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Merged
aylward merged 4 commits into from
Apr 17, 2026
Merged

ENH:VTK_To_USD and ConvertVTKToUSD consolidation #44

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e5015a6
Consolidate VTK-to-USD conversion under ConvertVTKToUSD as single API
claude Apr 16, 2026
dbceaaf
STYLE: Fix ruff formatting
aylward Apr 16, 2026
974333b
FIX: Harden ConvertVTKToUSD input validation and label time-code alig…
aylward Apr 17, 2026
6204d5c
ENH: Cache topology-validation mesh data; always author time-varying …
aylward Apr 17, 2026
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127 changes: 65 additions & 62 deletions docs/API_MAP.md
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94 changes: 36 additions & 58 deletions experiments/Convert_VTK_To_USD/convert_chop_alterra_valve_to_usd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,15 +37,11 @@
# Import USDTools for post-processing colormap
from physiomotion4d.usd_tools import USDTools

# Import the vtk_to_usd library
from physiomotion4d.vtk_to_usd import (
ConversionSettings,
MaterialData,
VTKToUSDConverter,
cell_type_name_for_vertex_count,
read_vtk_file,
validate_time_series_topology,
)
from physiomotion4d import ConvertVTKToUSD

# cell_type_name_for_vertex_count and read_vtk_file are internal APIs used for diagnostics
from physiomotion4d.vtk_to_usd import cell_type_name_for_vertex_count
from physiomotion4d.vtk_to_usd.vtk_reader import read_vtk_file

# %% [markdown]
# ## 1. Discover and Organize Time-Series Files
Expand All @@ -71,25 +67,10 @@
colormap_range_min = 25
colormap_range_max = 200

conversion_settings = ConversionSettings(
triangulate_meshes=True,
compute_normals=False, # Use existing normals if available
preserve_point_arrays=True,
preserve_cell_arrays=True,
separate_objects_by_cell_type=False,
separate_objects_by_connectivity=True, # Essential for alterra vtk file
up_axis="Y",
times_per_second=60.0, # 60 FPS for smooth animation
use_time_samples=True,
)

stent_material = MaterialData(
name="Alterra_valve",
diffuse_color=(0.5, 0.5, 0.5),
roughness=0.4,
metallic=0.9,
use_vertex_colors=False,
)
# Conversion parameters
separate_by = "connectivity" # Essential for alterra vtk file
times_per_second = 60.0
solid_color = (0.5, 0.5, 0.5)

# %%
output_dir.mkdir(parents=True, exist_ok=True)
Expand Down Expand Up @@ -155,8 +136,6 @@
# ## 3. Convert TPV25

# %%
converter = VTKToUSDConverter(conversion_settings)

alterra_files = [file_path for _, file_path in alterra_series]
alterra_times = [float(time_step) for time_step, _ in alterra_series]

Expand All @@ -168,39 +147,38 @@
print(f"Number of time steps: {len(alterra_times)}")
print("\nThis may take several minutes...\n")

# Read MeshData
mesh_data_sequence = [read_vtk_file(f, extract_surface=True) for f in alterra_files]

# Validate topology consistency across time series
validation_report = validate_time_series_topology(
mesh_data_sequence, filenames=alterra_files
)
if not validation_report["is_consistent"]:
print(
f"Warning: Found {len(validation_report['warnings'])} topology/primvar issues"
)
if validation_report["topology_changes"]:
print(
f" Topology changes in {len(validation_report['topology_changes'])} frames"
)

# Convert to USD (preserves all primvars from VTK)
stage = converter.convert_mesh_data_sequence(
mesh_data_sequence=mesh_data_sequence,
output_usd=output_usd,
mesh_name="AlterraValve",
# topology validation and conversion happen inside from_files()
stage = ConvertVTKToUSD.from_files(
data_basename="AlterraValve",
vtk_files=alterra_files,
extract_surface=True,
separate_by=separate_by,
times_per_second=times_per_second,
solid_color=solid_color,
time_codes=alterra_times,
material=stent_material,
)
).convert(str(output_usd))

# %%
usd_tools = USDTools()
if conversion_settings.separate_objects_by_connectivity is True:
vessel_path = "/World/Meshes/AlterraValve_object3"
elif conversion_settings.separate_objects_by_cell_type is True:
vessel_path = "/World/Meshes/AlterraValve_triangle1"
# ConvertVTKToUSD places prims at /World/{basename}/{part_name}.
# Discover the target prim dynamically so the path stays valid regardless
# of how many connected components or cell types the VTK file produces.
if separate_by == "connectivity":
mesh_paths = usd_tools.list_mesh_paths_under(
stage, parent_path="/World/AlterraValve"
)
candidates = [
p for p in mesh_paths if p.split("/")[-1].startswith("AlterraValve_object")
]
vessel_path = candidates[-1] if candidates else "/World/AlterraValve/Mesh"
elif separate_by == "cell_type":
mesh_paths = usd_tools.list_mesh_paths_under(
stage, parent_path="/World/AlterraValve"
)
triangle_paths = [p for p in mesh_paths if p.split("/")[-1].endswith("_Triangle")]
vessel_path = triangle_paths[0] if triangle_paths else "/World/AlterraValve/Mesh"
else:
vessel_path = "/World/Meshes/AlterraValve"
vessel_path = "/World/AlterraValve/Mesh"

