tiff/0000755000175100001440000000000014531324160011217 5ustar hornikuserstiff/NAMESPACE0000644000175100001440000000007714531222327012444 0ustar hornikusersuseDynLib(tiff, read_tiff, write_tiff) exportPattern(".*TIFF") tiff/tools/0000755000175100001440000000000014531222327012361 5ustar hornikuserstiff/tools/winlibs.R0000644000175100001440000000060314531222327014152 0ustar hornikusers# Build against libtiff compiled with Rtools if (!file.exists("../windows/libtiff-4.1.0/mingw64/include/tiff.h")) { if(getRversion() < "3.3.0") setInternet2() download.file("https://github.com/rwinlib/libtiff/archive/v4.1.0.zip", "lib.zip", quiet = TRUE) dir.create("../windows", showWarnings = FALSE) unzip("lib.zip", exdir = "../windows") unlink("lib.zip") } tiff/man/0000755000175100001440000000000014531222327011774 5ustar hornikuserstiff/man/writeTIFF.Rd0000644000175100001440000000452514531222327014074 0ustar hornikusers\name{writeTIFF} \alias{writeTIFF} \title{ Write one or more bitmap images in TIFF format } \description{ Writes images into a TIFF file or a raw vector representing such. } \usage{ writeTIFF(what, where, bits.per.sample = 8L, compression = c("LZW", "none", "PackBits", "RLE", "JPEG", "deflate"), reduce = TRUE) } \arguments{ \item{what}{either an image or a list of images. An image is a real matrix or array of three dimensions, or an object of the class \code{"nativeRaster"}.} \item{where}{file name or a raw vector} \item{bits.per.sample}{number of bits per sample (numeric scalar). Supported values in this version are 8, 16, and 32.} \item{compression}{desired compression algorithm (string). Optionally, it can be specified as a numeric value corresponding to the compression TIFF tag, but it needs to be also supported by the underlying TIFF library} \item{reduce}{if \code{TRUE} then \code{writeTIFF} will attempt to reduce the number of planes in native rasters by analyzing the image to choose one of RGBA, RGB, GA or G formats, whichever uses the least planes without any loss. Otherwise the image is always saved with four planes (RGBA).} } \value{ If \code{where} is a raw vector then the value is the raw vector containg the TIFF contents, otherwise a scalar integer specifying the number of images written in the file. } %\references{ %} \author{ Simon Urbanek } \details{ By default \code{writeTIFF} uses the same number of planes as there are planes in the input image. For native images it is always four unless \code{reduce = TRUE} is set (see above). Consequently, color maps are not used. The output always uses contiguous planar configuration (baseline TIFF). The output is tagged with a photometric tag of either RGB (3 or 4 planes) or zero-is-black (1 or 2 planes). If \code{what} is a list then the TIFF output will be a directory of the corresponding number of images (in TIFF speak - not to be confused with file directories). } \seealso{ \code{\link{readTIFF}} } \examples{ img <- readTIFF(system.file("img", "Rlogo.tiff", package="tiff")) # write without the alpha channel tiff <- writeTIFF(img[,,-4], raw(0)) # read as native i2 <- readTIFF(tiff, native=TRUE) # write reduced - should be the same as tiff t2 <- writeTIFF(i2, raw(0), reduce=TRUE) } \keyword{IO} tiff/man/readTIFF.Rd0000644000175100001440000001315714531222327013656 0ustar hornikusers\name{readTIFF} \alias{readTIFF} \title{ Read a bitmap image stored in the TIFF format } \description{ Reads an image from a TIFF file/content into a raster array. } \usage{ readTIFF(source, native = FALSE, all = FALSE, convert = FALSE, info = FALSE, indexed = FALSE, as.is = FALSE, payload = TRUE) } \arguments{ \item{source}{Either name of the file to read from or a raw vector representing the TIFF file content.} \item{native}{logical, determines the image representation - if \code{FALSE} (the default) then the result is an array, if \code{TRUE} then the result is a native raster representation (suitable for plotting).} \item{all}{logical scalar or integer vector. TIFF files can contain more than one image. If \code{all=TRUE} then all images are returned in a list of images. If \code{all} is a vector, it gives the (1-based) indices of images to return. Otherwise only the first image is returned.} \item{convert}{logical, if \code{TRUE} then first convert the image into 8-bit RGBA samples and then to an array, see below for details.} \item{info}{logical, if set to \code{TRUE} then the resulting image(s) will also contain information from TIFF tags as attributes} \item{indexed}{logical, if set to \code{TRUE} then indexed images will be returned in the indexed form, i.e., as a matrix of integer indices referencing into a color map which is returned in the \code{"color.map"} attribute. This flag cannot be combined with \code{convert} or \code{native} and has no effect on images that are not indexed.} \item{as.is}{logical, if \code{TRUE} an attempt will be made to return the original integer values without re-scaling where possible} \item{payload}{logical, if \code{FALSE} then only metadata about the image(s) is returned, but not the actual image. Implies \code{info=TRUE} and all image-related flags are ignored.} } \value{ If \code{native} is \code{FALSE} then an array of the dimensions height x width x channels. If there is only one channel the result is a matrix. The values are reals between 0 and 1 (except for 32-bit floating point sample storage which are unscaled reals, and for indexed and \code{as.is=TRUE} which are integers). If \code{native} is \code{TRUE} then an object of the class \code{nativeRaster} is returned instead. The latter cannot be easily computed on but is the most efficient way to draw using \code{rasterImage}. If \code{all} is \code{TRUE} or a vector of image indices, then the result is a list of the above with zero or more elements. If \code{all} is a vector of indices, the result will have exactly the same length as \code{all}. If an index does not appear in the file, the corresponding list entry will be \code{NULL}. If \code{payload=FALSE} then the result is equivalent to \code{info=TRUE} but without the image data and returned as a data frame. If \code{all} is either \code{TRUE} or a vector then the result will be a data frame with each row corresponding to one image. } \details{ Most common files decompress into RGB (3 channels), RGBA (4 channels), Grayscale (1 channel) or GA (2 channels). Note that G and GA images cannot be directly used in \code{\link{rasterImage}} unless \code{native} is set to \code{TRUE} because \code{rasterImage} requires RGB or RGBA format (\code{nativeRaster} is always 8-bit RGBA). TIFF images can have a wide range of internal representations, but only the most common in image processing are directly supported (8-bit, 16-bit integer and 32-bit float samples). Other formats (color maps, sub-8-bit images, etc.) are only supported via \code{convert=TRUE} which uses the built-in facilities of the TIFF library to convert the image into RGBA format with 8-bit samples (i.e. total of 32-bit per pixel) and then store the relevant components from there into real arrays. This is the same path as used by \code{native=TRUE} and so differs only in the output value. Note that conversion may result in different values than direct acccess as it is intended mainly for viewing and not computation. } %\references{ %} \author{ Simon Urbanek Kent Johnson } \note{ Some non-standard formats such as 12-bit TIFFs are partially supported (there is no standard for packing order for TIFFs beoynd 8-bit so we assume big-endian packing similar to the default fill order and only support single channel or indexed). The \code{as.is=TRUE} option is experimental, cannot be used with \code{native} or \code{convert} and only works for integer storage TIFFs. } \seealso{ \code{\link{rasterImage}}, \code{\link{writeTIFF}} } \examples{ Rlogo <- system.file("img", "Rlogo.tiff", package="tiff") # read a sample file (R logo) img <- readTIFF(Rlogo) # read it also in native format img.n <- readTIFF(Rlogo, native=TRUE) # and also in converted img.c <- readTIFF(Rlogo, convert=TRUE) # read all contained images str(readTIFF(Rlogo, all=TRUE)) # pick some images str(readTIFF(Rlogo, all=c(5, 1, 3))) # only show information str(readTIFF(Rlogo, payload=FALSE)) # if your R supports it, we'll plot it if (exists("rasterImage")) { # can plot only in R 2.11.0 and higher plot(1:2, type='n') if (names(dev.cur()) == "windows") { # windows device doesn't support semi-transparency so we'll need # to flatten the image transparent <- img[,,4] == 