{
"cells": [
{
"cell_type": "markdown",
"id": "8a8e95e7",
"metadata": {},
"source": [
"# **multimoda-rs**: Intravascular Module – Notebook Tutorial\n",
"\n",
"This notebook follows the [Intravascular Alignment Tutorial](../tutorial_intravascular.rst) step-by-step:\n",
"\n",
"1. General note on segmentation preparation\n",
"2. Workflow from CSV files (AIVUS-CAA format)\n",
"3. Workflow from numpy arrays — including parameter fine-tuning\n",
"4. Alignment with a CCTA centerline\n",
"5. Saving geometries as `.obj` files\n",
"6. Utility functions: `to_array` and `numpy_to_geometry`\n",
"7. Class-level methods for `PyContour`, `PyFrame`, and `PyGeometry`\n",
"\n",
"> **Performance note:** Alignment is compute-intensive. Running the notebook via the console is faster than interactive cell-by-cell execution."
]
},
{
"cell_type": "markdown",
"id": "539ebfaf",
"metadata": {},
"source": [
"## 1. General note on segmentation preparation\n",
"\n",
"The package works with segmented intravascular images from IVUS or OCT.\n",
"Segmentation must follow specific conventions for optimal results:\n",
"\n",
"- Files follow AIVUS-CAA convention: `diastolic_contours.csv`, `systolic_contours.csv`,\n",
" `diastolic_reference_points.csv`, `systolic_reference_points.csv`.\n",
"- Each file has columns `(frame_index, x_mm, y_mm, z_mm)` — **no header row**.\n",
"- A correct anatomical **reference point** is essential for downstream centerline co-registration.\n",
"\n",
"For CAD a bifurcation serves as reference; for AAOCA the reference is placed at the aortic side of\n",
"the most proximal fully closed lumen contour (see tutorial for details).\n",
"\n",
"**Four processing modes**\n",
"\n",
"| Mode | Inputs | Typical use-case |\n",
"|------|--------|-----------------|\n",
"| `full` | 4 states (rest-dia, rest-sys, stress-dia, stress-sys) | AAOCA pulsatile lumen analysis |\n",
"| `doublepair` | 2 independent pullbacks, each with dia+sys | Pre/post-stenting across both phases |\n",
"| `singlepair` | 1 pullback with dia+sys | CAD: diastole vs. systole within one pullback |\n",
"| `single` | 1 pullback (dia or sys only) | Standalone reconstruction (CAD, OCT) |"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "f7b1f230",
"metadata": {
"execution": {
"iopub.execute_input": "2026-05-04T15:13:32.349348Z",
"iopub.status.busy": "2026-05-04T15:13:32.349130Z",
"iopub.status.idle": "2026-05-04T15:13:50.293709Z",
"shell.execute_reply": "2026-05-04T15:13:50.292360Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Working directory: /mnt/c/WorkingData/Documents/2_Coding/Rust/multimodars/examples/data\n"
]
}
],
"source": [
"import os\n",
"from pathlib import Path\n",
"import numpy as np\n",
"import multimodars as mm\n",
"\n",
"cwd = Path.cwd()\n",
"for candidate in [cwd, cwd.parent, cwd.parent.parent]:\n",
" if (candidate / \"examples\" / \"data\").exists():\n",
" os.chdir(candidate / \"examples\" / \"data\")\n",
" break\n",
" elif (candidate / \"data\").exists():\n",
" os.chdir(candidate / \"data\")\n",
" break\n",
"print(f\"Working directory: {os.getcwd()}\")"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "996ea018",
"metadata": {
"execution": {
"iopub.execute_input": "2026-05-04T15:13:50.296342Z",
"iopub.status.busy": "2026-05-04T15:13:50.295949Z",
"iopub.status.idle": "2026-05-04T15:13:59.154174Z",
"shell.execute_reply": "2026-05-04T15:13:59.153230Z"
},
"tags": [
"remove-input"
]
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Note: you may need to restart the kernel to use updated packages.\n"
]
}
],
"source": [
"%pip --disable-pip-version-check install trimesh plotly scipy nbformat | grep -v 'already satisfied'\n",
"\n",
"\n",
"import trimesh\n",
"import plotly.graph_objects as go\n",
"import plotly.io as pio\n",
"pio.renderers.default = \"notebook_connected\"\n",
"from plotly.subplots import make_subplots\n",
"\n",
"\n",
"def trimesh_to_mesh3d(mesh, color, name, opacity=0.6):\n",
" verts = mesh.vertices\n",
" faces = mesh.faces\n",
" return go.Mesh3d(\n",
" x=verts[:, 0], y=verts[:, 1], z=verts[:, 2],\n",
" i=faces[:, 0], j=faces[:, 1], k=faces[:, 2],\n",
" color=color, opacity=opacity, name=name, flatshading=True,\n",
" )\n",
"\n",
"\n",
"def plot_pair(before_paths, after_paths, colors, titles):\n",
" \"\"\"Side-by-side 3D comparison of two mesh lists.\"\"\"\n",
" before_meshes = [trimesh.load(p) for p in before_paths]\n",
" after_meshes = [trimesh.load(p) for p in after_paths]\n",
" fig = make_subplots(\n",
" rows=1, cols=2,\n",
" specs=[[{\"type\": \"scene\"}, {\"type\": \"scene\"}]],\n",
" subplot_titles=titles,\n",
" )\n",
" labels = [\"diastole\", \"systole\"]\n",
" for mesh, color, label in zip(before_meshes, colors, labels):\n",
" fig.add_trace(trimesh_to_mesh3d(mesh, color, f\"before_{label}\"), row=1, col=1)\n",
" for mesh, color, label in zip(after_meshes, colors, labels):\n",
" fig.add_trace(trimesh_to_mesh3d(mesh, color, f\"after_{label}\"), row=1, col=2)\n",
" camera = dict(eye=dict(x=1.5, y=1.5, z=1.0))\n",
" fig.update_layout(\n",
" width=900, height=450,\n",
" scene_camera=camera, scene2_camera=camera,\n",
" scene=dict(aspectmode=\"data\"), scene2=dict(aspectmode=\"data\"),\n",
" margin=dict(l=0, r=0, t=30, b=0),\n",
" )\n",
" fig.show()"
]
},
{
"cell_type": "markdown",
"id": "3418ff43",
"metadata": {},
"source": [
"## 2. Workflow from CSV files\n",
"\n",
"This section uses AIVUS-CAA CSV files.\n",
"`from_file_full` processes all four states simultaneously (rest-diastole, rest-systole,\n",
"stress-diastole, stress-systole) and writes aligned meshes to four output directories.\n",
"\n",
"See the [tutorial](../tutorial_intravascular.rst) for a detailed description of the CSV format."
