Box Geometry Model files
Box Geometry Model files are text files that store a spatially-explicit model domain used by the Atlantis Ecosystem Model.
The model domain consists of boxes (polygons) composed of faces (line segments) and an overall boundary that delimits the domain of the model.
The boundary will include boundary polygons that are not boxes in the model, but some box edges are on this boundary, for example some models bounded by land do not have boundary boxes on this edge.
The rbgm package includes tools to read the BGM format, returning tables of all X/Y vertices and tables of indices for the boxes and faces.
library(rbgm)
library(dplyr)
library(tibble)
mfile <- bgmfiles::bgmfiles()[1]
bgm <- bgmfile(mfile)
names(bgm)
## [1] "vertices" "facesXverts" "faces"
## [4] "facesXboxes" "boxesXverts" "boxes"
## [7] "boundaryvertices" "extra"
Box and face attributes, and model topology
Both boxes and faces have attributes stored row-wise in the respective table.
These are the box attributes for this example
## # A tibble: 35 x 9
## label nconn botz area vertmix horizmix insideX insideY .bx0
## <chr> <int> <dbl> <dbl> <int> <int> <dbl> <dbl> <dbl>
## 1 Box0 7 -53.7 9254788445 1 1 3430169 3073000 0
## 2 Box1 81 -48.9 1996056923 1 1 3498567 3029308 1
## 3 Box2 120 -55.7 3922348664 1 1 3521055 3050400 2
## 4 Box3 105 -53.4 3576072582 1 1 3523085 3077300 3
## 5 Box4 83 -30.0 1672921591 1 1 3522699 3102469 4
## 6 Box5 12 -24.1 411048577 1 1 3496968 3124359 5
## 7 Box6 16 -10.2 447377917 1 1 3520947 3133926 6
## 8 Box7 18 0.0 402661184 1 1 3523883 3122610 7
## 9 Box8 13 -15.0 705100219 1 1 3562646 3115917 8
## 10 Box9 3 -5.4 93312196 1 1 3581060 3127380 9
## # ... with 25 more rows
and these are the face attributes.
## # A tibble: 824 x 7
## cosine sine left right length .fx0 label
## <dbl> <dbl> <int> <int> <dbl> <dbl> <chr>
## 1 0.1117110 0.9937407 34 32 29876.1751 0 face0
## 2 0.5063539 0.8623257 32 33 17890.9481 1 face1
## 3 0.1156084 0.9932949 34 33 10168.5158 2 face2
## 4 0.1166131 0.9931774 34 33 155.3584 3 face3
## 5 0.8692497 0.4943733 33 27 9390.6169 4 face4
## 6 0.1178758 0.9930283 34 27 12817.8024 5 face5
## 7 0.1211979 0.9926284 34 27 21316.3942 6 face6
## 8 0.2764643 0.9610242 32 33 25393.5801 7 face7
## 9 0.5142367 0.8576483 32 33 8425.2753 8 face8
## 10 0.1356335 0.9907591 32 30 14366.1017 9 face9
## # ... with 814 more rows
By using relations between these tables we can reconstruct the geometry appropriately. (This is pretty painful, but shows that we have all the information required.)
bgm$boxes %>%
filter(label %in% c("Box1", "Box11")) %>%
inner_join(bgm$boxesXverts, ".bx0") %>%
print()
## # A tibble: 115 x 10
## label nconn botz area vertmix horizmix insideX insideY .bx0
## <chr> <int> <dbl> <dbl> <int> <int> <dbl> <dbl> <dbl>
## 1 Box1 81 -48.9 1996056923 1 1 3498567 3029308 1
## 2 Box1 81 -48.9 1996056923 1 1 3498567 3029308 1
## 3 Box1 81 -48.9 1996056923 1 1 3498567 3029308 1
## 4 Box1 81 -48.9 1996056923 1 1 3498567 3029308 1
## 5 Box1 81 -48.9 1996056923 1 1 3498567 3029308 1
## 6 Box1 81 -48.9 1996056923 1 1 3498567 3029308 1
## 7 Box1 81 -48.9 1996056923 1 1 3498567 3029308 1
## 8 Box1 81 -48.9 1996056923 1 1 3498567 3029308 1
## 9 Box1 81 -48.9 1996056923 1 1 3498567 3029308 1
## 10 Box1 81 -48.9 1996056923 1 1 3498567 3029308 1
## # ... with 105 more rows, and 1 more variables: .vx0 <int>
Convert to Spatial objects
To avoid constructing boxes and faces manually, rbgm provides several helper functions to create the boxes, faces, coordinates, and boundary as Spatial objects from the sp package.
Since Spatial objects cannot store the full connectivity of the BGM structure, it is best to consider these as one-way conversions, keeping all the details in the raw tables as above.
To generate an object with just “Box1” and “Box11”, use the function boxSpatial and then subset on box labels.
boxes <- subset(boxSpatial(bgm), label %in% c("Box2", "Box16"))
To determine which faces belong to these boxes, first create all faces and then join.
allfaces <- faceSpatial(bgm)
faces <- allfaces[match(bgm$facesXboxes$iface[which(bgm$facesXboxes$.bx0 %in% boxes$.bx0)], allfaces$.fx0), ]
## this method needs spdplyr
#face <- romsface %>% inner_join(as.data.frame(box) %>% inner_join(bgm$facesXboxes, ".bx0") %>% transmute(.fx0 = iface), ".fx0")
Plot the two layers together.
plot(boxes, main = "boxes only")
text(coordinates(boxes), lab = sprintf("%s\nnconn: %s", boxes$label, boxes$nconn))
plot(boxes, main = "boxes and faces overlaid")
text(coordinates(boxes), lab = sprintf("%s\nnconn: %s", boxes$label, boxes$nconn))
plot(faces, col = c("firebrick"), lwd = 1, add = TRUE)
(Future releases will provide simpler tools to do this kind of matching).