0 img <- as.raster(img[,,1:3]) img[transparent] <- NA # interpolate must be FALSE on Windows, otherwise R will # try to interpolate transparency and fail rasterImage(img, 1.2, 1.27, 1.8, 1.73, interpolate=FALSE) } else { # any reasonable device will be fine using alpha rasterImage(img, 1.2, 1.27, 1.8, 1.73) rasterImage(img.n, 1.5, 1.5, 1.9, 1.8) } } } \keyword{IO} tiff/DESCRIPTION0000644000175100001440000000123014531324160012721 0ustar hornikusersPackage: tiff Version: 0.1-12 Title: Read and Write TIFF Images Author: Simon Urbanek [aut, cre], Kent Johnson [ctb] Maintainer: Simon Urbanek Depends: R (>= 2.9.0) Description: Functions to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors, including native image representation. License: GPL-2 | GPL-3 SystemRequirements: tiff and jpeg libraries URL: https://www.rforge.net/tiff/ NeedsCompilation: yes Packaged: 2023-11-27 23:23:08 UTC; rforge Repository: CRAN Date/Publication: 2023-11-28 08:44:32 UTC tiff/configure.ac0000644000175100001440000000545414531222327013517 0ustar hornikusersAC_INIT([tiff],[1.0],[Simon.Urbanek@r-project.org]) AC_CONFIG_SRCDIR(src/common.c) # find R home and set correct compiler + flags : ${R_HOME="`R RHOME`"} if test -z "${R_HOME}"; then AC_MSG_ERROR([cannot determine R_HOME. Make sure you use R CMD INSTALL!]) fi RBIN="${R_HOME}/bin/R" : ${PKG_MODULE=libtiff-4} # pick all flags for testing from R : ${CC=`"${RBIN}" CMD config CC`} : ${CFLAGS=`"${RBIN}" CMD config CFLAGS`} : ${CPPFLAGS=`"${RBIN}" CMD config CPPFLAGS`} : ${LDFLAGS=`"${RBIN}" CMD config LDFLAGS`} : ${CPP="$CC -E"} # honor PKG_xx overrides LIBS="${LIBS} ${PKG_LIBS}" # for CPPFLAGS we will superfluously double R's flags # since we'll set PKG_CPPFLAGS with this, but that shouldn't hurt CPPFLAGS="${CPPFLAGS} ${PKG_CPPFLAGS}" AC_PATH_PROG([PKG_CONFIG], [pkg-config]) AC_LANG(C) AC_CHECK_HEADERS([unistd.h]) AC_CHECK_LIB([tiff],[TIFFClientOpen],,[ AC_MSG_NOTICE([Using libtiff directly doesn't work, falling back to pkg-config.]) AC_MSG_NOTICE([Note that you can provide correct PKG_LIBS to allow installation without pkg-config.]) AC_MSG_CHECKING([for pkg-config]) AS_IF(["$PKG_CONFIG" --version], , [AC_MSG_RESULT([no]) AC_MSG_ERROR([Provided flags don't work and pkg-config is not present. You can either set PKG_LIBS to the correct flags or install pkg-config.])]) AC_MSG_CHECKING([whether pkg-config knows about $PKG_MODULE]) AS_IF([$PKG_CONFIG $PKG_MODULE], [AC_MSG_RESULT(yes)], [AC_MSG_RESULT([no]) AC_MSG_ERROR([Install libtiff-dev or equivalent first (or set PKG_MODULE if non-standard)])]) TIFF_CPPFLAGS="`$PKG_CONFIG --cflags $PKG_MODULE`" TIFF_LIBS="`$PKG_CONFIG --libs $PKG_MODULE`" LIBS0="$LIBS" LIBS="$LIBS0 ${TIFF_LIBS}" CPPFLAGS="$CPPFLAGS ${TIFF_CPPFLAGS}" AC_MSG_CHECKING([whether ${TIFF_CPPFLAGS} ${TIFF_LIBS} works]) AC_LINK_IFELSE([AC_LANG_CALL([], [TIFFClientOpen])], AC_MSG_RESULT([yes]), [ AC_MSG_RESULT([no]) AC_MSG_CHECKING([whether --static helps]) TIFF_LIBS="`$PKG_CONFIG --static --libs $PKG_MODULE`" LIBS="$LIBS0 ${TIFF_LIBS}" AC_LINK_IFELSE([AC_LANG_CALL([], [TIFFClientOpen])], AC_MSG_RESULT([yes]),,[ AC_MSG_RESULT([no]) AC_MSG_ERROR([Cannot get libtiff to work, check config.log for details.]) ]) ]) ]) AC_MSG_NOTICE([ PKG_CPPFLAGS: $CPPFLAGS]) AC_MSG_NOTICE([ PKG_LIBS : $LIBS]) ## check headers only after we're done with pkg-config AC_CHECK_HEADERS([tiff.h tiffio.h],, [AC_MSG_ERROR([TIFF headers are not usable. Please make sure you have installed development files for libtiff.])]) AC_ARG_VAR([PKG_CPPFLAGS],[custom C preprocessor flags for package compilation]) AC_ARG_VAR([PKG_LIBS],[custom libraries for package compilation]) AC_ARG_VAR([PKG_CONFIG],[path to the pkg-config executable (pkg-config)]) AC_ARG_VAR([PKG_MODULE],[name of the tiff pkg-config module (libtiff-4)]) AC_CONFIG_FILES(src/Makevars) AC_OUTPUT tiff/src/0000755000175100001440000000000014531222327012010 5ustar hornikuserstiff/src/read.c0000644000175100001440000005550014531222327013074 0ustar hornikusers#include #include #include #include #include "common.h" #include /* avoid protection issues with setAttrib where new symbols may trigger GC problems */ static void setAttr(SEXP x, const char *name, SEXP val) { PROTECT(val); setAttrib(x, Rf_install(name), val); UNPROTECT(1); } /* add information attributes according to the TIFF tags. Only a somewhat random set (albeit mostly baseline) is supported */ static void TIFF_add_info(TIFF *tiff, SEXP res) { uint32_t i32; uint16_t i16; float f; char *c = 0; if (TIFFGetField(tiff, TIFFTAG_IMAGEWIDTH, &i32)) setAttr(res, "width", ScalarInteger(i32)); if (TIFFGetField(tiff, TIFFTAG_IMAGELENGTH, &i32)) setAttr(res, "length", ScalarInteger(i32)); if (TIFFGetField(tiff, TIFFTAG_IMAGEDEPTH, &i32)) setAttr(res, "depth", ScalarInteger(i32)); if (TIFFGetField(tiff, TIFFTAG_BITSPERSAMPLE, &i16)) setAttr(res, "bits.per.sample", ScalarInteger(i16)); if (TIFFGetField(tiff, TIFFTAG_SAMPLESPERPIXEL, &i16)) setAttr(res, "samples.per.pixel", ScalarInteger(i16)); if (TIFFGetField(tiff, TIFFTAG_SAMPLEFORMAT, &i16)) { char uv[24]; const char *name = 0; switch (i16) { case 1: name = "uint"; break; case 2: name = "int"; break; case 3: name = "float"; break; case 4: name = "undefined"; break; case 5: name = "complex int"; break; case 6: name = "complex float"; break; default: snprintf(uv, sizeof(uv), "unknown (%d)", i16); name = uv; } setAttr(res, "sample.format", mkString(name)); } if (TIFFGetField(tiff, TIFFTAG_PLANARCONFIG, &i16)) { if (i16 == PLANARCONFIG_CONTIG) setAttr(res, "planar.config", mkString("contiguous")); else if (i16 == PLANARCONFIG_SEPARATE) setAttr(res, "planar.config", mkString("separate")); else { char uv[24]; snprintf(uv, sizeof(uv), "unknown (%d)", i16); setAttr(res, "planar.config", mkString(uv)); } } if (TIFFGetField(tiff, TIFFTAG_ROWSPERSTRIP, &i32)) setAttr(res, "rows.per.strip", ScalarInteger(i32)); if (TIFFGetField(tiff, TIFFTAG_TILEWIDTH, &i32)) { setAttr(res, "tile.width", ScalarInteger(i32)); TIFFGetField(tiff, TIFFTAG_TILELENGTH, &i32); setAttr(res, "tile.length", ScalarInteger(i32)); } if (TIFFGetField(tiff, TIFFTAG_COMPRESSION, &i16)) { char uv[24]; const char *name = 0; switch (i16) { case 1: name = "none"; break; case 2: name = "CCITT RLE"; break; case 32773: name = "PackBits"; break; case 3: name = "CCITT Group 3 fax"; break; case 4: name = "CCITT Group 4 fax"; break; case 5: name = "LZW"; break; case 6: name = "old JPEG"; break; case 7: name = "JPEG"; break; case 8: name = "deflate"; break; case 9: name = "JBIG b/w"; break; case 10: name = "JBIG color"; break; default: snprintf(uv, sizeof(uv), "unknown (%d)", i16); name = uv; } setAttr(res, "compression", mkString(name)); } if (TIFFGetField(tiff, TIFFTAG_THRESHHOLDING, &i16)) setAttr(res, "threshholding", ScalarInteger(i16)); if (TIFFGetField(tiff, TIFFTAG_XRESOLUTION, &f)) setAttr(res, "x.resolution", ScalarReal(f)); if (TIFFGetField(tiff, TIFFTAG_YRESOLUTION, &f)) setAttr(res, "y.resolution", ScalarReal(f)); if (TIFFGetField(tiff, TIFFTAG_XPOSITION, &f)) setAttr(res, "x.position", ScalarReal(f)); if (TIFFGetField(tiff, TIFFTAG_YPOSITION, &f)) setAttr(res, "y.position", ScalarReal(f)); if (TIFFGetField(tiff, TIFFTAG_RESOLUTIONUNIT, &i16)) { const char *name = "unknown"; switch (i16) { case 1: name = "none"; break; case 2: name = "inch"; break; case 3: name = "cm"; break; } setAttr(res, "resolution.unit", mkString(name)); } #ifdef TIFFTAG_INDEXED /* very recent in libtiff even though it's an old tag */ if (TIFFGetField(tiff, TIFFTAG_INDEXED, &i16)) setAttr(res, "indexed", ScalarLogical(i16)); #endif if (TIFFGetField(tiff, TIFFTAG_ORIENTATION, &i16)) { const char *name = ""; switch (i16) { case 1: name = "top.left"; break; case 2: name = "top.right"; break; case 3: name = "bottom.right"; break; case 4: name = "bottom.left"; break; case 5: name = "left.top"; break; case 6: name = "right.top"; break; case 7: name = "right.bottom"; break; case 8: name = "left.bottom"; break; } setAttr(res, "orientation", mkString(name)); } if (TIFFGetField(tiff, TIFFTAG_COPYRIGHT, &c) && c) setAttr(res, "copyright", mkString(c)); if (TIFFGetField(tiff, TIFFTAG_ARTIST, &c) && c) setAttr(res, "artist", mkString(c)); if (TIFFGetField(tiff, TIFFTAG_DOCUMENTNAME, &c) && c) setAttr(res, "document.name", mkString(c)); if (TIFFGetField(tiff, TIFFTAG_DATETIME, &c) && c) setAttr(res, "date.time", mkString(c)); if (TIFFGetField(tiff, TIFFTAG_IMAGEDESCRIPTION, &c) && c) setAttr(res, "description", mkString(c)); if (TIFFGetField(tiff, TIFFTAG_SOFTWARE, &c) && c) setAttr(res, "software", mkString(c)); if (TIFFGetField(tiff, TIFFTAG_PHOTOMETRIC, &i16)) { char uv[24]; const char *name = 0; switch (i16) { case 0: name = "white is zero"; break; case 1: name = "black is zero"; break; case 2: name = "RGB"; break; case 3: name = "palette"; break; case 4: name = "mask"; break; case 5: name = "separated"; break; case 6: name = "YCbCr"; break; case 8: name = "CIELAB"; break; case 9: name = "ICCLab"; break; case 10: name = "ITULab"; break; default: snprintf(uv, sizeof(uv), "unknown (%d)", i16); name = uv; } setAttr(res, "color.space", mkString(name)); } } SEXP read_tiff(SEXP sFn, SEXP sNative, SEXP sAll, SEXP sConvert, SEXP sInfo, SEXP sIndexed, SEXP sOriginal, SEXP sPayload) { SEXP res = R_NilValue, multi_res = R_NilValue, multi_tail = R_NilValue, dim = R_NilValue; const char *fn; int native = asInteger(sNative), all = (isLogical(sAll) && asInteger(sAll) > 0), n_img = 0, convert = (asInteger(sConvert) == 1), add_info = (asInteger(sInfo) == 1), indexed = (asInteger(sIndexed) == 1), original = (asInteger(sOriginal) == 1), info_only = (asInteger(sPayload) == 0); tiff_job_t rj; TIFF *tiff; FILE *f; int *pick = (isInteger(sAll) ? INTEGER(sAll) : 0); int picks = pick ? LENGTH(sAll) : 0; SEXP pick_res = pick ? PROTECT(allocVector(VECSXP, picks)) : 0; /* make sure people don't use vector logicals - they must use which() if that's what they want */ if (!((isLogical(sAll) && LENGTH(sAll) == 1) || isInteger(sAll))) Rf_error("`all' must be either a scalar logical (TRUE/FALSE) or an integer vector"); if (indexed && (convert || native)) Rf_error("indexed and native/convert cannot both be TRUE as they are mutually exclusive"); if (TYPEOF(sFn) == RAWSXP) { rj.data = (char*) RAW(sFn); rj.len = LENGTH(sFn); rj.alloc = rj.ptr = 0; rj.f = f = 0; } else { if (TYPEOF(sFn) != STRSXP || LENGTH(sFn) < 1) Rf_error("invalid filename"); fn = CHAR(STRING_ELT(sFn, 0)); f = fopen(fn, "rb"); if (!f) Rf_error("unable to open %s", fn); rj.f = f; } tiff = TIFF_Open("rmc", &rj); /* no mmap, no chopping */ if (!tiff) Rf_error("Unable to open TIFF"); int cur_dir = 0; /* 1-based image number */ int nprot = 0; while (1) { /* loop over separate image in a directory if desired */ int pick_index = -1; /* not picked */ cur_dir++; /* If sAll is a numeric vector, only read images referenced in it */ if (pick) { /* We don't use match() as it re-builds the hash table on every call. */ int i = 0; while (i < picks) { if (pick[i] == cur_dir) { pick_index = i; break; } i++; } if (pick_index == -1) { /* No match */ if (TIFFReadDirectory(tiff)) /* skip */ continue; else break; } } if (info_only) { /* dummy result object */ res = PROTECT(allocVector(INTSXP, 0)); TIFF_add_info(tiff, res); if (isLogical(sAll) && asInteger(sAll) == 0) { UNPROTECT(1); TIFFClose(tiff); return res; } n_img++; if (pick_index >= 0) SET_VECTOR_ELT(pick_res, pick_index, res); else { if (multi_res == R_NilValue) { multi_tail = multi_res = CONS(res, R_NilValue); PROTECT(multi_res); nprot++; } else { SEXP q = CONS(res, R_NilValue); SETCDR(multi_tail, q); multi_tail = q; } } UNPROTECT(1); if (!TIFFReadDirectory(tiff)) break; continue; } uint32_t imageWidth = 0, imageLength = 0, imageDepth; uint32_t tileWidth, tileLength; uint32_t x, y; uint16_t config, bps = 8, spp = 1, sformat = 1, out_spp; tdata_t buf; double *ra = 0; uint16_t *colormap[3] = {0, 0, 0}; int is_float = 0; TIFFGetField(tiff, TIFFTAG_IMAGEWIDTH, &imageWidth); TIFFGetField(tiff, TIFFTAG_IMAGELENGTH, &imageLength); if (!TIFFGetField(tiff, TIFFTAG_IMAGEDEPTH, &imageDepth)) imageDepth = 0; if (TIFFGetField(tiff, TIFFTAG_TILEWIDTH, &tileWidth)) TIFFGetField(tiff, TIFFTAG_TILELENGTH, &tileLength); else /* no tiles */ tileWidth = tileLength = 0; TIFFGetField(tiff, TIFFTAG_PLANARCONFIG, &config); TIFFGetField(tiff, TIFFTAG_BITSPERSAMPLE, &bps); TIFFGetField(tiff, TIFFTAG_SAMPLESPERPIXEL, &spp); out_spp = spp; TIFFGetField(tiff, TIFFTAG_COLORMAP, colormap, colormap + 1, colormap + 2); if (TIFFGetField(tiff, TIFFTAG_SAMPLEFORMAT, &sformat) && sformat == SAMPLEFORMAT_IEEEFP) is_float = 1; if (spp == 1 && !indexed) { /* modify out_spp for colormaps */ if (colormap[2]) out_spp = 3; else if (colormap[1]) out_spp = 2; } #ifdef TIFF_DEBUG Rprintf("image %d x %d x %d, tiles %d x %d, bps = %d, spp = %d (output %d), config = %d, colormap = %s,\n", imageWidth, imageLength, imageDepth, tileWidth, tileLength, bps, spp, out_spp, config, colormap[0] ? "yes" : "no"); Rprintf(" float = %d\n", is_float); #endif if (native || convert) { /* use built-in RGBA conversion - fortunately, libtiff uses exactly the same RGBA representation as R ... *but* flipped y coordinate :( */ SEXP tmp = R_NilValue; /* FIXME: TIFF handle leak in case this fails */ if (convert) PROTECT(tmp = allocVector(REALSXP, imageWidth * imageLength * out_spp)); res = PROTECT(allocVector(INTSXP, imageWidth * imageLength)); TIFFReadRGBAImage(tiff, imageWidth, imageLength, (uint32_t*) INTEGER(res), 0); /* TIFF uses flipped y-axis, so we need to invert it .. argh ... */ if (imageLength > 1) { int *line = INTEGER(allocVector(INTSXP, imageWidth)); int *src = INTEGER(res), *dst = INTEGER(res) + imageWidth * (imageLength - 1), ls = imageWidth * sizeof(int); int *el = src + imageWidth * (imageLength / 2); while (src < el) { memcpy(line, src, ls); memcpy(src, dst, ls); memcpy(dst, line, ls); src += imageWidth; dst -= imageWidth; } } if (convert) { uint16_t s; uint32_t *data = (uint32_t*) INTEGER(res); ra = REAL(tmp); for (x = 0; x < imageWidth; x++) for (y = 0; y < imageLength; y++) { if (out_spp == 1) { /* single plane (gray) just take R */ ra[imageLength * x + y] = ((double)(data[x + y * imageWidth] & 255)) / 255.0; } else if (out_spp == 2 /* G+A */) { /* this is a bit odd as we need to copy R and A */ ra[imageLength * x + y] = ((double)(data[x + y * imageWidth] & 255)) / 255.0; ra[imageWidth * imageLength + imageLength * x + y] = ((double)((data[x + y * imageWidth] >> 16) & 255)) / 255.0; } else /* 3-4 are simply sequential copies */ for (s = 0; s < out_spp; s++) ra[(imageLength * imageWidth * s) + imageLength * x + y] = ((double) ((data[x + y * imageWidth] >> (s * 8)) & 255)) / 255.0; } UNPROTECT(1); /* res */ res = tmp; dim = allocVector(INTSXP, (out_spp > 1) ? 3 : 2); INTEGER(dim)[0] = imageLength; INTEGER(dim)[1] = imageWidth; if (out_spp > 1) INTEGER(dim)[2] = out_spp; setAttrib(res, R_DimSymbol, dim); if (add_info) TIFF_add_info(tiff, res); UNPROTECT(1); } else { SEXP R_ChannelsSymbol = Rf_install("channels"); dim = allocVector(INTSXP, 2); INTEGER(dim)[0] = imageLength; INTEGER(dim)[1] = imageWidth; setAttrib(res, R_DimSymbol, dim); setAttrib(res, R_ClassSymbol, mkString("nativeRaster")); setAttrib(res, R_ChannelsSymbol, ScalarInteger(out_spp)); if (add_info) TIFF_add_info(tiff, res); UNPROTECT(1); } if (!all && !picks) { TIFFClose(tiff); return res; } n_img++; if (pick_index >= 0) SET_VECTOR_ELT(pick_res, pick_index, res); else { if (multi_res == R_NilValue) { multi_tail = multi_res = CONS(res, R_NilValue); PROTECT(multi_res); nprot++; } else { SEXP q = CONS(res, R_NilValue); SETCDR(multi_tail, q); multi_tail = q; } } if (!TIFFReadDirectory(tiff)) break; continue; } /* end native || convert */ if (bps != 8 && bps != 16 && bps != 32 && ( bps != 12 || spp != 1 )) { TIFFClose(tiff); Rf_error("image has %d bits/sample which is unsupported in direct mode - use native=TRUE or convert=TRUE", bps); } if (original && is_float) { TIFFClose(tiff); Rf_error("as.is=TRUE is not supported for floating point images"); } if (sformat == SAMPLEFORMAT_INT && !original) Rf_warning("tiff package currently only supports unsigned integer or float sample formats in direct mode, but the image contains signed integer format - it will be treated as unsigned (use as.is=TRUE, native=TRUE or convert=TRUE depending on your intent)"); /* FIXME: TIFF handle leak in case this fails */ res = allocVector((spp == 1 && (original || (indexed && colormap[0]))) ? INTSXP : REALSXP, imageWidth * imageLength * out_spp); if (!