R/RcppExports.R

In IFC: Tools for Imaging Flow Cytometry

# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

#' @title Get Current Compilation Bits Depth
#' @name cpp_getBits
#' @description
#' Retrieve size of std::size_t.
#' @return an unsigned integer
#' @keywords internal
NULL

#' @title Spatial Offsets Image Correction
#' @name cpp_align
#' @description
#' This function uses bilinear interpolation to apply spatial offset correction on image
#' @param mat, a NumericMatrix.
#' @param dx, a double x spatial offset. It has to be within ]-1,+1[. Default is NA_REAL for no change.
#' @param dy, a double y spatial offset. It has to be within ]-1,+1[. Default is NA_REAL for no change.
#' @details It is intended to be applied on raw images matrices from .rif files so has to generate spatial offset corrected image matrices.\cr
#' See William E. Ortyn et al. Sensitivity Measurement and Compensation in Spectral Imaging. Cytometry A 69 852-862 (2006).
#' \doi{10.1002/cyto.a.20306}
#' @return a NumericMatrix.
#' @keywords internal
NULL

#' @title Input Parameters Assertive Tool
#' @name cpp_assert
#' @description
#' Ensures that x respects several parameters
#' @param len IntegerVector, of allowed length for x. Default is NULL, for not checking this parameter.
#' @param cla CharacterVector, of allowed classes of x. Default is NULL, for not checking this parameter.
#' @param typ CharacterVector, of allowed types of x. Default is NULL, for not checking this parameter.
#' @param Robject of allowed values for x (will be passed to cpp_allowed). Default is NULL, for not checking this parameter.
#' @param fun CharacterVector, function to execute when mandatory parameters are not met. Default is "stop". Allowed are "stop","warning","message","return".
#' fun is placed in cpp_assert() in order to check it is correct before being used in assert() function.
#' @keywords internal
NULL

#' @title Ellipse Boundaries to Coordinates
#' @name cpp_ell_coord
#' @description
#' Transforms ellipse boundaries to usefull coordinates.
#' @param bound_x NumericVector, x-boundaries of the ellipse.
#' @param bound_y NumericVector, y-boundaries of the ellipse.
#' @keywords internal
NULL

#' @title Point in Gate
#' @name cpp_pnt_in_gate
#' @description
#' This function checks if points lie in a polygon or ellipse.
#' @param pnts NumericMatrix, a 2-columns matrix with (x and y) coordinates of the points of interest.
#' @param gate NumericMatrix, a 2-columns matrix defining polygon vertices or ellipse boundaries.
#' @param algorithm int, used for computation. Default is 1.\cr
#' 1: Trigonometry.\cr
#' 2: Special case = axes-aligned rectangle.\cr
#' 3: Special case = axes-aligned ellipse.
#' @param epsilon double, epsilon threshold value. Default is 0.000000000001
#' @keywords internal
NULL

#' @title Multiple Pattern Fixed Matching
#' @name cpp_mpfmatch
#' @description
#' String matching with multiple pattern.
#' @param x,pattern Nullable Rcpp CharacterVector.
#' @details equivalent of as.logical(sum(unlist(lapply(pattern, grepl, x = x, fixed = TRUE)))).
#' @return a bool
#' @keywords internal
NULL

#' @title Sequence of Strings Matching
#' @name cpp_seqmatch
#' @description
#' Match a sequence of strings in another string
#' @param x,y StringVector to match
#' @details smallest sequence will be searched into the largest one.
#' @return the index (starting at 1) when a match has been found. Otherwise 0.
#' @keywords internal
NULL

#' @title Use Rcpp to Apply Any on Matrix Rows
#' @name cpp_fast_rowAny
#' @description
#' Computes any across matrix rows.
#' @param M_ a Nullable LogicalVector. /!\ But cast to LogicalMatrix
#' @return a LogicalVector.
#' @keywords internal
NULL

#' @title Use Rcpp to Apply Any on List members
#' @name cpp_fast_listAny
#' @description
#' Computes any across list members
#' @param L_ a Nullable List.
#' @return a LogicalVector.
#' @keywords internal
NULL

#' @title Use Rcpp for Range
#' @name cpp_fast_range
#' @description
#' Determines range of numeric vector
#' @param x_ a Nullable NumericVector.
#' @details the behaviour is the same as R base::range(x_, na.rm = TRUE, finite = TRUE) without creating warnings
#' @return a NumericVector.
#' @keywords internal
NULL

#' @title Use Rcpp for Sampling
#' @name cpp_fast_sample
#' @description
#' Create a sample of integers
#' @param n a R_len_t, max number integers to choose from.
#' @param size a R_len_t the desired size of return integers.
#' @param replace a bool determining if sampling should be done with replacement. Default is false.
#' @keywords internal
NULL

#' @title Get Bytes Order
#' @name cpp_get_bytes_order
#' @description
#' This function expands bytes order to the whole data
#' @param obj number of objects in the data.
#' @param byt_ IntegerVector of number of bytes to take from 'ord_'.
#' @param ord_ IntegerVector bytes order. 
#' @param rev bool whether to reverse order or not. Default is false.
#' @keywords internal
NULL

#' @title Non Finite Values Replacement
#' @name cpp_replace_non_finite
#' @description
#' This function replaces non finite values (NA, NaN -Inf and +Inf)
#' @param V_ a NumericVector.
#' @param by a double used as replcaement value. Default is 0.0
#' @keywords internal
NULL

