phenopix: Process Digital Images of a Vegetation Cover

A collection of functions to process digital images, depict greennes index trajectories and extract relevant phenological stages.

AuthorGianluca Filippa, Edoardo Cremonese, Mirco Migliavacca, Marta Galvagno, Matthias Folker, Andrew D. Richardson, Enrico Tomelleri
Date of publication2017-03-16 14:54:46
MaintainerGianluca Filippa <>

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Man pages

autoFilter: A multiple-approach filtering procedure

bartlett2009: Bartlett 2009 raw data

bartlett2009.filtered: Bartlett 2009 dataset filtered

bartlett2009.fitted: Bartlett 2009 dataset with computed fitting and uncertainty...

bartlett2009.processed: Bartlett 2009 dataset processed by greenExplore function

BeckFit: A function to fit a double logisitic function to a vector...

combineUncertainty: An evolution of 'greenProcess' for the combination of...

convert: A function to convert in data.frame a 'zoo' or 'ts' objct

CutSeason: A function to cut time series by visual estimation

DrawROI: Draw Region of Interest

editExposure: Change erroneous exposure values by hand

ElmoreFit: A function to fit a double logisitic function to a vector...

extract: A function to extract items from an object of class phenopix

extractDateFilename: Estract dates from filenames

extractParameters: Extract fitting parameters from a pixel-based analysis

extractVIs: Extracts various vegetation indexes in a ROI

FitDoubleLogBeck: A fit

FitDoubleLogElmore: A fit

FitDoubleLogGu: A function to fit a double logisitic function to a vector...

FitDoubleLogKlHeavy: A function to fit a double logisitic function to a vector...

FitDoubleLogKlLight: A function to fit a double logisitic function to a vector...

fitted.phenopix: Returns predicted values from 'phenopix' objects.

getCoords: Extract given coordinates (in pixels) from a given JPEG image

getExposure: Extract exposure from stardot (or similar) images

get.options: Returns default options for function 'autoFilter'.

greenClusters: A function to perform a cluster analysis on data in output...

greenExplore: Explore all possible fitting and theshold methods from the...

greenProcess: A function to fit a curve and extract thresholds from...

GuFit: A function to fit a double logisitic function to a vector...

hydrodoy: Converts from and to hydrological day of year

KlostermanFit: A function to fit a double logisitic function to a vector...

matchExposure: Match exposures retrieved from the header of (stardot)...

NDVI: Compute NDVI

PasteSeason: A plotting facility for seasonal data with multiple cycles

PhenoBP: A function to extract breakpoints on a time series

PhenoDeriv: A function to extract thresholds

PhenoExtract: A function that extracts phenological thresholds

PhenoGu: A function to extract phenological thresholds according to Gu...

PhenoKl: A function to extract phenological thresholds according to...

phenopix-package: A package to process images of a vegetation cover

PhenoPlot: A plotting function for phenological thresholds

PhenoTrs: A fitting function

plotBP: A function to plot results of function 'PhenoBP'

plotExplore: Plot an object in output from the greenExplore function

plot.phenopix: Plotting 'phenopix' objects.

plotSpatial: Plot pixel-based analysis results from spatialGreen and...

plotSum: An evolution of 'greenProcess' for the combination of...

plotVI: Plot RGB DN, RGB indices and brightness

print.phenopix: Print 'phenopix' objects.

PrintROI: Print an already drawn region of interest

resizeImage: Resize an image (and a tROI) to a given pixel resolution

spatialFilter: Explore all possible fitting and theshold methods from the...

spatialGreen: Process pixel-based greenness indexes

SplineFit: A function to fit a smoothed spline to Phenological Data

splitROI: Splits a ROI into multiple subrois for spatial analysis

structureFolder: Fast structuration of a folder for phenopix process

summarizePhases: An evolution of 'greenProcess' for the combination of...

summary.phenopix: Summary of 'phenopix' objects.

trainOCR: Extract a training dataset for OCR procedure

update.phenopix: Update 'phenopix' objects.

