docker update, merge polygon error fix

broadinstitute · Aug 12, 2024 · 350de53 · 350de53
1 parent 0405bfa
commit 350de53
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Showing 3 changed files with 11 additions and 5 deletions.
diff --git a/common_python_scripts/merge_polygons.py b/common_python_scripts/merge_polygons.py
@@ -12,7 +12,8 @@
 
 
 def main(cell_outlines, intervals):
-
+
+    tolerance = 0.001
     cell_outlines = cell_outlines.split(",")
 
     def list_blobs_paths(bucket, prefix):
@@ -160,10 +161,15 @@ def string_to_polygon(coord_string):
 
             poly_1 = gdf.loc[cell_1, 'geometry']
 
-            area_1 = poly_1.area
-
             poly_2 = gdf.loc[cell_2, 'geometry']
 
+            poly_1 = make_valid(poly_1).buffer(0)
+            poly_2 = make_valid(poly_2).buffer(0)
+
+            poly_1 = poly_1.simplify(tolerance)
+            poly_2 = poly_2.simplify(tolerance)
+
+            area_1 = poly_1.area
             area_2 = poly_2.area
 
             area_intersection = poly_1.intersection(poly_2).area

diff --git a/segmentation_pipeline/miniwdl/modular_wdl_scripts/merge.wdl b/segmentation_pipeline/miniwdl/modular_wdl_scripts/merge.wdl
@@ -18,7 +18,7 @@ task merge_segmentation_dfs {
     }
 
     runtime {
-        docker: "jishar7/merge_polygons_for_mac@sha256:602f352e4e36bdf8729eceeb0985980e44e1ebe5d740b2a0c7e4ff30c61e5fc0"
+        docker: "jishar7/merge_polygons_for_mac@sha256:9bfc60cad9ba233712e1d1b77ed0123cb66fde7690ea6f86744b46ba2ebf1786"
         memory: "10GB"
         preemptible: 2
         disks: "local-disk 200 HDD"

diff --git a/segmentation_pipeline/terra/modular_wdl_scripts/merge.wdl b/segmentation_pipeline/terra/modular_wdl_scripts/merge.wdl
@@ -18,7 +18,7 @@ task merge_segmentation_dfs {
     }
 
     runtime {
-        docker: "jishar7/merge_polygons_for_terra@sha256:736a6537d50c431379a7049d6966dc059fde617a9e6f32fc7acc92f971aab586"
+        docker: "jishar7/merge_polygons_for_terra@sha256:2b91062544ff9eadcce4a6237adff34071bef97bfeb79528a81c4753fd841538"
         memory: "50GB"
         preemptible: 2
         disks: "local-disk 200 HDD"