(spp == 1 && (original || (indexed && colormap[0])))) ra = REAL(res); #define DE12A(v) ((((unsigned int) v[0]) << 4) | (((unsigned int) v[1]) >> 4)) #define DE12B(v) (((((unsigned int) v[1]) & 0x0f) << 8) | ((unsigned int) v[2])) if (tileWidth == 0) { tstrip_t strip; tsize_t plane_offset = 0; x = 0; y = 0; buf = _TIFFmalloc(TIFFStripSize(tiff)); #ifdef TIFF_DEBUG Rprintf(" - %d x %d strips\n", TIFFNumberOfStrips(tiff), TIFFStripSize(tiff)); #endif for (strip = 0; strip < TIFFNumberOfStrips(tiff); strip++) { tsize_t n = TIFFReadEncodedStrip(tiff, strip, buf, (tsize_t) -1); if (spp == 1) { /* config doesn't matter for spp == 1 */ if (colormap[0] && !indexed) { tsize_t i, step = bps / 8; int *ia = original ? INTEGER(res) : 0; if (bps == 12) step += 2; for (i = 0; i < n; i += step) { unsigned int ci = 0, ci2 = 0; const unsigned char *v = (const unsigned char*) buf + i; if (bps == 8) ci = v[0]; else if (bps == 16) ci = ((const unsigned short int*)v)[0]; else if (bps == 32) ci = ((const unsigned int*)v)[0]; else if (bps == 12) { ci = DE12A(v); ci2 = DE12B(v); } if (original) { ia[imageLength * x + y] = colormap[0][ci]; /* color maps are always 16-bit */ /* FIXME: bps==12 is broken with color map lookup !!! */ if (bps == 12) ia[imageLength * ++x + y] = colormap[0][ci2]; if (colormap[1]) { ia[(imageLength * imageWidth) + imageLength * x + y] = colormap[1][ci]; if (colormap[2]) ia[(2 * imageLength * imageWidth) + imageLength * x + y] = colormap[2][ci]; } } else { ra[imageLength * x + y] = ((double)colormap[0][ci]) / 65535.0; /* color maps are always 16-bit */ if (bps == 12) ra[imageLength * ++x + y] = ((double)colormap[0][ci2]) / 65535.0; if (colormap[1]) { ra[(imageLength * imageWidth) + imageLength * x + y] = ((double)colormap[1][ci]) / 65535.0; if (colormap[2]) ra[(2 * imageLength * imageWidth) + imageLength * x + y] = ((double)colormap[2][ci]) / 65535.0; } } x++; if (x >= imageWidth) { x -= imageWidth; y++; } } } else if (colormap[0] || original) { /* indexed requested */ tsize_t i, step = bps / 8; int *ia = INTEGER(res), ix_base = original ? 0 : 1; if (bps == 12) step = 3; for (i = 0; i < n; i += step) { int val = NA_INTEGER; const unsigned char *v = (const unsigned char*) buf + i; if (bps == 8) val = ix_base + v[0]; else if (bps == 16) val = ix_base + ((const unsigned short int*)v)[0]; else if (bps == 32) val = ix_base + ((const unsigned int*)v)[0]; else if (bps == 12) { ia[imageLength * x++ + y] = ix_base + DE12A(v); val = ix_base + DE12B(v); } ia[imageLength * x++ + y] = val; if (x >= imageWidth) { x -= imageWidth; y++; } } } else { /* direct gray */ tsize_t i, step = bps / 8; if (bps == 12) step = 3; for (i = 0; i < n; i += step) { double val = NA_REAL; const unsigned char *v = (const unsigned char*) buf + i; if (bps == 8) val = ((double) v[0]) / 255.0; else if (bps == 16) val = ((double) ((const unsigned short int*)v)[0]) / 65535.0; else if (bps == 32) { if (is_float) val = (double) ((const float*)v)[0]; else val = ((double) ((const unsigned int*)v)[0]) / 4294967296.0; } if (bps == 12) { ra[imageLength * x++ + y] = ((double) DE12A(v)) / 4096.0; val = ((double) DE12B(v)) / 4096.0; } ra[imageLength * x + y] = val; x++; if (x >= imageWidth) { x -= imageWidth; y++; } } } } else if (config == PLANARCONFIG_CONTIG) { /* interlaced */ tsize_t i, j, step = spp * bps / 8; for (i = 0; i < n; i += step) { const unsigned char *v = (const unsigned char*) buf + i; if (bps == 8) { for (j = 0; j < spp; j++) ra[(imageLength * imageWidth * j) + imageLength * x + y] = ((double) v[j]) / 255.0; } else if (bps == 16) { for (j = 0; j < spp; j++) ra[(imageLength * imageWidth * j) + imageLength * x + y] = ((double) ((const unsigned short int*)v)[j]) / 65535.0; } else if (bps == 32 && !is_float) { for (j = 0; j < spp; j++) ra[(imageLength * imageWidth * j) + imageLength * x + y] = ((double) ((const unsigned int*)v)[j]) / 4294967296.0; } else if (bps == 32 && is_float) { for (j = 0; j < spp; j++) ra[(imageLength * imageWidth * j) + imageLength * x + y] = (double) ((const float*)v)[j]; } x++; if (x >= imageWidth) { x -= imageWidth; y++; } } } else { /* separate */ tsize_t step = bps / 8, i; for (i = 0; i < n; i += step) { const unsigned char *v = (const unsigned char*) buf + i; if (bps == 8) ra[plane_offset + imageLength * x + y] = ((double) v[0]) / 255.0; else if (bps == 16) ra[plane_offset + imageLength * x + y] = ((double) ((const unsigned short int*)v)[0]) / 65535.0; else if (bps == 32 && !is_float) ra[plane_offset + imageLength * x + y] = ((double) ((const unsigned int*)v)[0]) / 4294967296.0; else if (bps == 32 && is_float) ra[plane_offset + imageLength * x + y] = (double) ((const float*)v)[0]; } x++; if (x >= imageWidth) { x -= imageWidth; y++; if (y >= imageLength) { y -= imageLength; plane_offset += imageWidth * imageLength; } } } } } else { /* tiled image */ if (indexed || colormap[0] || bps == 12) Rf_error("Indexed and 12-bit tiled images are not supported."); if (spp > 1 && config != PLANARCONFIG_CONTIG) Rf_error("Planar format tiled images are not supported"); #ifdef TIFF_DEBUG Rprintf(" - %d x %d tiles\n", TIFFNumberOfTiles(tiff), TIFFTileSize(tiff)); #endif x = 0; y = 0; buf = _TIFFmalloc(TIFFTileSize(tiff)); for (y = 0; y < imageLength; y += tileLength) for (x = 0; x < imageWidth; x += tileWidth) { tsize_t n = TIFFReadTile(tiff, buf, x, y, 0 /*depth*/, 0 /*plane*/); if (spp == 1) { /* config doesn't matter for spp == 1 */ /* direct gray */ tsize_t i, step = bps / 8; uint32_t xoff=0, yoff=0; for (i = 0; i < n; i += step) { double val = NA_REAL; const unsigned char *v = (const unsigned char*) buf + i; if (bps == 8) val = ((double) v[0]) / 255.0; else if (bps == 16) val = ((double) ((const unsigned short int*)v)[0]) / 65535.0; else if (bps == 32) { if (is_float) val = (double) ((const float*)v)[0]; else val = ((double) ((const unsigned int*)v)[0]) / 4294967296.0; } if (x + xoff < imageWidth && y + yoff < imageLength) ra[imageLength * (x + xoff) + y + yoff] = val; xoff++; if (xoff >= tileWidth) { xoff -= tileWidth; yoff++; } } } else if (config == PLANARCONFIG_CONTIG) { /* interlaced */ tsize_t i, j, step = spp * bps / 8; uint32_t xoff=0, yoff=0; for (i = 0; i < n; i += step) { const unsigned char *v = (const unsigned char*) buf + i; if (x + xoff < imageWidth && y + yoff < imageLength) { if (bps == 8) { for (j = 0; j < spp; j++) ra[(imageLength * imageWidth * j) + imageLength * (x + xoff) + y + yoff] = ((double) v[j]) / 255.0; } else if (bps == 16) { for (j = 0; j < spp; j++) ra[(imageLength * imageWidth * j) + imageLength * (x + xoff) + y + yoff] = ((double) ((const unsigned short int*)v)[j]) / 65535.0; } else if (bps == 32 && !is_float) { for (j = 0; j < spp; j++) ra[(imageLength * imageWidth * j) + imageLength * (x + xoff) + y + yoff] = ((double) ((const unsigned int*)v)[j]) / 4294967296.0; } else if (bps == 32 && is_float) { for (j = 0; j < spp; j++) ra[(imageLength * imageWidth * j) + imageLength * (x + xoff) + y + yoff] = (double) ((const float*)v)[j]; } } xoff++; if (xoff >= tileWidth) { xoff -= tileWidth; yoff++; } } /* for i */ } /* PLANARCONFIG_CONTIG */ } /* for x */ } _TIFFfree(buf); PROTECT(res); dim = allocVector(INTSXP, (out_spp > 1) ? 3 : 2); INTEGER(dim)[0] = imageLength; INTEGER(dim)[1] = imageWidth; if (out_spp > 1) INTEGER(dim)[2] = out_spp; setAttrib(res, R_DimSymbol, dim); if (colormap[0] && TYPEOF(res) == INTSXP && indexed) { int nc = 1 << bps, i; SEXP cm = allocMatrix(REALSXP, 3, nc); double *d = REAL(cm); for (i = 0; i < nc; i++) { d[3 * i] = ((double) colormap[0][i]) / 65535.0; d[3 * i + 1] = ((double) colormap[1][i]) / 65535.0; d[3 * i + 2] = ((double) colormap[2][i]) / 65535.0; } setAttr(res, "color.map", cm); } if (add_info) TIFF_add_info(tiff, res); UNPROTECT(1); if (isLogical(sAll) && asInteger(sAll) == 0) { TIFFClose(tiff); return res; } n_img++; if (pick_index >= 0) SET_VECTOR_ELT(pick_res, pick_index, res); else { if (multi_res == R_NilValue) { multi_tail = multi_res = CONS(res, R_NilValue); PROTECT(multi_res); nprot++; } else { SEXP q = CONS(res, R_NilValue); SETCDR(multi_tail, q); multi_tail = q; } } if (!TIFFReadDirectory(tiff)) break; } TIFFClose(tiff); /* if picked, we already have the result list */ if (pick) { UNPROTECT(nprot + 1 /* pick_res is the +1 */); return pick_res; } /* convert LISTSXP into VECSXP */ PROTECT(res = allocVector(VECSXP, n_img)); nprot++; { int i = 0; while (multi_res != R_NilValue) { SET_VECTOR_ELT(res, i, CAR(multi_res)); i++; multi_res = CDR(multi_res); } } UNPROTECT(nprot); return res; } tiff/src/reg.c0000644000175100001440000000113714531222327012733 0ustar hornikusers#include #include #include /* read.c */ extern SEXP read_tiff(SEXP sFn, SEXP sNative, SEXP sAll, SEXP sConvert, SEXP sInfo, SEXP sIndexed, SEXP sOriginal, SEXP sPayload); /* write.c */ extern SEXP write_tiff(SEXP image, SEXP where, SEXP sBPS, SEXP sCompr, SEXP sReduce); static const R_CallMethodDef CAPI[] = { {"read_tiff", (DL_FUNC) &read_tiff , 8}, {"write_tiff", (DL_FUNC) &write_tiff, 5}, {NULL, NULL, 0} }; void R_init_tiff(DllInfo *dll) { R_registerRoutines(dll, NULL, CAPI, NULL, NULL); R_useDynamicSymbols(dll, FALSE); } tiff/src/write.c0000644000175100001440000001765714531222327013326 0ustar hornikusers#include #include #include #include #include "common.h" #include #include #define INIT_SIZE (256 * 1024) #define HAS_ALPHA 0x01 #define IS_GRAY 0x02 #define IS_RGB 0x04 /* if neither GRAY/RGB is set then it's B/W */ int analyze_native(const unsigned int *what, int length) { int alpha = 0, ac = 0, i; for (i = 0; i < length; i++) { if (!alpha && (what[i] & 0xff000000) != 0xff000000) alpha = 1; if (ac < 2 && ((what[i] & 0xff) != ((what[i] >> 8) & 0xff) || (what[i] & 0xff) != ((what[i] >> 16) & 0xff))) ac = 2; if (ac == 0 && (what[i] & 0xffffff) != 0xffffff && (what[i] & 0xffffff)) ac = 1; if (ac == 2 && alpha) break; /* no need to continue */ } return alpha | (ac << 1); } SEXP write_tiff(SEXP image, SEXP where, SEXP sBPS, SEXP sCompr, SEXP sReduce) { SEXP dims, img_list = 0; tiff_job_t rj; TIFF *tiff; FILE *f; int native = 0, raw_array = 0, bps = asInteger(sBPS), compression = asInteger(sCompr), reduce = asInteger(sReduce), img_index = 0, n_img = 1; uint32_t width, height, planes = 1; if (TYPEOF(image) == VECSXP) { if ((n_img = LENGTH(image)) == 0) { Rf_warning("empty image list, nothing to do"); return R_NilValue; } img_list = image; } if (bps != 8 && bps != 16 && bps != 32) Rf_error("currently bits.per.sample must be 8, 16 or 32"); if (TYPEOF(where) == RAWSXP) { rj.alloc = INIT_SIZE; if (!(rj.data = malloc(rj.alloc))) Rf_error("unable to allocate memory for the in-memory output buffer"); rj.len = 0; rj.ptr = 0; rj.f = f = 0; } else { const char *fn; if (TYPEOF(where) != STRSXP || LENGTH(where) < 1) Rf_error("invalid filename"); fn = CHAR(STRING_ELT(where, 0)); f = fopen(fn, "w+b"); if (!f) Rf_error("unable to create %s", fn); rj.f = f; } tiff = TIFF_Open("wm", &rj); if (!tiff) { if (!rj.f) free(rj.data); Rf_error("cannot create TIFF structure"); } while (1) { if (img_list) image = VECTOR_ELT(img_list, img_index++); if (inherits(image, "nativeRaster") && TYPEOF(image) == INTSXP) native = 1; if (TYPEOF(image) == RAWSXP) raw_array = 1; if (!native && !raw_array && TYPEOF(image) != REALSXP) Rf_error("image must be a matrix or array of raw or real numbers"); dims = Rf_getAttrib(image, R_DimSymbol); if (dims == R_NilValue || TYPEOF(dims) != INTSXP || LENGTH(dims) < 2 || LENGTH(dims) > 3) Rf_error("image must be a matrix or an array of two or three dimensions"); if (raw_array && LENGTH(dims) == 3) { /* raw arrays have either bpp, width, height or width, height dimensions */ planes = INTEGER(dims)[0]; width = INTEGER(dims)[1]; height = INTEGER(dims)[2]; } else { /* others have width, height[, bpp] */ width = INTEGER(dims)[1]; height = INTEGER(dims)[0]; if (LENGTH(dims) == 3) planes = INTEGER(dims)[2]; } if (planes < 1 || planes > 4) Rf_error("image must have either 1 (grayscale), 2 (GA), 3 (RGB) or 4 (RGBA) planes"); if (native) { /* nativeRaster should have a "channels" attribute if it has anything else than 4 channels */ SEXP cha = getAttrib(image, install("channels")); if (cha != R_NilValue) { planes = asInteger(cha); if (planes < 1 || planes > 4) planes = 4; } else planes = 4; } if (raw_array) { if (planes != 4) Rf_error("Only RGBA format is supported as raw data"); native = 1; /* from now on we treat raw arrays like native */ } TIFFSetField(tiff, TIFFTAG_IMAGEWIDTH, width); TIFFSetField(tiff, TIFFTAG_IMAGELENGTH, height); TIFFSetField(tiff, TIFFTAG_PLANARCONFIG, 1); TIFFSetField(tiff, TIFFTAG_SOFTWARE, "tiff package, R " R_MAJOR "." R_MINOR); if (native) { TIFFSetField(tiff, TIFFTAG_BITSPERSAMPLE, 8); if (reduce) { int an = analyze_native((const unsigned int*) INTEGER(image), width * height); if (an == (HAS_ALPHA | IS_RGB)) reduce = 0; else { /* we only reduce to RGB, GA or G */ int out_spp = ((an & HAS_ALPHA) ? 1 : 0 ) + ((an & IS_RGB) ? 3 : 1); uint32_t i = 1, n = width * height; tdata_t buf; unsigned char *data8; const unsigned int *nd = (const unsigned int*) INTEGER(image); TIFFSetField(tiff, TIFFTAG_SAMPLESPERPIXEL, out_spp); TIFFSetField(tiff, TIFFTAG_ROWSPERSTRIP, height); TIFFSetField(tiff, TIFFTAG_COMPRESSION, compression); TIFFSetField(tiff, TIFFTAG_PHOTOMETRIC, (out_spp > 2) ? PHOTOMETRIC_RGB : PHOTOMETRIC_MINISBLACK); buf = _TIFFmalloc(width * height * out_spp); data8 = (unsigned char*) buf; if (out_spp == 1) for (i = 0; i < n; i++) /* G */ data8[i] = nd[i] & 255; else if (out_spp == 2) { if (((const char*)&i)[0] == 1) /* little-endian */ for (i = 0; i < n; i++) { /* GA */ *(data8++) = nd[i] & 255; *(data8++) = (nd[i] >> 24) & 255; } else /* big-endian */ for (i = 0; i < n; i++) { /* GA */ *(data8++) = (nd[i] >> 24) & 255; *(data8++) = nd[i] & 255; } } else if (out_spp == 3) { if (((const char*)&i)[0] == 1) /* little-endian */ for (i = 0; i < n; i++) { /* RGB */ *(data8++) = nd[i] & 255; *(data8++) = (nd[i] >> 8) & 255; *(data8++) = (nd[i] >> 16) & 255; } else /* big-endian */ for (i = 0; i < n; i++) { /* RGB */ *(data8++) = (nd[i] >> 16) & 255; *(data8++) = (nd[i] >> 8) & 255; *(data8++) = nd[i] & 255; } } TIFFWriteEncodedStrip(tiff, 0, buf, width * height * out_spp); _TIFFfree(buf); } } if (!reduce) { TIFFSetField(tiff, TIFFTAG_SAMPLESPERPIXEL, 4); TIFFSetField(tiff, TIFFTAG_ROWSPERSTRIP, height); TIFFSetField(tiff, TIFFTAG_COMPRESSION, compression); TIFFSetField(tiff, TIFFTAG_PHOTOMETRIC, PHOTOMETRIC_RGB); TIFFWriteEncodedStrip(tiff, 0, INTEGER(image), width * height * 4); } } else { uint32_t x, y, pl; tdata_t buf; unsigned char *data8; unsigned short *data16; unsigned int *data32; double *ra = REAL(image); uint32_t i, N = LENGTH(image); for (i = 0; i < N; i++) /* do a pre-flight check */ if (ra[i] < 0.0 || ra[i] > 1.0) { Rf_warning("The input contains values outside the [0, 1] range - storage of such values is undefined"); break; } TIFFSetField(tiff, TIFFTAG_BITSPERSAMPLE, bps); TIFFSetField(tiff, TIFFTAG_SAMPLESPERPIXEL, planes); TIFFSetField(tiff, TIFFTAG_ROWSPERSTRIP, height); TIFFSetField(tiff, TIFFTAG_COMPRESSION, compression); TIFFSetField(tiff, TIFFTAG_PHOTOMETRIC, (planes > 2) ? PHOTOMETRIC_RGB : PHOTOMETRIC_MINISBLACK); buf = _TIFFmalloc(width * height * planes * (bps / 8)); data8 = (unsigned char*) buf; data16 = (unsigned short*) buf; data32 = (unsigned int*) buf; if (!buf) Rf_error("cannot allocate output image buffer"); if (bps == 8) for (y = 0; y < height; y++) for (x = 0; x < width; x++) for (pl = 0; pl < planes; pl++) data8[(x + y * width) * planes + pl] = (unsigned char) (ra[y + x * height + pl * width * height] * 255.0); else if (bps == 16) for (y = 0; y < height; y++) for (x = 0; x < width; x++) for (pl = 0; pl < planes; pl++) data16[(x + y * width) * planes + pl] = (unsigned short) (ra[y + x * height + pl * width * height] * 65535.0); else if (bps == 32) for (y = 0; y < height; y++) for (x = 0; x < width; x++) for (pl = 0; pl < planes; pl++) data32[(x + y * width) * planes + pl] = (unsigned int) (ra[y + x * height + pl * width * height] * 4294967295.0); TIFFWriteEncodedStrip(tiff, 0, buf, width * height * planes * (bps / 8)); _TIFFfree(buf); } if (img_list && img_index < n_img) TIFFWriteDirectory(tiff); else break; } if (!rj.f) { SEXP res; TIFFFlush(tiff); res = allocVector(RAWSXP, rj.len); #if TIFF_DEBUG Rprintf("convert to raw %d bytes (ptr=%d, alloc=%d)\n", rj.len, rj.ptr, rj.alloc); #endif memcpy(RAW(res), rj.data, rj.len); TIFFClose(tiff); return res; } TIFFClose(tiff); return ScalarInteger(n_img); } tiff/src/common.c0000644000175100001440000001167714531222327013460 0ustar hornikusers#include "common.h" #include #include #include static int need_init = 1; static char txtbuf[2048]; static TIFF *last_tiff; /* this to avoid leaks */ static void TIFFWarningHandler_(const char* module, const char* fmt, va_list ap) { /* we can't pass it directly since R has no vprintf entry point */ vsnprintf(txtbuf, sizeof(txtbuf), fmt, ap); Rf_warning("%s: %s", module, txtbuf); } static int err_reenter = 0; static void TIFFErrorHandler_(const char* module, const char* fmt, va_list ap) { if (err_reenter) return; /* prevent re-entrance which can happen as TIFF is happy to call another error from Close */ err_reenter = 1; /* FIXME: if TIFFClose below fails we may get stuck without errors!! */ /* we can't pass it directly since R has no vprintf entry point */ vsnprintf(txtbuf, sizeof(txtbuf), fmt, ap); /* we have to close the TIFF that caused it as it will not come back -- recursive calls won't work under errors but that is hopefully unlikely/impossible */ if (last_tiff) TIFFClose(last_tiff); /* this will also