median_filter: Smooth and median filters with options for handling NAs.
In nandb: Number and Brightness Image Analysis

Description Usage Arguments Details Value Examples

These are alternatives to EBImage::filter2() and EBImage::medianFilter() for smooth and median filtering respectively. These functions have many options for dealing with NA values which EBImage's functions lack.

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median_filter(mat, size = 1L, na_rm = FALSE, na_count = FALSE)

smooth_filter(mat, size = 1L, na_rm = FALSE, na_count = FALSE)

`mat`	A matrix (representing an image).
`size`	An integer; the median filter radius.
`na_rm`	Should `NA`s be ignored?
`na_count`	If this is TRUE, in each median calculation, if the majority of arguments are `NA`s, `NA` is returned but if the `NA`s are in the minority, they are ignored as in `median(x, na.rm = TRUE)`.

The behavior at image boundaries is such as the source image has been padded with pixels whose values equal the nearest border pixel value.

A matrix (the median filtered image).

m <- matrix(1:9, nrow = 3)
m[2:3, 2:3] <- NA
print(m)
median_filter(m)
median_filter(m, na_rm = TRUE)
median_filter(m, na_count = TRUE)

smooth_filter(m)
smooth_filter(m, na_rm = TRUE)
smooth_filter(m, na_count = TRUE)