makeChipsDF

Create data frame and CSV file listing image chips and associated masks

Usage

makeChipsDF(
  folder,
  outCSV,
  extension = ".tif",
  mode = "All",
  shuffle = FALSE,
  saveCSV = FALSE,
  useEdgeDist = FALSE
)

Arguments

folder

Full path or path relative to the working directory to the folder containing the image chips and associated masks. You must include the final forward slash in the path (e.g., "C:/data/chips/").

outCSV

File name and full path or path relative to the working directory for the resulting CSV file with a ".csv" extension.

extension

The extension of the image and mask raster data (e.g., ".tif", ".png", ".jpeg", or ".img"). The default is ".tif" since this is the file format used by the utilities in this package. This option is provided if chips are generated using another method.

mode

Either "All", "Positive", or "Divided". This should match the setting used in the makeChips() function. If the makeChipsMultiClass() function was used, this should be set to "All" or left as the default. The default is "All".

shuffle

TRUE or FALSE. Whether or not to shuffle the rows in the table. Rows can be shuffled to potentially reduced autocorrelation in the data. The default is FALSE.

saveCSV

TRUE or FALSE. Whether or not to save the CSV file or just return the data frame. If this is set to FALSE then the outCSV parameter is ignored and no CSV file is generated. The default is FALSE.

useEdgeDist

TRUE or FALSE. Whether to include a distPth column pointing to the distance-to-class-boundary grids produced by makeBoundaryDistance. Supported for all modes. Default is FALSE.

Value

Data frame with three columns (chpN, chpPth, and mskPth) and, optionally, a CSV file written to disk. If mode = "Divided", a division column is added to differentiate "positive" and "background" samples. If useEdgeDist = TRUE, an additional distPth column is included.

Details

This function creates a data frame and, optionally, a CSV file that lists all of the image chips and associated masks in a directory. Three columns are produced. The chpN column provides the name of the chip, the chpPth column provides the path to the chip, and the chpMsk column provides the path to the associated mask. All paths are relative to the input folder as opposed to the full file path so that the results can still be used if the data are copied to a new location on disk or to a new computer.

If useEdgeDist = TRUE, a fourth column distPth is added that points to the corresponding distance-to-class-boundary grid produced by makeBoundaryDistance. All three modes are supported. For mode = "All" or mode = "Positive" the paths resolve to dist/<name>.tif; for mode = "Divided" they resolve to dist/positive/<name>.tif or dist/background/<name>.tif to match the layout written by makeBoundaryDistance when it detects the divided folder structure.

Examples

if (FALSE) { # \dontrun{
chpDF <- makeChipsDF(folder = "PATHT TO CHIPS FOLDER",
                      outCSV = "OUTPUT CSV FILE AND PATH",
                      extension = ".tif",
                      mode="Positive",
                      shuffle=TRUE,
                      saveCSV=TRUE,
                      useEdgeDist=TRUE)
} # }