either one or the other. Path to file(s) to read from for 'fileName' or list of 'IFC_data' objects for obj.

indices of desired graphs. It can be provided as an integer vector or as a matrix.
In such case, the layout of the matrix will reflect the layout of the extracted graphs for each 'fileName' or ”obj'.
NA value will result in an empty place. When missing, it will be determined by the whole layout of 1st 'fileName' or 'obj' with 'gating' applied when provided

pattern used to export file(s). Placeholders, like c("%d/%s_fromR.pdf", "%d/%s_fromR.csv"), will be substituted:
-%d: with full path directory
-%p: with first parent directory
-%e: with extension (without leading .)
-%s: with shortname (i.e. basename without extension).
Exported file(s) extension(s) will be deduced from this pattern using either 1st 'fileName' or 'obj'. Note that has to be a .pdf and/or .csv.

whether to overwrite file or not. Default is FALSE. Note that if TRUE, it will overwrite file. In addition a warning message will be sent.

an 'IFC_gating' object as extracted by readGatingStrategy(). Default is missing. If not missing, each ‘IFC_data' provided in ’obj' or read from 'fileName' will be passed to applyGatingStrategy() before creating the report.

the main title of the document. Default is missing.

whether to add selected graphs for each file by row or not. Default is FALSE.

number of files to add before starting a new row or column (depending on 'byrow').

Whether to extract colors in white or black mode. Default is "white".

whether to draw a "global" key under title or in the first "panel" or "both". Default is "panel".
Accepted values are either: FALSE, "panel", "global", "both" or c("panel", "global").
Note that it only applies when display is seen as overlaying populations.

when graphs is a 2D scatter with population overlay, this argument controls amount of information displayed. Default is "light".
-"light", the default, will only display points of same coordinates that are among the other layers.
-"full" will display all the layers.

maximum number of characters to display for labels. Default is 38.

name of the transformation function for density graphs. If missing the default, the BasePop[[1]]$densitytrans, if any, will be retrieved, otherwise "asinh" will be used.

default number of bin used for histogram. Default is missing.

Either "ideas", "data" or "max" defining limits used for the graph. Default is "ideas".
-"ideas" will use same limits as the one defined in ideas.
-"data" will use data to define limits.
-"max" will use data and regions drawn to define limits.

backend used for drawing. Allowed are "lattice", "base", "raster". Default is "lattice".
-"lattice" is the original one used in IFC using lattice,
-"base" will produce the plot using base,
-"raster" uses "base" for plotting but 2D graphs points will be produced as rasterImage.
This has the main advantage of being super fast allowing for plotting a huge amount of points while generating smaller objects (in bytes). However, plot quality is impacted with "raster" method and resizing can lead to unpleasant looking.

whether to display a progress bar. Default is TRUE.

other parameters to be passed.

either one or the other. Path to file(s) to read from for 'fileName' or list of 'IFC_data' objects for obj.

template defining stats to compute as extracted by getSTATSREPORT().

an 'IFC_gating' object as extracted by readGatingStrategy(). Default is missing. If not missing, each ‘IFC_data' provided in ’obj' or read from 'fileName' will be passed to applyGatingStrategy() before creating the report.

whether to display a progress bar. Default is TRUE.

other parameters to be passed.

an 'IFC_data' object extracted with features extracted.

indices of desired graphs. It can be provided as an integer vector or as a matrix.
In such case, the layout of the matrix will reflect the layout of the extracted graphs.
NA value will result in an empty place.
Otherwise, when 'selection' is provided as a vector not identical to seq_along(obj$graphs), 'onepage' parameter will be set to FALSE.
Note that indices are read from left to right, from top to bottom. Default is missing for extracting all graphs.

whether to generate a pdf with all graphs on one page or not. Default is TRUE.

Whether to extract colors from obj in white or black mode. Default is "white".

whether to draw a "global" key under title or in the first "panel" or "both". Default is "panel".
Accepted values are either: FALSE, "panel", "global", "both" or c("panel", "global").
Note that it only applies when display is seen as overlaying populations.

when graphs is a 2D scatter with population overlay, this argument controls amount of information displayed. Default is "light".
-"light", the default, will only display points of same coordinates that are among the other layers.
-"full" will display all the layers.

maximum number of characters to display for labels. Default is 38.

name of the transformation function for density graphs. If missing the default, the BasePop[[1]]$densitytrans, if any, will be retrieved, otherwise "asinh" will be used.

default number of bin used for histogram. Default is missing.

Either "ideas", "data" or "max" defining limits used for the graph. Default is "ideas".
-"ideas" will use same limits as the one defined in ideas.
-"data" will use data to define limits.
-"max" will use data and regions drawn to define limits.

backend used for drawing. Allowed are "lattice", "base", "raster". Default is "lattice".
-"lattice" is the original one used in IFC using lattice,
-"base" will produce the plot using base,
-"raster" uses "base" for plotting but 2D graphs points will be produced as rasterImage.
This has the main advantage of being super fast allowing for plotting a huge amount of points while generating smaller objects (in bytes). However, plot quality is impacted with "raster" method and resizing can lead to unpleasant looking.

whether to display a progress bar. Default is TRUE.

other parameters to be passed.

arguments to be passed to objectExtract with the exception of 'ifd' and 'bypass'(=TRUE).
If 'param' is provided 'export'(="base64") and the above parameters will be overwritten.
If 'offsets' are not provided extra arguments can also be passed with ... to getOffsets.
/!\ If not any of 'fileName', 'info' and 'param' can be found in ... then attr(offsets, "fileName_image") will be used as 'fileName' input parameter to pass to objectParam.

integer vector, IDEAS objects ids numbers to use. This argument is not mandatory, if missing, the default, all objects will be used.

object of class 'IFC_offset'. This argument is not mandatory but it may allow to save time for repeated image export on same file.

image_type of desired offsets. Either "img" or "msk". Default is "img".

a character vector of [acquired channels + 'composite' images] members to export. Default is missing to export everything.
Note that members can be missing to be removed from final display.
Note that members not found will be automatically removed and a warning will be thrown.

id of the datatable container. Default is DisplayGallery.

whether to display caption name or not. Default is FALSE.

integer, number of objects to display per page. Default is 10.

string, page dimension when exporting to pdf. Default is "A2".

string, page orientation when exporting to pdf. Default is "landscape". Allowed are "landscape" or "portrait".

integer, desired image resolution. Default is 96, for full resolution.

maximum number of objects to extract. Default is 10. Use +Inf to extract all.

whether to sample objects or not. Default is FALSE.

whether to display a progress bar. Default is TRUE.

(objectParam argument) color mode export. Either "rgb" or "gray". Default is "rgb".

an 'IFC_data' object extracted with features extracted.

whether to display a progress bar. Default is TRUE.

other parameters to be passed.

list of batch nodes as created by buildBatch.

path of file to read data from.

pattern used to export file. Placeholders, like "%d/%s_fromR.%e", will be substituted:
-%d: with full path directory of 'fileName'
-%p: with first parent directory of 'fileName'
-%e: with extension of 'fileName' (without leading .)
-%s: with shortname from 'fileName' (i.e. basename without extension).
Exported file extension will be deduced from this pattern. Note that has to be a .daf.

list of population(s) to export. Will be coerced to exportable format by buildPopulation.

list of region(s) to export. Will be coerced to exportable format by buildRegion.

list of feature(s) to export.

list of graph(s) to export. Not yet implemented.

list of mask(s) to export. Not yet implemented.

Character String. Allow user to change displayed population. Default is 'All'.

The endian-ness ("big" or "little") of the target system for the file. Default is .Platform$endian.
Endianness describes the bytes order of data stored within the files. This parameter may not be modified.

whether to display information (use for debugging purpose). Default is FALSE.

whether to overwrite file or not. Default is FALSE. Note that if TRUE, it will overwrite exported file if path of 'fileName' and deduced from 'write_to' arguments are different. Otherwise, you will get an error saying that overwriting source file is not allowed.
Note also that an original file, i.e. generated by IDEAS(R) or INSPIRE(R), will never be overwritten.
Otherwise, you will get an error saying that overwriting original file is not allowed.

whether to export daf file with full name of its corresponding cif, if found. Default is TRUE. If cif can't be found, daf file will be exported with the original cif file name.

the path of the directory to initially look to cif file. Default is dirname(fileName). Only apply when 'fullname' is set to TRUE.

number of times ExportToDAF will be allowed to find corresponding cif file. Default is +Inf. Only apply when 'fullname' is set to TRUE.

other arguments to be passed.

an 'IFC_data' object extracted with features extracted.

pattern used to export file. Placeholders, like "%d/%s_fromR.%e", will be substituted:
-%d: with full path directory of 'obj$fileName'
-%p: with first parent directory of 'obj$fileName'
-%e: with extension of 'obj$fileName' (without leading .)
-%s: with shortname from 'obj$fileName' (i.e. basename without extension).
Exported file extension will be deduced from this pattern. Note that it has to be a .fcs.

whether to overwrite file or not. Default is FALSE. Note that if TRUE, it will overwrite exported file if path of 'fileName' and deduced from 'write_to' arguments are different. Otherwise, you will get an error saying that overwriting source file is not allowed.
Note also that an original file will never be overwritten.

an ASCII character to separate the FCS keyword-value pairs. Default is : "/".

string, if provided it will be used to fill $CYT keyword.
However, when missing $CYT will be filled with obj$description$FCS$instrument if found, or "Image Stream" otherwise.

other arguments to be passed. keyword-value pairs can be passed here.

arguments to be passed to objectExtract with the exception of 'ifd' and 'bypass'(=TRUE).
If 'param' is provided 'mode'(="rgb") and the above parameters will be overwritten.
If 'offsets' are not provided extra arguments can also be passed with ... getOffsets.
/!\ If not any of 'fileName', 'info' and 'param' can be found in ... then attr(offsets, "fileName_image") will be used as 'fileName' input parameter to pass to objectParam.

integer vector, IDEAS objects ids numbers to use. This argument is not mandatory, if missing, the default, all objects will be used.

object of class 'IFC_offset'. This argument is not mandatory but it may allow to save time for repeated image export on same file.

image_type of desired offsets. Either "img" or "msk". Default is "img".

a character vector of [acquired channels + 'composite' images] members to export. Default is missing to export everything. Note that members can be missing to be removed from final gallery export. Note that members not found will be automatically removed and a warning will be thrown.

export format. Either "file", "matrix", "base64". Default is "matrix".

