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Identify the ROXAS (AI) files in a directory

Source: R/read_rxs_metadata.R
get_roxas_files.Rd

Returns a data frame with the full path names of the relevant ROXAS (AI) files (i.e., images, cell measurements, ring measurements, and ROXAS settings resp. ROXAS AI metadata files) found within the given directory. The function 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.

Usage

get_roxas_files(path_in, roxas_version, exclude_dirs = NULL)

Arguments

path_in

path of the input directory.

roxas_version

which ROXAS version was used to create the files (classic "roxas" or new AI version "roxas_ai").

exclude_dirs

directory names / keywords that should be ignored when searching for ROXAS files (e.g., "unused_files", optional)

Value

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

Details

For ROXAS, the required files per image are:

  • Image file ({IMAGEID}.jpg or .jpeg)

  • Cells output ({IMAGEID}_Output_Cells.txt)

  • Rings output ({IMAGEID}_Output_Rings.txt)

  • Settings file ({IMAGEID}_ROXAS_Settings.txt)

For ROXAS AI, the required files per image are:

  • Image file ({IMAGEID}.scan.jpg or .jpeg)

  • Cells table ({IMAGEID}.cells_table.csv)

  • Rings table ({IMAGEID}.rings_table.csv)

  • Metadata file ({IMAGEID}.metadata.json)