luz_metric_f1score

luz_metric function to calculate the macro-averaged, class aggregated F1-score

Usage

luz_metric_f1score(
  nCls = 1,
  smooth = 1,
  mode = "multiclass",
  biThresh = 0.5,
  clsWghts = rep(1, nCls),
  zeroStart = TRUE,
  usedDS = FALSE
)

Arguments

nCls

Number of classes being differentiated.

smooth

A smoothing factor to avoid divide by zero errors. Default is 1.

mode

Either "binary" or "multiclass". If "binary", only the logit for the positive class prediction should be provided. If both the positive and negative or background class probability is provided for a binary classification, use the "multiclass" mode. Note that this package is designed to treat all predictions as multiclass. The "binary" mode is only provided for use outside of the standard geodl workflow.

biThresh

Probability threshold to define postive case prediction. Default is 0.5.

clsWghts

Vector of class weightings loss calculatokn. Default is equal weightings.

zeroStart

TRUE or FALSE. If class indices start at 0 as opposed to 1, this should be set to TRUE. This is required to implement one-hot encoding since R starts indexing at 1. Default is TRUE.

usedDS

TRUE or FALSE. If deep supervision was implemented and masks are produced at varying scales using the defineSegDataSetDS() function, this should be set to TRUE. Only the original resolution is used to calculate assessment metrics. Default is FALSE.

Value

Calculated metric returned as a base-R vector as opposed to tensor.

Details

Calculates F1-score based on luz_metric() for use within training and validation loops.

Examples

library(terra)
library(torch)
#Generate example data as SpatRasters
ref <- terra::rast(matrix(sample(c(1, 2, 3), 625, replace=TRUE), nrow=25, ncol=25))
pred1 <- terra::rast(matrix(sample(c(1:150), 625, replace=TRUE), nrow=25, ncol=25))
pred2 <- terra::rast(matrix(sample(c(1:150), 625, replace=TRUE), nrow=25, ncol=25))
pred3 <- terra::rast(matrix(sample(c(1:150), 625, replace=TRUE), nrow=25, ncol=25))
pred <- c(pred2, pred2, pred3)

#Convert SpatRaster to array
ref <- terra::as.array(ref)
pred <- terra::as.array(pred)

#Convert arrays to tensors and reshape
ref <- torch::torch_tensor(ref, dtype=torch::torch_long())
pred <- torch::torch_tensor(pred, dtype=torch::torch_float32())
ref <- ref$permute(c(3,1,2))
pred <- pred$permute(c(3,1,2))

#Add mini-batch dimension
ref <- ref$unsqueeze(1)
pred <- pred$unsqueeze(1)

#Duplicate tensors to have a batch of two
ref <- torch::torch_cat(list(ref, ref), dim=1)
pred <- torch::torch_cat(list(pred, pred), dim=1)

#Calculate Macro-Averaged, Class Aggregated F1-Score
metric<-luz_metric_f1score(nCls=3,
                           smooth=1e-8,
                           mode = "multiclass",
                           zeroStart=FALSE,
                           usedDS=FALSE)
metric<-metric$new()
metric$update(pred,ref)
metric$compute()
#> [1] 0.4232165