used when 'export' is "file" or "base64" to compute respectively filename or base64 id attribute. Exported type will be deduced from this pattern. Allowed export are '.bmp', '.jpg', '.jpeg', '.png', '.tif', '.tiff'. Note that '.bmp' are faster but not compressed producing bigger data.
Placeholders, if found, will be substituted:
-%d: with full path directory
-%p: with first parent directory
-%e: with extension (without leading .)
-%s: with shortname (i.e. basename without extension)
-%o: with objects (at most 10, will be collapse with "_", if more than one).
-%c: with channel_id (will be collapse with "_", if more than one, composite in any will be bracketed). A good trick is to use:
-"%d/%s_gallery_Obj[%o]_Ch[%c].tiff", when 'export' is "file"
-"%s_gallery.bmp", when 'export' is "base64".
Note that if missing and 'export' is not "file", 'write_to' will be set to "%s_gallery.bmp".

whether to add id attribute to base64 exported object. Default is TRUE.
Only applied when 'export' is "base64".

attributes to add to base64 exported object. Default is "".
Only applied when export is "base64". For example, use "class=draggable".
Note that id (if base64_id is TRUE) and width and height are already used.

whether to overwrite file or not. Default is FALSE.

main title that will be displayed on top center of the image. If too large it will be clipped.

whether to add channels names. Default is TRUE.

integer, indice of column to mark objects ids number. Default is 1. If add_ids < 1, no ids are added.

integer, size of separating lines between objects. Default is 1. If add_lines < 1, no separating lines are added.

background color for main, channels and separating lines. Default is "grey20".

integer, the resolution of the image in DPI (dots per inch). Default is 300.
Please note that whetever this parameter is final resolution will be 96 dpi.
However image will be scaled according this parameter and magnification factor will be equal to this parameter divided by 96.

a named list whose members are 'size', 'style', 'color', 'xoff', 'yoff'. Default is list() to draw no scale. Otherwise,
-'size' positive integer. Scale's bar size in micro-meter. Default is '7'.
This parameter can't be lesser than 6px nor higher than image width + scale text.
-'style' a character string. Scale's bar style, either "dash" or "line". Default is "dash".
-'color' a character string. color of the scale. Default is "white".
-'xoff' positive integer. x offset in image to draw scale, starting from bottom left corner.
-'yoff' positive integer. y offset in image to draw scale, starting from bottom left corner.

maximum number of objects to extract. Default is 10. Use +Inf to extract all.

whether to sample objects or not. Default is FALSE.

whether to display a progress bar. Default is TRUE.

arguments to be passed to objectExtract with the exception of 'ifd' and 'bypass'(=TRUE).
/!\ If not any of 'fileName', 'info' and 'param' can be found in '...' then attr(offsets, "fileName_image") will be used as 'fileName' input parameter to pass to objectParam.

integer vector, IDEAS objects ids numbers to use. This argument is not mandatory, if missing, the default, all objects will be used.

object of class 'IFC_offset'. This argument is not mandatory but it may allow to save time for repeated image export on same file.
If 'offsets' are not provided, extra arguments can also be passed with '...' to getOffsets.

type of desired object offsets. Either "img" or "msk". Default is "img".

a length 2 integer vector of final dimensions of the image, height 1st and width 2nd. Default is c(64,64).

whether to use information in 'info' to fill 'size'. Default is FALSE. When set to TRUE, width of 'size' argument will be overwritten.

whether to display a progress bar. Default is TRUE.

path to python. Default is Sys.getenv("RETICULATE_PYTHON").
Note that numpy should be available in this python to allow export to ".npy" file, otherwise 'export' will be forced to "matrix".

desired arrays data-type. Default is "double". Allowed are "uint8", "int16", "uint16" or "double". If 'mode' is "raw", this parameter will be forced to "int16".

(objectParam argument) color mode export. Either "raw", "gray". Default is "raw".

export format. Either "file", "matrix". Default is "matrix".
Note that you will need reticulate package installed to be able to export to ".npy" file, otherwise 'export' will be forced to "matrix".

used when 'export' is "file" to compute exported file name and type. Exported type will be deduced from this pattern. Allowed exported file extension is ".npy".
Placeholders, if found, will be substituted:
-%d: with full path directory
-%p: with first parent directory
-%e: with extension of (without leading .)
-%s: with shortname (i.e. basename without extension)
-%o: with objects (at most 10, will be collapse with "_", if more than one).
-%c: with channel_id (will be collapse with "_", if more than one, composite in any will be bracketed). A good trick is to use:
-"%d/%s_Obj[%o]_Ch[%c].npy", when 'export' is "file".

whether to overwrite file or not. Default is FALSE.

an 'IFC_data' object extracted with features extracted.

indices of desired graphs. It can be provided as an integer vector or as a matrix.
In such case, the layout of the matrix will reflect the layout of the extracted graphs.
NA value will result in an empty place.
Otherwise, when 'selection' is provided as a vector not identical to seq_along(obj$graphs), 'onepage' parameter will be set to FALSE.
Note that indices are read from left to right, from top to bottom. Default is missing for extracting all graphs.

pattern used to export file(s). Placeholders, like c("%d/%s_fromR.pdf", "%d/%s_fromR.csv"), will be substituted:
-%d: with full path directory of 'obj$fileName'
-%p: with first parent directory of 'obj$fileName'
-%e: with extension of 'obj$fileName' (without leading .)
-%s: with shortname from 'obj$fileName' (i.e. basename without extension).
Exported file(s) extension(s) will be deduced from this pattern. Note that has to be a .pdf and/or .csv.

whether to overwrite file or not. Default is FALSE. Note that if TRUE, it will overwrite file. In addition a warning message will be sent.

whether to generate a pdf with all graphs on one page or not. Default is TRUE.

Whether to extract colors from obj in white or black mode. Default is "white".

whether to draw a "global" key under title or in the first "panel" or "both". Default is "panel".
Accepted values are either: FALSE, "panel", "global", "both" or c("panel", "global").
Note that it only applies when display is seen as overlaying populations.

when graphs is a 2D scatter with population overlay, this argument controls amount of information displayed. Default is "light".
-"light", the default, will only display points of same coordinates that are amoung the other layers.
-"full" will display all the layers.

maximum number of characters to display for labels. Default is 38.

name of the transformation function for density graphs. If missing the default, the BasePop[[1]]$densitytrans, if any, will be retrieved, otherwise "asinh" will be used.

default number of bin used for histogram. Default is missing.

Either "ideas", "data" or "max" defining limits used for the graph. Default is "ideas".
-"ideas" will use same limits as the one defined in ideas.
-"data" will use data to define limits.
-"max" will use data and regions drawn to define limits.

backend used for drawing. Allowed are "lattice", "base", "raster". Default is "lattice".
-"lattice" is the original one used in IFC using lattice,
-"base" will produce the plot using base,
-"raster" uses "base" for plotting but 2D graphs points will be produced as rasterImage.
This has the main advantage of being super fast allowing for plotting a huge amount of points while generating smaller objects (in bytes). However, plot quality is impacted with "raster" method and resizing can lead to unpleasant looking.

whether to display a progress bar. Default is TRUE.

other parameters to be passed.

path(s) of file(s) to subset or merge. If multiple files are provided they will be merged. Otherwise, if only one file is input it will be subsetted. All files have to be either '.rif' or '.cif' files. All files should have same channels.

pattern used to export file. Placeholders, like "%d/%s_fromR.%e", will be substituted:
-%d: with full path directory of first element of 'fileName'
-%p: with first parent directory of first element of 'fileName'
-%e: with extension of first element of 'fileName' (without leading .)
-%s: with shortname from of first element of 'fileName' (i.e. basename without extension).
Exported file extension will be deduced from this pattern. It has to be the same as 'fileName', i.e. .cif or .rif.

integer vector, IDEAS objects ids numbers to use. If missing, the default, all objects will be used. Only apply for subsetting.

object of class ‘IFC_offset'. If missing, the default, offsets will be extracted from ’fileName'.
This param is not mandatory but it may allow to save time for repeated XIF export on same file. Only apply for subsetting.

whether to fast extract 'objects' or not. Default is TRUE. Meaning that 'objects' will be extracted expecting that 'objects' are stored in ascending order.
Note that a warning will be sent if an 'object' is found at an unexpected order. In such a case you may need to rerun function with 'fast' = FALSE. If set to FALSE, all object_ids will be scanned from 'fileName' to ensure extraction of desired 'objects'.
IMPORTANT: whatever this argument is, features are extracted assuming an ascending order of storage in file.
Only apply for subsetting.

whether to try to extract features. Default is FALSE. IMPORTANT: it is not clear if how features are stored and which objects they rely to when input file is already a merge or a subset. For this reason it should be carefully checked. Note that features extraction is not implemented for merging.

the endian-ness ("big" or "little") of the target system for the file. Default is .Platform$endian.
Endianness describes the bytes order of data stored within the files. This parameter may not be modified.

whether to display information (use for debugging purpose). Default is FALSE.

quantity of information displayed when verbose is TRUE; 1: normal, 2: rich. Default is 1.

whether to overwrite file or not. Default is FALSE.
Note that if TRUE, it will overwrite exported file if path(s) of file(s) in 'fileName' and deduced from 'write_to' arguments are different. Otherwise, you will get an error saying that overwriting source file is not allowed.
Note also that an original file, i.e. generated by IDEAS(R) or INSPIRE(R), will never be overwritten. Otherwise, you will get an error saying that overwriting original file is not allowed.

whether to display a progress bar. Default is TRUE.

whether to register files' paths and objects' ids in the exported file. Default is TRUE.

other arguments to be passed.

path to file.

whether to extract features (and graphs, pops and regions) from file. Default is TRUE.

whether to extract images information from file. Default is TRUE.

whether to extract IFDs offsets from corresponding. Default is TRUE.
See getOffsets for further details.

whether to extract population statistics. Default is TRUE.

The endian-ness ("big" or "little") of the target system for the file. Default is .Platform$endian.
Endianness describes the bytes order of data stored within the files. This parameter may not be modified.

algorithm used to determine if object belongs to a polygon region or not. Default is 1.
Note that for the moment only 1(Trigonometry) is available.

epsilon to determine if object belongs to a polygon region or not. It only applies when algorithm is 1. Default is 1e-12.

whether to display a progress bar. Default is TRUE.