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "45003053",
"metadata": {
"execution": {
"iopub.execute_input": "2026-05-04T15:13:59.156581Z",
"iopub.status.busy": "2026-05-04T15:13:59.156372Z",
"iopub.status.idle": "2026-05-04T15:14:15.511118Z",
"shell.execute_reply": "2026-05-04T15:14:15.510168Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"✅ Successfully built geometry from path\n",
"-----------------------------------------\n",
"✅ Lumen\n",
"❌ Eem\n",
"❌ Calcification\n",
"❌ Sidebranch\n",
"✅ Catheter\n",
"-----------------------------------------\n",
"Label: rest_dia\n",
"Diastole phase: Yes\n",
"\n",
"\n",
"✅ Successfully built geometry from path\n",
"-----------------------------------------\n",
"✅ Lumen\n",
"❌ Eem\n",
"❌ Calcification\n",
"❌ Sidebranch\n",
"✅ Catheter\n",
"-----------------------------------------\n",
"Label: rest_sys\n",
"Diastole phase: No\n",
"\n",
"\n",
"✅ Successfully built geometry from path\n",
"-----------------------------------------\n",
"✅ Lumen\n",
"❌ Eem\n",
"❌ Calcification\n",
"❌ Sidebranch\n",
"✅ Catheter\n",
"-----------------------------------------\n",
"Label: stress_dia\n",
"Diastole phase: Yes\n",
"\n",
"\n",
"✅ Successfully built geometry from path\n",
"-----------------------------------------\n",
"✅ Lumen\n",
"❌ Eem\n",
"❌ Calcification\n",
"❌ Sidebranch\n",
"✅ Catheter\n",
"-----------------------------------------\n",
"Label: stress_sys\n",
"Diastole phase: No\n",
"\n",
"\n",
"+--------------------------------------------------------------------+\n",
"| ✅ Finished aligning 'rest_sys' (anomalous: true) |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"| Contour | Matched To | Rotation (°) | Tx | Ty | Centroid |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"| 1 | 0 | -2.30 | -0.19 | -0.01 | (3.63,5.12) |\n",
"| 2 | 1 | 12.20 | -0.54 | 0.15 | (3.63,5.12) |\n",
"| 3 | 2 | -10.30 | -0.44 | 0.53 | (3.63,5.12) |\n",
"| 4 | 3 | -4.10 | -0.72 | 0.94 | (3.63,5.12) |\n",
"| 5 | 4 | 0.80 | -0.75 | 0.26 | (3.63,5.12) |\n",
"| 6 | 5 | 5.10 | -0.79 | 0.65 | (3.63,5.12) |\n",
"| 7 | 6 | -6.50 | -1.21 | 0.69 | (3.63,5.12) |\n",
"| 8 | 7 | 14.70 | -1.08 | 0.81 | (3.63,5.12) |\n",
"| 9 | 8 | -35.30 | -1.03 | 0.24 | (3.63,5.12) |\n",
"| 10 | 9 | 25.50 | -1.46 | 0.28 | (3.63,5.12) |\n",
"| 11 | 10 | 41.30 | -2.40 | 0.73 | (3.63,5.12) |\n",
"| 12 | 11 | -21.20 | -1.95 | 0.68 | (3.63,5.12) |\n",
"| 13 | 12 | 4.80 | -2.06 | 0.66 | (3.63,5.12) |\n",
"| 14 | 13 | -6.90 | -2.14 | 0.52 | (3.63,5.12) |\n",
"| 15 | 14 | 23.40 | -2.27 | 0.46 | (3.63,5.12) |\n",
"| 16 | 15 | 7.30 | -2.28 | 0.53 | (3.63,5.12) |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"\n",
"+--------------------------------------------------------------------+\n",
"| ✅ Finished aligning 'stress_dia' (anomalous: true) |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"| Contour | Matched To | Rotation (°) | Tx | Ty | Centroid |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"| 1 | 0 | 3.80 | -0.10 | 0.02 | (3.60,4.59) |\n",
"| 2 | 1 | 6.20 | -0.38 | 0.40 | (3.60,4.59) |\n",
"| 3 | 2 | 1.90 | -0.24 | 0.42 | (3.60,4.59) |\n",
"| 4 | 3 | -1.60 | -0.11 | 0.49 | (3.60,4.59) |\n",
"| 5 | 4 | -1.90 | -0.22 | 0.50 | (3.60,4.59) |\n",
"| 6 | 5 | 0.70 | -0.03 | 0.10 | (3.60,4.59) |\n",
"| 7 | 6 | 3.20 | -0.05 | 0.09 | (3.60,4.59) |\n",
"| 8 | 7 | 0.80 | -0.11 | -0.09 | (3.60,4.59) |\n",
"| 9 | 8 | 2.40 | -0.14 | -0.13 | (3.60,4.59) |\n",
"| 10 | 9 | 14.60 | -0.75 | 0.01 | (3.60,4.59) |\n",
"| 11 | 10 | 0.00 | -1.08 | 0.08 | (3.60,4.59) |\n",
"| 12 | 11 | 8.80 | -1.21 | 0.08 | (3.60,4.59) |\n",
"| 13 | 12 | 11.80 | -1.28 | 0.20 | (3.60,4.59) |\n",
"| 14 | 13 | -14.20 | -1.46 | -0.02 | (3.60,4.59) |\n",
"| 15 | 14 | 22.50 | -1.55 | 0.29 | (3.60,4.59) |\n",
"| 16 | 15 | -13.20 | -1.72 | 0.16 | (3.60,4.59) |\n",
"| 17 | 16 | -18.90 | -1.61 | -0.27 | (3.60,4.59) |\n",
"| 18 | 17 | -2.70 | -1.41 | -0.44 | (3.60,4.59) |\n",
"| 19 | 18 | 7.50 | -1.74 | -0.31 | (3.60,4.59) |\n",
"| 20 | 19 | 10.70 | -1.77 | -0.55 | (3.60,4.59) |\n",
"| 21 | 20 | 18.00 | -2.30 | -0.37 | (3.60,4.59) |\n",
"| 22 | 21 | 0.00 | -2.04 | -0.25 | (3.60,4.59) |\n",
"| 23 | 22 | 24.70 | -2.34 | 0.36 | (3.60,4.59) |\n",
"| 24 | 23 | 4.10 | -2.29 | 0.78 | (3.60,4.59) |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"\n",
"+--------------------------------------------------------------------+\n",
"| ✅ Finished aligning 'rest_dia' (anomalous: true) |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"| Contour | Matched To | Rotation (°) | Tx | Ty | Centroid |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"| 1 | 0 | 7.70 | 0.12 | -0.36 | (3.72,5.25) |\n",
"| 2 | 1 | 0.70 | 0.04 | -0.16 | (3.72,5.25) |\n",
"| 3 | 2 | 6.20 | -0.28 | 0.03 | (3.72,5.25) |\n",
"| 4 | 3 | -13.10 | -0.16 | 0.45 | (3.72,5.25) |\n",
"| 5 | 4 | -23.90 | -0.32 | 0.89 | (3.72,5.25) |\n",
"| 6 | 5 | -5.10 | -0.48 | 1.10 | (3.72,5.25) |\n",
"| 7 | 6 | -29.80 | -0.94 | 0.82 | (3.72,5.25) |\n",
"| 8 | 7 | -18.00 | -1.29 | 0.87 | (3.72,5.25) |\n",
