GeometryCollectionLegacy polygon format

*Requested by Matthew Cai*

CHANGELOG.md

@@ -1,5 +1,9 @@
 ## [Upcoming]
 
+### Added
+
+- `--polygon-format=GeometryCollectionLegacy` format similar to `GeometryCollection`, but with integer cell IDs. Used for compatibility with Xenium Ranger. This option will be deprecated after Xenium Ranger is updated.
+
 ### Fixed
 
 - CLI argument parsing

src/cli/main.jl

@@ -28,9 +28,11 @@ Run cell segmentation
                                         (default: 4)
 - `-o, --output=<path>`:                Name of the output file or path to the output directory (default: "segmentation.csv")
 - `--polygon-format=<format>`:          Format to save estimated cell boundary polygons to a file with a specified `format`.
-                                        Two types of 'GeoJSON' format are currently supported: 'FeatureCollection' produces the
-                                        same output as Xenium Ranger and 'GeometryCollection' is the old Baysor format. Set to "none"
-                                        to disable saving polygons. (default: 'FeatureCollection').
+                                        Two main types of 'GeoJSON' format are currently supported: 'FeatureCollection' produces the
+                                        same output as Xenium Ranger and 'GeometryCollection' is the old Baysor format. Additionally,
+                                        `GeometryCollectionLegacy` format is similar to `GeometryCollection`, but with integer cell IDs
+                                        *(used for compatibility with Xenium Ranger, this option will be deprecated after Xenium Ranger
+                                        is updated)*. Set to "none" to disable saving polygons. (default: 'FeatureCollection').
 - `--scale-std=<ss>`:                   Standard deviation of scale across cells. Can be either number, which means absolute value of
                                         the std, or string ended with '%' to set it relative to scale (default: "25%")
 - `-s, --scale=<s>`:                    Scale parameter, which suggest approximate cell radius for the algorithm. Must be in the same

src/data_loading/cli_wrappers.jl

@@ -72,15 +72,21 @@ function save_molecule_counts(
     return file
 end
 
-
 """
     polygons_to_geojson(polygons::PolygonCollection; format::String="FeatureCollection")
 
     Converts a collection of polygons to GeoJSON format.
-    Uses either `FeatureCollection` (compatible with 10x Xenium Ranger) or `GeometryCollection` (original Baysor) format.
+    Uses either `FeatureCollection` (10x Xenium Ranger output), `GeometryCollection` (original Baysor) or `GeometryCollectionLegacy` (Baysor v0.6 with integer cell IDs) format.
 """
 function polygons_to_geojson(polygons::PolygonCollection; format::String="FeatureCollection")
     format_lc = lowercase(format)
+    if format_lc == "geometrycollectionlegacy"
+        if eltype(keys(polygons)) <: AbstractString
+            polygons = Dict(parse(Int, split(k, '-')[2]) => p for (k,p) in polygons)
+        end
+
+        format_lc = "geometrycollection"
+    end
     if format_lc == "geometrycollection"
         geoms = [Dict("type" => "Polygon", "coordinates" => [collect.(eachrow(p))], "cell" => c) for (c,p) in polygons]
         return Dict("type" => "GeometryCollection", "geometries" => geoms);