Change to adaptive number of boundary points and add test for moving …

…domain meshing + data
KVSlab · Oct 24, 2023 · 88520a3 · 88520a3
1 parent b7e4a25
commit 88520a3
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Showing 8 changed files with 59 additions and 13 deletions.
diff --git a/src/vampy/automatedPreprocessing/preprocessing_common.py b/src/vampy/automatedPreprocessing/preprocessing_common.py
@@ -801,7 +801,7 @@ def add_flow_extension(surface, centerlines, is_inlet, extension_length=2.0, ext
     flowExtensionsFilter.SetInputData(surface)
     flowExtensionsFilter.SetCenterlines(centerlines)
     flowExtensionsFilter.SetAdaptiveExtensionLength(1)
-    flowExtensionsFilter.SetAdaptiveNumberOfBoundaryPoints(0)
+    flowExtensionsFilter.SetAdaptiveNumberOfBoundaryPoints(1)
     flowExtensionsFilter.SetExtensionRatio(extension_length)
     flowExtensionsFilter.SetTransitionRatio(1.0)
     flowExtensionsFilter.SetCenterlineNormalEstimationDistanceRatio(1.0)

diff --git a/tests/test_data/artery/artery.stl b/tests/test_data/artery/artery.stl
diff --git a/tests/test_data/artery/artery_moved/artery_moved_00.stl b/tests/test_data/artery/artery_moved/artery_moved_00.stl
diff --git a/tests/test_data/artery/artery_moved/artery_moved_01.stl b/tests/test_data/artery/artery_moved/artery_moved_01.stl
diff --git a/tests/test_data/artery/artery_moved/artery_moved_02.stl b/tests/test_data/artery/artery_moved/artery_moved_02.stl
diff --git a/tests/test_data/artery/artery_moved/artery_moved_03.stl b/tests/test_data/artery/artery_moved/artery_moved_03.stl
diff --git a/tests/test_data/artery/artery_moved/artery_moved_04.stl b/tests/test_data/artery/artery_moved/artery_moved_04.stl
diff --git a/tests/test_pre_processing.py b/tests/test_pre_processing.py
@@ -1,5 +1,5 @@
-import os
-from os import path
+import shutil
+from os import path, listdir, remove
 
 from dolfin import Mesh
 
@@ -16,7 +16,7 @@ def test_mesh_model_with_one_inlet():
                              smoothing_method="taubin",
                              refine_region=False,
                              coarsening_factor=1.3,
-                             visualize=True,
+                             visualize=False,
                              compress_mesh=False,
                              outlet_flow_extension_length=1,
                              inlet_flow_extension_length=1
@@ -31,13 +31,13 @@ def test_mesh_model_with_one_inlet():
     output_files = [model_name + suffix for suffix in ['.vtu', '.xml', '_info.json', '_probe_point.json']]
     check_files(output_files)
 
-    num_points = 3473
-    num_cells = 19208
+    num_points = 3524
+    num_cells = 19465
     check_mesh(output_files, num_points=num_points, num_cells=num_cells)
 
     # Remove output files
     for output_file in output_files:
-        os.remove(output_file)
+        remove(output_file)
 
 
 def test_mesh_model_with_one_inlet_and_two_outlets():
@@ -65,13 +65,13 @@ def test_mesh_model_with_one_inlet_and_two_outlets():
     check_files(output_files)
 
     # Check that mesh is not empty with VTK/morphMan and FEniCS and contains correct amount of points and cells
-    num_points = 13247
-    num_cells = 74861
+    num_points = 12908
+    num_cells = 72688
     check_mesh(output_files, num_points=num_points, num_cells=num_cells)
 
     # Remove output files
     for output_file in output_files:
-        os.remove(output_file)
+        remove(output_file)
 
 
 def test_mesh_model_with_constant_edge_length():
@@ -97,13 +97,58 @@ def test_mesh_model_with_constant_edge_length():
     output_files = [model_name + suffix for suffix in ['.vtu', '.xml.gz', '_info.json', '_probe_point.json']]
     check_files(output_files)
 
-    num_points = 6964
-    num_cells = 38531
+    num_points = 6944
+    num_cells = 38647
     check_mesh(output_files, num_points=num_points, num_cells=num_cells)
 
     # Remove output files
     for output_file in output_files:
-        os.remove(output_file)
+        remove(output_file)
+
+
+def test_moving_domain_meshing():
+    model_path = "tests/test_data/artery/artery.stl"
+    # Get default input parameters
+    common_input = read_command_line(model_path)
+    common_input.update(dict(meshing_method="constant",
+                             edge_length=0.35,
+                             smoothing_method="laplace",
+                             moving_mesh=True,
+                             clamp_boundaries=True,
+                             refine_region=False,
+                             visualize=False,
+                             compress_mesh=True,
+                             add_boundary_layer=False,
+                             outlet_flow_extension_length=1,
+                             inlet_flow_extension_length=1
+                             ))
+
+    # Run pre processing
+    run_pre_processing(**common_input)
+
+    model_name = model_path.replace(".stl", "")
+
+    # Check that output files exist (standard output files plus artery_points.np)
+    output_files = [model_name + suffix for suffix in ['.vtu', '.xml.gz', '_info.json', '_probe_point.json']]
+    check_files(output_files)
+
+    # Check moving domain meshing files
+    displacement_file = [model_name + "_points.np"]
+    check_files(displacement_file)
+
+    extended_folder = model_name + "_extended"
+    assert path.exists(extended_folder)
+    assert listdir(extended_folder) != []
+
+    num_points = 3982
+    num_cells = 21619
+    check_mesh(output_files, num_points=num_points, num_cells=num_cells)
+
+    # Remove output files
+    for output_file in output_files + displacement_file:
+        remove(output_file)
+
+    shutil.rmtree(extended_folder)
 
 
 def check_files(output_files):
@@ -128,3 +173,4 @@ def check_mesh(output_files, num_points, num_cells):
     test_mesh_model_with_one_inlet()
     test_mesh_model_with_one_inlet_and_two_outlets()
     test_mesh_model_with_constant_edge_length()
+    test_moving_domain_meshing()