#' @title Gamma Computation
#' @name cpp_computeGamma
#' @description
#' This function computes image gamma transformation value.
#' @param V named NumericVector of channel display properties containing 'xmin', 'xmax', 'xmid' and 'ymid'.
#' @keywords internal
NULL

#' @title Raw to Base64 Conversion
#' @name cpp_base64_encode
#' @description
#' Converts a raw vector to base64 string.
#' @param x RawVector.
#' @return a string, representing the base64 encoding of x.
#' @keywords internal
NULL

#' @title BMP Writer
#' @name cpp_writeBMP
#' @description
#' Transforms 3D [0,1] image to uncompressed bmp
#' @param image, a [0,1] normalized image matrix or 3D array. If 3D array, 3rd dimension should be of length 1 or 3.
#' @keywords internal
NULL

#' @title TIFF Checker
#' @name cpp_checkTIFF
#' @description
#' Checks if file is a TIFF.
#' @details If file is a TIFF it returns endianness of file, 'big' or 'little.
#' Otherwise, it shows an error and returns an empty string.
#' @param fname string, path to file.
#' @source TIFF 6.0 specifications archived from web \url{https://web.archive.org/web/20211209104854/https://www.adobe.io/open/standards/TIFF.html}
#' @keywords internal
NULL

#' @title IFC_offsets Computation without Id Determination
#' @name cpp_getoffsets_noid
#' @description
#' Returns offsets of the IFDs (Image Field Directory) within a TIFF file.
#' @param fname string, path to file.
#' @param obj_count R_len_t, numbers of objects present in the file. Default is 0.
#' If obj_count <= 0 then progress_bar is forced to false.
#' @param display_progress bool, whether to display a progress bar. Default is false.
#' @param pb a List of class `IFC_progress` containing a progress bar of class `txtProgressBar`, `winProgressBar` or `Progress`. Default is R_Nilvalue.
#' @param verbose bool, whether to display information (use for debugging purpose). Default is false.
#' @source TIFF 6.0 specifications archived from web \url{https://web.archive.org/web/20211209104854/https://www.adobe.io/open/standards/TIFF.html}
#' @return an numeric vector with offsets of IFDs found.
#' @keywords internal
NULL

#' @title IFD Tags Extraction
#' @name cpp_getTAGS
#' @description
#' Returns TAGS contained within an IFD (Image Field Directory) entry.
#' @param fname string, path to file.
#' @param offset std::size_t, position of the IFD beginning.
#' @param verbose bool, whether to display information (use for debugging purpose). Default is 'false'.
#' @param trunc_bytes uint32_t maximal number of individual scalar to extract BYTE/ASCII/SBYTE/UNDEFINED for TAGS (1, 2, 6 or 7). Default is 12.\cr
#' However, if less is found, less is returned in map.
#' Note that, if 0 is provided, it will be automatically set to 1.
#' @param force_trunc whether to force truncation for all TAGS types. Default is FALSE.\cr
#' If 'true', 'trunc_bytes' will be used for TAGS (3, 4, 5, 8, 9, 10, 11 and 12) to extract desired number of individual scalar corresponding to each types.
#' @source TIFF 6.0 specifications archived from web \url{https://web.archive.org/web/20211209104854/https://www.adobe.io/open/standards/TIFF.html}
#' @keywords internal
NULL

#' @title IFD Fast Tags Extraction
#' @name cpp_fastTAGS
#' @description
#' Returns TAGS contained within an IFD (Image Field Directory) entry.
#' @param fname string, path to file.
#' @param offset std::size_t, position of the IFD beginning.
#' @param swap bool, whether to swap bytes or not. Default is 'false'.
#' @source TIFF 6.0 specifications archived from web \url{https://web.archive.org/web/20211209104854/https://www.adobe.io/open/standards/TIFF.html}
#' @keywords internal
NULL

#' @title IFC_offsets Computation with Object Identification
#' @name cpp_getoffsets_wid
#' @description
#' Returns offsets of the IFD (Image Field Directory) within a TIFF file.
#' @param fname string, path to file.
#' @param obj_count R_len_t, numbers of objects present in the file. Default is 0.
#' If obj_count <= 0 then progress_bar is forced to false.
#' @param display_progress bool, whether to display a progress bar. Default is false.
#' @param pb a List of class `IFC_progress` containing a progress bar of class `txtProgressBar`, `winProgressBar` or `Progress`. Default is R_Nilvalue.
#' @param verbose bool, whether to display information (use for debugging purpose). Default is false.
#' @source TIFF 6.0 specifications archived from web \url{https://web.archive.org/web/20211209104854/https://www.adobe.io/open/standards/TIFF.html}
#' @return a list of numeric vectors with OBJECT_ID, TYPE and OFFSET of IFDs found.
#' @keywords internal
NULL

#' @title Checksum for RIF/CIF
#' @name cpp_checksum
#' @description
#' Computes sum of img IFDs (Image Field Directory) offsets of objects 0, 1, 2, 3 and 4.
#' @param fname string, path to file.
#' @source TIFF 6.0 specifications archived from web \url{https://web.archive.org/web/20211209104854/https://www.adobe.io/open/standards/TIFF.html}
#' @keywords internal
NULL

