Extract mean/median spectra for a spectral cube

Usage

at_extract_spectrum(
  project,
  img = NULL,
  stat = "mean",
  layer = NULL,
  label = NULL,
  level = 0L,
  call = rlang::caller_env(),
  nonfinite = c("propagate", "omit", "error")
)

Arguments

project: An annot_project.
img: An annot_image; defaults to the project's image. Supplying an alternate image asserts spatial registration on the same level-0 pixel grid. Its level-0 extent must match; differing pyramid dimensions are handled using the alternate image's actual level dimensions.
stat: "mean" (default) or "median".
layer, label: Optional filters.
level: Integer pyramid level. Default 0.
call: The calling environment, for error reporting.
nonfinite: Policy for NA, NaN and infinite samples: "propagate" (default) returns NA statistics for any affected ROI/band; "omit" uses finite samples only; "error" aborts on selected nonfinite samples. n always counts selected pixels. A wholly invalid selection has NA statistics under omit (including sum); singleton sample SD is NA.

Value

The long tibble of at_extract(), restricted to spectral bands and sorted by ROI, declared unit, wavelength, then band index. Values are not converted between units; equal wavelengths retain band order.

Examples

cube <- at_example_image("cube")
proj <- at_project(cube, at_layer_add(at_layer("roi"),
                                      at_roi_circle(16, 16, 5, label = "roi")))
at_extract_spectrum(proj)
#> # A tibble: 40 × 12
#>    roi_id        layer label  band band_name wavelength unit  stat   value  n_px
#>    <chr>         <chr> <chr> <int> <chr>          <dbl> <chr> <chr>  <dbl> <int>
#>  1 roi_000000022 roi   roi       1 Band 1          450  nm    mean  32760.    80
#>  2 roi_000000022 roi   roi       2 Band 2          462. nm    mean  36680.    80
#>  3 roi_000000022 roi   roi       3 Band 3          473. nm    mean  40125.    80
#>  4 roi_000000022 roi   roi       4 Band 4          485. nm    mean  43501.    80
#>  5 roi_000000022 roi   roi       5 Band 5          496. nm    mean  46419.    80
#>  6 roi_000000022 roi   roi       6 Band 6          508. nm    mean  49054.    80
#>  7 roi_000000022 roi   roi       7 Band 7          519. nm    mean  50767.    80
#>  8 roi_000000022 roi   roi       8 Band 8          531. nm    mean  51994.    80
#>  9 roi_000000022 roi   roi       9 Band 9          542. nm    mean  52439.    80
#> 10 roi_000000022 roi   roi      10 Band 10         554. nm    mean  52137.    80
#> # ℹ 30 more rows
#> # ℹ 2 more variables: n_valid <int>, n_invalid <int>

Extract mean/median spectra for a spectral cube

Usage

Arguments

Value

See also

Examples