OpenSpecy (version 1.5.3)

collapse_spec: Define features

Description

Functions for analyzing features, like particles, fragments, or fibers, in spectral map oriented OpenSpecy object.

Usage

collapse_spec(x, ...)
# S3 method for default
collapse_spec(x, ...)
# S3 method for OpenSpecy
collapse_spec(x, fun = median, column = "feature_id", ...)
def_features(x, ...)
# S3 method for default
def_features(x, ...)
# S3 method for OpenSpecy
def_features(
  x,
  features,
  shape_kernel = c(3, 3),
  shape_type = "box",
  close = F,
  close_kernel = c(4, 4),
  close_type = "box",
  img = NULL,
  bottom_left = NULL,
  top_right = NULL,
  ...
)

Value

An OpenSpecy object appended with metadata about the features or collapsed for the features. All units are in pixels. Metadata described below.

x

x coordinate of the pixel or centroid if collapsed

y

y coordinate of the pixel or centroid if collapsed

feature_id

unique identifier of each feature

area

area in pixels of the feature

perimeter

perimeter of the convex hull of the feature

feret_min

feret_max divided by the area

feret_max

largest dimension of the convex hull of the feature

convex_hull_area

area of the convex hull

centroid_x

mean x coordinate of the feature

centroid_y

mean y coordinate of the feature

first_x

first x coordinate of the feature

first_y

first y coordinate of the feature

rand_x

random x coordinate from the feature

rand_y

random y coordinate from the feature

r

if using visual imagery overlay, the red band value at that location

g

if using visual imagery overlay, the green band value at that location

b

if using visual imagery overlay, the blue band value at that location

Arguments

x

an OpenSpecy object

fun

function name to collapse by.

column

column name in metadata to collapse by.

features

a logical vector or character vector describing which of the spectra are of features (TRUE) and which are not (FALSE). If a character vector is provided, it should represent the different feature types present in the spectra.

shape_kernel

the width and height of the area in pixels to search for connecting features, c(3,3) is typically used but larger numbers will smooth connections between particles more.

shape_type

character, options are for the shape used to find connections c("box", "disc", "diamond")

close

logical, whether a closing should be performed using the shape kernel before estimating components.

close_kernel

width and height of the area to close if using the close option.

close_type

character, options are for the shape used to find connections c("box", "disc", "diamond")

img

a file location where a visual image is that corresponds to the spectral image.

bottom_left

a two value vector specifying the x,y location in image pixels where the bottom left of the spectral map begins. y values are from the top down while x values are left to right.

top_right

a two value vector specifying the x,y location in the visual image pixels where the top right of the spectral map extent is. y values are from the top down while x values are left to right.

...

additional arguments passed to subfunctions.

Author

Win Cowger, Zacharias Steinmetz

Details

def_features() accepts an OpenSpecy object and a logical or character vector describing which pixels correspond to particles. collapse_spec() takes an OpenSpecy object with particle-specific metadata (from def_features()) and collapses the spectra with a function intensities for each unique particle. It also updates the metadata with centroid coordinates, while preserving the feature information on area and Feret max.

Examples

data.table::setDTthreads(2)
tiny_map <- read_extdata("CA_tiny_map.zip") |> read_any()
identified_map <- def_features(tiny_map, tiny_map$metadata$x == 0)
collapse_spec(identified_map)