#' @title Matrix HSV to RGB Conversion
#' @name cpp_M_HSV2RGB
#' @description
#' Converts grayscale [0,1] mat to 3D rgb array according to hsv space.
#' hue and saturation determines tint whereas v is given by each element of mat
#' @param mat NumericMatrix, [0,1].
#' @param h double, [0,1], hue. Default is 0.0
#' @param s double, [0,1], saturation. Default is 0.0
#' @return a NumericVector with 3 dimensions attribute i.e. a 3D array
#' - 1st Dim is matrix rows count,
#' - 2nd Dim is matrix cols count,
#' - 3rd Dim is RGB
#' @keywords internal
NULL

#' @title Smooth LinLog Transformation with Rcpp
#' @name cpp_smoothLinLog
#' @description
#' Takes a numeric vector and return its transformation:
#' - to linear, if abs(x) < hyper.
#' - to log, if abs(x) > hyper.
#' @param x NumericVector.
#' @param hyper double, value where transition between Lin/Log is applied.
#' @param base double, base of Log scale.
#' @param lin_comp double, value that is used to smooth transition between Lin/Log.
#' @keywords internal
NULL

#' @title Inverse Smooth LinLog Transformation with Rcpp
#' @name cpp_inv_smoothLinLog
#' @description
#' Takes a numeric vector and return its transformation:
#' - to linear, if abs(x) < log(base) / lin_comp.
#' - to exp, if abs(x) > log(base) / lin_comp.
#' @param x NumericVector.
#' @param hyper double, value where transition between Lin/Log is applied.
#' @param base double, base of Log scale.
#' @param lin_comp double, value that is used to smooth transition between Lin/Log.
#' @keywords internal
NULL

#' @title Uint32 to Raw Conversion
#' @name cpp_uint32_to_raw
#' @description
#' Converts unsigned 32bits integer to raw
#' @param x uint32_t.
#' @keywords internal
NULL

#' @title Int32 to Uint32 32bits Conversion
#' @name cpp_int32_to_uint32
#' @description
#' Converts 32bits integer from signed to unsigned
#' @param x int32_t.
#' @keywords internal
NULL

#' @title Offset to Raw Conversion
#' @name cpp_offset_to_raw
#' @description
#' Converts offset to raw
#' @param x double.
#' @param swap bool, whether to swap or not.
#' @keywords internal
NULL

#' @title Offset to Raw Conversion
#' @name cpp_raw_to_offset
#' @description
#' Converts raw to offset
#' @param x RawVector.
#' @param swap bool, whether to swap or not.
#' @keywords internal
NULL

#' @title Uint32 to Int32 32bits Conversion
#' @name cpp_uint32_to_int32
#' @description
#' Converts 32bits integer from unsigned to signed
#' @param x uint32_t.
#' @keywords internal
NULL

#' @title Int64 to Uint64 64bits Conversion
#' @name cpp_int64_to_uint64
#' @description
#' Converts 64bits integer from signed to unsigned
#' @param x int64_t.
#' @keywords internal
NULL

#' @title Uint64 to Int64 64bits Conversion
#' @name cpp_uint64_to_int64
#' @description
#' Converts 64bits integer from unsigned to signed
#' @param x uint64_t.
#' @keywords internal
NULL

#' @title Vectorize Int32 to Uint32 32bits Conversion
#' @name cpp_v_int32_to_uint32
#' @description
#' Converts 32bits vector of integers from unsigned to signed
#' @param V a NumericVector
#' @keywords internal
NULL

#' @title Vectorize Int64 to Uint64 64bits Conversion
#' @name cpp_v_int64_to_uint64
#' @description
#' Converts 64bits vector of integers from unsigned to signed
#' @param V a NumericVector
#' @keywords internal
NULL

#' @title File Scanner
#' @name cpp_scanFirst
#' @description
#' Scans file for 1st occurence of a target string.
#' If found, it returns the position in bytes of the target.
#' Otherwise, it returns 0.
#' @param fname string, path to file.
#' @param raw a Rcpp::RawVector, exact target to be searched for. When converted to string it should be of at least 1 character and not exceed 1024 characters.
#' @param start size_t, position where to begin search.
#' It can't be superior or equal than file size or end (when end is different from 0 and inferior than file size).
#' @param end size_t, position where to stop searching. Default is 0.
#' Search will end up at this position unless it is higher than file size.
#' In such case, search will end up when file end will be reached.
#' @param buf_size uint8_t, size of buffer used to search for target (in kilo-Bytes, will be forced to be between 2 and 1024). Default is 64.
#' @return size_t index of first target character found within target plus 1 or 0 if not found.
#' @keywords internal
NULL

#' @title Fast Factorize Vector
#' @name cpp_fast_factor
#' @description
#' Makes factor with Rcpp
#' @param x a SEXP only NILSXP, LGLSXP, INTSXP, REALSXP, STRSXP, RAWSXP are handled.
#' @param handleNA a bool specifying if NA should be returned as NA or if they should be attributed a unique integer.
#' @details returned object should not be of class `factor` so has to prevent malformed factor' error when printing the result in R.
#' For this reason, it is aimed to be wrap in an R function to handle factor class / handleNA balance.\cr
#' e.g. either:
#' - structure(cpp_fast_factor(df, TRUE), class = "factor"), or,
#' - structure(cpp_fast_factor(unclass(df), FALSE), levels = NULL)
#' @source adaptation from Kevin Ushey code \url{https://gallery.rcpp.org/articles/fast-factor-generation/}
#' @return an IntegerVector, with attributes "levels" being the non-NA unique value(s) found
#' and "lvs" the total number of unique values found (including NA).
#' @keywords internal
NULL