# Select primvar for coloring
primvars = usd_tools.list_mesh_primvars(str(output_usd), vessel_path)
Expand Down
90 changes: 32 additions & 58 deletions experiments/Convert_VTK_To_USD/convert_chop_tpv25_valve_to_usd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,15 +36,11 @@
# Import USDTools for post-processing colormap
from physiomotion4d.usd_tools import USDTools

# Import the vtk_to_usd library
from physiomotion4d.vtk_to_usd import (
ConversionSettings,
MaterialData,
VTKToUSDConverter,
cell_type_name_for_vertex_count,
read_vtk_file,
validate_time_series_topology,
)
from physiomotion4d import ConvertVTKToUSD

# cell_type_name_for_vertex_count and read_vtk_file are internal APIs used for diagnostics
from physiomotion4d.vtk_to_usd import cell_type_name_for_vertex_count
from physiomotion4d.vtk_to_usd.vtk_reader import read_vtk_file

# %% [markdown]
# ## 1. Discover and Organize Time-Series Files
Expand All @@ -70,25 +66,10 @@
colormap_range_min = 25
colormap_range_max = 200

conversion_settings = ConversionSettings(
triangulate_meshes=True,
compute_normals=False, # Use existing normals if available
preserve_point_arrays=True,
preserve_cell_arrays=True,
separate_objects_by_cell_type=False,
separate_objects_by_connectivity=True, # Essential for tpv25 vtk file
up_axis="Y",
times_per_second=60.0, # 60 FPS for smooth animation
use_time_samples=True,
)

stent_material = MaterialData(
name="tpv25_valve",
diffuse_color=(0.5, 0.5, 0.5),
roughness=0.4,
metallic=0.9,
use_vertex_colors=False,
)
# Conversion parameters
separate_by = "connectivity" # Essential for tpv25 vtk file
times_per_second = 60.0
solid_color = (0.5, 0.5, 0.5)

# %%
output_dir.mkdir(parents=True, exist_ok=True)
Expand Down Expand Up @@ -154,8 +135,6 @@
# ## 3. Convert TPV25

# %%
converter = VTKToUSDConverter(conversion_settings)

tpv25_files = [file_path for _, file_path in tpv25_series]
tpv25_times = [float(time_step) for time_step, _ in tpv25_series]

Expand All @@ -167,39 +146,34 @@
print(f"Number of time steps: {len(tpv25_times)}")
print("\nThis may take several minutes...\n")

# Read MeshData
mesh_data_sequence = [read_vtk_file(f, extract_surface=True) for f in tpv25_files]

# Validate topology consistency across time series
validation_report = validate_time_series_topology(
mesh_data_sequence, filenames=tpv25_files
)
if not validation_report["is_consistent"]:
print(
f"Warning: Found {len(validation_report['warnings'])} topology/primvar issues"
)
if validation_report["topology_changes"]:
print(
f" Topology changes in {len(validation_report['topology_changes'])} frames"
)

# Convert to USD (preserves all primvars from VTK)
stage = converter.convert_mesh_data_sequence(
mesh_data_sequence=mesh_data_sequence,
output_usd=output_usd,
mesh_name="TPV25Valve",
# topology validation and conversion happen inside from_files()
stage = ConvertVTKToUSD.from_files(
data_basename="TPV25Valve",
vtk_files=tpv25_files,
extract_surface=True,
separate_by=separate_by,
times_per_second=times_per_second,
solid_color=solid_color,
time_codes=tpv25_times,
material=stent_material,
)
).convert(str(output_usd))

# %%
usd_tools = USDTools()
if conversion_settings.separate_objects_by_connectivity is True:
vessel_path = "/World/Meshes/TPV25Valve_object4"
elif conversion_settings.separate_objects_by_cell_type is True:
vessel_path = "/World/Meshes/TPV25Valve_triangle1"
# ConvertVTKToUSD places prims at /World/{basename}/{part_name}.
# Discover the target prim dynamically so the path stays valid regardless
# of how many connected components or cell types the VTK file produces.
if separate_by == "connectivity":
mesh_paths = usd_tools.list_mesh_paths_under(stage, parent_path="/World/TPV25Valve")
candidates = [
p for p in mesh_paths if p.split("/")[-1].startswith("TPV25Valve_object")
]
vessel_path = candidates[-1] if candidates else "/World/TPV25Valve/Mesh"
elif separate_by == "cell_type":
mesh_paths = usd_tools.list_mesh_paths_under(stage, parent_path="/World/TPV25Valve")
triangle_paths = [p for p in mesh_paths if p.split("/")[-1].endswith("_Triangle")]
vessel_path = triangle_paths[0] if triangle_paths else "/World/TPV25Valve/Mesh"
else:
vessel_path = "/World/Meshes/TPV25Valve"
vessel_path = "/World/TPV25Valve/Mesh"

# Select primvar for coloring
primvars = usd_tools.list_mesh_primvars(str(output_usd), vessel_path)
Expand Down
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