Add mesh inversion functions

Author: mogres

cellpack_analysis/lib/mesh_tools.py

@@ -1024,3 +1024,19 @@ def get_weights_from_distances(
     else:
         weights = 1 - scaled_distances
     return weights
+
+
+def invert_mesh_faces(input_mesh_path: str | Path, output_mesh_path: str | Path) -> None:
+    """
+    Invert the faces of a mesh and save to a new file.
+
+    Parameters
+    ----------
+    input_mesh_path
+        Path to the input mesh file
+    output_mesh_path
+        Path to save the inverted mesh file
+    """
+    mesh = trimesh.load_mesh(input_mesh_path)
+    mesh.invert()
+    mesh.export(output_mesh_path)

cellpack_analysis/notebooks/export_simularium_paths_as_csv.py

@@ -15,12 +15,14 @@
 # TODO: inverted meshes?
 # %%
 import json
+import shutil
 
 import boto3
 import pandas as pd
 from tqdm import tqdm
 
 from cellpack_analysis.lib.file_io import get_datadir_path, get_results_path
+from cellpack_analysis.lib.mesh_tools import invert_mesh_faces
 
 # %%
 base_datadir = get_datadir_path()
@@ -39,6 +41,7 @@
 simularium_path = (
     base_datadir / "packing_outputs" / dataset / condition / rule / structure_name / "spheresSST"
 )
+figure_path = simularium_path / "figures"
 # %%
 records = []
 base_s3_mesh_url = (
@@ -47,10 +50,22 @@
 base_s3_simularium_url = "https://cellpack-analysis-data.s3.us-west-2.amazonaws.com/"
 s3_client = boto3.client("s3")
 # %%
-# Update meshes in s3 bucket
-mesh_path = base_datadir / "structure_data" / structure_id / "meshes"
-for file_path in tqdm(mesh_path.rglob("*")):
+# Invert and upload meshes to s3 bucket
+invert_meshes = False
+mesh_dir = base_datadir / "structure_data" / structure_id / "meshes"
+for file_path in tqdm(mesh_dir.rglob("*")):
     if file_path.is_file():
+        # invert mem meshes
+        if invert_meshes and "mem" in file_path.name and "original" not in file_path.name:
+            orig_mesh_path = file_path.parent / f"{file_path.stem}_original.obj"
+            # copy original file with suffix
+            shutil.copy(
+                file_path,
+                orig_mesh_path,
+            )
+            invert_mesh_faces(input_mesh_path=orig_mesh_path, output_mesh_path=file_path)
+
+        # upload to s3
         s3_key = file_path.relative_to(base_datadir).as_posix()
         s3_client.upload_file(str(file_path), "cellpack-analysis-data", s3_key)
         s3_client.put_object_acl(
@@ -59,6 +74,7 @@
             Key=s3_key,
         )
 # %%
+reupload = False
 # Update simularium files and upload to s3
 for file_path in tqdm(simularium_path.rglob("*.simularium")):
     # update mesh paths in simularium file
@@ -69,17 +85,25 @@
             mapping["geometry"]["url"] = f"{base_s3_mesh_url}{mapping['geometry']['url']}"
     with open(file_path, "w") as f:
         json.dump(sim_data, f, indent=2)
-    # try:
-    #     s3_client.head_object(Bucket="cellpack-analysis-data", Key=s3_key)
-    # except s3_client.exceptions.ClientError:
-    # upload to s3
+
     s3_key = file_path.relative_to(base_datadir).as_posix()
-    s3_client.upload_file(str(file_path), "cellpack-analysis-data", s3_key)
-    s3_client.put_object_acl(
-        ACL="public-read",
-        Bucket="cellpack-analysis-data",
-        Key=s3_key,
-    )
+
+    should_upload = reupload
+    if not reupload:
+        try:
+            s3_client.head_object(Bucket="cellpack-analysis-data", Key=s3_key)
+            should_upload = False
+        except s3_client.exceptions.ClientError:
+            should_upload = True
+
+    if should_upload:
+        s3_client.upload_file(str(file_path), "cellpack-analysis-data", s3_key)
+        s3_client.put_object_acl(
+            ACL="public-read",
+            Bucket="cellpack-analysis-data",
+            Key=s3_key,
+        )
+
     s3_path = f"{base_s3_simularium_url}{s3_key}"
     record = {
         "File Path": str(s3_path),