#' @title Data Frame Merge Groups with Rcpp
#' @name cpp_group_df
#' @description
#' Computes global grouping factor from data.frame columns
#' @param df a DataFrame.
#' @return an IntegerVector with the resulting global grouping factor and a "table" attribute representing the amount of scalar in each resulting level.
#' @keywords internal
NULL

#' @title Coordinates to Pixels
#' @name cpp_coord_to_px
#' @description low-level function to compute pixels coordinates
#' @param x NumericVector of x-coordinates of the points.
#' @param y NumericVector of y-coordinates of the points.
#' @param param NumericVector of parameters to scale raw points coordinates to pixels coordinates.
#' @return a 2 columns NumericMatrix of x and y pixels coordinates.
#' @keywords internal
NULL

#' @title Image to Native Raster Conversion
#' @name cpp_as_nativeRaster
#' @description Converts 3D image array to nativeRaster
#' @param x an IntegerVecter /!\ It should be coercible to 3D array [height, width, rgba]
#' @return a nativeRaster IntegerMatrix
#' @keywords internal
NULL

#' @title Draw Shape to Image
#' @name cpp_draw
#' @description low-level function to add shape on image
#' @param img an IntegerVector. A non null array of dimensions [nrow, ncol, 4].
#' @param coords an IntegerMatrix whose rows are points to draw and with:\cr
#' - 1st column being img col coordinate in px,\cr
#' - 2nd column being img row coordinate in px.
#' @param mask a LogicalMatrix where every true value will be added to the image.
#' @param color, a 4 rows IntegerMatrix specifying rgba, from 0 to 255.
#' @param blur_size, a R_len_t the size of the gaussian blurring kernel. Default is 9.
#' @param blur_sd, a double the sd of the gaussian blurring kernel. Default is 3.0.
#' @details shape according to 'mask' will be drawn on 'img' centered at coordinates coords[, 1], coords[, 0]
#' and every pixels being part of the shape will be filled with 'color'.
#' If only one 'color' is provided, this 'color' will be used for each points.
#' If more than one 'color' is provided, then if number of colors (ncol) equals the number of points 'color' will be used as is for each single point.
#' Otherwise, 'color' will be considered as a color-gradient and density will be computed.
#' /!\ please note that IFC:::densCols() is faster to compute color based on density for n < 20000 points, so it's worth using it when number of points are lower.
#' @keywords internal
#' @return /!\ nothing is returned but img is modified in-place
NULL

#' @title Raster Image
#' @name cpp_raster
#' @description low-level function to create plot raster
#' @param width a uint16_t determining the returned image width.
#' @param height a uint16_t determining the returned image height.
#' @param obj a List containing drawing information:\cr
#' - pch, an integer specifying a symbol to draw. Handled are [0-20]. Otherwise only a pixel will be drawn.\cr
#' - size, an integer specifying the size in pixel of the shape, from 1 to 255.\cr
#' - color a 4 rows IntegerMatrix (rgba) of the color used to draw the shape.\cr
#' - coords, an IntegerMatrix whose rows are points to draw and with:\cr
#' -* 1st column being img col coordinate in px,\cr
#' -* 2nd column being img row coordinate in px.
#' - blur_size an integer controlling the size of the blurring gaussian kernel.\cr
#' - blur_sd a double controlling the sd of the blurring gaussian kernel.
#' @param bg_ a Nullable IntegerVector that will be cast to 3D array when not NULL. Default is R_NilValue.\cr
#' When not NULL, its dimensions should be the same as required by 'width' and 'height', otherwise an error will be thrown.\cr
#' When not NULL, it will serve as a background to draw new points on top of it.
#' @details shape according to 'pch' will be drawn centered at coordinates obj$coord[, 1], obj$coord[, 0]
#' and every pixels being part of the shape will be filled with 'color'.
#' If only one 'color' is provided, this 'color' will be used for each points.
#' If more than one 'color' is provided, then if number of colors (ncol) equals the number of points 'color' will be used as is for each single point.
#' Otherwise, 'color' will be considered as a color-gradient and density will be computed.
#' /!\ please note that IFC:::densCols() is faster to compute color based on density for n < 20000 points, so it's worth using it when number of points are lower.
#' @return an IntegerVector with dimensions [height, width, 4]
#' @keywords internal
NULL

#' @title Matrix Cropping
#' @name cpp_crop
#' @description
#' Crops mat according to new_height and new_width parameters.
#' @param mat a numeric matrix.
#' @param new_height an unsigned integer, giving the new height of returned mat. Default is 0 for no change.
#' @param new_width an unsigned integer, giving the new width of returned mat. Default is 0 for no change.
#' @return a cropped matrix.
#' @keywords internal
NULL

#' @title Matrix Resizing
#' @name cpp_resize
#' @description
#' Resizes mat according to new_height and new_width parameters.
#' @param mat a numeric matrix.
#' @param new_height an unsigned integer, giving the new height of returned mat. Default is 0 for no change.
#' @param new_width an unsigned integer, giving the new width of returned mat. Default is 0 for no change.
#' @param add_noise logical, if true adds normal noise when at least one new dimension is larger than original mat dimensions 
#' Rcpp::rnorm() function is used. Default is true.
#' @param bg double, mean value of the background added if add_noise is true. Default is 0.
#' @param sd double, standard deviation of the background added if add_noise is true. Default is 0.
#' @return a resized matrix with padding background if new_height or new_width is larger than original mat dimensions.
#' @keywords internal
NULL