"| 9 | 8 | 1.50 | -1.36 | 0.86 | (3.72,5.25) |\n",
"| 10 | 9 | -1.20 | -1.68 | 1.27 | (3.72,5.25) |\n",
"| 11 | 10 | 47.40 | -1.54 | 1.87 | (3.72,5.25) |\n",
"| 12 | 11 | 3.30 | -1.45 | 1.95 | (3.72,5.25) |\n",
"| 13 | 12 | 1.00 | -1.51 | 2.08 | (3.72,5.25) |\n",
"| 14 | 13 | 30.60 | -0.96 | 2.12 | (3.72,5.25) |\n",
"| 15 | 14 | -7.00 | -1.11 | 1.93 | (3.72,5.25) |\n",
"| 16 | 15 | 19.40 | -0.68 | 2"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"sidebranch file not found, skipping: \"ivus_rest/branch_diastolic_contours.csv\"\n",
"process_directory: unknown mapping name 'catheter', skipping\n",
"eem file not found, skipping: \"ivus_rest/eem_diastolic_contours.csv\"\n",
"calcification file not found, skipping: \"ivus_rest/calcium_diastolic_contours.csv\"\n",
"process_directory: unknown mapping name 'catheter', skipping\n",
"calcification file not found, skipping: \"ivus_rest/calcium_systolic_contours.csv\"\n",
"eem file not found, skipping: \"ivus_rest/eem_systolic_contours.csv\"\n",
"sidebranch file not found, skipping: \"ivus_rest/branch_systolic_contours.csv\"\n",
"sidebranch file not found, skipping: \"ivus_stress/branch_diastolic_contours.csv\"\n",
"calcification file not found, skipping: \"ivus_stress/calcium_diastolic_contours.csv\"\n",
"eem file not found, skipping: \"ivus_stress/eem_diastolic_contours.csv\"\n",
"process_directory: unknown mapping name 'catheter', skipping\n",
"sidebranch file not found, skipping: \"ivus_stress/branch_systolic_contours.csv\"\n",
"calcification file not found, skipping: \"ivus_stress/calcium_systolic_contours.csv\"\n",
"process_directory: unknown mapping name 'catheter', skipping\n",
"eem file not found, skipping: \"ivus_stress/eem_systolic_contours.csv\"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
".47 | (3.72,5.25) |\n",
"| 17 | 16 | 3.40 | -0.50 | 2.35 | (3.72,5.25) |\n",
"| 18 | 17 | -0.90 | -0.58 | 2.24 | (3.72,5.25) |\n",
"| 19 | 18 | -11.00 | -0.95 | 2.37 | (3.72,5.25) |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"\n",
"+--------------------------------------------------------------------+\n",
"| ✅ Finished aligning 'stress_sys' (anomalous: true) |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"| Contour | Matched To | Rotation (°) | Tx | Ty | Centroid |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"| 1 | 0 | 0.00 | -0.22 | 0.10 | (3.80,4.64) |\n",
"| 2 | 1 | 1.00 | -0.19 | 0.14 | (3.80,4.64) |\n",
"| 3 | 2 | 0.00 | -0.04 | 0.17 | (3.80,4.64) |\n",
"| 4 | 3 | -1.20 | 0.08 | 0.15 | (3.80,4.64) |\n",
"| 5 | 4 | -1.10 | 0.03 | 0.09 | (3.80,4.64) |\n",
"| 6 | 5 | 0.20 | 0.06 | 0.06 | (3.80,4.64) |\n",
"| 7 | 6 | 7.30 | 0.06 | 0.24 | (3.80,4.64) |\n",
"| 8 | 7 | 2.60 | -0.30 | 0.00 | (3.80,4.64) |\n",
"| 9 | 8 | 11.50 | -0.32 | -0.18 | (3.80,4.64) |\n",
"| 10 | 9 | 9.50 | -0.57 | -0.32 | (3.80,4.64) |\n",
"| 11 | 10 | -1.00 | -0.53 | -0.36 | (3.80,4.64) |\n",
"| 12 | 11 | 3.40 | -0.49 | -0.39 | (3.80,4.64) |\n",
"| 13 | 12 | -4.10 | -0.52 | -0.46 | (3.80,4.64) |\n",
"| 14 | 13 | 8.40 | -0.63 | -0.37 | (3.80,4.64) |\n",
"| 15 | 14 | -2.10 | -0.76 | -0.43 | (3.80,4.64) |\n",
"| 16 | 15 | 8.50 | -0.79 | -0.41 | (3.80,4.64) |\n",
"| 17 | 16 | -6.00 | -0.81 | -0.81 | (3.80,4.64) |\n",
"| 18 | 17 | 0.00 | -0.83 | -1.10 | (3.80,4.64) |\n",
"| 19 | 18 | 0.40 | -0.82 | -1.12 | (3.80,4.64) |\n",
"| 20 | 19 | 3.20 | -0.89 | -1.13 | (3.80,4.64) |\n",
"| 21 | 20 | 9.50 | -0.96 | -1.14 | (3.80,4.64) |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"\n",
"✅ Aligned geometry 'stress_sys' to 'stress_dia'\n",
"-----------------------------------------\n",
"Applied initial translation: (-0.20, -0.05, 0.00) mm\n",
"Found best rotation of 2.70° with parameters: \n",
"range: 90.00° \n",
"step size: 0.1°\n",
"Applied final translation: ( 0, 0.00, 0.00) mm\n",
"-----------------------------------------\n",
"\n",
"✅ Aligned geometry 'rest_sys' to 'rest_dia'\n",
"-----------------------------------------\n",
"Applied initial translation: (0.09, 0.13, -3.94) mm\n",
"Found best rotation of 3.00° with parameters: \n",
"range: 90.00° \n",
"step size: 0.1°\n",
"Applied final translation: ( 0, 0.00, 0.00) mm\n",
"-----------------------------------------\n",
"\n",
"✅ Aligned geometry 'stress_sys' to 'rest_sys'\n",
"-----------------------------------------\n",
"Applied initial translation: (0.12, 0.66, 0.00) mm\n",
"Found best rotation of 1.80° with parameters: \n",
"range: 90.00° \n",
"step size: 0.1°\n",
"Applied final translation: ( 0, 0.00, 0.00) mm\n",
"-----------------------------------------\n",
"\n",
"✅ Aligned geometry 'stress_dia' to 'rest_dia'\n",
"-----------------------------------------\n",
"Applied initial translation: (0.12, 0.66, 0.00) mm\n",
"Found best rotation of 17.80° with parameters: \n",
"range: 90.00° \n",
"step size: 0.1°\n",
"Applied final translation: ( 0, 0.00, 0.00) mm\n",
"-----------------------------------------\n",
"\n",
"Saving files for 'rest_dia - rest_sys' to 'output/rest'\n",
"LUMEN .obj files: 30/30 written successfully\n",