Other arguments to be passed.

path(s) of file(s). If multiple files are provided they will be merged and populations will be created to identify each single file within returned 'IFC_data' object.

other arguments to be passed to readFCS function, with the exception of 'options$text_only'.

path to file.

whether to extract features from file. Default is TRUE.
If TRUE, ExtractFromXIF will try to export features. It it fails a message will be sent.
Otherwise, graphs, pops and regions will be also extracted.

whether to extract images information from file. Default is FALSE.

whether to extract IFDs offsets from corresponding. Default is FALSE.
See getOffsets for further details.

whether to extract population statistics. Default is TRUE.

algorithm used to determine if object belongs to a polygon region or not. Default is 1.
Note that for the moment only 1(Trigonometry) is available.

epsilon to determine if object belongs to a polygon region or not. It only applies when algorithm is 1. Default is 1e-12.

when display information can't be retrieved whether to use default values. Default is TRUE.

whether to display information (use for debugging purpose). Default is FALSE.

quantity of information displayed when verbose is TRUE; 1: normal, 2: rich. Default is 1.

whether to display a progress bar. Default is TRUE.

whether to fast extract 'objects' or not. Default is TRUE.
Meaning that offsets will be extracted expecting that 'objects' are stored in ascending order. if extract_images is FALSE, a message will be thrown since extraction method does not ensure correct mapping between objects and offsets.
if extract_images is TRUE, a warning will be sent if an object is found at an unexpected order.

whether to recursively apply ExtractFromXIF on files defining input fileName when it is a merged. Default is FALSE.

Other arguments to be passed.

arguments to be passed to objectExtract with the exception of 'ifd' and 'bypass'(=TRUE).
/!\ If not any of 'fileName', 'info' and 'param' can be found in '...' then attr(offsets, "fileName_image") will be used as 'fileName' input parameter to pass to objectParam.

integer vector, IDEAS objects ids numbers to use. This argument is not mandatory, if missing, the default, all objects will be used.

object of class 'IFC_offset'. This argument is not mandatory but it may allow to save time for repeated image export on same file.
If 'offsets' are not provided, extra arguments can also be passed with '...' to getOffsets.

whether to display a progress bar. Default is TRUE.

(objectParam argument) color mode export. Either "rgb", "gray". Default is "rgb".

used to compute respectively exported file name.
Exported base64 data-uri will be deduced from this pattern. Allowed export are ".bmp", ".jpg", ".jpeg", ".png", ".tif", ".tiff". Note that ".bmp" is faster but files are not compressed producing bigger data.
Placeholders, if found, will be substituted:
-%d: with full path directory
-%p: with first parent directory
-%e: with extension (without leading .)
-%s: with shortname (i.e. basename without extension)
-%o: with object_id
-%c: with channel_id
A good trick is to use: "%o_%c.bmp".

whether to add id attribute to base64 exported object.

attributes to add to base64 exported object.
For example, use "class='draggable'".
Note that id (if 'base64_id' is TRUE) and width and height are already used.

arguments to be passed to objectExtract with the exception of 'ifd' and 'bypass'(=TRUE).
/!\ If not any of 'fileName', 'info' and 'param' can be found in '...' then attr(offsets, "fileName_image") will be used as 'fileName' input parameter to pass to objectParam.

integer vector, IDEAS objects ids numbers to use. This argument is not mandatory, if missing, the default, all objects will be used.

object of class 'IFC_offset'. This argument is not mandatory but it may allow to save time for repeated image export on same file.
If 'offsets' are not provided, extra arguments can also be passed with '...' to getOffsets.

whether to display a progress bar. Default is TRUE.

(objectParam argument) color mode export. Either "rgb", "gray". Default is "rgb".

used to compute respectively exported file name.
Exported "file" extension will be deduced from this pattern. Allowed export are ".bmp", ".jpg", ".jpeg", ".png", ".tif", ".tiff". Note that ".bmp" is faster but files are not compressed producing bigger data.
Placeholders, if found, will be substituted:
-%d: with full path directory
-%p: with first parent directory
-%e: with extension (without leading .)
-%s: with shortname (i.e. basename without extension)
-%o: with object_id
-%c: with channel_id
A good trick is to use: "%d/%s/%s_%o_%c.tiff".

whether to overwrite file or not. Default is FALSE.

arguments to be passed to objectExtract with the exception of 'ifd' and 'bypass'(=TRUE).
/!\ If not any of 'fileName', 'info' and 'param' can be found in '...' then attr(offsets, "fileName_image") will be used as 'fileName' input parameter to pass to objectParam.

integer vector, IDEAS objects ids numbers to use. This argument is not mandatory, if missing, the default, all objects will be used.

object of class 'IFC_offset'. This argument is not mandatory but it may allow to save time for repeated image export on same file.
If 'offsets' are not provided, extra arguments can also be passed with '...' to getOffsets.

whether to display a progress bar. Default is TRUE.

arguments to be passed to objectExtract with the exception of 'ifd' and 'bypass'(=TRUE).
/!\ If not any of 'fileName', 'info' and 'param' can be found in '...' then attr(offsets, "fileName_image") will be used as 'fileName' input parameter to pass to objectParam.

integer vector, IDEAS objects ids numbers to use. This argument is not mandatory, if missing, the default, all objects will be used.

object of class 'IFC_offset'. This argument is not mandatory but it may allow to save time for repeated image export on same file.
If 'offsets' are not provided, extra arguments can also be passed with '...' to getOffsets.

whether to display a progress bar. Default is TRUE.

(objectParam argument) color mode export. Either "rgb", "gray". Default is "rgb".

used to compute respectively exported file name.
Exported base64 data-uri will be deduced from this pattern. Allowed export are ".bmp", ".jpg", ".jpeg", ".png", ".tif", ".tiff". Note that ".bmp" is faster but files are not compressed producing bigger data.
Placeholders, if found, will be substituted:
-%d: with full path directory
-%p: with first parent directory
-%e: with extension (without leading .)
-%s: with shortname (i.e. basename without extension)
-%o: with object_id
-%c: with channel_id
A good trick is to use: "%o_%c.bmp".

whether to add id attribute to base64 exported object.

attributes to add to base64 exported object.
For example, use "class='draggable'".
Note that id (if 'base64_id' is TRUE) and width and height are already used.

arguments to be passed to objectExtract with the exception of 'ifd' and 'bypass'(=TRUE).
/!\ If not any of 'fileName', 'info' and 'param' can be found in '...' then attr(offsets, "fileName_image") will be used as 'fileName' input parameter to pass to objectParam.

integer vector, IDEAS objects ids numbers to use. This argument is not mandatory, if missing, the default, all objects will be used.

object of class 'IFC_offset'. This argument is not mandatory but it may allow to save time for repeated image export on same file.
If 'offsets' are not provided, extra arguments can also be passed with '...' to getOffsets.

whether to display a progress bar. Default is TRUE.

(objectParam argument) color mode export. Either "rgb", "gray". Default is "rgb".

used to compute respectively exported file name.
Exported "file" extension will be deduced from this pattern. Allowed export are ".bmp", ".jpg", ".jpeg", ".png", ".tif", ".tiff". Note that ".bmp" is faster but files are not compressed producing bigger data.
Placeholders, if found, will be substituted:
-%d: with full path directory
-%p: with first parent directory
-%e: with extension (without leading .)
-%s: with shortname (i.e. basename without extension)
-%o: with object_id
-%c: with channel_id
A good trick is to use: "%d/%s/%s_%o_%c.tiff".

whether to overwrite file or not. Default is FALSE.

arguments to be passed to objectExtract with the exception of 'ifd' and 'bypass'(=TRUE).
/!\ If not any of 'fileName', 'info' and 'param' can be found in '...' then attr(offsets, "fileName_image") will be used as 'fileName' input parameter to pass to objectParam.

integer vector, IDEAS objects ids numbers to use. This argument is not mandatory, if missing, the default, all objects will be used.

object of class 'IFC_offset'. This argument is not mandatory but it may allow to save time for repeated image export on same file.
If 'offsets' are not provided, extra arguments can also be passed with '...' to getOffsets.

whether to display a progress bar. Default is TRUE.

a named list of keywords values.

delimiter used to separate keyword-value pairs. /!\ NOTE that files with 0x00 'delimiter' can _NOT_ be parsed.

version to check keywords compliance against. Default is 3.0.

name of the encoding for raw to character conversion. Default is "UTF-8".

function to execute when mandatory parameters are not met. Default is "warning". Allowed are "stop","warning","message","return".

other arguments to be passed.

'IFC_fcs' object as extracted by readFCS().

other arguments to be passed.

'IFC_fcs' object as extracted by readFCS().

other arguments to be passed.

'IFC_fcs' object as extracted by readFCS().

other arguments to be passed.

an 'IFC_data' object.

template defining stats to compute as extracted by getSTATSREPORT().

path of file to subset. It has to be a '.rif' or '.cif' file.

pattern used to export file. Placeholders, like "%d/%s_fromR.%e", will be substituted:
-%d: with full path directory of 'fileName'
-%p: with first parent directory of 'fileName'
-%e: with extension of 'fileName' (without leading .)
-%s: with shortname from 'fileName' (i.e. basename without extension).
Exported file extension has to be .tif or .tiff.

integer vector, IDEAS objects ids numbers to use. If missing, the default, all objects will be used.

object of class ‘IFC_offset'. If missing, the default, offsets will be extracted from ’fileName'.
This param is not mandatory but it may allow to save time for repeated XIF export on same file.

whether to fast extract 'objects' or not. Default is TRUE. Meaning that 'objects' will be extracted expecting that 'objects' are stored in ascending order.
Note that a warning will be sent if an 'object' is found at an unexpected order. In such a case you may need to rerun function with 'fast' = FALSE. If set to FALSE, all raw object_ids will be scanned from 'fileName' to ensure extraction of desired 'objects'.
IMPORTANT: whatever this argument is, features are extracted assuming an ascending order of storage in file.