#' @title IFC_object Decompression
#' @name cpp_decomp
#' @description
#' Operates decompression of compressed image stored in TIFF file.
#' @param fname string, path to file.
#' @param offset std::size_t, position of the beginning of compressed image.
#' @param nbytes uint32_t, number of bytes of compressed image.
#' @param imgWidth R_len_t, Width of the decompressed image. Default is 1.
#' @param imgHeight R_len_t, Height of the decompressed image. Default is 1.
#' @param nb_channels R_len_t, number of channels of the decompressed image. Default is 1.
#' @param removal uint8_t, object removal method. Only apply for 30818 compression. Default is 0.\cr
#' -1, for clipped removal: height OR width clipped pixels will be set to -1.\cr
#' -2, height clipped removal: height clipped pixels will be set to -1.\cr
#' -3, width clipped removal: width clipped pixels will be set to -1.\cr
#' -4, only keep background: background pixels will be set to 1 and all others to 0.\cr
#' -5, only keep foreground: foreground pixels will be set to 1 and all others to 0.
#' @param compression uint32_t, compression algorithm used. Default is 30818.
#' @param verbose bool, whether to display information (use for debugging purpose). Default is false.
#' @source For image decompression, Lee Kamentsky's code porting from \url{https://github.com/ome/bioformats/blob/4146b9a1797501f0fec7d6cfe69124959bff96ee/components/formats-bsd/src/loci/formats/in/FlowSightReader.java}\cr
#' cited in \url{https://linkinghub.elsevier.com/retrieve/pii/S1046-2023(16)30291-2}\cr
#' \verb{
#' BSD implementations of Bio-Formats readers and writers
#' %%
#' Copyright (C) 2005 - 2017 Open Microscopy Environment:
#'   - Board of Regents of the University of Wisconsin-Madison
#'   - Glencoe Software, Inc.
#'   - University of Dundee
#' %%
#' Redistribution and use in source and binary forms, with or without
#' modification, are permitted provided that the following conditions are met:
#' 
#' 1. Redistributions of source code must retain the above copyright notice,
#'    this list of conditions and the following disclaimer.
#' 2. Redistributions in binary form must reproduce the above copyright notice,
#'    this list of conditions and the following disclaimer in the documentation
#'    and/or other materials provided with the distribution.
#' 
#' THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
#' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
#' IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
#' ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
#' LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
#' CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
#' SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
#' INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
#' CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
#' ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
#' POSSIBILITY OF SUCH DAMAGE.
#' }
#' @keywords internal
NULL

#' @title IFC_object Decompression to RAW
#' @name cpp_rawdecomp
#' @description
#' Operates decompression to raw of compressed image stored in TIFF file.
#' @param fname string, path to file.
#' @param offset std::size_t, position of the beginning of compressed image.
#' @param nbytes uint32_t, number of bytes of compressed image.
#' @param imgWidth uint32_t, Width of the decompressed image. Default is 1.
#' @param imgHeight uint32_t, Height of the decompressed image. Default is 1.
#' @param compression uint32_t, compression algorithm used. Default is 30818.
#' @param swap bool, whether to swap bytes or not. Default is false.
#' @param verbose bool, whether to display information (use for debugging purpose). Default is false.
#' @source For image decompression, Lee Kamentsky's code porting from \url{https://github.com/ome/bioformats/blob/4146b9a1797501f0fec7d6cfe69124959bff96ee/components/formats-bsd/src/loci/formats/in/FlowSightReader.java}\cr
#' cited in \url{https://linkinghub.elsevier.com/retrieve/pii/S1046-2023(16)30291-2}\cr
#' \verb{
#' BSD implementations of Bio-Formats readers and writers
#' %%
#' Copyright (C) 2005 - 2017 Open Microscopy Environment:
#'   - Board of Regents of the University of Wisconsin-Madison
#'   - Glencoe Software, Inc.
#'   - University of Dundee
#' %%
#' Redistribution and use in source and binary forms, with or without
#' modification, are permitted provided that the following conditions are met:
#' 
#' 1. Redistributions of source code must retain the above copyright notice,
#'    this list of conditions and the following disclaimer.
#' 2. Redistributions in binary form must reproduce the above copyright notice,
#'    this list of conditions and the following disclaimer in the documentation
#'    and/or other materials provided with the distribution.
#' 
#' THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
#' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
#' IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
#' ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
#' LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
#' CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
#' SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
#' INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
#' CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
#' ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
#' POSSIBILITY OF SUCH DAMAGE.
#' }
#' @keywords internal
NULL

#' @title Matrix Normalization
#' @name cpp_normalize
#' @description
#' Normalizes a finite matrix to [0,1]
#' @param mat a finite NumericMatrix.
#' @param input_range a finite NumericVector, sets the range of the input intensity values. Values outside this range are clipped. Default is \code{[0.0,4095.0]}.
#' @param full_range if \code{'full_range'} is \code{true}, then \code{'input_range'} will be set to \code{[0.0,4095.0]} and \code{'gamma'} forced to \code{1.0}. Default is \code{false}.
#' @param force_range if \code{'force_range'} is \code{true}, then \code{'input_range'} will be adjusted to \code{'mat'} range in \code{[-4095.0, +inf]} and \code{'gamma'} forced to \code{1.0}. Default is \code{false}.\cr
#' Note that this parameter takes the precedence over \code{'input_range'} and \code{'full_range'}.
#' @param gamma correction. Default is \code{1.0}, for no correction.
#' @keywords internal
NULL

