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Package ‘rtiff’
July16,2015
Type Package
Title ReadandWriteTIFFFiles
Version 1.4.5
Date 2015-07-15
Depends pixmap
Author EricKort<eric.kort@vai.org>
Maintainer EricKort<eric.kort@vai.org>
SystemRequirements libtiff
Description ReadsandwritesTIFFformatimagesand
returnsthemasapixmapobject.Becausetheresultingobject
canbeverylargeforevenmodestlysizedTIFFimages,images
canbereducedastheyarereadforimprovedperformance. This
packageisawrapperaroundlibtiff(www.libtiff.org),onwhich
itdepends(i.e.thelibtiffsharedlibrarymustbeonyour
PATHforthebinarytowork,andtiffio.hmustbeonyour
systemtobuildthepackagefromsource).Byusinglibtiff's
highlevelTIFFReadRGBAImagefunction,thispackageinherently
supportsawiderangeofimageformatsandcompressionschemes.
ThispackagealsoprovidesanimplementationoftheRidler
Autothresholdingalgorithmforeasygenerationofbinarymasks.
License GPL-3
Repository CRAN
Date/Publication 2015-07-1614:38:53
NeedsCompilation yes
Rtopicsdocumented:
rtiff-package. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
autoThreshold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
getDescription. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
newPixmapRGB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
plot.matrix. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1
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2
rtiff-package
readTiff . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
updateDescription . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
writeTiff . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Index
10
rtiff-package
AtiffreaderforR.
Description
This packagewill readTIFF format images and return them asapixmap object. Because the
resultingobjectcanbeverylargeforevenmodestlysizedTIFFimages,imagescanbereducedas
theyarereadforimprovedperformance.Thispackageisawrapperaroundlibtiff(www.libtiff.org),
on whichit depends. Byusinglibtiff’shighlevelTIFFReadRGBAImagefunction,thispackage
inherentlysupport awiderangeofimageformatsandcompressionschemes. Thispackagealso
providesanimplementationoftheRidlerAutothresholdingalgorithmforeasygenerationofbinary
masks.
Details
Package: rtiff
Type:
Package
Version: 1.0
Date:
2005-12-20
License: GPL
AtiffimagecanbeloadedusingreadTiff,andthenplotted,orprocessed. Regardlessofthecol-
orspaceoftheoriginal image, thisfunction returnsanRGBpixmap. Theimagerasterscanbe
accessedthroughthered,green,andblueslotsofthepixmapobjectreturned.Theserastersmaybe
furtherprocessedusinganyofthewidelydescribedimageanalysisalorithms. Asafirststep,and
autoThresholdfunctionisprovidedbythispackagetocreatebinarymasksofpixmapchannelsof
interest.
Author(s)
EricKort<eric.kort@vai.org>Maintainer:EricKort<eric.kort@vai.org>
References
www.libtiff.org
Examples
library(rtiff)
tif <- readTiff(system.file("tiff", "jello.tif", package="rtiff"))
plot(tif)
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autoThreshold
3
plot(tif@blue)
plot(tif@blue> autoThreshold(tif@blue)[3])
autoThreshold
Suggeststhresholdlevelstouseinbinarizinganimagechannel.
Description
ThisisanimplementationoftheRidlermethodforbinarization(seereferences).NOTE:Theorder
ofthevaluesreturneddidnotmatchwhatisdescribedinthe"value"sectionbelow.Thisisfixedin
thisversion.
Usage
autoThreshold(d.m, est = 0.5)
Arguments
d.m
Adatamatrixrepresentingthepixelintensitiesforasingleimagechannel(e.g.
readTiff("image.tif")@red).
est
Theinitialthresholdingestimatetoworkfrom. Thedefaultonlyworksifthe
pixelintensitiesarebetween0and1,otherwisethemeanintensityoftheentire
channelislikelyareasonablestartingpoint.Theselectionoftheestimateshould
notinfluencethefinalthresholdselected.
