Read _raw sheets from a CPCe output workbook

CPCe output workbooks often contain one worksheet per image, with raw point annotation worksheets named like image_name_raw. This function reads only those raw worksheets, skips deep_cres_..._raw worksheets by default, keeps the raw worksheet columns, adds image_name and point_index as the first columns, and adds a full major_category column using a label crosswalk. point_index is a 1-based row index within each raw worksheet, matching the CPCe point order.

Usage

read_cpce_output_raw_tabs(
  path,
  crosswalk = NULL,
  skip_deep_cres = TRUE,
  sheet_pattern = "_raw$"
)

Arguments

path

Path to a CPCe output .xls or .xlsx workbook.

crosswalk

Optional label crosswalk data frame or path. When NULL, the bundled example crosswalk is used. The raw CPCe label in the workbook is joined to raw_code or raw_label.

skip_deep_cres

Whether to skip worksheets whose names start with deep_cres_. Those sheets use a different layout.

sheet_pattern

Regular expression used to identify raw worksheets. Defaults to sheets ending in _raw.

Value

A tibble combining all selected raw worksheets. The first columns are image_name and point_index. The original CPCe raw major/group column is preserved as cpce_major_category when present.

Examples

xlsx <- system.file(
  "extdata", "pointcoral_example_cpce_output_raw_tabs.xlsx",
  package = "pointcoral"
)
read_cpce_output_raw_tabs(xlsx)
#> # A tibble: 7 × 11
#>   image_name point_index raw_data notes cpce_major_category frame_limits
#>   <chr>            <int> <chr>    <lgl> <chr>               <chr>       
#> 1 Sample_A             1 SPO      NA    S                   *           
#> 2 Sample_A             2 PEYS     NA    MA                  NA          
#> 3 Sample_A             3 S        NA    SPR                 NA          
#> 4 Sample_A             4 CALG     NA    CA                  NA          
#> 5 Sample_B             1 LOBO     NA    MA                  NA          
#> 6 Sample_B             2 SS       NA    C                   NA          
#> 7 Sample_B             3 P        NA    SPR                 NA          
#> # ℹ 5 more variables: frame_image_name <chr>, cpc_filename <chr>,
#> #   major_category <chr>, start_stop <chr>, image_cpc_file <chr>