reset last_tiff */ err_reenter = 0; Rf_error("%s: %s", module, txtbuf); } static void init_tiff(void) { if (need_init) { TIFFSetWarningHandler(TIFFWarningHandler_); TIFFSetErrorHandler(TIFFErrorHandler_); need_init = 0; } } static tsize_t TIFFReadProc_(thandle_t usr, tdata_t buf, tsize_t length) { tiff_job_t *rj = (tiff_job_t*) usr; tsize_t to_read = length; if (rj->f) return fread(buf, 1, to_read, rj->f); #if TIFF_DEBUG Rprintf("read [@%d %d/%d] -> %d\n", rj->ptr, rj->len, rj->alloc, length); #endif if (to_read > (rj->len - rj->ptr)) to_read = (rj->len - rj->ptr); if (to_read > 0) { memcpy(buf, rj->data + rj->ptr, to_read); rj->ptr += to_read; } return to_read; } static int guarantee_write_buffer(tiff_job_t *rj, long where) { if (where > rj->alloc) { /* need to resize buffer? */ void *new_data; unsigned long new_alloc = rj->alloc; while (new_alloc <= where) new_alloc <<= 1; new_data = realloc(rj->data, new_alloc); if (!new_data) /* FAILED */ return 0; rj->data = new_data; rj->alloc = new_alloc; } return 1; } static tsize_t TIFFWriteProc_(thandle_t usr, tdata_t buf, tsize_t length) { tiff_job_t *rj = (tiff_job_t*) usr; if (rj->f) return (tsize_t) fwrite(buf, 1, length, rj->f); #if TIFF_DEBUG Rprintf("write [@%d %d/%d] <- %d\n", rj->ptr, rj->len, rj->alloc, length); #endif if (!guarantee_write_buffer(rj, rj->ptr + length)) return 0; memcpy(rj->data + rj->ptr, buf, length); rj->ptr += length; if (rj->ptr > rj->len) rj->len = rj->ptr; return length; } static toff_t TIFFSeekProc_(thandle_t usr, toff_t offset, int whence) { tiff_job_t *rj = (tiff_job_t*) usr; if (rj->f) { int e = fseeko(rj->f, offset, whence); if (e != 0) { Rf_warning("fseek failed on a file in TIFFSeekProc"); return -1; } return ftello(rj->f); } #if TIFF_DEBUG Rprintf("seek [@%d %d/%d] %d (%d)\n", rj->ptr, rj->len, rj->alloc, offset, whence); #endif if (whence == SEEK_CUR) offset += rj->ptr; else if (whence == SEEK_END) offset += rj->len; else if (whence != SEEK_SET) { Rf_warning("invalid `whence' argument to TIFFSeekProc callback called by libtiff"); return -1; } if (rj->alloc && rj->len < offset) { if (offset >= rj->alloc) { /* need more space? */ if (!guarantee_write_buffer(rj, offset)) return -1; } else /* enough space but need to zero out */ memset(rj->data + rj->len, 0, offset - rj->len); rj->len = offset; } if (offset < 0 || offset > rj->len) { Rf_warning("libtiff attempted to seek beyond the data end"); return -1; } return (toff_t) (rj->ptr = offset); } static int TIFFCloseProc_(thandle_t usr) { tiff_job_t *rj = (tiff_job_t*) usr; if (rj->f) fclose(rj->f); else if (rj->alloc) { free(rj->data); rj->data = 0; rj->alloc = 0; } last_tiff = 0; return 0; } static toff_t TIFFSizeProc_(thandle_t usr) { tiff_job_t *rj = (tiff_job_t*) usr; if (rj->f) { off_t cur = ftello(rj->f), end; fseek(rj->f, 0, SEEK_END); end = ftello(rj->f); fseeko(rj->f, cur, SEEK_SET); return end; } return (toff_t) rj->len; } static int TIFFMapFileProc_(thandle_t usr, tdata_t* map, toff_t* off) { Rf_warning("libtiff attempted to use TIFFMapFileProc on non-file which is unsupported"); return -1; } static void TIFFUnmapFileProc_(thandle_t usr, tdata_t map, toff_t off) { Rf_warning("libtiff attempted to use TIFFUnmapFileProc on non-file which is unsupported"); } /* actual interface */ TIFF *TIFF_Open(const char *mode, tiff_job_t *rj) { if (need_init) init_tiff(); #if AGGRESSIVE_CLEANUP if (last_tiff) TIFFClose(last_tiff); #endif return (last_tiff = TIFFClientOpen("pkg:tiff", mode, (thandle_t) rj, TIFFReadProc_, TIFFWriteProc_, TIFFSeekProc_, TIFFCloseProc_, TIFFSizeProc_, TIFFMapFileProc_, TIFFUnmapFileProc_) ); } tiff/src/Makevars.win0000644000175100001440000000040114531222327014273 0ustar hornikusersRWINLIB = ../windows/libtiff-4.1.0/mingw$(WIN) PKG_CPPFLAGS = -I$(RWINLIB)/include PKG_LIBS = -L$(RWINLIB)/lib -ltiff -ljpeg -lz all: clean winlibs winlibs: "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" "../tools/winlibs.R" clean: rm -f $(SHLIB) $(OBJECTS) tiff/src/Makevars.ucrt0000644000175100001440000000047414531222327014465 0ustar hornikusersifeq (,$(shell pkg-config --version 2>/dev/null)) LIBSHARPYUV = $(or $(and $(wildcard $(R_TOOLS_SOFT)/lib/libsharpyuv.a),-lsharpyuv),) PKG_LIBS = -ltiff -ljpeg -lz -lzstd -lwebp $(LIBSHARPYUV) -llzma else PKG_LIBS = $(shell pkg-config --libs libtiff-4) endif all: clean clean: rm -f $(SHLIB) $(OBJECTS) tiff/src/common.h0000644000175100001440000000041614531222327013452 0ustar hornikusers#ifndef PKG_TIFF_COMMON_H__ #define PKG_TIFF_COMMON_H__ #include #include #include typedef struct tiff_job { FILE *f; long ptr, len, alloc; char *data; } tiff_job_t; TIFF *TIFF_Open(const char *mode, tiff_job_t *rj); #endif tiff/src/Makevars.in0000644000175100001440000000005014531222327014104 0ustar hornikusersPKG_LIBS=@LIBS@ PKG_CPPFLAGS=@CPPFLAGS@ tiff/NEWS0000644000175100001440000000475314531222327011731 0ustar hornikusersNEWS/Changelog 0.1-12 2023-11-28 o updated Windows flags (#12) o replace () with (void) in a declaration 0.1-11 2022-01-31 o add Windows UCRT support 0.1-10 2021-11-05 o Silence benign warnings in some compilers. 0.1-9 2021-08-13 o bugfix: readTIFF(..., native=TRUE) returned incorrect results when the all parameter was used to pick individual images. (#10) 0.1-8 2021-03-31 o add support for readTIFF(..., payload=FALSE) which only retrieves metadata information from the file -- The following features have been inspired or ported from https://github.com/akoyabio/tiff fork by Kent Johnson: o Add limited support for tiled images. Supports 8-, 16- and 32-bit integer and float images with spp=1 or 3. No support for indexed, color map, as.is, or planar format color. o add the ability to read (or get info on) selected images by passing a vector in the `all` parameter o add width, length, x.position, y.position, and, if available, rows.per.strip, tile.width, tile.length to the directory info returned when `info=TRUE`. o stop with an error if `as.is=TRUE` is used with a float image o fixed documentation typos o writeTIFF() uses path.expand() on supplied path 0.1-7 2021-02-04 o unix: use autoconf to detect libtiff flags to support static builds and optional tiff capabilities o add C-level function registration o minor updates to DESCRIPTION 0.1-5 2013-09-03 o bugfix: output of readTIFF(..., as.is=TRUE) with integer values was shifted by one (i.e., stored integer value x was returned as x + 1) o writeTIFF() now supports 32-bit (integer) output o writeTIFF() issues a warning if the input data range is outside [0, 1] 0.1-4 2013-02-19 o remove debugging output (it is now only shown if tiff is compiled with -DTIFF_DEBUG=1) 0.1-3 2012-11-05 o add support for 12-bit grayscale TIFF images in readTIFF() (Note that 12-bit TIFFs are outside of the standard, so we assume big-endian packing order) o add readTIFF(..., as.is=TRUE) which preserves the integer values used in the TIFF as they are (if applicable) instead of rescaling to reals 0.1-2 2012-08-30 o fixed a bug in writeTIFF() for 16-bit images 0.1-1 2012-08-24 o add readTIFF(..., indexed=TRUE) which return indexed images as color map and an index matrix. o fixed a bug in writing a TIFF file consisting of multiple subimages o prevent TIFF from re-entering error calls 0.1-0 2012-08-04 o first CRAN release tiff/R/0000755000175100001440000000000014531222327011422 5ustar hornikuserstiff/R/read.R0000644000175100001440000000240114531222327012455 0ustar hornikusersreadTIFF <- function(source, native=FALSE, all=FALSE, convert=FALSE, info=FALSE, indexed=FALSE, as.is=FALSE, payload=TRUE) { if (payload) .Call(read_tiff, if (is.raw(source)) source else path.expand(source), native, if (is.numeric(all)) as.integer(all) else all, convert, info, indexed, as.is, TRUE) else { ## for payload=FALSE we have to extract the info from the attributes x <- .Call(read_tiff, if (is.raw(source)) source else path.expand(source), FALSE, if (is.numeric(all)) as.integer(all) else all, FALSE, TRUE, FALSE, FALSE, FALSE) if (is.integer(x)) as.data.frame(attributes(x), stringsAsFactors=FALSE) else { ## fetch tag from each image x <- lapply(x, attributes) ## construct a union of all tags u <- unique(unlist(lapply(x, names))) ## match tags from each image using NA for missing d <- do.call("rbind.data.frame", lapply(x, function(o) { o <- c(o, list(`NA`=NA)) d <- o[match(u, names(o), length(o))] names(d)=u d })) ## clear row names so they are sequential row.names(d) <- NULL d } } } tiff/R/write.R0000644000175100001440000000111514531222327012675 0ustar hornikuserswriteTIFF <- function(what, where, bits.per.sample = 8L, compression = c("LZW", "none", "PackBits", "RLE", "JPEG", "deflate"), reduce = TRUE) { if (!is.numeric(compression) || length(compression) != 1L) { compressions <- c(none=1L, RLE=2L, PackBits=32773L, fax3=3L, fax4=4L, LZW=5L, JPEG=7L, deflate=8L) compression <- match.arg(compression) compression <- compressions[match(compression, names(compressions))] } .Call(write_tiff, what, if (is.raw(where)) where else path.expand(where), bits.per.sample, compression, reduce) } tiff/MD50000644000175100001440000000157614531324160011540 0ustar hornikusers5c7dbf3570bccc39d967b51e7c6b913d *DESCRIPTION 859acc2878dcf689f6f87e8a0fb49db2 *NAMESPACE 475a599f4870ecdbe96db4a60b92e2ad *NEWS aea7b2318135c79490d3613e068b4602 *R/read.R 2b6be5244a4db18f0f8e2cb953446569 *R/write.R 4b24b3df7af69b95e62bc5ebc3f7d2b7 *configure 3e0d087f1526501cae02410692be99fd *configure.ac 39ab4d2a0fc38ce4f556b2f4ce71104e *inst/img/Rlogo.tiff a88de4ef20cfe6bbbf4185a3584067f9 *man/readTIFF.Rd 1246a701cce89e0856ecfa18ad76a273 *man/writeTIFF.Rd 299df8e9b2039f8cda14d88c0570feeb *src/Makevars.in 9f14c7a5a5701ccc4de8fef90afd5bae *src/Makevars.ucrt 839ae60a23783c249b43d20392ed7404 *src/Makevars.win 6c6f6bf403df67f189ead04760e81d82 *src/common.c ca1d1edf6d0f3392afcb3d6ec20c43cc *src/common.h f39cda8fa1e651811450ccd7aadf7241 *src/read.c 64c902cd7021e19cea22a7e2c08cb32d *src/reg.c 6f12dbd9c7535d1f52a3a62fe4bfc314 *src/write.c 995e002271189bab1928d405626865c6 *tools/winlibs.R tiff/inst/0000755000175100001440000000000014531222327012176 5ustar hornikuserstiff/inst/img/0000755000175100001440000000000014531222327012752 5ustar hornikuserstiff/inst/img/Rlogo.tiff0000644000175100001440000003314014531222327014707 0ustar hornikusersMM*5n€ P8$ „BaP¸d6ˆD`ìfCÒi´BOwÃØ<øß’0«úLÊAÒgè Ÿ¯çèúœ=·ÜÑüîP^#¬Gt„‚!'(D%tˆ$GìJ­W¬VkUºåv½_°C“IäÀãgN"×ü˜Y3 ­¯á Íú ”¿À›ÜSÀïRù³îG~âovØzÅÞ¯˜ûìA|à@.gÖ@­ h0Î$‘ɱp°\þ°ìv[=¦×mX`0—À£Y¨+z½^„aþâ_Œž@çôzPn„>øì$o¸,ùÏÇ_ð@õþçäó_äÛ.ÃÏëòLò €Þ¢1ðŒ _õ|!aœ+Š‚ʪÛÁL«åa^UÇ!ÊrgÌ,(9BS¼ Š# ÇCÎŒ>ƺNªÍ/®s¨è¥-ƒê§ä»`‚>njôò²S“GqúLòHok⪸ò<`šHƒ°ª [? Yf 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It has function prototypes and stuff, but not \xHH hex character constants. These do not provoke an error unfortunately, instead are silently treated as an "x". The following induces an error, until -std is added to get proper ANSI mode. Curiously \x00 != x always comes out true, for an array size at least. It is necessary to write \x00 == 0 to get something that is true only with -std. */ int osf4_cc_array ['\''\x00'\'' == 0 ? 1 : -1]; /* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters inside strings and character constants. */ #define FOO(x) '\''x'\'' int xlc6_cc_array[FOO(a) == '\''x'\'' ? 1 : -1]; int test (int i, double x); struct s1 {int (*f) (int a);}; struct s2 {int (*f) (double a);}; int pairnames (int, char **, int *(*)(struct buf *, struct stat *, int), int, int);' # Test code for whether the C compiler supports C89 (body of main). ac_c_conftest_c89_main=' ok |= (argc == 0 || f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]); ' # Test code for whether the C compiler supports C99 (global declarations) ac_c_conftest_c99_globals=' // Does the compiler advertise C99 conformance? #if !defined __STDC_VERSION__ || __STDC_VERSION__ < 199901L # error "Compiler does not advertise C99 conformance" #endif #include extern int puts (const char *); extern int printf (const char *, ...); extern int dprintf (int, const char *, ...); extern void *malloc (size_t); // Check varargs macros. These examples are taken from C99 6.10.3.5. // dprintf is used instead of fprintf to avoid needing to declare // FILE and stderr. #define debug(...) dprintf (2, __VA_ARGS__) #define showlist(...) puts (#__VA_ARGS__) #define report(test,...) ((test) ? puts (#test) : printf (__VA_ARGS__)) static void test_varargs_macros (void) { int x = 1234; int y = 5678; debug ("Flag"); debug ("X = %d\n", x); showlist (The first, second, and third items.); report (x>y, "x is %d but y is %d", x, y); } // Check long long types. #define BIG64 18446744073709551615ull #define BIG32 4294967295ul #define BIG_OK (BIG64 / BIG32 == 4294967297ull && BIG64 % BIG32 == 0) #if !BIG_OK #error "your preprocessor is broken" #endif #if BIG_OK #else #error "your preprocessor is broken" #endif static long long int bignum = -9223372036854775807LL; static unsigned long long int ubignum = BIG64; struct incomplete_array { int datasize; double data[]; }; struct named_init { int number; const wchar_t *name; double average; }; typedef const char *ccp; static inline int test_restrict (ccp restrict text) { // See if C++-style comments work. // Iterate through items via the restricted pointer. // Also check for declarations in for loops. for (unsigned int i = 0; *(text+i) != '\''\0'\''; ++i) continue; return 0; } // Check varargs and va_copy. static bool test_varargs (const char *format, ...) { va_list args; va_start (args, format); va_list args_copy; va_copy (args_copy, args); const char *str = ""; int number = 0; float fnumber = 0; while (*format) { switch (*format++) { case '\''s'\'': // string str = va_arg (args_copy, const char *); break; case '\''d'\'': // int number = va_arg (args_copy, int); break; case '\''f'\'': // float fnumber = va_arg (args_copy, double); break; default: break; } } va_end (args_copy); va_end (args); return *str && number && fnumber; } ' # Test code for whether the C compiler supports C99 (body of main). ac_c_conftest_c99_main=' // Check bool. _Bool success = false; success |= (argc != 0); // Check restrict. if (test_restrict ("String literal") == 0) success = true; char *restrict newvar = "Another string"; // Check varargs. success &= test_varargs ("s, d'\'' f .", "string", 65, 34.234); test_varargs_macros (); // Check flexible array members. struct incomplete_array *ia = malloc (sizeof (struct incomplete_array) + (sizeof (double) * 10)); ia->datasize = 10; for (int i = 0; i < ia->datasize; ++i) ia->data[i] = i * 1.234; // Check named initializers. struct named_init ni = { .number = 34, .name = L"Test wide string", .average = 543.34343, }; ni.number = 58; int dynamic_array[ni.number]; dynamic_array[0] = argv[0][0]; dynamic_array[ni.number - 1] = 543; // work around unused variable warnings ok |= (!success || bignum == 0LL || ubignum == 0uLL || newvar[0] == '\''x'\'' || dynamic_array[ni.number - 1] != 543); ' # Test code for whether the C compiler supports C11 (global declarations) ac_c_conftest_c11_globals=' // Does the compiler advertise C11 conformance? #if !defined __STDC_VERSION__ || __STDC_VERSION__ < 201112L # error "Compiler does not advertise C11 conformance" #endif // Check _Alignas. char _Alignas (double) aligned_as_double; char _Alignas (0) no_special_alignment; extern char aligned_as_int; char _Alignas (0) _Alignas (int) aligned_as_int; // Check _Alignof. enum { int_alignment = _Alignof (int), int_array_alignment = _Alignof (int[100]), char_alignment = _Alignof (char) }; _Static_assert (0 < -_Alignof (int), "_Alignof is signed"); // Check _Noreturn. int _Noreturn does_not_return (void) { for (;;) continue; } // Check _Static_assert. struct test_static_assert { int x; _Static_assert (sizeof (int) <= sizeof (long int), "_Static_assert does not work in struct"); long int y; }; // Check UTF-8 literals. #define u8 syntax error! char const utf8_literal[] = u8"happens to be ASCII" "another string"; // Check duplicate typedefs. typedef long *long_ptr; typedef long int *long_ptr; typedef long_ptr long_ptr; // Anonymous structures and unions -- taken from C11 6.7.2.1 Example 1. struct anonymous { union { struct { int i; int j; }; struct { int k; long int l; } w; }; int m; } v1; ' # Test code for whether the C compiler supports C11 (body of main). ac_c_conftest_c11_main=' _Static_assert ((offsetof (struct anonymous, i) == offsetof (struct anonymous, w.k)), "Anonymous union alignment botch"); v1.i = 2; v1.w.k = 5; ok |= v1.i != 5; ' # Test code for whether the C compiler supports C11 (complete). ac_c_conftest_c11_program="${ac_c_conftest_c89_globals} ${ac_c_conftest_c99_globals} ${ac_c_conftest_c11_globals} int main (int argc, char **argv) { int ok = 0; ${ac_c_conftest_c89_main} ${ac_c_conftest_c99_main} ${ac_c_conftest_c11_main} return ok; } " # Test code for whether the C compiler supports C99 (complete). ac_c_conftest_c99_program="${ac_c_conftest_c89_globals} ${ac_c_conftest_c99_globals} int main (int argc, char **argv) { int ok = 0; ${ac_c_conftest_c89_main} ${ac_c_conftest_c99_main} return ok; } " # Test code for