"CATHETER .obj files: 30/30 written successfully\n",
"WALL .obj files: 30/30 written successfully\n",
"\n",
"Saving files for 'stress_dia - stress_sys' to 'output/stress'\n",
"LUMEN .obj files: 30/30 written successfully\n",
"CATHETER .obj files: 30/30 written successfully\n",
"WALL .obj files: 30/30 written successfully\n",
"\n",
"Saving files for 'rest_dia - stress_dia' to 'output/diastole'\n",
"LUMEN .obj files: 30/30 written successfully\n",
"CATHETER .obj files: 30/30 written successfully\n",
"WALL .obj files: 30/30 written successfully\n",
"\n",
"Saving files for 'rest_sys - stress_sys' to 'output/systole'\n",
"LUMEN .obj files: 30/30 written successfully\n",
"CATHETER .obj files: 30/30 written successfully\n",
"WALL .obj files: 30/30 written successfully\n"
]
}
],
"source": [
"# Full 4-state workflow: rest vs. stress, diastole vs. systole\n",
"rest, stress, dia, sys, _ = mm.from_file_full(\n",
" input_path_ab=\"ivus_rest\",\n",
" input_path_cd=\"ivus_stress\",\n",
" labels=[\"rest_dia\", \"rest_sys\", \"stress_dia\", \"stress_sys\"],\n",
" step_rotation_deg=0.1,\n",
" range_rotation_deg=90,\n",
" image_center=(4.5, 4.5),\n",
" radius=0.5,\n",
" n_points=20,\n",
" write_obj=True,\n",
" watertight=False,\n",
" contour_types=[mm.PyContourType.Lumen, mm.PyContourType.Catheter, mm.PyContourType.Wall],\n",
" output_path_ab=\"output/rest\",\n",
" output_path_cd=\"output/stress\",\n",
" output_path_ac=\"output/diastole\",\n",
" output_path_bd=\"output/systole\",\n",
" interpolation_steps=28,\n",
")"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "6650d4ec",
"metadata": {
"execution": {
"iopub.execute_input": "2026-05-04T15:14:15.512728Z",
"iopub.status.busy": "2026-05-04T15:14:15.512536Z",
"iopub.status.idle": "2026-05-04T15:14:15.995755Z",
"shell.execute_reply": "2026-05-04T15:14:15.994611Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Successfully wrote lumen to output/before/dia_lumen.obj\n",
"Successfully wrote lumen to output/before/sys_lumen.obj\n",
"Successfully wrote lumen to output/after/dia_lumen.obj\n",
"Successfully wrote lumen to output/after/sys_lumen.obj\n"
]
}
],
"source": [
"# Build \"before\" meshes from raw CSV, then write explicit .obj files for comparison\n",
"rest_dia_raw = np.genfromtxt(\"ivus_rest/diastolic_contours.csv\")\n",
"rest_dia_ref = np.genfromtxt(\"ivus_rest/diastolic_reference_points.csv\")\n",
"rest_sys_raw = np.genfromtxt(\"ivus_rest/systolic_contours.csv\")\n",
"rest_sys_ref = np.genfromtxt(\"ivus_rest/systolic_reference_points.csv\")\n",
"\n",
"rest_dia_before = mm.numpy_to_geometry(\n",
" lumen_arr=rest_dia_raw, eem_arr=np.array([]), catheter_arr=np.array([]),\n",
" wall_arr=np.array([]), reference_arr=rest_dia_ref, label=\"dia_before\",\n",
")\n",
"rest_sys_before = mm.numpy_to_geometry(\n",
" lumen_arr=rest_sys_raw, eem_arr=np.array([]), catheter_arr=np.array([]),\n",
" wall_arr=np.array([]), reference_arr=rest_sys_ref, label=\"sys_before\",\n",
")\n",
"rest_dia_before.frames = np.array([f.sort_frame_points() for f in rest_dia_before.frames])\n",
"rest_sys_before.frames = np.array([f.sort_frame_points() for f in rest_sys_before.frames])\n",
"\n",
"# Write before (unprocessed) and after (aligned) meshes with explicit names\n",
"mm.to_obj(rest_dia_before, \"output/before\", watertight=False,\n",
" contour_types=[mm.PyContourType.Lumen], filename_prefix=\"dia\")\n",
"mm.to_obj(rest_sys_before, \"output/before\", watertight=False,\n",
" contour_types=[mm.PyContourType.Lumen], filename_prefix=\"sys\")\n",
"mm.to_obj(rest.geom_a, \"output/after\", watertight=False,\n",
" contour_types=[mm.PyContourType.Lumen], filename_prefix=\"dia\")\n",
"mm.to_obj(rest.geom_b, \"output/after\", watertight=False,\n",
" contour_types=[mm.PyContourType.Lumen], filename_prefix=\"sys\")"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "2f1d5bea",
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"execution": {
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"outputs": [
{
"data": {
"text/html": [
" \n",
" \n",
" "
]
},
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"output_type": "display_data"
},
{
"data": {
"text/html": [
""
]
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"metadata": {},
"output_type": "display_data"
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],
"source": [
"plot_pair(\n",
" before_paths=[\"output/before/dia_lumen.obj\", \"output/before/sys_lumen.obj\"],\n",
" after_paths=[\"output/after/dia_lumen.obj\", \"output/after/sys_lumen.obj\"],\n",
" colors=[\"royalblue\", \"firebrick\"],\n",
" titles=[\"Before Processing\", \"After Processing\"],\n",
")"
]
},
{
"cell_type": "markdown",
"id": "90585578",
"metadata": {},
"source": [
"The data is now neatly ordered in pairs (diastolic and systolic geometry). Every geometry contains\n",
"contours for lumen, wall, and a synthetic catheter. The reference point is used for centerline\n",
"co-registration. All points belonging to a contour are stored in a `PyContour` struct."
