cpp_extract: IFC_object Extraction

In IFC: Tools for Imaging Flow Cytometry

IFC_object Extraction

Description

Extracts object from ifd

Arguments

fname	string, path to file
ifd	List, ifd information of class IFC_ifd
colors	List of colors to use.
channels	DataFrame, channels information.
physicalChannel	CharacterVector of indices for each channel.
xmin	NumericVector of minimal values for each channel.
xmax	NumericVector of maximal values for each channel.
spatialX	NumericVector of X spatial offset correction for each channel.
spatialY	NumericVector of Y spatial offset correction for each channel.
removal	IntegerVector of removal method to be used for each channel.
add_noise	LogicalVector of whether to 'add_noise' for each channel.
full_range	LogicalVector of whether to use 'full_range' for each channel.
force_range	LogicalVector of whether to use 'force_range' for each channel.
gamma	NumericVector of the 'gamma' for each channel.
chan_to_extract	IntegerVector, channels to extract.
extract_msk	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.
mode	string, color mode export. Either "rgb", "gray" or "raw". Default is "raw".
size	a length 2 IntegerVector of final dimensions (height,width) of the image. Default is 0,0 for no change.
verbose	bool, whether to display information (use for debugging purpose). Default is false.

Details

When 'add_noise' is false, background will be automatically set to minimal pixel value for "masked" and "MC" 'removal' method.

IFC documentation built on Sept. 14, 2023, 1:08 a.m.