Value
Avector(v)ofestimates,the3rdelementofwhichisthetrueRidlerestimate.However,experience
demonstratesthatsometimesalower(elements1or2)orhigher(elements4or5)estimateperforms
betterforagiven application. TheRidlerestimateisthemeanbetweentheaverageintensityof
brightregionsintherasterandtheaverageintensityofdimregions.Thisisv[3].v[1]istheaverage
of dimregions,v[5]istheaverageof dimregions,andv[2]and v[4]arethemean between the
Ridlerestimateandv[1]andv[2],respectively.
Author(s)
EricKort<eric.kort@vai.org>
References
RidlerT,CalvardS.Picturethresholdingusinganiterativeselectionmethod. IEEETransonSys-
temsManandCybernetics,SMC8;630-2.
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getDescription
Examples
tif <- readTiff(system.file("tiff", "jello.tif", package="rtiff"))
threshold <- autoThreshold(tif@red)
plot(tif)
plot(tif@red >threshold[3])
getDescription
GetthedescriptiononaTIFFfile.
Description
GetstheTIFFdescriptionfield(tag270)foraTIFFfile.
Usage
getDescription(fn)
Arguments
fn
Thenameofthetifffile.
Value
AstringwiththedescriptionfieldfromtheTIFFfile,orNAifthereisnosuchfield.
Author(s)
EricKort<eric.kort@vai.org>
Examples
# This has nodescription
getDescription(system.file("tiff", "jello.tif", package="rtiff"))
# but this has
getDescription(system.file("tiff", "t1.tif", package="rtiff"))
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newPixmapRGB
5
newPixmapRGB
CreateanRGBpixmap
Description
AutilityfunctiontocreateanRGBpixmapobjectoutof3rasters.
Usage
newPixmapRGB(red = NULL, green = NULL, blue = NULL)
Arguments
red
Theredraster(amatrix)
green
Thegreenraster(amatrix)
blue
Theblueraster(amatrix)
Value
AnobjectoftypepixmaprepresentingtheresultingRGBimage.
Author(s)
EricKort<eric.kort@vai.org>
Examples
#this is tautological, but demonstrates the syntax...
tif <- readTiff(system.file("tiff", "jello.tif", package="rtiff"))
myPixmap <- newPixmapRGB(tif@red, tif@green, tif@blue)
plot(myPixmap)
#lets scramble the color channels just for fun
getOption("device")()
myPixmap <- newPixmapRGB(tif@blue, tif@red, tif@green)
plot(myPixmap)
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readTiff
plot.matrix
Overloadtheplotfunctionformatrices
Description
ThisisasimpleS3methodfortheplotfunctionwhichtakesamatrix,convertsittoanRGBpixmap
(byreplicatingit3times,onceforeachchannel),andthenplottingtheresultingimage.
Usage
## S3 method for class matrix
plot(x, ...)
Arguments
x
Amatrixrepresentinganimageraster.
...
Additionalargumentstosendtoplot.
Value
None.
Author(s)
EricKort<eric.kort@vai.org>
Examples
tif <- readTiff(system.file("tiff", "jello.tif", package="rtiff"))
plot(tif@red)
readTiff
AfunctiontoloadTIFFimagesintoapixmap.
Description
LoadsaTIFFimagefromafileandreturnstheimageasapixmapobject,withoptionalscaling.
Usage
readTiff(fn, page = 0, reduce = 0, pixmap = TRUE)
readTiff
7
Arguments
fn
Filename(thetiffimagetoload)
page
Inthecaseofmulti-pagetiffs,whichpagedoyouwant?
reduce
Optional scalingfactortoimproveperformancewithlargeimages,shouldbe
avaluebetween0and 1(i.e. adecimal representationofapercentage). See
details.
pixmap
Bydefault,readTiffreturnsapixmapobject,idealforplotting.Howeverpixmap
rescales thevalues to [0..1]. If you want the raw values from thefile, set
pixmap=FALSEtogetalistofr,g,andbvalues,unscaled.