The endian-ness ("big" or "little") of the target system for the file. Default is .Platform$endian.
Endianness describes the bytes order of data stored within the files. This parameter may not be modified.

whether to display information (use for debugging purpose). Default is FALSE.

quantity of information displayed when verbose is TRUE; 1: normal, 2: rich. Default is 1.

whether to overwrite file or not. Default is FALSE.
Note that if TRUE, it will overwrite exported file if path of 'fileName' and deduced from 'write_to' arguments are different. Otherwise, you will get an error saying that overwriting source file is not allowed.
Note also that an original file, i.e. generated by IDEAS(R) or INSPIRE(R), will never be overwritten. Otherwise, you will get an error saying that overwriting original file is not allowed.

whether to display a progress bar. Default is TRUE.

whether to register files' paths and objects' ids in the exported file. Default is TRUE.

other arguments to be passed.

a [0,1] image.

positive integer. Scale's bar size in micro-meter. Default is '7'.
This parameter can't be lesser than 6px and higher than image width + scale text.

a character string. Scale's bar style, either 'dash' or 'line'. Default is 'dash'.

a character string. color of the scale. Default is 'white'.

positive integer. Resolution in ppi of 'image'. Default is '96'.

positive integer. x offset in image to draw scale, starting from bottom left corner.

positive integer. y offset in image to draw scale, starting from bottom left corner.

a [0,1] image.

a character string.

a character string. color of the text.

positive integer. x offset in image to start writing text.

positive integer. y offset in image to start writing text.

a character string. where to position text in the image. Allowed are "TL", "TR", "BL", "BR", for top-left, top-right, bottom-left, bottom-right, respectively.

an object of class 'IFC_data' extracted by ExtractFromDAF(extract_features = TRUE) or ExtractFromXIF(extract_features = TRUE).

a graph from 'obj' or a list that can be coerced by buildGraph.

whether to try to adjust graph(s) when possible. Default is TRUE.
-TRUE, graph(s) will be kept if possible using only regions, pops it depends that can be found in 'obj',
-FALSE, graph(s) will be kept only if all features, regions, pops it refers to are found in 'obj',
-NA, graph(s) will be removed no matter if features, regions, pops it refers to are found in 'obj'.

other arguments to be passed.

an 'IFC_data' object extracted with features extracted.

an 'IFC_gating' object extracted by readGatingStrategy.

names of population(s) that should not be overwritten using 'gating'.

whether to display a progress bar. Default is TRUE.

whether to display information (use for debugging purpose). Default is FALSE.

other arguments to be passed.

a numeric vector.

the object returned by parseTrans().

whether or not to apply the inverse transformation. Default is FALSE.

variable to test

integer vector of allowed length for x. Default is NULL, for not checking this parameter.

character vector of allowed classes of x. Default is NULL, for not checking this parameter.

character vector of allowed types of x. Default is NULL, for not checking this parameter.

allowed values for x. Default is NULL, for not checking this parameter.

function to execute when mandatory parameters are not met. Default is "stop". Allowed are "stop","warning","message","return".

an 'IFC_data' object extracted by ExtractFromDAF(extract_features = TRUE) or ExtractFromXIF(extract_features = TRUE).

one or several populations present in 'obj'. Default is NULL.
If provided, autoplot will try to display these populations. See details when not provided.

autoplot will try to determine x and y and their transformations based on 'shown_pops' parameter. If all populations provided in 'shown_pops' are siblings, region(s) from which 'shown_pops' were defined will be displayed.
In case 'shown_pops' are not siblings, they will be treated as populations and a graph will be generating with an overlay of these populations. Order of this overlay is given by order of 'shown_pops'.
Finally, changing any of the following arguments (x, x_trans, y, y_trans, type) to something else than the one detected from 'shown_pops' will prevent from displaying region(s) and 'shown_pops' populations will be displayed as overlay.
However, please consider that if original type is 'histogram' changing x_trans transformation will have no impact on this.

a population present in 'obj'. Default is NULL. Background population that will be used to generate graph. This argument will not be used when graph is an histogram. If this argument is filled with a different population than what can be determined thanks to 'shown_pops', Then 'shown_pops' will be treated as overlay. However, 'shown_pops' argument can still be used to determine x, y axis and their transformation

feature for x-axis. Default is NULL. When empty, autoplot will try to determine if automatically from 'shown_pops' argument. If provided, x feature has to be a name from 'obj' features. Note that providing x feature : - takes precedence on automatic x-axis detection. - will reset x-axis transformation to "P" except if 'x_trans' is filled.

parameter for x-axis transformation. Default is NULL. If not provided, transformation will be determined thanks to 'shown_pops'. It takes precedence when provided and if provided it has to be be either "P" or coercible to a positive numeric. "P" will leave x-axis as is but a positive numeric will be passed has hyper argument of smoothLinLog to transform x-axis.

feature for y-axis. Default is NULL. When empty, autoplot will try to determine it automatically from 'shown_pops' argument. If provided, y feature has to be a name from obj features. Note that providing y feature - takes precedence on automatic y-axis detection. - will reset y-axis transformation to "P" except if 'y_trans' is filled.

parameter for y-axis transformation. Default is NULL. If not provided, transformation will be determined thanks to 'shown_pops'. It takes precedence when provided and and if provided it has to be be either "P" or coercible to a positive numeric. "P" will leave y-axis as is but a positive numeric will be passed has hyper argument of smoothLinLog to transform y-axis. Note that it is irrelevant for "histogram".

type of plot. Default is NULL to allow autoplot to detemine 'type' automatically. If provided it has to be either "histogram", "scatter", "density". Note that when "histogram" is choosen, 'subset' parameter will not be used. Note that "density" will be possible only when 'subset' will be automatically determined or filled with only one population. Note that when autoplot has determined, thanks to 'shown_pops' that original plot is an "histogram", "Object Number" will be used as y-axis by default when 'type' is forced to "scatter" or "density".

when type of graph is "histogram", whether to smooth it or not. Default is NULL. Should be an integer [0:20] Note that 0 means no smoothing and other values will produce smoothing

when type of graph is "histogram", whether to normalize it or not. Default is NULL. Should be a logical.

number of bins when graph's type is "histogram" / number of equally spaced grid points for density. Default is missing to allow autoplot to determine it by itself.

Either "ideas", "data" or "max" defining limits used for the graph. Default is "ideas".
-"ideas" will use same limits as the one defined in ideas.
-"data" will use data to define limits.
-"max" will use data and regions drawn to define limits.

when graphs is a 2D scatter with population overlay, this argument controls amount of information displayed. Default is "light".
-"light", the default, will only display points of same coordinates that are amoung the other layers.
-"full" will display all the layers.

Whether to extract colors from obj in white or black mode. Default is "white".

whether to draw plot. Default is TRUE.

Other arguments to be passed.

a raw vector.

vector of length 2 of axis extents.

transformation applied. Defaut is "P".

positive integer value indicating (approximately) the desired number of intervals. Default is 10.

a vector of values for which the histogram is desired.

histogram type. Default is missing. Allowed are "count" and "percent".

breakpoints given an interval and the number of pieces to break it into.

whether to normalize. Default is missing.

whether to fill. Default is missing.

whether to smooth. Default is missing.

graphical parameters. See par() from package 'graphics'.

logical; if TRUE, an x[i] equal to the breaks value will be included in the first (or last, for right = FALSE) bar. This will be ignored (with a warning) unless breaks is a vector.

logical; if TRUE, the histogram cells are right-closed (left open) intervals.

path of files to batch.

path to compensation file.

path to analysis file.

directory where batches are stored.
It can be found in IDEAS(R) software, under Options -> Application Defaults -> Directories -> Default Batch Report Files Directory.
If missing, the default, it will be deduced from IDEAS(R) config file, However, if it can't be deduced then tempdir(check = TRUE) from base will be used.
This argument takes precedence over 'config_file' and filling 'default_batch_dir' prevents the use of 'config_file' argument.

path to IDEAS(R) config file.
It may depends on IDEAS(R) software installation but one may use "C:/Users/%USER%/AppData/Roaming/Amnis Corporation/userconfig.xml".

name of batch. Default is "Batch1".

whether to use acquisition as analysis template. Default is FALSE.

suffix to add to files when batched. Default is "".

whether to allow building batch when all files were not acquired with same channels. Default is FALSE.

whether to overwrite files or not. Default is TRUE.

size of file segmentation. Default is "None", for no segmentation.
Allowed are "None", "100", "1K", "5K", "10K", "50K", "100K".

A list of arguments to be passed.
If missing, the default, options will be set to:
-"Brightfield compensation"=TRUE,
-"EDF deconvolution"=TRUE,
-"Camera background"=TRUE,
-"Spatial alignment"=TRUE.
Allowed are TRUE or FALSE for all, excepted for 'Spatial aligment' which can also be path to .rif file.

feature's name. If missing, it will be determined thanks to def.

feature's type. Default is "single". Allowed are "single", "combined", "computed".

definition of the feature. Default is "Camera Line Number".

a coercible to numeric vector of feature values. Default is NULL.
Note that although not mandatory for buildFeatureit has to be provided to allow feature export in ExportToDAF and data_add_features.

Other arguments to be passed.

Graph's type. Either "histogram", "scatter" or "density". Default is "density".

Integer. Graph's x location. Default is 0.

Integer. Graph's x location. Default is 0.

Character. Graph x axis parameter. Default is "Object Number".

Character. Graph y axis parameter. Default is "Object Number". Only used when 'type' is not "histogram".

Integer. Graph scale. Either 0 (auto), 1 (manual). Default is 1.

Double. Graph's xmin. Default -1.

Double. Graph's xmax. Default 1.

Double. Graph's xmin. Default 0.

Double. Graph's xmax. Default 1.

Character. Graph title label. Default will use names of BasePop collapse with ', '.

Character. Graph x axis label.

Character. Graph y axis label.

Integer. Axis label font size. Default is 10. Allowed are: 8, 9, 10, 11, 12, 14, 16, 18, 20, 22, 24, 26, 28.
Checked but not yet implemented.

Integer. Axis tick font size. Default is 10. Allowed are: 8, 9, 10, 11, 12, 14, 16, 18, 20, 22, 24, 26, 28.
Checked but not yet implemented.

Integer. Axis title font size. Default is 12. Allowed are: 8, 9, 10, 11, 12, 14, 16, 18, 20, 22, 24, 26, 28.
Checked but not yet implemented.

Integer. Axis region font size. Default is 10. Allowed are: 8, 9, 10, 11, 12, 14, 16, 18, 20, 22, 24, 26, 28.
Checked but not yet implemented.

Integer. Histogram bin count. Default is 0. Allowed are: 0, 8, 16, 32, 64, 128, 256, 512, 1024.

Character. Histogram with frequency normalization of not. Default is "T", allowed are "T" or "F".

Integer. Histogram smoothing factor. Allowed are [0-20]. Only partly implemented, default is 0 for no smoothing other values will produce same smoothing.

determines transformation instruction for x-axis. Default is "P" for no transformation.

determines transformation instruction for y-axis. Default is "P" for no transformation.

determines the maximum number of points to display. Default is +Inf to display all points.
If provided, values from ]0,1] will be used as a proportion of the total number of points to show.
While values values superior to 1 will be interpreted as the maximal number of points to show.
It only applies to 2D graphs. When 'type' is "histogram", +Inf will be used whatever the value provided as input.

