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Identify the ROXAS (AI) files in a directory

Source: R/get_roxas_files.R
get_roxas_files.Rd

Returns a data frame with the full paths of the four types of relevant ROXAS (AI) files (i.e., images, cell measurements, ring measurements, and ROXAS settings resp. ROXAS AI metadata files) found within the given directory. Recurses into any subdirectories except those explicitly excluded. The files are identified by matching on the standard naming suffixes produced by ROXAS resp. ROXAS AI, see the Details below.

Usage

get_roxas_files(path_in, roxas_version, exclude_dirs = NULL)

Arguments

path_in

The path of the input directory.

roxas_version

Which software was used to create the files, either "roxas" or "roxas_ai".

exclude_dirs

Optional character vector of subdirectory names that should not be searched for ROXAS (AI) files (e.g., "unused_files").

Value

A data frame with columns prefix, fname_image, fname_settings, fname_cells and fname_rings containing the common prefixes and full file paths.

Details

For ROXAS, the required files per image are:

  • The original image file ({IMAGEID}.jpg or .jpeg).

  • The ROXAS settings file ({IMAGEID}_ROXAS_Settings.txt).

  • The cell measurements output ({IMAGEID}_Output_Cells.txt).

  • The ring measurements output ({IMAGEID}_Output_Rings.txt).

For ROXAS AI, the required files per image are:

  • The original image file ({IMAGEID}.scan.jpg or .jpeg).

  • The ROXAS AI metadata file ({IMAGEID}.metadata.json).

  • The cell measurements table ({IMAGEID}.cells_table.csv or .txt).

  • The ring measurements table ({IMAGEID}.rings_table.csv or .txt).