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Pre-process data for U-Net

Source: R/unet_prep.R
unet_prep.Rd

Creates numpy arrays ready for fitting in U-Net. Result files are placed in <site>/unet/<model>.

Usage

unet_prep(
  model,
  save_gis = FALSE,
  resources = NULL,
  local = FALSE,
  trap = TRUE,
  comment = NULL
)

Arguments

model

The model name, which is also the name of a .yml parameter file in the pars directory. This file must contain the following:

  • years: the year(s) of field data to fit

  • orthos: file names of all orthophotos to include

  • patch: size in pixels

  • depth: number of of downsampling stages

  • classes: vector of target classes

  • transects: base name of field transects shapefile (default: "transects")

  • holdout_col: holdout set to use (uses bypoly). Holdout sets are created by gather, numbering each poly from 1 to 10, repeating if necessary. There are 5 sets to choose from.

  • cv: number of cross-validations. Use 1 for a single model, up to 5 for five-fold cross-validation. Cross-validations are systematic, not random. Since there are only 10 sets in each bypoly, the number of cross-validations is limited by the values of val and test.

  • val: validation polys from holdout_col. Use NULL to skip validation, or a vector of the validation polys for the first cross-validation (these will be incremented for subsequent validations). For 20% validation holdout, use val = c(1, 6). This will use bypoly01 %in% c(1,6)`` for the first cross-validation, c(2, 7)` for the second, and so on.

  • test: test polys from holdout_col, as with val.

  • overlap: Proportion overlap of patches

  • upscale: number of cells to upscale (default = 1). Use 3 to upscale to 3x3, 5 for 5x5, etc.

  • smooth: number of cells to include in moving window mean (default = 1). Use 3 to smooth to 3x3, etc.

save_gis

If TRUE, saves GIS data for assessment and debugging

resources

Slurm launch resources. See launch. These take priority over the function's defaults.

local

If TRUE, run locally; otherwise, spawn a batch run on Unity

trap

If TRUE, trap errors in local mode; if FALSE, use normal R error handling. Use this for debugging. If you get unrecovered errors, the job won't be added to the jobs database. Has no effect if local = FALSE.

comment

Optional slurmcollie comment

Details

Try this to test: unet_prep('unet01', local = TRUE)