Character. Either "true" or "false" to display stats. Default is "false".

Integer. Graph's x size. Default is 320 for small. Regular are: 320 (small), 480 (medium), 640 (big). Checked but not yet implemented.

Integer. Graph's y size. Default is 'ysize' + 'splitterdistance' when 'stats' is set to "true". Checked but not yet implemented.

Integer. Default is 120. Checked but not yet implemented.

Character. x stats to be computed. Default is 'Count|%Gated|Mean'. It has to be a filled with the concatenation of 'Count', '%Total', '%Gated', '%Plotted', 'Objects/mL', 'Mean', 'Median', 'Std. Dev.', 'MAD', 'CV', 'Minimum', 'Maximum', 'Geo. Mean', 'Mode', 'Variance' and /or 'NaN', collapse with '|'. Checked but not yet implemented.

Character. y stats to be computed. Should be identical to 'xstats'. Default is xstats. Checked but not yet implemented.

Character. Order to display populations. When 'type' is "density" it will be BasePop[[1]]$name. When 'type' is "histogram" or "density" 'ShownPop' are not allowed Otherwise, it will use each of 'GraphRegion', 'BasePop' and 'ShownPop' names, collapse with '|'.

Character. Order of stat rows. It will use each of 'GraphRegion' names & each of 'BasePop' names, reverted and collapse with '|'.

Default is list(list(onoff='false',x='0',y='0',witdh='96',height='128')). Not yet implemented.

Default is list(list()). See details.

Default is list(list()). Only allowed member are sub-list(s) with only one character component named 'name'.

Default is list(list()). Only allowed member are sub-list(s) with only one character component named 'name'.

Other arguments to be passed.

the value of the IFD

desired IFD type

the desired IFD 'tag'

the desired endian-ness ("big" or "little"). Default is .Platform$endian.
Endianness describes the bytes order of data stored within the files. This parameter may not be modified.

the channel. Default is 1. Allowed are [1-12].

other arguments to be passed. See members in returned value.

should 'physicalChannel' channel be considered as brightfield. Default is FALSE.

collection mode (as retrieved by getInfo) determining the range. Default is 1.

an 'IFC_masks' object or a data.frame containing masks definition and name. Default is missing.

a data.frame containing images definition. Default is missing.

whether to compute masks definition or masks names. Default is TRUE, to compute definition.

a vector of masks names to use for matching 'masks' names. Default is NULL

a vector of masks names to use for replacing 'masks' names. Default is NULL

a vector of images names to use for matching 'images' names. Default is NULL

a vector of images names to use for replacing 'images' names. Default is NULL

Other arguments to be passed.

name of the population.

type of population. Either "B", "C", "G" or "T" for Base, Combined, Graphical or Tagged, respectively.
If missing, the default, 'type' will be deduced from other parameters. If 'name' is "All" type will be "B". Otherwise, if 'fx' is given type will be "G". Otherwise, "T", if 'definition' is missing but not 'obj' or "C" if 'definition' is not missing.

which population is based on. It will be base="All", for 'type' "T" and "C" and base="", for 'type' "B". It is only needed when type = "G".

color of the population. See paletteIFC for allowed colors. If not provided, it will be sampled.

lightModeColor of the population. See paletteIFC for allowed colors. If not provided, it will be sampled.

style of the population. Either 20, 4, 3, 1, 5, 0, 2, 18, 15, 17, respectively for: "Simple Dot", "Cross", "Plus", "Empty Circle", "Empty Diamond", "Empty Square", "Empty Triangle", "Solid Diamond", "Solid Square", "Solid Triangle".

Only if type="G". Name of the region defining the population.

Only needed if type="G". Name of the x-feature defining the population.

Only needed if type="G" and only if region is defined in 2D. Name of the y-feature defining the population.

Only needed if type="C". Parameters defining the population.

Only needed if type="T". Either a:
-Logical vector of same length as "All" population indicating if a cell belongs to the population or not.
-Integer vector of indices of cells that belongs to the population. Note that first object is 0.

Other arguments to be passed.

Region's type. Either "line", "rect", "poly" or "oval".

label of the region.

x label's position. If not provided x center will be used.

y label's position. If not provided y center will be used.

color of the region. See paletteIFC for allowed colors.

lightcolor of the region. See paletteIFC for allowed colors.

Default is 'false'. Allowed are 'true' or 'false'. Used for compatibility with amnis file but role remains unknown.

Default is 'false'. Allowed are 'true' or 'false'. Used for compatibility with amnis file but role remains unknown.

determines transformation instruction for x-axis. Default is "P" for no transformation.

determines transformation instruction for y-axis. Default is "P" for no transformation.

vector of x vertices values.

vector of y vertices values.

Other arguments to be passed.

an 'IFC_data' object

list of statistics instructions, whose members are list containing 3 instructions:
- 'type' stats's type. Allowed are "COUNT","PERCENT_GATED","CONCENTRATION","PERCENT","MEAN","MEDIAN","STDDEV","MAD","CV","MINIMUM","MAXIMUM","GEOMETRIC_MEAN","MODE","VARIANCE","NAN","MEAN_RD","MEDIAN_RD".
- 'title' stats's title. If missing, it will be determined thanks to def.
- 'def' definition of the stats.
Default is:
list(list(type="COUNT",title="Count",def=""),
list(type="PERCENT_GATED",title="%Gated",def=""))

desired width. Default is 80 * (1 + length(stats)).

desired height Default is 400.

x location in analysis workspace. Default is 0.

y location in analysis workspace. Default is 0.

Other arguments to be passed.

a character string.

an 'IFC_data' object.

path to file.

The endian-ness ("big" or "little") of the target system for the file. Default is .Platform$endian.
Endianness describes the bytes order of data stored within the files. This parameter may not be modified.

other arguments to be passed.

path to file.

arguments to pass to checksumDAF or checksumXIF.

path to file.

other arguments to be passed.

a list of raw vectors.

a raw vector used to collapse. Default is as.raw(0x7c)

channel display properties containing 'xmin', 'xmax', 'xmid' and 'ymid'.

either a spillover matrix or a spillover keyword

coordinates in user system. A matrix where rows are points and with at least 2 columns named "x" and "y" for x and y coordinates, respectively.

current device adjusted coordinates. Default is missing.

whether points outside of plotting region should be bounded on the edge. Default is FALSE to clip points.

NumericMatrix, [0,1].

double, [0,1], hue. Default is 0.0

double, [0,1], saturation. Default is 0.0

a NumericMatrix.

a double x spatial offset. It has to be within ]-1,+1[. Default is NA_REAL for no change.

a double y spatial offset. It has to be within ]-1,+1[. Default is NA_REAL for no change.

an IntegerVecter /!\ It should be coercible to 3D array [height, width, rgba]

IntegerVector, of allowed length for x. Default is NULL, for not checking this parameter.

CharacterVector, of allowed classes of x. Default is NULL, for not checking this parameter.

CharacterVector, of allowed types of x. Default is NULL, for not checking this parameter.

of allowed values for x (will be passed to cpp_allowed). Default is NULL, for not checking this parameter.

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.

RawVector.

string, path to file.

string, path to file.

a NumericMatrix.

a IntegerMatrix.

bool, whether to add normal noise or not, Rcpp::Rf_rnorm(bg, sd) function is used. Default is true.

double, mean value of the background added if 'add_noise' is true. Default is 0.0.

double, standard deviation of the background added if 'add_noise' is true. Default is 0.0.

named NumericVector of channel display properties containing 'xmin', 'xmax', 'xmid' and 'ymid'.

NumericVector of x-coordinates of the points.

NumericVector of y-coordinates of the points.

NumericVector of parameters to scale raw points coordinates to pixels coordinates.

a numeric matrix.

an unsigned integer, giving the new height of returned mat. Default is 0 for no change.

an unsigned integer, giving the new width of returned mat. Default is 0 for no change.

string, path to file.

std::size_t, position of the beginning of compressed image.

uint32_t, number of bytes of compressed image.

R_len_t, Width of the decompressed image. Default is 1.

R_len_t, Height of the decompressed image. Default is 1.

R_len_t, number of channels of the decompressed image. Default is 1.

uint8_t, object removal method. Only apply for 30818 compression. Default is 0.
-1, for clipped removal: height OR width clipped pixels will be set to -1.
-2, height clipped removal: height clipped pixels will be set to -1.
-3, width clipped removal: width clipped pixels will be set to -1.
-4, only keep background: background pixels will be set to 1 and all others to 0.
-5, only keep foreground: foreground pixels will be set to 1 and all others to 0.

uint32_t, compression algorithm used. Default is 30818.

bool, whether to display information (use for debugging purpose). Default is false.

an IntegerVector. A non null array of dimensions [nrow, ncol, 4].

an IntegerMatrix whose rows are points to draw and with:
- 1st column being img col coordinate in px,
- 2nd column being img row coordinate in px.

a LogicalMatrix where every true value will be added to the image.

a 4 rows IntegerMatrix specifying rgba, from 0 to 255.

a R_len_t the size of the gaussian blurring kernel. Default is 9.

a double the sd of the gaussian blurring kernel. Default is 3.0.

NumericVector, x-boundaries of the ellipse.

NumericVector, y-boundaries of the ellipse.

string, path to file

List, ifd information of class IFC_ifd

List of colors to use.

DataFrame, channels information.

CharacterVector of indices for each channel.

NumericVector of minimal values for each channel.

NumericVector of maximal values for each channel.

NumericVector of X spatial offset correction for each channel.

NumericVector of Y spatial offset correction for each channel.

IntegerVector of removal method to be used for each channel.

LogicalVector of whether to 'add_noise' for each channel.

LogicalVector of whether to use 'full_range' for each channel.

LogicalVector of whether to use 'force_range' for each channel.

NumericVector of the 'gamma' for each channel.

