Subsetting images in Giotto objects

[rbutleriii]

Hi @jiajic , I know you mentioned in #1067 that you are working on more comprehensive control of images, but I wanted to ask if there is a better way to crop an image to a polygon (like from region selection for example). I tried an approach below, and it works to drop all images that are not in the subsetGiotto object, but it appears to apply the crop to the spatial extent of the data, not using the polygon as a mask as I think terra can do (mask = TRUE)? Realistically this would help for non-rectangular selection regions.

#' Subset giotto object by a polygon
#' 
#' @param gobj giotto object to subset
#' @param poly string, polygon type. must be added as spat_unit and cell metadata
#' @param name string, which polygon value to subset
#' 
#' @return A subset Giotto object with extra images dropped
subGiottoPoly <- function(gobj, poly, name) {
  # subset most Giotto data by cells
  cells <- pDataDT(gobj)[get(poly) == name, cell_ID] 
  g1 <- subsetGiotto(gobj, cell_ids = cells)
   
  # filter images to be those in the polygon
  imgs <- lapply(gobj@images, function(i) {
    tryCatch(
      expr = crop(x = i, y = gobj@spatial_info[[poly]][name]), 
      error = function(e) return(NULL)
    )
  })
  g1@images <- Filter(Negate(is.null), imgs)
  
  # remove extra spat_unit
  g1 <- sliceGiotto(g1, spat_unit = "cell")
  return(g1)
}



# Plot spatial cells/spots with tissue on the background
gobj %>%
  spatPlot2D(
    cell_color = ctype,
    cell_color_code = fourty,
    point_size = 0.5,
    point_alpha = 0.5,
    show_image = TRUE,
    image_name = img_list,
    return_plot = TRUE,
    show_plot = FALSE
  ) %>%
  plotInteractivePolygons() -> my_polygon_coords

# add to the gobj
polygons = createGiottoPolygonsFromDfr(
  my_polygon_coords, 
  name = 'subregion',
  calc_centroids = TRUE
)

# calculate overlaps
gobj %>%
  addGiottoPolygons(gpolygons = list(polygons)) %>%
  addPolygonCells(polygon_name = 'subregion') -> gobj

# Subset the gobj by subregion for further analysis ------------------------
# subset including images
gobjs <- lapply(gobj@spatial_info$subregion$poly_ID, function(i) {
  subGiottoPoly(gobj, 'subregion', i)
})
setattr(gobjs, 'names', gobj@spatial_info$subregion$poly_ID)

}

Below image should have the lower right corner clipped based on a polygon