Details
Thispackageisawrapperaroundlibtiff(www.libtiff.org),onwhichitdepends.Byusinglibtiff’s
highlevelTIFFReadRGBAImagefunction,thispackageinherentlysupportawiderangeofimage
formatsandcompressionschemes(interestingly,thankstolibtiff,thispackagecanloadanumber
ofTIFFformatsthattoolslikeWindow’sPaintortheopensourceGimpapplicationwillnotload).
Highresolution images(by which Imean imagesthat contain a"large"number ofpixels)will
occupyquiteabitofmemoryandwillalsoplotveryslowly.Ifyoudonotneedalltheresolutionfor
yourpurposes,youscanspecifyascalingfactor(reduce=x)todownsampletheimage.Thefactor
istheamountyouwanttheimagescaledBY,notTO.Inotherwords,reduce=.90willreducethe
imageby90yieldinganimage10approachisused. Sincewearereducingandnotenlarging,I
hopethiswillbesuitableforyourapplications.
Forsimplicity, an RGBpixmapisgenerated regardlessofthecolorspaceof theoriginal image
(includinggrayscaleimages, inwhich casetheR,G, and Brastersareidentical). Thepixmap
objectrequirespixelintensitiestobebetween0and1,sotheintensitiesintheorginalimagefile
arescaledaccordingly.Alternatively,specifypixmap=FALSEtoreturnalistofunscaler,g,andb
valuesinsteadofapixmapobject.
Value
Apixmapobjectcontainingtheimagerasters.
Author(s)
EricKort<eric.kort@vai.org>
Examples
tif <- readTiff(system.file("tiff", "jello.tif", package="rtiff"))
plot(tif)
8
writeTiff
updateDescription
SetthedescriptiononaTIFFfile.
Description
SetstheTIFFdescriptionfield(tag270)foraTIFFfile.
Usage
updateDescription(fn, description)
Arguments
fn
Thenameofthetifffile.
description
Thetexttosetthedescriptionto.
Value
None.
Author(s)
EricKort<eric.kort@vai.org>
writeTiff
AfunctiontoloadTIFFimagesintoapixmap.
Description
LoadsaTIFFimagefromafileandreturnstheimageasapixmapobject,withoptionalscaling.
Usage
writeTiff(pixmap, fn)
Arguments
pixmap
EitherapixmapRGBormatrixcontainingtheimagetosave. Inthecaseofa
matrix,anewpixmapRGBwillbecreatedfromit.TheresultingTIFFfilewill
beRGB,butwillappeargreybecauseeachchannelwillbeidentical.
fn
Whattocallthenewtifffile.
Details
This function savesthegiven pixmap or matrix rasterasan unencrypted TIFFimage,utilizing
libtiff’sTIFFWriteEncodedStrip,withtheentirerasterinasinglestrip(forsimplicity).
writeTiff
9
Value
None.Usedforitshandysideeffectofcreatingatifffile.
Author(s)
EricKort<eric.kort@vai.org>
Examples
tif <- readTiff(system.file("tiff", "jello.tif", package="rtiff"))
writeTiff(tif@red, "atesttif.tif")
Index
Topic
IO
autoThreshold,3
getDescription,4
readTiff,6
rtiff-package,2
updateDescription,8
writeTiff,8
Topic
file
autoThreshold,3
getDescription,4
readTiff,6
updateDescription,8
writeTiff,8
Topic
utilities
autoThreshold,3
getDescription,4
newPixmapRGB,5
plot.matrix,6
readTiff,6
updateDescription,8
writeTiff,8
autoThreshold,3
getDescription,4
newPixmapRGB,5
plot.matrix,6
readTiff,6
rtiff(rtiff-package),2
rtiff-package,2
updateDescription,8
writeTiff,8
10
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