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Define features

Source: R/def_features.R
def_features.Rd

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

Usage

collapse_spec(x, ...)

# Default S3 method
collapse_spec(x, ...)

# S3 method for class 'OpenSpecy'
collapse_spec(x, fun = median, column = "feature_id", ...)

def_features(x, ...)

# Default S3 method
def_features(x, ...)

# S3 method for class '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,
  ...
)

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.

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

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.

Author

Win Cowger, Zacharias Steinmetz

Examples

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)
#>      wavenumber          1        -88
#>           <num>      <num>      <num>
#>   1:     717.42 -0.3454294 -0.1846190
#>   2:     725.13 -0.3505079 -0.2030258
#>   3:     732.85 -0.3595735 -0.2236059
#>   4:     740.56 -0.3662870 -0.2380186
#>   5:     748.28 -0.3689005 -0.2436821
#>  ---                                 
#> 423:    3972.81 -0.4140871 -0.3092059
#> 424:    3980.52 -0.4108835 -0.3107601
#> 425:    3988.24 -0.4105957 -0.3180229
#> 426:    3995.95 -0.4125072 -0.3195935
#> 427:    4003.67 -0.4132366 -0.3126730
#> 
#> $metadata
#>        x     y feature_id  area perimeter feret_min feret_max convex_hull_area
#>    <num> <num>     <char> <int>     <num>     <num>     <num>            <num>
#> 1:     0     0          1    13        24         1        13                0
#> 2:     1     0        -88    NA        NA        NA        NA               NA
#>          file_name  license
#>             <char>   <char>
#> 1: CA small UF.dat CC BY-NC
#> 2: CA small UF.dat CC BY-NC
#>                                                     description samples lines
#>                                                          <char>   <num> <num>
#> 1: Pixel 15, XPos=12549.72, YPos= 589.82, X=12362.22, Y= 614.82      16    13
#> 2: Pixel 15, XPos=12549.72, YPos= 589.82, X=12362.22, Y= 614.82      16    13
#>    bands header offset data type interleave                  z plot titles
#>    <num>         <num>     <num>     <char>                         <char>
#> 1:   427             0         4        bip Wavenumbers (cm-1), Absorbance
#> 2:   427             0         4        bip Wavenumbers (cm-1), Absorbance
#>                  pixel size col_id
#>                      <char> <char>
#> 1: 0.000025000, 0.000025000    0_0
#> 2: 0.000025000, 0.000025000    0_1
#>                                                           session_id
#>                                                               <char>
#> 1: ecda43264a8678214ae194e7d1bd2078/b112b38eae2fd98e0568643174fff2df
#> 2: ecda43264a8678214ae194e7d1bd2078/b112b38eae2fd98e0568643174fff2df
#>                             file_id centroid_x centroid_y first_x first_y
#>                              <char>      <num>      <num>   <num>   <num>
#> 1: 215a0fd7e0dc3b1001799214618ce6eb          0          6       0       0
#> 2: 215a0fd7e0dc3b1001799214618ce6eb          8          6       1       0
#>    rand_x rand_y
#>     <num>  <num>
#> 1:      0     10
#> 2:     14      1