From 350de53e23ea7149cb8dd694c2408026e9dc8991 Mon Sep 17 00:00:00 2001 From: Jaspreet Ishar Date: Mon, 12 Aug 2024 12:24:48 -0400 Subject: [PATCH] docker update, merge polygon error fix --- common_python_scripts/merge_polygons.py | 12 +++++++++--- .../miniwdl/modular_wdl_scripts/merge.wdl | 2 +- .../terra/modular_wdl_scripts/merge.wdl | 2 +- 3 files changed, 11 insertions(+), 5 deletions(-) diff --git a/common_python_scripts/merge_polygons.py b/common_python_scripts/merge_polygons.py index d4669e3..e852a06 100644 --- 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 index bb26bce..95ad080 100644 --- 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 index c7bbee4..263bac8 100644 --- 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"