#' @title Matrix Cleanser
#' @name cpp_cleanse
#' @description
#' Replaces values in matrix mat according to mask msk.
#' Depending of \code{'add_noise'} parameter, values of \code{'mat'} will be replaced with noise or not.
#' @param mat a NumericMatrix.
#' @param msk a IntegerMatrix.
#' @param add_noise bool, whether to add normal noise or not, \code{Rcpp::Rf_rnorm(bg, sd)} function is used. Default is \code{true}.
#' @param bg double, mean value of the background added if \code{'add_noise'} is \code{true}. Default is \code{0.0}.
#' @param sd double, standard deviation of the background added if \code{'add_noise'} is \code{true}. Default is \code{0.0}.
#' @return a NumericMatrix cleansed according to \code{'msk'}.
#' @keywords internal
NULL

#' @title Equal Sized Matrix to Matrix Writer According to Mask
#' @name cpp_mask
#' @description
#' Writes matrix \code{'B'} in matrix \code{'A'} according to \code{'mask'}.
#' If \code{'mask'} is not \code{0.0} \code{'B'} is written, \code{'A'} otherwise.
#' @param A a NumericMatrix.
#' @param B a NumericMatrix.
#' @param mask a NumericMatrix.
#' @keywords internal
NULL

#' @title Matrix to Matrix Writer According to Mask with Offsets
#' @name cpp_mark
#' @description
#' Writes matrix \code{'B'} in matrix \code{'A'} according to \code{'mask'}.
#' @param A a NumericMatrix.
#' @param B a NumericMatrix.
#' @param mask a NumericMatrix.
#' @param xoff x offset in \code{'A'} to start writing \code{'B'}.
#' @param yoff x offset in \code{'A'} to start writing \code{'B'}.
#' @param invert a logical. Default is \code{false}.
#' When \code{false}, the default, values of \code{'B'} are written into \code{'A'} when \code{'mask'} is not \code{0.0}.
#' When \code{true}, values of '\code{1-B}' are written into \code{'A'} when \code{'mask'} is not \code{0.0}.
#' @keywords internal
NULL

#' @title Matrix Transformation
#' @name cpp_transform
#' @description
#' Function to normalize, colorize and add background to images.
#' @param mat NumericMatrix.
#' @param color NumericVector, whose members are h,s,v color.
#' This vector has to be named with 1st name being the name of this color.
#' @param msk IntegerMatrix.
#' @param size a length 2 IntegerVector, of final dimensions (height,width) of the image. Default is \code{0,0} for no change.
#' @param mode string, color mode export. Either \code{"rgb"}, \code{"gray"} or \code{"raw"}. Default is \code{"raw"}.
#' @param type uint16_t image object type. Default is \code{2}.
#' @param input_range a finite NumericVector, only apply when \code{'mode'} is not \code{"raw"}, sets the range of the input intensity values. Values outside this range are clipped. Default is \code{[0.0,4095.0]}.
#' @param add_noise bool, whether to add normal noise or not. Default is \code{true}.
#' @param bg double, mean value of the background added if \code{'add_noise'} is \code{true}. Default is \code{0.0}.
#' @param sd double, standard deviation of the background added if \code{'add_noise'} is \code{true}. Default is \code{0.0}.
#' @param full_range bool, only apply when \code{'mode'} is not \code{"raw"}, if \code{'full_range'} is \code{true}, then \code{'input_range'} will be set to \code{[0.0,4095.0]} and \code{'gamma'} forced to \code{1.0}. Default is \code{false}.
#' @param force_range bool, only apply when \code{'mode'} is not \code{"raw"}, if \code{'force_range'} is \code{true}, then \code{'input_range'} will be adjusted to object range in \code{[-4095.0, +inf]} and \code{'gamma'} forced to \code{1.0}. Default is \code{false}.\cr
#' Note that this parameter takes the precedence over \code{'input_range'} and \code{'full_range'}.
#' @param gamma correction. Default is \code{1.0}, for no correction.
#' @param spatialX X offset correction. Default is \code{0.0} for no change.
#' @param spatialY Y offset correction. Default is \code{0.0} for no change.
#' @details When a mask is detected, \code{'add_noise'}, \code{'full_range'} and \code{'force_range'} are set to \code{false}, \code{'bg'} and \code{'sd'} to \code{0.0}, \code{'input_range'} to \code{[0.0,3.0]} and \code{'gamma'} to \code{1.0}.\cr\cr
#' Experimental (as of v0.2.0.501): when \code{'mode'} is not \code{"raw"}, if \code{'input_range'} is within \code{]0,1[}, it will be used as \code{'probs'} argument to \link[stats]{quantile} to determine clipping range from image object, in addition, \code{'gamma'} will be forced to \code{1.0}.
#' @keywords internal
NULL