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "852594dc",
"metadata": {
"execution": {
"iopub.execute_input": "2026-05-04T15:14:17.106324Z",
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"shell.execute_reply": "2026-05-04T15:14:17.114889Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"PyGeometryPair:\n",
"GeometryPair rest_dia - rest_sys (diastolic: 14 frames, systolic: 14 frames)\n",
"PyGeometry:\n",
"Geometry(14 frames, label='rest_dia')\n",
"PyFrame:\n",
"Frame(id=0, centroid=(3.72, 5.25, 0.00), lumen=Contour(id=0, frame=385, points=501, centroid=(3.72, 5.25, 0.00), kind=Lumen), extras=2)\n",
"PyContour:\n",
"Contour(id=0, frame=385, points=501, centroid=(3.72, 5.25, 0.00), kind=Lumen)\n",
"Extras:\n",
"{'Catheter': Contour(id=0, frame=385, points=20, centroid=(3.84, 6.33, 0.00), kind=Catheter), 'Wall': Contour(id=0, frame=385, points=501, centroid=(3.72, 5.25, 0.00), kind=Wall)}\n",
"PyContourPoint:\n",
"Point(frame_id=19, pt_id=0, x=3.80, y=7.90, z=0.00, aortic=false)\n"
]
}
],
"source": [
"print(f\"PyGeometryPair:\\n{rest}\")\n",
"print(f\"PyGeometry:\\n{rest.geom_a}\")\n",
"print(f\"PyFrame:\\n{rest.geom_a.frames[0]}\")\n",
"print(f\"PyContour:\\n{rest.geom_a.frames[0].lumen}\")\n",
"print(f\"Extras:\\n{rest.geom_a.frames[0].extras}\")\n",
"print(f\"PyContourPoint:\\n{rest.geom_a.frames[0].lumen.points[0]}\")"
]
},
{
"cell_type": "markdown",
"id": "4213f69a",
"metadata": {},
"source": [
"Different stenosis measurements can be obtained directly from the objects:"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "4a93dd04",
"metadata": {
"execution": {
"iopub.execute_input": "2026-05-04T15:14:17.117396Z",
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"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"+----+----------+-----------+----------+-----------+-------+\n",
"| id | area_dia | ellip_dia | area_sys | ellip_sys | z |\n",
"+----+----------+-----------+----------+-----------+-------+\n",
"PyGeometryPair summary (dia_geom: (mla [mm²], max. stenosis, stenosis length [mm])):\n",
"((5.559206007496853, 0.6780775439844883, 10.364606842105268), (6.111481670202526, 0.663038559502465, 7.7734551315789515))\n",
"Deformation table:\n",
"[[ 0. 5.63662776 4.58651358 6.11148167 4.35376487 0. ]\n",
" [ 1. 5.79662471 4.75220339 6.25936689 3.38956113 1.29557586]\n",
" [ 2. 5.70440311 3.69759593 6.49106359 2.85326248 2.59115171]\n",
" [ 3. 5.55920601 2.56932308 6.84671006 2.17905332 3.88672757]\n",
" [ 4. 5.5883072 1.63583386 7.59416089 1.90836576 5.18230342]\n",
" [ 5. 6.41743783 1.50724622 7.57484592 1.67549107 6.47787928]\n",
" [ 6. 7.25510456 1.36697234 7.3074273 1.63078837 7.77345513]\n",
" [ 7. 7.74398201 1.24613112 10.23430197 1.32956583 9.06903099]\n",
" [ 8. 7.77347285 1.43038361 11.90101937 1.19922679 10.36460684]\n",
" [ 9. 9.05387612 1.32700846 14.15414345 1.08910895 11.6601827 ]\n",
" [10. 11.91520903 1.18319293 11.7040278 1.17176063 12.95575855]\n",
" [11. 15.27166328 1.08294811 13.56639023 1.14517785 14.25133441]\n",
" [12. 17.26877359 1.05840795 15.42409292 1.11280753 15.54691026]\n",
" [13. 16.34175131 1.0407399 18.13703568 1.06629346 16.84248612]]\n",
"| 0 | 5.64 | 4.59 | 6.11 | 4.35 | 0.00 |\n",
"| 1 | 5.80 | 4.75 | 6.26 | 3.39 | 1.30 |\n",
"| 2 | 5.70 | 3.70 | 6.49 | 2.85 | 2.59 |\n",
"| 3 | 5.56 | 2.57 | 6.85 | 2.18 | 3.89 |\n",
"| 4 | 5.59 | 1.64 | 7.59 | 1.91 | 5.18 |\n",
"| 5 | 6.42 | 1.51 | 7.57 | 1.68 | 6.48 |\n",
"| 6 | 7.26 | 1.37 | 7.31 | 1.63 | 7.77 |\n",
"| 7 | 7.74 | 1.25 | 10.23 | 1.33 | 9.07 |\n",
"| 8 | 7.77 | 1.43 | 11.90 | 1.20 | 10.36 |\n",
"| 9 | 9.05 | 1.33 | 14.15 | 1.09 | 11.66 |\n",
"| 10 | 11.92 | 1.18 | 11.70 | 1.17 | 12.96 |\n",
"| 11 | 15.27 | 1.08 | 13.57 | 1.15 | 14.25 |\n",
"| 12 | 17.27 | 1.06 | 15.42 | 1.11 | 15.55 |\n",
"| 13 | 16.34 | 1.04 | 18.14 | 1.07 | 16.84 |\n",
"+----+----------+-----------+----------+-----------+-------+\n",
"\n",
"PyGeometry summary:\n",
"5.559206007496853\n",
"\n",
"Contour area [mm²]: 5.6366\n",
"Elliptic ratio: 1.0407\n"
]
}
],
"source": [
"# Summary over PyGeometryPair\n",
"summary_pair, deform_table = rest.get_summary()\n",
"print(f\"PyGeometryPair summary (dia_geom: (mla [mm²], max. stenosis, stenosis length [mm])):\\n{summary_pair}\")\n",
"print(f\"Deformation table:\\n{np.array(deform_table)}\")\n",
"\n",
"# Summary over PyGeometry\n",
"print(f\"\\nPyGeometry summary:\\n{rest.geom_a.get_summary()[0]}\")\n",
"\n",
"# Per-contour measurements\n",
"print(f\"\\nContour area [mm²]: {rest.geom_a.frames[0].lumen.get_area():.4f}\")\n",
"print(f\"Elliptic ratio: {rest.geom_a.frames[-1].lumen.get_elliptic_ratio():.4f}\")"
]
},
{
"cell_type": "markdown",
"id": "31b03e3a",
"metadata": {},
"source": [
"The four pairs represent all four possible comparisons in gated images — particularly relevant for\n",
"coronary artery anomalies (AAOCA): rest pulsatile, stress pulsatile, stress-induced diastolic, and\n",
"stress-induced systolic lumen deformation.\n",
"\n",
"The `interpolation_steps` parameter generates intermediate meshes between paired states, useful for\n",
"deformation animations in Blender. Set `interpolation_steps=0` to skip interpolation.\n",
"\n",
"### Coronary Artery Disease\n",
"\n",
"`from_file_single` reconstructs a single pullback with all contour layers (lumen, EEM, wall, catheter):"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "9e30d724",
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"execution": {