IntegerVector, channels to extract.

uint8_t, type of mask to extract:
-0: no mask,
-1: at least one "raw",
-2: at least one "clipped",
-3: at least one "masked",
-4: at least one "MC" mask.

string, color mode export. Either "rgb", "gray" or "raw". Default is "raw".

a length 2 IntegerVector of final dimensions (height,width) of the image. Default is 0,0 for no change.

bool, whether to display information (use for debugging purpose). Default is false.

string, path to file.

std::size_t, position of the IFD beginning.

bool, whether to swap bytes or not. Default is 'false'.

a SEXP only NILSXP, LGLSXP, INTSXP, REALSXP, STRSXP, RAWSXP are handled.

a bool specifying if NA should be returned as NA or if they should be attributed a unique integer.

a Nullable List.

a Nullable NumericVector.

a Nullable LogicalVector. /!\ But cast to LogicalMatrix

a R_len_t, max number integers to choose from.

a R_len_t the desired size of return integers.

a bool determining if sampling should be done with replacement. Default is false.

string, path to file.

std::size_t, position of the IFD beginning.

bool, whether to display information (use for debugging purpose). Default is 'false'.

uint32_t maximal number of individual scalar to extract BYTE/ASCII/SBYTE/UNDEFINED for TAGS (1, 2, 6 or 7). Default is 12.
However, if less is found, less is returned in map. Note that, if 0 is provided, it will be automatically set to 1.

whether to force truncation for all TAGS types. Default is FALSE.
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.

number of objects in the data.

IntegerVector of number of bytes to take from 'ord_'.

IntegerVector bytes order.

bool whether to reverse order or not. Default is false.

string, path to file.

R_len_t, numbers of objects present in the file. Default is 0. If obj_count <= 0 then progress_bar is forced to false.

bool, whether to display a progress bar. Default is false.

a List of class 'IFC_progress' containing a progress bar of class 'txtProgressBar', 'winProgressBar' or 'Progress'. Default is R_Nilvalue.

bool, whether to display information (use for debugging purpose). Default is false.

string, path to file.

R_len_t, numbers of objects present in the file. Default is 0. If obj_count <= 0 then progress_bar is forced to false.

bool, whether to display a progress bar. Default is false.

a List of class 'IFC_progress' containing a progress bar of class 'txtProgressBar', 'winProgressBar' or 'Progress'. Default is R_Nilvalue.

bool, whether to display information (use for debugging purpose). Default is false.

a DataFrame.

int32_t.

int64_t.

NumericVector.

double, value where transition between Lin/Log is applied.

double, base of Log scale.

double, value that is used to smooth transition between Lin/Log.

a NumericMatrix.

a NumericMatrix.

a NumericMatrix.

x offset in 'A' to start writing 'B'.

x offset in 'A' to start writing 'B'.

a logical. Default is false. When false, the default, values of 'B' are written into 'A' when 'mask' is not 0.0. When true, values of '1-B' are written into 'A' when 'mask' is not 0.0.

a NumericMatrix.

a NumericMatrix.

a NumericMatrix.

Nullable Rcpp CharacterVector.

a finite NumericMatrix.

a finite NumericVector, sets the range of the input intensity values. Values outside this range are clipped. Default is [0.0,4095.0].

if 'full_range' is true, then 'input_range' will be set to [0.0,4095.0] and 'gamma' forced to 1.0. Default is false.

if 'force_range' is true, then 'input_range' will be adjusted to 'mat' range in [-4095.0, +inf] and 'gamma' forced to 1.0. Default is false.
Note that this parameter takes the precedence over 'input_range' and 'full_range'.

correction. Default is 1.0, for no correction.

double.

bool, whether to swap or not.

NumericMatrix, a 2-columns matrix with (x and y) coordinates of the points of interest.

NumericMatrix, a 2-columns matrix defining polygon vertices or ellipse boundaries.

int, used for computation. Default is 1.
1: Trigonometry.
2: Special case = axes-aligned rectangle.
3: Special case = axes-aligned ellipse.

double, epsilon threshold value. Default is 0.000000000001

a uint16_t determining the returned image width.

a uint16_t determining the returned image height.

a List containing drawing information:
- pch, an integer specifying a symbol to draw. Handled are [0-20]. Otherwise only a pixel will be drawn.
- size, an integer specifying the size in pixel of the shape, from 1 to 255.
- color a 4 rows IntegerMatrix (rgba) of the color used to draw the shape.
- coords, an IntegerMatrix whose rows are points to draw and with:
-* 1st column being img col coordinate in px,
-* 2nd column being img row coordinate in px. - blur_size an integer controlling the size of the blurring gaussian kernel.
- blur_sd a double controlling the sd of the blurring gaussian kernel.

a Nullable IntegerVector that will be cast to 3D array when not NULL. Default is R_NilValue.
When not NULL, its dimensions should be the same as required by 'width' and 'height', otherwise an error will be thrown.
When not NULL, it will serve as a background to draw new points on top of it.

RawVector.

bool, whether to swap or not.

string, path to file.

std::size_t, position of the beginning of compressed image.

uint32_t, number of bytes of compressed image.

uint32_t, Width of the decompressed image. Default is 1.

uint32_t, Height of the decompressed image. Default is 1.

uint32_t, compression algorithm used. Default is 30818.

bool, whether to swap bytes or not. Default is false.

bool, whether to display information (use for debugging purpose). Default is false.

a NumericVector.

a double used as replcaement value. Default is 0.0

a numeric matrix.

an unsigned integer, giving the new height of returned mat. Default is 0 for no change.

an unsigned integer, giving the new width of returned mat. Default is 0 for no change.

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.

double, mean value of the background added if add_noise is true. Default is 0.

double, standard deviation of the background added if add_noise is true. Default is 0.

string, path to file.

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.

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).

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.

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.

StringVector to match

NumericVector.

double, value where transition between Lin/Log is applied.

double, base of Log scale.

double, value that is used to smooth transition between Lin/Log.

NumericMatrix.

NumericVector, whose members are h,s,v color. This vector has to be named with 1st name being the name of this color.

IntegerMatrix.

a length 2 IntegerVector, of final dimensions (height,width) of the image. Default is 0,0 for no change.

string, color mode export. Either "rgb", "gray" or "raw". Default is "raw".

uint16_t image object type. Default is 2.

a finite NumericVector, only apply when 'mode' is not "raw", sets the range of the input intensity values. Values outside this range are clipped. Default is [0.0,4095.0].

bool, whether to add normal noise or not. Default is true.

double, mean value of the background added if 'add_noise' is true. Default is 0.0.

double, standard deviation of the background added if 'add_noise' is true. Default is 0.0.

bool, only apply when 'mode' is not "raw", if 'full_range' is true, then 'input_range' will be set to [0.0,4095.0] and 'gamma' forced to 1.0. Default is false.

bool, only apply when 'mode' is not "raw", if 'force_range' is true, then 'input_range' will be adjusted to object range in [-4095.0, +inf] and 'gamma' forced to 1.0. Default is false.
Note that this parameter takes the precedence over 'input_range' and 'full_range'.

correction. Default is 1.0, for no correction.

X offset correction. Default is 0.0 for no change.

Y offset correction. Default is 0.0 for no change.

uint32_t.

uint32_t.

uint64_t.

a NumericVector

a NumericVector

a [0,1] normalized image matrix or 3D array. If 3D array, 3rd dimension should be of length 1 or 3.

an 'IFC_data' object extracted by ExtractFromDAF(extract_features = TRUE) or ExtractFromXIF(extract_features = TRUE).

a list of features to add to obj. Each element of this list will be coerced by buildFeature.

Other arguments to be passed.

an 'IFC_data' object extracted by ExtractFromDAF(extract_features = TRUE) or ExtractFromXIF(extract_features = TRUE).

a list of graph(s) to add to obj. Each element of this list will be coerced by buildGraph.

whether to try to adjust graph(s) when possible. Default is TRUE.
-TRUE, graph(s) will be kept if possible using only regions, pops it depends that can be found in 'obj',
-FALSE, graph(s) will be kept only if all features, regions, pops it refers to are found in 'obj',
-NA, is not allowed and will throw an error.

Other arguments to be passed.

an 'IFC_data' object extracted by ExtractFromDAF(extract_features = TRUE) or ExtractFromXIF(extract_features = TRUE).

name of the population to sample.

a non-negative integer giving the number of items to choose.

name of the exported population.

a list of elements to pass to set.seed or a single value, interpreted as an integer, or NULL to be used when 'add_noise' is set to TRUE. Default is NULL. Note that NA_integer_ or list(seed = NA_integer_) can be used to not call set.seed at all.

Other arguments to be passed.

an 'IFC_data' object extracted by ExtractFromDAF(extract_features = TRUE) or ExtractFromXIF(extract_features = TRUE).

a list of population(s) to add to 'obj'. Each element of this list will be coerced by buildPopulation.

algorithm used to determine if object belongs to a polygon region or not. Default is 1.
Note that for the moment only 1(Trigonometry) is available.

epsilon to determine if object belongs to a polygon region or not. It only applies when algorithm is 1. Default is 1e-12.

whether to display a progress bar. Default is TRUE.

Other arguments to be passed.

an 'IFC_data' object extracted by ExtractFromDAF(extract_features = TRUE) or ExtractFromXIF(extract_features = TRUE).

a list of region(s) to add to obj. Each element of this list will be coerced by buildRegion.

Other arguments to be passed.

an 'IFC_data' object extracted by ExtractFromDAF(extract_features = TRUE) or ExtractFromXIF(extract_features = TRUE).

a list of population(s) to modify in 'obj'. Each element of this list will be coerced by buildPopulation.

whether to display a progress bar. Default is TRUE.

Other arguments to be passed.

an 'IFC_data' object extracted by ExtractFromDAF(extract_features = TRUE) or ExtractFromXIF(extract_features = TRUE).

a list of region(s) to modify in 'obj'. Each element of this list will be coerced by buildRegion.

whether to display a progress bar. Default is TRUE.

Other arguments to be passed.

an 'IFC_data' object extracted by ExtractFromDAF(extract_features = TRUE) or ExtractFromXIF(extract_features = TRUE).

a character vector of features names to remove within 'obj'. Note that "Object Number" is not allowed and will be excluded from 'features' if present.

whether to return a list of elements that will be impacted by the removal. Default is TRUE. If FALSE then modified object will be returned.

whether to try to adjust graph(s) when possible. Default is TRUE.
-TRUE, graph(s) will be kept if possible using only regions, pops it depends that can be found in 'obj',
-FALSE, graph(s) will be kept only if all features, regions, pops it refers to are found in 'obj',
-NA, graph(s) will be removed no matter if features, regions, pops it refers to are found in 'obj'.