#' @title IFC_object Extraction
#' @name cpp_extract
#' @description
#' Extracts object from ifd
#' @param fname string, path to file
#' @param ifd List, ifd information of class IFC_ifd
#' @param colors List of colors to use.
#' @param channels DataFrame, channels information.
#' @param physicalChannel CharacterVector of indices for each channel.
#' @param xmin NumericVector of minimal values for each channel.
#' @param xmax NumericVector of maximal values for each channel.
#' @param spatialX NumericVector of X spatial offset correction for each channel.
#' @param spatialY NumericVector of Y spatial offset correction for each channel.
#' @param removal IntegerVector of removal method to be used for each channel.
#' @param add_noise LogicalVector of whether to \code{'add_noise'} for each channel.
#' @param full_range LogicalVector of whether to use \code{'full_range'} for each channel.
#' @param force_range LogicalVector of whether to use \code{'force_range'} for each channel.
#' @param gamma NumericVector of the \code{'gamma'} for each channel.
#' @param chan_to_extract IntegerVector, channels to extract.
#' @param extract_msk uint8_t, type of mask to extract:\cr
#' -\code{0}: no mask,\cr
#' -\code{1}: at least one \code{"raw"},\cr
#' -\code{2}: at least one \code{"clipped"},\cr
#' -\code{3}: at least one \code{"masked"},\cr
#' -\code{4}: at least one \code{"MC"} mask.
#' @param mode string, color mode export. Either \code{"rgb"}, \code{"gray"} or \code{"raw"}. Default is \code{"raw"}.
#' @param size a length 2 IntegerVector of final dimensions (height,width) of the image. Default is \code{0,0} for no change.
#' @param verbose bool, whether to display information (use for debugging purpose). Default is \code{false}.
#' @details When \code{'add_noise'} is \code{false}, background will be automatically set to minimal pixel value for \code{"masked"} and \code{"MC"} \code{'removal'} method.
#' @keywords internal
NULL

cpp_getBits <- function() {
    .Call(`_IFC_cpp_getBits`)
}

cpp_align <- function(mat, dx = NA_real_, dy = NA_real_) {
    .Call(`_IFC_cpp_align`, mat, dx, dy)
}

cpp_assert <- function(x, len = NULL, cla = NULL, typ = NULL, alw = NULL, fun = "stop") {
    .Call(`_IFC_cpp_assert`, x, len, cla, typ, alw, fun)
}

cpp_ell_coord <- function(bound_x, bound_y) {
    .Call(`_IFC_cpp_ell_coord`, bound_x, bound_y)
}

cpp_pnt_in_gate <- function(pnts, gate, algorithm = 1L, epsilon = 0.000000000001) {
    .Call(`_IFC_cpp_pnt_in_gate`, pnts, gate, algorithm, epsilon)
}

cpp_mpfmatch <- function(x = NULL, pattern = NULL) {
    .Call(`_IFC_cpp_mpfmatch`, x, pattern)
}

cpp_seqmatch <- function(x, y) {
    .Call(`_IFC_cpp_seqmatch`, x, y)
}

cpp_fast_rowAny <- function(M_ = NULL) {
    .Call(`_IFC_cpp_fast_rowAny`, M_)
}

cpp_fast_listAny <- function(L_ = NULL) {
    .Call(`_IFC_cpp_fast_listAny`, L_)
}

cpp_fast_range <- function(x_ = NULL) {
    .Call(`_IFC_cpp_fast_range`, x_)
}

cpp_fast_sample <- function(n = 0L, size = 0L, replace = FALSE) {
    .Call(`_IFC_cpp_fast_sample`, n, size, replace)
}

cpp_get_bytes_order <- function(obj = 0L, byt_ = NULL, ord_ = NULL, rev = FALSE) {
    .Call(`_IFC_cpp_get_bytes_order`, obj, byt_, ord_, rev)
}

cpp_replace_non_finite <- function(V_ = NULL, by = 0.0) {
    .Call(`_IFC_cpp_replace_non_finite`, V_, by)
}

cpp_computeGamma <- function(V) {
    .Call(`_IFC_cpp_computeGamma`, V)
}

cpp_base64_encode <- function(x) {
    .Call(`_IFC_cpp_base64_encode`, x)
}

cpp_writeBMP <- function(image) {
    .Call(`_IFC_cpp_writeBMP`, image)
}

cpp_checkTIFF <- function(fname) {
    .Call(`_IFC_cpp_checkTIFF`, fname)
}

cpp_getoffsets_noid <- function(fname, obj_count = 0L, display_progress = FALSE, pb = NULL, verbose = FALSE) {
    .Call(`_IFC_cpp_getoffsets_noid`, fname, obj_count, display_progress, pb, verbose)
}

cpp_getTAGS <- function(fname, offset, verbose = FALSE, trunc_bytes = 12L, force_trunc = FALSE) {
    .Call(`_IFC_cpp_getTAGS`, fname, offset, verbose, trunc_bytes, force_trunc)
}

cpp_fastTAGS <- function(fname, offset, swap = FALSE) {
    .Call(`_IFC_cpp_fastTAGS`, fname, offset, swap)
}

cpp_getoffsets_wid <- function(fname, obj_count = 0L, display_progress = FALSE, pb = NULL, verbose = FALSE) {
    .Call(`_IFC_cpp_getoffsets_wid`, fname, obj_count, display_progress, pb, verbose)
}

cpp_checksum <- function(fname) {
    .Call(`_IFC_cpp_checksum`, fname)
}

cpp_M_HSV2RGB <- function(mat, h = 0.0, s = 0.0) {
    .Call(`_IFC_cpp_M_HSV2RGB`, mat, h, s)
}

cpp_smoothLinLog <- function(x, hyper = 1000.0, base = 10.0, lin_comp = 2.302585) {
    .Call(`_IFC_cpp_smoothLinLog`, x, hyper, base, lin_comp)
}

cpp_inv_smoothLinLog <- function(x, hyper = 1000.0, base = 10.0, lin_comp = 2.302585) {
    .Call(`_IFC_cpp_inv_smoothLinLog`, x, hyper, base, lin_comp)
}