whether the C compiler supports C89 (complete). ac_c_conftest_c89_program="${ac_c_conftest_c89_globals} int main (int argc, char **argv) { int ok = 0; ${ac_c_conftest_c89_main} return ok; } " as_fn_append ac_header_c_list " stdio.h stdio_h HAVE_STDIO_H" as_fn_append ac_header_c_list " stdlib.h stdlib_h HAVE_STDLIB_H" as_fn_append ac_header_c_list " string.h string_h HAVE_STRING_H" as_fn_append ac_header_c_list " inttypes.h inttypes_h HAVE_INTTYPES_H" as_fn_append ac_header_c_list " stdint.h stdint_h HAVE_STDINT_H" as_fn_append ac_header_c_list " strings.h strings_h HAVE_STRINGS_H" as_fn_append ac_header_c_list " sys/stat.h sys_stat_h HAVE_SYS_STAT_H" as_fn_append ac_header_c_list " sys/types.h sys_types_h HAVE_SYS_TYPES_H" as_fn_append ac_header_c_list " unistd.h unistd_h HAVE_UNISTD_H" # Check that the precious variables saved in the cache have kept the same # value. ac_cache_corrupted=false for ac_var in $ac_precious_vars; do eval ac_old_set=\$ac_cv_env_${ac_var}_set eval ac_new_set=\$ac_env_${ac_var}_set eval ac_old_val=\$ac_cv_env_${ac_var}_value eval ac_new_val=\$ac_env_${ac_var}_value case $ac_old_set,$ac_new_set in set,) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5 printf "%s\n" "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;} ac_cache_corrupted=: ;; ,set) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5 printf "%s\n" "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} ac_cache_corrupted=: ;; ,);; *) if test "x$ac_old_val" != "x$ac_new_val"; then # differences in whitespace do not lead to failure. ac_old_val_w=`echo x $ac_old_val` ac_new_val_w=`echo x $ac_new_val` if test "$ac_old_val_w" != "$ac_new_val_w"; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5 printf "%s\n" "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;} ac_cache_corrupted=: else { printf "%s\n" "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5 printf "%s\n" "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;} eval $ac_var=\$ac_old_val fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5 printf "%s\n" "$as_me: former value: \`$ac_old_val'" >&2;} { printf "%s\n" "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5 printf "%s\n" "$as_me: current value: \`$ac_new_val'" >&2;} fi;; esac # Pass precious variables to config.status. if test "$ac_new_set" = set; then case $ac_new_val in *\'*) ac_arg=$ac_var=`printf "%s\n" "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;; *) ac_arg=$ac_var=$ac_new_val ;; esac case " $ac_configure_args " in *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy. *) as_fn_append ac_configure_args " '$ac_arg'" ;; esac fi done if $ac_cache_corrupted; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 printf "%s\n" "$as_me: error: in \`$ac_pwd':" >&2;} { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5 printf "%s\n" "$as_me: error: changes in the environment can compromise the build" >&2;} as_fn_error $? "run \`${MAKE-make} distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5 fi ## -------------------- ## ## Main body of script. ## ## -------------------- ## ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu # find R home and set correct compiler + flags : ${R_HOME="`R RHOME`"} if test -z "${R_HOME}"; then as_fn_error $? "cannot determine R_HOME. Make sure you use R CMD INSTALL!" "$LINENO" 5 fi RBIN="${R_HOME}/bin/R" : ${PKG_MODULE=libtiff-4} # pick all flags for testing from R : ${CC=`"${RBIN}" CMD config CC`} : ${CFLAGS=`"${RBIN}" CMD config CFLAGS`} : ${CPPFLAGS=`"${RBIN}" CMD config CPPFLAGS`} : ${LDFLAGS=`"${RBIN}" CMD config LDFLAGS`} : ${CPP="$CC -E"} # honor PKG_xx overrides LIBS="${LIBS} ${PKG_LIBS}" # for CPPFLAGS we will superfluously double R's flags # since we'll set PKG_CPPFLAGS with this, but that shouldn't hurt CPPFLAGS="${CPPFLAGS} ${PKG_CPPFLAGS}" # Extract the first word of "pkg-config", so it can be a program name with args. set dummy pkg-config; ac_word=$2 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 printf %s "checking for $ac_word... " >&6; } if test ${ac_cv_path_PKG_CONFIG+y} then : printf %s "(cached) " >&6 else $as_nop case $PKG_CONFIG in [\\/]* | ?:[\\/]*) ac_cv_path_PKG_CONFIG="$PKG_CONFIG" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS case $as_dir in #((( '') as_dir=./ ;; */) ;; *) as_dir=$as_dir/ ;; esac for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then ac_cv_path_PKG_CONFIG="$as_dir$ac_word$ac_exec_ext" printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS ;; esac fi PKG_CONFIG=$ac_cv_path_PKG_CONFIG if test -n "$PKG_CONFIG"; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $PKG_CONFIG" >&5 printf "%s\n" "$PKG_CONFIG" >&6; } else { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } fi ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args. set dummy ${ac_tool_prefix}gcc; ac_word=$2 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 printf %s "checking for $ac_word... " >&6; } if test ${ac_cv_prog_CC+y} then : printf %s "(cached) " >&6 else $as_nop if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS case $as_dir in #((( '') as_dir=./ ;; */) ;; *) as_dir=$as_dir/ ;; esac for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then ac_cv_prog_CC="${ac_tool_prefix}gcc" printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 printf "%s\n" "$CC" >&6; } else { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } fi fi if test -z "$ac_cv_prog_CC"; then ac_ct_CC=$CC # Extract the first word of "gcc", so it can be a program name with args. set dummy gcc; ac_word=$2 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 printf %s "checking for $ac_word... " >&6; } if test ${ac_cv_prog_ac_ct_CC+y} then : printf %s "(cached) " >&6 else $as_nop if test -n "$ac_ct_CC"; then ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS case $as_dir in #((( '') as_dir=./ ;; */) ;; *) as_dir=$as_dir/ ;; esac for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_CC="gcc" printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 printf "%s\n" "$ac_ct_CC" >&6; } else { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } fi if test "x$ac_ct_CC" = x; then CC="" else case $cross_compiling:$ac_tool_warned in yes:) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 printf "%s\n" "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac CC=$ac_ct_CC fi else CC="$ac_cv_prog_CC" fi if test -z "$CC"; then if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. set dummy ${ac_tool_prefix}cc; ac_word=$2 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 printf %s "checking for $ac_word... " >&6; } if test ${ac_cv_prog_CC+y} then : printf %s "(cached) " >&6 else $as_nop if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS case $as_dir in #((( '') as_dir=./ ;; */) ;; *) as_dir=$as_dir/ ;; esac for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then ac_cv_prog_CC="${ac_tool_prefix}cc" printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 printf "%s\n" "$CC" >&6; } else { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } fi fi fi if test -z "$CC"; then # Extract the first word of "cc", so it can be a program name with args. set dummy cc; ac_word=$2 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 printf %s "checking for $ac_word... " >&6; } if test ${ac_cv_prog_CC+y} then : printf %s "(cached) " >&6 else $as_nop if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. else ac_prog_rejected=no as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS case $as_dir in #((( '') as_dir=./ ;; */) ;; *) as_dir=$as_dir/ ;; esac for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then if test "$as_dir$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then ac_prog_rejected=yes continue fi ac_cv_prog_CC="cc" printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS if test $ac_prog_rejected = yes; then # We found a bogon in the path, so make sure we never use it. set dummy $ac_cv_prog_CC shift if test $# != 0; then # We chose a different compiler from the bogus one. # However, it has the same basename, so the bogon will be chosen # first if we set CC to just the basename; use the full file name. shift ac_cv_prog_CC="$as_dir$ac_word${1+' '}$@" fi fi fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 printf "%s\n" "$CC" >&6; } else { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } fi fi if test -z "$CC"; then if test -n "$ac_tool_prefix"; then for ac_prog in cl.exe do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 printf %s "checking for $ac_word... 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