Other arguments to be passed.

an 'IFC_data' object extracted by ExtractFromDAF(extract_features = TRUE) or ExtractFromXIF(extract_features = TRUE).

an integer vector of graph(s) to remove within 'obj'.

whether to return a list of elements that will be impacted by the removal. Default is TRUE. If FALSE then modified object will be returned.

whether to try to adjust graph(s) when possible. Default is TRUE.
-TRUE, graph(s) will be kept if possible using only regions, pops it depends that can be found in 'obj',
-FALSE, graph(s) will be kept only if all features, regions, pops it refers to are found in 'obj',
-NA, graph(s) will be removed no matter if features, regions, pops it refers to are found in 'obj'.

Other arguments to be passed.

an 'IFC_data' object extracted by ExtractFromDAF(extract_features = TRUE) or ExtractFromXIF(extract_features = TRUE).

a character vector of population names to remove within 'obj'. Note that "All" and "" are not allowed and will be excluded from 'pops' if present.

whether to return a list of elements that will be impacted by the removal. Default is TRUE. If FALSE then modified object will be returned.

whether to try to adjust graph(s) when possible. Default is TRUE.
-TRUE, graph(s) will be kept if possible using only regions, pops it depends that can be found in 'obj',
-FALSE, graph(s) will be kept only if all features, regions, pops it refers to are found in 'obj',
-NA, graph(s) will be removed no matter if features, regions, pops it refers to are found in 'obj'.

Other arguments to be passed.

an 'IFC_data' object extracted by ExtractFromDAF(extract_features = TRUE) or ExtractFromXIF(extract_features = TRUE).

a character vector of regions names to remove within 'obj'.

whether to return a list of elements that will be impacted by the removal. Default is TRUE. If FALSE then modified object will be returned.

whether to try to adjust graph(s) when possible. Default is TRUE.
-TRUE, graph(s) will be kept if possible using only regions, pops it depends that can be found in 'obj',
-FALSE, graph(s) will be kept only if all features, regions, pops it refers to are found in 'obj',
-NA, graph(s) will be removed no matter if features, regions, pops it refers to are found in 'obj'.

Other arguments to be passed.

an 'IFC_data' object extracted with features extracted.

pattern used to export file. Placeholders, like "%d/%s_fromR.%e", will be substituted:
-%d: with full path directory of 'obj$fileName'
-%p: with first parent directory of 'obj$fileName'
-%e: with extension of 'obj$fileName' (without leading .)
-%s: with shortname from 'obj$fileName' (i.e. basename without extension).
Exported file extension will be deduced from this pattern. Note that it has to be a .ast.

Character String. Allow user to change displayed population. Default is 'All'.

whether to overwrite file or not. Default is FALSE. Note that if TRUE, it will overwrite exported file if path of 'obj$fileName' and deduced from 'write_to' arguments are different. Otherwise, you will get an error saying that overwriting source file is not allowed.
Note also that an original file, i.e. generated by IDEAS(R) or INSPIRE(R), will never be overwritten. Otherwise, you will get an error saying that overwriting original file is not allowed.

whether to display a progress bar. Default is TRUE.

whether to display information (use for debugging purpose). Default is FALSE.

other arguments to be passed.

an 'IFC_data' object extracted with features extracted.

pattern used to export file. Placeholders, like "%d/%s_fromR.%e", will be substituted:
-%d: with full path directory of 'obj$fileName'
-%p: with first parent directory of 'obj$fileName'
-%e: with extension of 'obj$fileName' (without leading .)
-%s: with shortname from 'obj$fileName' (i.e. basename without extension).
Exported file extension will be deduced from this pattern. Note that it has to be a .daf.

Character String. Allow user to change displayed population. Default is 'All'.

whether to overwrite file or not. Default is FALSE. Note that if TRUE, it will overwrite exported file if path of 'obj$fileName' and deduced from 'write_to' arguments are different. Otherwise, you will get an error saying that overwriting source file is not allowed.
Note also that an original file, i.e. generated by IDEAS(R) or INSPIRE(R), will never be overwritten. Otherwise, you will get an error saying that overwriting original file is not allowed.

whether to write object to file in binary mode or not. Default is TRUE.
Note that it can represent a convenient way to make file written in binary mode back-compatible with former version of IDEAS software.
/!\ However unexpected behaviour may happen if features, regions, pops, ... are depending on masks (e.g. AdaptiveErode, Component, LevelSet, Watershed) introduced in newer version of IDEAS software.
/!\ Important please note that conversion from binary to non-binary and back to binary may create some rounding adjustment resulting in some features/image values changes.
Finally, if data originate from FCS, 'binary' will be forced to FALSE.

The endian-ness ("big" or "little") of the target system for the file. Default is .Platform$endian.
Endianness describes the bytes order of data stored within the files. This parameter may not be modified.

whether to display a progress bar. Default is TRUE.

whether to display information (use for debugging purpose). Default is FALSE.

whether to export daf file with full name of its corresponding cif, if found. Default is TRUE. If cif can't be found, daf file will be exported with the original cif file name.

the path of the directory to initially look to cif file. Default is dirname(obj$fileName). Only apply when 'fullname' is set to TRUE.

number of times data_to_DAF will be allowed to find corresponding cif file. Default is +Inf. Only apply when 'fullname' is set to TRUE.

other arguments to be passed.

an object of class 'IFC_progress' containing a progress bar of class 'txtProgressBar', 'winProgressBar' or 'Progress'.

value return by xml2::as_list. Default is 5.

value return by xml2::as_list.

maximum number of recurrence into subnodes. Default is 5.

an 'IFC_data' object

a feature name.

character string describing transformation used and its parameters. See parseTrans().

either a list or an object coercible to logical matrix

an object either a data.frame, a list or something coercible to numeric matrix.

an object either a data.frame, a list or something coercible to numeric matrix.

a bool determining if 1st column of returned object should be given 1 to nrow integers

list containing feature definition

a list of elements to pass to set.seed or a single value, interpreted as an integer, or NULL. NA_integer_ or list(seed = NA_integer_) can be used to prevent 'seed' argument from being passed to set.seed. Default is NA_integer_.

object returned by splitp.

object returned by splitf. It will be used to substitute %d, %p, %s and %e.

string to be used to substitute %c

string to be used to substitute %o

a set of xml_nodes

type of the gate to extract

a character vector.

number of characters of the desired returned name. Default is 10.

forbidden character vector. Default is character().

a list of elements to pass to set.seed or a single value, interpreted as an integer, or NULL. Default is list(seed = 0xFC, "Mersenne-Twister", "Inversion", "Rounding"). Note that NA_integer_ or list(seed = NA_integer_) can be used to not call set.seed at all. Note also that the default is chosen because it is compatible with old R version.

path to file..

other arguments to be passed.

path to file containing aborted information.
If missing, the default, a dialog box will be displayed to choose this file. Note, that if provided 'default_batch_dir' and 'config_file' will not be used.

directory where batches are stored.
It can be found in IDEAS(R) software, under Options -> Application Defaults -> Directories -> Default Batch Report Files Directory. If missing, the default, it will be deduced from IDEAS(R) config file, However, if it can't be deduced then current working directory will be used.
This argument takes precedence over 'config_file' and filling 'default_batch_dir' prevents the use of 'config_file' argument.

path to IDEAS(R) config file.
It may depends on IDEAS(R) software installation but one may use "C:/Users/%USER%/AppData/Roaming/Amnis Corporation/userconfig.xml".

a data.frame of features, typically an object of class 'IFC_features'.

a list of features definitions, typically an object of class 'IFC_features_def'.

operators used. Default is c("+", "-", "*", "/", "(", ")", "ABS", "COS", "SIN", "SQR", "SQRT").

string used for splitting. Default is "|".

path to file.

an object of class 'IFC_ifd_list' extracted by getIFD.

scalar, integer (index) or the name of 'IFD' sub-element to extract 'tag' from. Default is 1 to extract 'tag' from the first member of 'IFD'.

scalar, integer (index) or the name of the IFD[[which]] of the desired 'tag'.

whether to return tag as a raw vector. Default is FALSE.

path to file.

either "all", "first" or an object of class 'IFC_offset'. Default is "first".

a positive integer maximal number of individual scalar to extract BYTE/ASCII/SBYTE/UNDEFINED for TAGS (1, 2, 6 or 7). Default is 12.
However, if less is found, less is returned in map. Note that, if 0 is provided, it will be automatically set to 1.

whether to force truncation for all TAGS types. Default is FALSE.
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.

whether to display information (use for debugging purpose). Default is FALSE.

quantity of information displayed when verbose is TRUE; 1: normal, 2: rich. Default is 1.

whether to display a progress bar. Default is FALSE.

whether to bypass checks on 'trunc_bytes', 'force_trunc', 'verbose', 'verbosity' and 'display_progress'. Default is FALSE.

other arguments to be passed.

path to file.

Object of class ‘IFC_offset'. If missing, the default, ’offsets' will be extracted from 'fileName'.
This param is not mandatory but it may allow to save time when exporting repeated image value on same file.

integer vector, IDEAS objects ids numbers to extract.
If missing, the default, images values from all objects will be extracted.

whether to display a progress bar. Default is FALSE.

when no 'offsets' are provided whether to fast extract 'objects' or not. Default is TRUE.
Meaning that 'objects' will be extracted expecting that 'objects' are stored in ascending order.
Only apply when 'offsets' are not provided.
Note that a warning will be sent if an object is found at an unexpected order.

other arguments to be passed.

path to file..

whether to extract information from 'acquisition' or 'analysis'. Default is 'analysis'.

whether to display information (use for debugging purpose). Default is FALSE.

quantity of information print to console when verbose is TRUE; 1: normal, 2: rich. Default is 1.

whether to send warning message when trying to read 'analysis' information from a 'rif' file. Default is TRUE.

when display information can't be retrieved whether to use default values. Default is TRUE.

the path of the directory to initially look to cif file. Default is dirname(fileName). Only apply when 'fileName' is a .daf file.

number of times getInfo will be allowed to find corresponding cif file. Default is +Inf. Only apply when 'fileName' is a .daf file. If cif can't be found, but 'ntry' is reached, then an error will be thrown.

other arguments to be passed.

a character string.

path to file.

whether to fast extract 'objects' or not. Default is TRUE.
Meaning that offsets will be extracted expecting that 'objects' are stored in ascending order.
A message will be thrown since fast extraction method does not ensure correct mapping between objects and offsets.
If set to FALSE, all object_ids will be scanned from 'fileName' to ensure extraction of desired offsets.

whether to display a progress bar. Default is TRUE.

whether to display information (use for debugging purpose). Default is FALSE.

path to file.

current device plotting region. Default is missing.

current device height in pixel. Default is grDevices::dev.size("px")[1].

current device width in pixel. Default is grDevices::dev.size("px")[2].

current device ratio. Default is graphics::par('din') / graphics::par('pin').

a feature definition as created by buildFeature.

a data.frame of features, typically an object of class 'IFC_features'.

vector of same length as features to use for substitution. It can be used to speed up the process.

operators used. Default is c("+", "-", "*", "/", "(", ")", "ABS", "COS", "SIN", "SQR", "SQRT").

string used for splitting. Default is "|".

list of populations

total number of objects.

a data.frame whose columns represent grouping factor.

a string used to collapse groups levels.

whether to keep NA levels resulting from groups merging

other arguments to be passed.

non empty character vectors.

whether to replace all instances of 'pattern' or only the 1st one. Default is TRUE, to replace all instances.