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"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"✅ Successfully built geometry from path\n",
"-----------------------------------------\n",
"✅ Lumen\n",
"✅ Eem\n",
"✅ Calcification\n",
"✅ Sidebranch\n",
"✅ Catheter\n",
"-----------------------------------------\n",
"Label: ivus_full\n",
"Diastole phase: Yes\n",
"\n",
"\n",
"+--------------------------------------------------------------------+\n",
"| ✅ Finished aligning 'ivus_full' (anomalous: false) |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"| Contour | Matched To | Rotation (°) | Tx | Ty | Centroid |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"| 1 | 0 | 0.00 | 0.04 | -0.07 | (4.38,4.06) |\n",
"| 2 | 1 | -0.60 | 0.11 | -0.15 | (4.38,4.06) |\n",
"| 3 | 2 | 19.20 | 0.04 | -0.24 | (4.38,4.06) |\n",
"| 4 | 3 | 90.00 | -0.12 | -0.46 | (4.38,4.06) |\n",
"| 5 | 4 | 5.30 | -0.24 | -0.36 | (4.38,4.06) |\n",
"| 6 | 5 | -36.00 | -0.16 | -0.44 | (4.38,4.06) |\n",
"| 7 | 6 | 18.00 | -0.21 | -0.50 | (4.38,4.06) |\n",
"| 8 | 7 | 2.70 | -0.12 | -0.52 | (4.38,4.06) |\n",
"| 9 | 8 | -18.00 | -0.08 | -0.46 | (4.38,4.06) |\n",
"| 10 | 9 | 0.00 | 0.02 | -0.39 | (4.38,4.06) |\n",
"| 11 | 10 | 0.00 | -0.06 | -0.42 | (4.38,4.06) |\n",
"| 12 | 11 | -90.00 | -0.14 | -0.34 | (4.38,4.06) |\n",
"| 13 | 12 | 69.40 | 0.05 | -0.52 | (4.38,4.06) |\n",
"| 14 | 13 | 0.00 | 0.29 | -0.53 | (4.38,4.06) |\n",
"| 15 | 14 | -5.90 | 0.32 | -0.51 | (4.38,4.06) |\n",
"| 16 | 15 | -12.30 | 0.36 | -0.50 | (4.38,4.06) |\n",
"| 17 | 16 | -6.90 | 0.35 | -0.36 | (4.38,4.06) |\n",
"| 18 | 17 | 0.00 | 0.38 | -0.40 | (4.38,4.06) |\n",
"| 19 | 18 | -8.60 | 0.35 | -0.35 | (4.38,4.06) |\n",
"| 20 | 19 | -0.80 | 0.43 | -0.35 | (4.38,4.06) |\n",
"| 21 | 20 | -19.60 | 0.35 | -0.23 | (4.38,4.06) |\n",
"| 22 | 21 | -10.50 | 0.39 | -0.05 | (4.38,4.06) |\n",
"| 23 | 22 | -3.70 | 0.31 | 0.03 | (4.38,4.06) |\n",
"| 24 "
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"process_directory: unknown mapping name 'catheter', skipping\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
" | 23 | -2.20 | 0.23 | 0.04 | (4.38,4.06) |\n",
"| 25 | 24 | 0.00 | 0.14 | -0.00 | (4.38,4.06) |\n",
"| 26 | 25 | 0.00 | 0.03 | -0.09 | (4.38,4.06) |\n",
"| 27 | 26 | -18.00 | -0.06 | -0.16 | (4.38,4.06) |\n",
"| 28 | 27 | 17.00 | -0.05 | -0.14 | (4.38,4.06) |\n",
"| 29 | 28 | 0.00 | -0.01 | -0.06 | (4.38,4.06) |\n",
"| 30 | 29 | 18.00 | 0.08 | -0.02 | (4.38,4.06) |\n",
"| 31 | 30 | 89.40 | 0.20 | -0.59 | (4.38,4.06) |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"Successfully wrote OBJ files for geometry ivus_full to output/cad\n",
"Successfully wrote lumen to output/cad/aligned_lumen.obj\n",
"Successfully wrote eem to output/cad/aligned_eem.obj\n",
"Successfully wrote wall to output/cad/aligned_wall.obj\n"
]
},
{
"data": {
"text/html": [
""
]
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"metadata": {},
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"source": [
"cad, _ = mm.from_file_single(\n",
" input_path=\"ivus_full\",\n",
" diastole=True,\n",
" step_rotation_deg=0.1,\n",
" range_rotation_deg=90,\n",
" image_center=(4.5, 4.5),\n",
" radius=0.5,\n",
" n_points=20,\n",
" write_obj=True,\n",
" watertight=False,\n",
" contour_types=[\n",
" mm.PyContourType.Lumen, mm.PyContourType.Eem,\n",
" mm.PyContourType.Catheter, mm.PyContourType.Wall,\n",
" ],\n",
" output_path=\"output/cad\",\n",
")\n",
"# Centre coordinate system on EEM and write both versions\n",
"cad_aligned = cad.center_to_contour(mm.PyContourType.Eem)\n",
"mm.to_obj(cad_aligned, \"output/cad\", watertight=False,\n",
" contour_types=[mm.PyContourType.Lumen, mm.PyContourType.Eem, mm.PyContourType.Wall],\n",
" filename_prefix=\"aligned\")\n",
"\n",
"# from_file_single writes files as {contour_type}_{input_path_name}.obj\n",
"lumen = trimesh.load(\"output/cad/lumen_ivus_full.obj\")\n",
"eem = trimesh.load(\"output/cad/eem_ivus_full.obj\")\n",
"wall = trimesh.load(\"output/cad/wall_ivus_full.obj\")\n",
"lumen_a = trimesh.load(\"output/cad/aligned_lumen.obj\")\n",
"eem_a = trimesh.load(\"output/cad/aligned_eem.obj\")\n",
"wall_a = trimesh.load(\"output/cad/aligned_wall.obj\")\n",
"\n",
"fig = make_subplots(\n",
" rows=1, cols=2,\n",
" specs=[[{\"type\": \"scene\"}, {\"type\": \"scene\"}]],\n",
" subplot_titles=(\"CAD (lumen-centred)\", \"CAD (EEM-centred)\"),\n",
")\n",
"camera = dict(eye=dict(x=1.5, y=1.5, z=1.0))\n",
"for t in [trimesh_to_mesh3d(lumen, \"firebrick\", \"Lumen\", 1.0),\n",
" trimesh_to_mesh3d(eem, \"royalblue\", \"EEM\", 0.6),\n",
" trimesh_to_mesh3d(wall, \"white\", \"Wall\", 0.5)]:\n",
" fig.add_trace(t, row=1, col=1)\n",
"for t in [trimesh_to_mesh3d(lumen_a, \"firebrick\", \"Lumen\", 1.0),\n",
" trimesh_to_mesh3d(eem_a, \"royalblue\", \"EEM\", 0.6),\n",
" trimesh_to_mesh3d(wall_a, \"white\", \"Wall\", 0.5)]:\n",
" fig.add_trace(t, row=1, col=2)\n",
"fig.update_layout(\n",
" width=900, height=450,\n",
" scene=dict(camera=camera, aspectmode=\"data\"),\n",
" scene2=dict(camera=camera, aspectmode=\"data\"),\n",
" margin=dict(l=0, r=0, t=40, b=0),\n",
")\n",
"fig.show()"
]
},
{
"cell_type": "markdown",
"id": "37a663e0",
"metadata": {},
"source": [
"### Pre- vs. Post-stenting\n",
"\n",
"For pre/post-stenting comparison across both cardiac phases, `from_file_full` is used with the\n",
"pre-stent pullback as `input_path_ab` and the post-stent pullback as `input_path_cd`."
