spatial cropping

crop subsets SpatialData elements according to a rectangular bounding box or arbitrary polygonal shapes.

For SpatialData objects, crop propagates the operation across all layers that share the coordinate space j.

For SpatialDataFrames (points and shapes), cropping relies on sf::st_intersects (i.e., instances that intersect the query region in any way are kept). For circle shapes, radii are currently ignored (i.e., a circle is kept if its centroid intersects the query region).

For SpatialDataArrays (images and labels), only bounding box cropping is supported. The requested spatial bounding box is projected into pixel coordinates, and the underlying array is sliced accordingly. The wh metadata is updated to reflect the new spatial extent.

Usage

# S4 method for class 'SpatialDataArray'
crop(x, y, j = 1, ...)

# S4 method for class 'SpatialDataFrame'
crop(x, y, j = 1, ...)

# S4 method for class 'SpatialData'
crop(x, y, j = 1, ...)

Arguments

x

SpatialData object or element.

y

query specification; bounding box: length-4 numeric list with names 'xmin/xmax/ymin/ymax', or an st_bbox; polygon: numeric matrix with 2 columns (= xy-coordinates), or an st_polygon (sfg) or sfc/sf object.

j

character string specifying a coordinate system.

...

optional arguments passed to and from other methods.

Value

same as input

Examples

zs <- file.path("extdata", "blobs.zarr")
zs <- system.file(zs, package="SpatialData")
sd <- readSpatialData(zs, tables=FALSE)

# bounding box crop of a SpatialData object
y <- list(xmin=10, xmax=50, ymin=10, ymax=50)
crop(sd, y, j="global")
#> class: SpatialData
#> - images(2):
#>   - blobs_image (3,40,40)
#>   - blobs_multiscale_image (3,40,40)
#> - labels(2):
#>   - blobs_labels (40,40)
#>   - blobs_multiscale_labels (40,40)
#> - points(1):
#>   - blobs_points (92)
#> - shapes(3):
#>   - blobs_circles (5,circle)
#>   - blobs_multipolygons (2,polygon)
#>   - blobs_polygons (5,polygon)
#> - tables(0):
#> coordinate systems(5):
#> - global(8): blobs_image blobs_multiscale_image ... blobs_polygons
#>   blobs_points
#> - scale(1): blobs_labels
#> - translation(1): blobs_labels
#> - affine(1): blobs_labels
#> - sequence(1): blobs_labels

# cropping individual elements
a <- sf::st_bbox(c(xmin=10, xmax=50, ymin=10, ymax=50))
b <- matrix(c(10,10, 25,50, 40,10, 10,10), ncol=2, byrow=TRUE)
p <- crop(point(sd), a)
q <- crop(point(sd), b)

plot(p$geometry, col="blue")
plot(q$geometry, col="red", add=TRUE)
plot(sf::st_as_sfc(a), add=TRUE)
lines(b, type="l")