A numeric vector.

value where transition between Lin/Log is applied.

base of Log scale.

value that is used to smooth transition between Lin/Log. Default is log(base).

an 'IFC_graphs' object extracted with features extracted.

a character vector Default is missing.

whether to convert color toR or back. Default is TRUE.

a pch (converted to integer) or a character vector. Default is missing.

whether to convert color toR or back. Default is FALSE.

paths of files to merge. All files have to be either '.rif' or '.cif' files. All files should have same channels.

pattern used to export file. Placeholders, like "%d/%s_fromR.%e", will be substituted:
-%d: with full path directory of first element of 'fileName'
-%p: with first parent directory of first element of 'fileName'
-%e: with extension of 'fileName' (without leading .)
-%s: with shortname from of first element of 'fileName' (i.e. basename without extension).
Exported file extension will be deduced from this pattern. It has to be the same as 'fileName', i.e. .cif or .rif.

whether to try to extract features. Default is FALSE. Not yet implemented.

the endian-ness ("big" or "little") of the target system for the file. Default is .Platform$endian.
Endianness describes the bytes order of data stored within the files. This parameter may not be modified.

whether to display information (use for debugging purpose). Default is FALSE.

quantity of information displayed when verbose is TRUE; 1: normal, 2: rich. Default is 1.

whether to overwrite file or not. Default is FALSE.
Note that if TRUE, it will overwrite exported file if paths of files in 'fileName' and deduced from 'write_to' arguments are different. Otherwise, you will get an error saying that overwriting source file is not allowed.
Note also that an original file, i.e. generated by IDEAS(R) or INSPIRE(R), will never be overwritten. Otherwise, you will get an error saying that overwriting original file is not allowed.

whether to display a progress bar. Default is TRUE.

whether to register files' paths and objects' ids in the exported file. Default is TRUE.

other arguments to be passed.

named NumericVector of channel display properties containing 'xmin', 'xmax', 'xmid' and 'ymid'.

gamma

character strings, giving the 'title'(='message' for shiny progress bar) and the 'label'(='detail' for shiny progress bar).

(finite) numeric values for the extremes of the progress bar. Must have 'min' < 'max'.

initial value for the progress bar.

(finite) numeric value for the number of individual chunk of the progress bar. Default is 21.

the width of the progress bar. If missing, the default, will be NA for "txtProgressBar" and 300 for "winProgressBar".

does not apply for "winProgressBar", the style of the bar. If missing, the default, will be 3 "txtProgressBar" and getShinyOption("progress.style", default = "notification") for shiny progress bar.

only apply for "txtProgressBar", the character (or character string) to form the progress bar.

only apply for "txtProgressBar", an open connection object or "" which indicates the console: stderr() might be useful here. Default is "".

Other arguments to be passed.

a string, current component.

an integer, representing current number of opened/closed bracket.

a string, alias used for population name.

a numeric vector.

number of significant decimal digits to keep. Default is 22.

a numeric matrix (image).

a numeric matrix (mask identifying abnormalities).

if TRUE adds normal noise to background using rnorm(), from Rcpp. Default is TRUE.

a list of elements to pass to set.seed or a single value, interpreted as an integer, or NULL to be used when 'add_noise' is set to TRUE. Default is NULL. Note that NA_integer_ or list(seed = NA_integer_) can be used to not call set.seed at all.

mean value of the background added if add_noise is TRUE. Default is 0.

standard deviation of the background added if add_noise is TRUE. Default is 0.

a [0,1] numeric matrix.

a color

An object extracted by objectExtract of class 'IFC_img' or 'IFC_msk'.
Note that a matrix with finite values can also be used.

a finite numeric vector of 2 values, sets the range of the input intensity values. Values outside this range are clipped. Default is [0,4095].

if 'full_range' is TRUE, then 'input_range' will be set to [0,4095] and 'gamma' forced to 1. Default is FALSE.

if 'force_range' is TRUE, then 'input_range' will be adjusted to 'image' range in [-4095,+inf] and 'gamma' forced to 1. Default is FALSE.
Note that this parameter takes the precedence over input_range' and full_range'.

'gamma' correction. Default is 1, for no correction.

a color. Default is "Green".

display resolution. Default is 300.

list of sub elements of IFD data information extracted by getIFD. This argument can't be missing.

object of class 'IFC_param', containing extraction parameters defined by objectParam.
This argument is not mandatory but it may allow to save time for repeated image export on same file. If this argument is missing, objectExtract will use named arguments in '...' as input to objectParam to control object extraction.
However, if 'param' is provided, '...' will be ignored.

whether to display information (use for debugging purpose). Default is FALSE.

whether to bypass checks on 'ifd' and 'param'. Default is FALSE.

Arguments passed on to objectParam

info

object of class 'IFC_info', rich information extracted by getInfo. This argument is not mandatory but it may allow to save time for repeated image export on same file. If missing, the default, 'info' will be extracted thanks to '...'.

mode

color mode export. Either "rgb", "gray" or "raw". Default is "raw". Note that "raw" is only possible when 'export' is "matrix".

export

format mode export. Either "file", "matrix", "base64". Default is "matrix".

write_to

used when export is "file" or "base64" to compute respectively exported file name or base64 id attribute.
Exported file extension and base64 MIME type will be deduced from this pattern. Allowed export are ".bmp", ".jpg", ".jpeg", ".png", ".tif", ".tiff". Note that ".bmp" are faster but not compressed producing bigger data.
Placeholders, if found, will be substituted:
-%d: with full path directory,
-%p: with first parent directory,
-%e: with extension (without leading .),
-%s: with shortname (i.e. basename without extension),
-%o: with object_id,
-%c: with channel_id.
A good trick is to use:
-"%d/%s/%s_%o_%c.tiff", when 'export' is "file",
-"%o_%c.bmp", when 'export' is "base64".
Note that if missing and 'export' is not "file", 'write_to' will be set to "%o_%c.bmp".

base64_id

whether to add id attribute to base64 exported object. Default is FALSE.
Only applied when export is "base64".

base64_att

attributes to add to base64 exported object. Default is "".
Only applied when export is "base64". For example, use "class='draggable'".
Note that id (if 'base64_id' is TRUE) and width and height are already used.

overwrite

only apply when 'export' is "file" whether to overwrite file or not. Default is FALSE.

composite

character vector of image composite. Default is "", for no image composite.
Should be like "1.05/2.4/4.55" for a composition of 5 perc. of channel 1, 40 perc. of channel 2 and 50 perc. of channel 55.
Note that channels should have been acquired and final image composition should be 100 perc., otherwise an error is thrown.
Note that each composite will be appended after 'selection'.

selection

physical channels to extract.
Note that this parameter will be ordered.
Default is "all" to extract all acquired channels.
Use "none" to only extract composite.

random_seed

a list of elements to pass to set.seed or a single value, interpreted as an integer, or NULL to be used when 'add_noise' is set to TRUE. Default is NULL. Note that NA_integer_ or list(seed = NA_integer_) can be used to not call set.seed at all.

size

a length 2 integer vector of final dimensions of the image, height 1st and width 2nd. Default is c(0,0) for no change.

force_width

whether to use information in 'info' to fill size. Default is TRUE. When set to TRUE, width of 'size' argument will be overwritten.

removal

removal method: Either "none", "raw", "clipped", "masked", "MC".
-"none", to keep image as is, no mask extraction will be performed resulting in faster extraction,
-"raw", to keep image as is, it provides a convenient way to retrieve "raw" value for the mask,
-"clipped", to remove clipped object from image,
-"masked", to only keep masked object from image,
-"MC", to keep MC masked object from image. This parameter will be repeated with rep_len() from base for every physical channel that needs to be extracted according to 'selection' and 'composite' parameters.

add_noise

if TRUE adds normal noise to background using Rcpp. Default is TRUE.
Note that it is better to set it to FALSE when 'removal' is "masked" or "MC". Doing so will allow to place masked object in a zero filled background, otherwise background will still be filled with noise. This parameter will be repeated with rep_len() from base for every physical channel that needs to be extracted according to 'selection' and 'composite' parameters.

full_range

only apply when 'mode' is not "raw", if 'full_range' is TRUE, then object range will be considered as 0 to 4095, it is like "raw" 'mode' but resulting in [0,4095] normalization to [0,1]. Default is FALSE.
This parameter will be repeated with rep_len() from base for every physical channel that needs to be extracted according to 'selection' and 'composite' parameters.

force_range

only apply when 'mode' is not "raw", if 'force_range' is TRUE, then range will be adjusted to object range in [-4095,+inf] resulting in normalization to [0,1]. Default is FALSE.
This parameter will be repeated with rep_len() from base for every physical channel that needs to be extracted according to 'selection' and 'composite' parameters.
Note that this parameter takes the precedence over 'full_range'.

spatial_correction

only apply on RIF file, whether to apply spatial correction. Default is FALSE.

a finite numeric matrix.

a finite numeric vector of 2 values, sets the range of the input intensity values. Values outside this range are clipped. Default is [0,4095].

if 'full_range' is TRUE, then 'input_range' will be set to [0,4095] and 'gamma' forced to 1. Default is FALSE.

if 'force_range' is TRUE, then 'input_range' will be adjusted to 'mat' range in [-4095,+inf] and 'gamma' forced to 1. Default is FALSE.
Note that this parameter takes the precedence over input_range' and full_range'.

'gamma' correction. Default is 1, for no correction.

arguments to be passed to getInfo, only if 'info' is not provided.

object of class 'IFC_info', rich information extracted by getInfo. This argument is not mandatory but it may allow to save time for repeated image export on same file. If missing, the default, 'info' will be extracted thanks to '...'.

color mode export. Either "rgb", "gray" or "raw". Default is "raw". Note that "raw" is only possible when 'export' is "matrix".