]
},
{
"cell_type": "code",
"execution_count": 9,
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"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"eem file not found, skipping: \"ivus_prestent/eem_diastolic_contours.csv\"\n",
"sidebranch file not found, skipping: \"ivus_prestent/branch_diastolic_contours.csv\"\n",
"calcification file not found, skipping: \"ivus_prestent/calcium_diastolic_contours.csv\"\n",
"process_directory: unknown mapping name 'catheter', skipping\n",
"sidebranch file not found, skipping: \"ivus_prestent/branch_systolic_contours.csv\"\n",
"process_directory: unknown mapping name 'catheter', skipping\n",
"calcification file not found, skipping: \"ivus_prestent/calcium_systolic_contours.csv\"\n",
"eem file not found, skipping: \"ivus_prestent/eem_systolic_contours.csv\"\n",
"sidebranch file not found, skipping: \"ivus_poststent/branch_diastolic_contours.csv\"\n",
"eem file not found, skipping: \"ivus_poststent/eem_diastolic_contours.csv\"\n",
"calcification file not found, skipping: \"ivus_poststent/calcium_diastolic_contours.csv\"\n",
"process_directory: unknown mapping name 'catheter', skipping\n",
"eem file not found, skipping: \"ivus_poststent/eem_systolic_contours.csv\"\n",
"sidebranch file not found, skipping: \"ivus_poststent/branch_systolic_contours.csv\"\n",
"calcification file not found, skipping: \"ivus_poststent/calcium_systolic_contours.csv\"\n",
"process_directory: unknown mapping name 'catheter', skipping\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"✅ Successfully built geometry from path\n",
"-----------------------------------------\n",
"✅ Lumen\n",
"❌ Eem\n",
"❌ Calcification\n",
"❌ Sidebranch\n",
"✅ Catheter\n",
"-----------------------------------------\n",
"Label: ivus_prestent\n",
"Diastole phase: Yes\n",
"\n",
"\n",
"✅ Successfully built geometry from path\n",
"-----------------------------------------\n",
"✅ Lumen\n",
"❌ Eem\n",
"❌ Calcification\n",
"❌ Sidebranch\n",
"✅ Catheter\n",
"-----------------------------------------\n",
"Label: ivus_prestent\n",
"Diastole phase: No\n",
"\n",
"\n",
"✅ Successfully built geometry from path\n",
"-----------------------------------------\n",
"✅ Lumen\n",
"❌ Eem\n",
"❌ Calcification\n",
"❌ Sidebranch\n",
"✅ Catheter\n",
"-----------------------------------------\n",
"Label: ivus_poststent\n",
"Diastole phase: Yes\n",
"\n",
"\n",
"✅ Successfully built geometry from path\n",
"-----------------------------------------\n",
"✅ Lumen\n",
"❌ Eem\n",
"❌ Calcification\n",
"❌ Sidebranch\n",
"✅ Catheter\n",
"-----------------------------------------\n",
"Label: ivus_poststent\n",
"Diastole phase: No\n",
"\n",
"\n",
"+--------------------------------------------------------------------+\n",
"| ✅ Finished aligning 'ivus_prestent' (anomalous: true) |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"| Contour | Matched To | Rotation (°) | Tx | Ty | Centroid |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"| 1 | 0 | -11.70 | 0.08 | 0.17 | (4.32,5.28) |\n",
"| 2 | 1 | -2.80 | 0.23 | 0.35 | (4.32,5.28) |\n",
"| 3 | 2 | -8.00 | 0.14 | 0.69 | (4.32,5.28) |\n",
"| 4 | 3 | 1.40 | 0.09 | 0.86 | (4.32,5.28) |\n",
"| 5 | 4 | 39.20 | -0.72 | -0.77 | (4.32,5.28) |\n",
"| 6 | 5 | -19.80 | -0.23 | -0.57 | (4.32,5.28) |\n",
"| 7 | 6 | 13.90 | -0.38 | -0.86 | (4.32,5.28) |\n",
"| 8 | 7 | 3.20 | -0.30 | -0.49 | (4.32,5.28) |\n",
"| 9 | 8 | -4.00 | -0.10 | -0.61 | (4.32,5.28) |\n",
"| 10 | 9 | 5.30 | -0.20 | -0.51 | (4.32,5.28) |\n",
"| 11 | 10 | -3.40 | -0.21 | -0.08 | (4.32,5.28) |\n",
"| 12 | 11 | -45.00 | 0.07 | 0.90 | (4.32,5.28) |\n",
"| 13 | 12 | 0.00 | -0.11 | 0.78 | (4.32,5.28) |\n",
"| 14 | 13 | 36.00 | -0.10 | 0.99 | (4.32,5.28) |\n",
"| 15 | 14 | -17.70 | -0.10 | 1.01 | (4.32,5.28) |\n",
"| 16 | 15 | -45.00 | -0.29 | 0.49 | (4.32,5.28) |\n",
"| 17 | 16 | 8.00 | -0.30 | 0.48 | (4.32,5.28) |\n",
"| 18 | 17 | 0.00 | -0.35 | 0.23 | (4.32,5.28) |\n",
"| 19 | 18 | -6.80 | -0.36 | 0.22 | (4.32,5.28) |\n",
"| 20 | 19 | -9.80 | -0.12 | 0.24 | (4.32,5.28) |\n",
"| 21 | 20 | -14.70 | 0.04 | 0.26 | (4.32,5.28) |\n",
"| 22 | 21 | -2.80 | 0.07 | 0.37 | (4.32,5.28) |\n",
"| 23 | 22 | -45.00 | 0.22 | 1.06 | (4.32,5.28) |\n",
"| 24 | 23 | -18.00 | 0.11 | 1.11 | (4.32,5.28) |\n",
