valData or trainPartition was specified. regression introduced in 0.1.3 (reported by Anna Stephani)
- spectralIndices valid value range of EVI/EVI2 now [-1,1]
- radCor returned smallest integer instead of NA for some NA pixels
- fix 'sdos' for non-contiguous bands in radCor (@BayAludra, #4)
- new logical argument
predict()for superClass. Disables prediction of full raster (validation is still conducted). - new generic predict() function for superClass objects. Useful to separate model training and prediction.
- new example data set (landcover training polygons) for lsat example data under /extdata/trainingPolygons.rds
- fix histMatch for single layers (affected also 'ihs' pan-sharpening)
- fix superClass validation sampling for factors (character based factors could lead to wrong factor conversions and wrong validation results)
- improved handling of of training polygons with overlaps and shared borders in superClass
- improved checks and error messages for insufficient training polygons
New model for superClass: maximum likelihood classification (model = "mlc")
- Restrict calculation of EVI/EVI2 to reflectance data (#3)
- Enforce valid value ranges in
radCor(): radiance: [0,+Inf], reflectance: [0,1]. Includes a new argumentclampto turn this on or off (on by default).
Added kernlab to suggested packages to be able to test \donttest{} examples
Initial release to CRAN (2015-09-05) with the following functions:
- classifyQA()
- cloudMask()
- cloudShadowMask()
- coregisterImages()
- decodeQA()
- encodeQA()
- estimateHaze()
- fortify.raster()
- fCover()
- getMeta()
- ggR()
- ggRGB()
- histMatch()
- ImageMetaData()
- normImage()
- panSharpen()
- pifMatch()
- radCor()
- rasterCVA()
- rasterEntropy()
- rasterPCA()
- readEE()
- readMeta()
- readRSTBX()
- readSLI()
- rescaleImage()
- rsOpts()
- sam()
- saveRSTBX()
- spectralIndices()
- stackMeta()
- superClass()
- tasseledCap()
- topCor()
- unsuperClass()
- writeSLI()
Included example data sets:
- data(srtm)
- data(lsat)
- data(rlogo)