Revert "Make extraction of the largest connected component optional (#…

…305)" This reverts commit 3ab0655.
eigenvivek · Jul 15, 2024 · 527ef53 · 527ef53
1 parent f773567
commit 527ef53
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Showing 2 changed files with 4 additions and 8 deletions.
diff --git a/diffdrr/visualization.py b/diffdrr/visualization.py
@@ -181,7 +181,6 @@ def drr_to_mesh(
     subject: Subject,  # torchio.Subject with a `volume` attribute
     method: str,  # Either `surface_nets` or `marching_cubes`
     threshold: float = 150,  # Min value for marching cubes (Hounsfield units)
-    extract_largest: bool = True,  # Extract the largest connected component from the mesh
     verbose: bool = True,  # Display progress bars for mesh processing steps
 ):
     """
@@ -191,7 +190,7 @@ def drr_to_mesh(
 
     The mesh processing steps are:
 
-    1. Keep only largest connected components (optional)
+    1. Keep only largest connected components
     2. Smooth
     3. Decimate (if `method=="marching_cubes"`)
     4. Fill any holes
@@ -230,8 +229,7 @@ def drr_to_mesh(
     mesh = mesh.transform(subject.volume.affine.squeeze())
 
     # Preprocess the mesh
-    if extract_largest:
-        mesh.extract_largest(inplace=True, progress_bar=verbose)
+    mesh.extract_largest(inplace=True, progress_bar=verbose)
     mesh.point_data.clear()
     mesh.cell_data.clear()
     mesh.smooth_taubin(

diff --git a/notebooks/api/04_visualization.ipynb b/notebooks/api/04_visualization.ipynb
@@ -286,7 +286,6 @@
     "    subject: Subject,  # torchio.Subject with a `volume` attribute\n",
     "    method: str,  # Either `surface_nets` or `marching_cubes`\n",
     "    threshold: float = 150,  # Min value for marching cubes (Hounsfield units)\n",
-    "    extract_largest: bool = True,  # Extract the largest connected component from the mesh\n",
     "    verbose: bool = True,  # Display progress bars for mesh processing steps\n",
     "):\n",
     "    \"\"\"\n",
@@ -296,7 +295,7 @@
     "\n",
     "    The mesh processing steps are:\n",
     "\n",
-    "    1. Keep only largest connected components (optional)\n",
+    "    1. Keep only largest connected components\n",
     "    2. Smooth\n",
     "    3. Decimate (if `method==\"marching_cubes\"`)\n",
     "    4. Fill any holes\n",
@@ -335,8 +334,7 @@
     "    mesh = mesh.transform(subject.volume.affine.squeeze())\n",
     "\n",
     "    # Preprocess the mesh\n",
-    "    if extract_largest:\n",
-    "        mesh.extract_largest(inplace=True, progress_bar=verbose)\n",
+    "    mesh.extract_largest(inplace=True, progress_bar=verbose)\n",
     "    mesh.point_data.clear()\n",
     "    mesh.cell_data.clear()\n",
     "    mesh.smooth_taubin(\n",