updateROI: Update pixels included in a ROI of different pixel size


autoFilter Man page
bartlett2009 Man page
bartlett2009.filtered Man page
bartlett2009.fitted Man page
bartlett2009.processed Man page
BeckFit Man page
combineUncertainty Man page
convert Man page
CutSeason Man page
DrawROI Man page
editExposure Man page
ElmoreFit Man page
extract Man page
extractDateFilename Man page
extractParameters Man page
extractVIs Man page
FitDoubleLogBeck Man page
FitDoubleLogElmore Man page
FitDoubleLogGu Man page
FitDoubleLogKlHeavy Man page
FitDoubleLogKlLight Man page
fitted.phenopix Man page
getCoords Man page
getExposure Man page
get.options Man page
greenClusters Man page
greenExplore Man page
greenProcess Man page
GuFit Man page
hydrodoy Man page
KlostermanFit Man page
matchExposure Man page
NDVI Man page
PasteSeason Man page
PhenoBP Man page
PhenoDeriv Man page
PhenoExtract Man page
PhenoGu Man page
PhenoKl Man page
phenopix Man page
phenopix-package Man page
PhenoPlot Man page
PhenoTrs Man page
plotBP Man page
plotExplore Man page
plot.phenopix Man page
plotSpatial Man page
plotSum Man page
plotVI Man page
print.phenopix Man page
PrintROI Man page
resizeImage Man page
spatialFilter Man page
spatialGreen Man page
SplineFit Man page
splitROI Man page
structureFolder Man page
summarizePhases Man page
summary.phenopix Man page
trainOCR Man page
update.phenopix Man page
updateROI Man page


R/BeckFit.R R/CutSeason.R R/DrawROI.R R/ElmoreFit.R R/FitDoubleLogBeck.R R/FitDoubleLogElmore.R R/FitDoubleLogGu.R R/FitDoubleLogKlHeavy.R R/FitDoubleLogKlLight.R R/GuFit.R R/KlostermanFit.R R/NDVI.R R/PasteSeason.R R/PhenoBP.R R/PhenoDeriv.R R/PhenoExtract.R R/PhenoGu.R R/PhenoKl.R R/PhenoPlot.R R/PhenoTrs.R R/PrintROI.R R/SplineFit.R R/autoFilter.R R/combineUncertainty.R R/convert.R R/editExposure.R R/extract.R R/extractDateFilename.R R/extractParameters.R R/extractVIs.R R/fitted.phenopix.R R/get.options.R R/getCoords.R R/getExposure.R R/greenClusters.R R/greenExplore.R R/greenProcess.R R/hydrodoy.R R/matchExposure.R R/plot.phenopix.R R/plotBP.R R/plotExplore.R R/plotSpatial.R R/plotSum.R R/plotVI.R R/print.phenopix.R R/resizeImage.R R/spatialFilter.R R/spatialGreen.R R/splitROI.R R/structureFolder.R R/summarizePhases.R R/summary.phenopix.R R/trainOCR.R R/update.phenopix.R R/updateROI.R
man/BeckFit.Rd man/CutSeason.Rd man/DrawROI.Rd man/ElmoreFit.Rd man/FitDoubleLogBeck.Rd man/FitDoubleLogElmore.Rd man/FitDoubleLogGu.Rd man/FitDoubleLogKlHeavy.Rd man/FitDoubleLogKlLight.Rd man/GuFit.Rd man/KlostermanFit.Rd man/NDVI.Rd man/PasteSeason.Rd man/PhenoBP.Rd man/PhenoDeriv.Rd man/PhenoExtract.Rd man/PhenoGu.Rd man/PhenoKl.Rd man/PhenoPlot.Rd man/PhenoTrs.Rd man/PrintROI.Rd man/SplineFit.Rd man/autoFilter.Rd man/bartlett2009.Rd man/bartlett2009.filtered.Rd man/bartlett2009.fitted.Rd man/bartlett2009.processed.Rd man/combineUncertainty.Rd man/convert.Rd man/editExposure.Rd man/extract.Rd man/extractDateFilename.Rd man/extractParameters.Rd man/extractVIs.Rd man/fitted.phenopix.Rd man/get.options.Rd man/getCoords.Rd man/getExposure.Rd man/greenClusters.Rd man/greenExplore.Rd man/greenProcess.Rd man/hydrodoy.Rd man/matchExposure.Rd man/phenopix-package.Rd man/plot.phenopix.Rd man/plotBP.Rd man/plotExplore.Rd man/plotSpatial.Rd man/plotSum.Rd man/plotVI.Rd man/print.phenopix.Rd man/resizeImage.Rd man/spatialFilter.Rd man/spatialGreen.Rd man/splitROI.Rd man/structureFolder.Rd man/summarizePhases.Rd man/summary.phenopix.Rd man/trainOCR.Rd man/update.phenopix.Rd man/updateROI.Rd

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