cpp_uint32_to_raw <- function(x) {
    .Call(`_IFC_cpp_uint32_to_raw`, x)
}

cpp_int32_to_uint32 <- function(x) {
    .Call(`_IFC_cpp_int32_to_uint32`, x)
}

cpp_offset_to_raw <- function(x, swap = FALSE) {
    .Call(`_IFC_cpp_offset_to_raw`, x, swap)
}

cpp_raw_to_offset <- function(x, swap = FALSE) {
    .Call(`_IFC_cpp_raw_to_offset`, x, swap)
}

cpp_uint32_to_int32 <- function(x) {
    .Call(`_IFC_cpp_uint32_to_int32`, x)
}

cpp_int64_to_uint64 <- function(x) {
    .Call(`_IFC_cpp_int64_to_uint64`, x)
}

cpp_uint64_to_int64 <- function(x) {
    .Call(`_IFC_cpp_uint64_to_int64`, x)
}

cpp_v_int32_to_uint32 <- function(V = NULL) {
    .Call(`_IFC_cpp_v_int32_to_uint32`, V)
}

cpp_v_int64_to_uint64 <- function(V = NULL) {
    .Call(`_IFC_cpp_v_int64_to_uint64`, V)
}

cpp_scanFirst <- function(fname, raw, start = 0L, end = 0L, buf_size = 64L) {
    .Call(`_IFC_cpp_scanFirst`, fname, raw, start, end, buf_size)
}

cpp_fast_factor <- function(x, handleNA = TRUE) {
    .Call(`_IFC_cpp_fast_factor`, x, handleNA)
}

cpp_group_df <- function(df) {
    .Call(`_IFC_cpp_group_df`, df)
}

cpp_coord_to_px <- function(x, y, param) {
    .Call(`_IFC_cpp_coord_to_px`, x, y, param)
}

cpp_as_nativeRaster <- function(x) {
    .Call(`_IFC_cpp_as_nativeRaster`, x)
}

cpp_draw <- function(img, coords = matrix(1,2), mask = matrix(1), color = matrix(4,1), blur_size = 9L, blur_sd = 3.0) {
    .Call(`_IFC_cpp_draw`, img, coords, mask, color, blur_size, blur_sd)
}

cpp_raster <- function(width, height, obj, bg_ = NULL) {
    .Call(`_IFC_cpp_raster`, width, height, obj, bg_)
}

cpp_crop <- function(mat, new_height = 0L, new_width = 0L) {
    .Call(`_IFC_cpp_crop`, mat, new_height, new_width)
}

cpp_resize <- function(mat, new_height = 0L, new_width = 0L, add_noise = TRUE, bg = 0.0, sd = 0.0) {
    .Call(`_IFC_cpp_resize`, mat, new_height, new_width, add_noise, bg, sd)
}

cpp_decomp <- function(fname, offset, nbytes, imgWidth = 1L, imgHeight = 1L, nb_channels = 1L, removal = 0L, compression = 30818L, verbose = FALSE) {
    .Call(`_IFC_cpp_decomp`, fname, offset, nbytes, imgWidth, imgHeight, nb_channels, removal, compression, verbose)
}

cpp_rawdecomp <- function(fname, offset, nbytes, imgWidth = 1L, imgHeight = 1L, compression = 30818L, swap = FALSE, verbose = FALSE) {
    .Call(`_IFC_cpp_rawdecomp`, fname, offset, nbytes, imgWidth, imgHeight, compression, swap, verbose)
}

cpp_normalize <- function(mat, input_range = as.numeric( c(0.0,4095.0)), full_range = FALSE, force_range = FALSE, gamma = 1.0) {
    .Call(`_IFC_cpp_normalize`, mat, input_range, full_range, force_range, gamma)
}

cpp_cleanse <- function(mat, msk, add_noise = TRUE, bg = 0.0, sd = 0.0) {
    .Call(`_IFC_cpp_cleanse`, mat, msk, add_noise, bg, sd)
}

cpp_mask <- function(A, B, mask) {
    .Call(`_IFC_cpp_mask`, A, B, mask)
}

cpp_mark <- function(A, B, mask, xoff = 0L, yoff = 0L, invert = FALSE) {
    .Call(`_IFC_cpp_mark`, A, B, mask, xoff, yoff, invert)
}

cpp_transform <- function(mat, color, msk, size = as.integer( c(0,0)), mode = "raw", type = 2L, input_range = as.numeric( c(0.0,4095.0)), add_noise = TRUE, bg = 0.0, sd = 0.0, full_range = FALSE, force_range = FALSE, gamma = 1.0, spatialX = 0.0, spatialY = 0.0) {
    .Call(`_IFC_cpp_transform`, mat, color, msk, size, mode, type, input_range, add_noise, bg, sd, full_range, force_range, gamma, spatialX, spatialY)
}

cpp_extract <- function(fname, ifd, colors, physicalChannel, xmin, xmax, spatialX, spatialY, removal, add_noise, full_range, force_range, gamma, chan_to_extract, extract_msk = 0L, mode = "raw", size = as.integer( c(0,0)), verbose = FALSE) {
    .Call(`_IFC_cpp_extract`, fname, ifd, colors, physicalChannel, xmin, xmax, spatialX, spatialY, removal, add_noise, full_range, force_range, gamma, chan_to_extract, extract_msk, mode, size, verbose)
}