"| 25 | 24 | 45.00 | 0.09 | 0.78 | (4.32,5.28) |\n",
"| 26 | 25 | 45.00 | -0.24 | 0.67 | (4.32,5.28) |\n",
"| 27 | 26 | 39.70 | -0.25 | 0.70 | (4.32,5.28) |\n",
"| 28 | 27 | 36.00 | -0.09 | 0.97 | (4.32,5.28) |\n",
"| 29 | 28 | -36.10 | -0.38 | 1.48 | (4.32,5.28) |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"⚠️\tHole detected! Attempting to fix using Geometry::insert_frame(...) (baseline spacing = 0.559)\n",
"✅ Fixed one-frame hole between Frame 24 and Frame 25 (dz = 0.909, ratio = 1.627)\n",
"✅ Fixed one-frame hole between Frame 31 and Frame 32 (dz = 0.876, ratio = 1.568)\n",
"✅ Fixed one-frame hole between Frame 33 and Frame 34 (dz = 0.842, ratio = 1.508)\n",
"⚠️\tHole detected! Attempting to fix using Geometry::insert_frame(...) (baseline spacing = 0.533)\n",
"✅ Fixed one-frame hole between Frame 19 and Frame 20 (dz = 1.099, ratio = 2.061)\n",
"\n",
"+-------------------------------------------------------------------+\n",
"| ✅ Finished aligning 'ivus_poststent' (anomalous: true) |\n",
"+---------+------------+---------------+------+-------+-------------+\n",
"| Contour | Matched To | Rotation (°) | Tx | Ty | Centroid |\n",
"+---------+------------+---------------+------+-------+-------------+\n",
"| 1 | 0 | 12.40 | 0.18 | -0.01 | (4.69,3.78) |\n",
"| 2 | 1 | 7.50 | 0.29 | 0.00 | (4.69,3.78) |\n",
"| 3 | 2 | -6.70 | 0.20 | 0.31 | (4.69,3.78) |\n",
"| 4 | 3 | 3.30 | 0.33 | 0.39 | (4.69,3.78) |\n",
"| 5 | 4 | 0.00 | 0.25 | 0.06 | (4.69,3.78) |\n",
"| 6 | 5 | 2.20 | 0.34 | 0.32 | (4.69,3.78) |\n",
"| 7 | 6 | 8.70 | 0.50 | 0.31 | (4.69,3.78) |\n",
"| 8 | 7 | -7.90 | 0.46 | 0.32 | (4.69,3.78) |\n",
"| 9 | 8 | 7.30 | 0.54 | 0.22 | (4.69,3.78) |\n",
"| 10 | 9 | 7.90 | 0.65 | 0.09 | (4.69,3.78) |\n",
"| 11 | 10 | 0.00 | 0.62 | 0.00 | (4.69,3.78) |\n",
"| 12 | 11 | 5.30 | 0.66 | -0.11 | (4.69,3.78) |\n",
"| 13 | 12 | -11.40 | 0.60 | -0.18 | (4.69,3.78) |\n",
"| 14 | 13 | -2.90 | 0.56 | -0.21 | (4.69,3.78) |\n",
"| 15 | 14 | 0.00 | 0.53 | -0.35 | (4.69,3.78) |\n",
"| 16 | 15 | 18.00 | 0.55 | -0.46 | (4.69,3.78) |\n",
"| 17 | 16 | 12.40 | 0.59 | -0.58 | (4.69,3.78) |\n",
"| 18 | 17 | 5.80 | 0.61 | -0.61 | (4.69,3.78) |\n",
"| 19 | 18 | 13.20 | 0.63 | -0.72 | (4.69,3.78) |\n",
"| 20 | 19 | 0.70 | 0.61 | -0.73 | (4.69,3.78) |\n",
"| 21 | 20 | 0.00 | 0.57 | -0.75 | (4.69,3.78) |\n",
"| 22 | 21 | -18.00 | 0.89 | -0.63 | (4.69,3.78) |\n",
"| 23 | 22 | -0.70 | 0.85 | -0.69 | (4.69,3.78) |\n",
"| 24 | 23 | -15.90 | 0.83 | -0.50 | (4.69,3.78) |\n",
"| 25 | 24 | 3.60 | 0.83 | -0.49 | (4.69,3.78) |\n",
"| 26 | 25 | 15.70 | 0.90 | -0.63 | (4.69,3.78) |\n",
"| 27 | 26 | 16.20 | 0.85 | -0.78 | (4.69,3.78) |\n",
"| 28 | 27 | -5.40 | 0.91 | -0.70 | (4.69,3.78) |\n",
"| 29 | 28 | 6.40 | 0.89 | -0.73 | (4.69,3.78) |\n",
"| 30 | 29 | 24.20 | 0.78 | -0.99 | (4.69,3.78) |\n",
"| 31 | 30 | -1.30 | 0.72 | -0.91 | (4.69,3.78) |\n",
"| 32 | 31 | 19.40 | 0.65 | -0.94 | (4.69,3.78) |\n",
"| 33 | 32 | 0.00 | 0.86 | -1.01 | (4.69,3.78) |\n",
"| 34 | 33 | 9.90 | 0.74 | -1.06 | (4.69,3.78) |\n",
"+---------+------------+---------------+------+-------+-------------+\n",
"\n",
"+--------------------------------------------------------------------+\n",
"| ✅ Finished aligning 'ivus_prestent' (anomalous: true) |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"| Contour | Matched To | Rotation (°) | Tx | Ty | Centroid |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"| 1 | 0 | 0.10 | 0.01 | 0.12 | (4.20,4.59) |\n",
"| 2 | 1 | -8.10 | -0.03 | 0.07 | (4.20,4.59) |\n",
"| 3 | 2 | 9.20 | -0.05 | -0.14 | (4.20,4.59) |\n",
"| 4 | 3 | -10.90 | 0.27 | -0.75 | (4.20,4.59) |\n",
"| 5 | 4 | 9.90 | 0.11 | -1.14 | (4.20,4.59) |\n",
"| 6 | 5 | -1.10 | 0.03 | -1.17 | (4.20,4.59) |\n",
"| 7 | 6 | 8.00 | -0.13 | -1.28 | (4.20,4.59) |\n",
"| 8 | 7 | -4.10 | -0.08 | -1.25 | (4.20,4.59) |\n",
"| 9 | 8 | -0.80 | -0.06 | -1.36 | (4.20,4.59) |\n",
"| 10 | 9 | -0.70 | 0.02 | -1.22 | (4.20,4.59) |\n",
"| 11 | 10 | 6.00 | -0.26 | -1.22 | (4.20,4.59) |\n",
"| 12 | 11 | -0.30 | -0.35 | -1.21 | (4.20,4.59) |\n",
"| 13 | 12 | -4.70 | -0.13 | -0.88 | (4.20,4.59) |\n",
"| 14 | 13 | -4.30 | -0.08 | -0.87 | (4.20,4.59) |\n",
"| 15 | 14 | 4.20 | -0.14 | -0.77 | (4.20,4.59) |\n",
"| 16 | 15 | -3.60 | -0.13 | -0.74 | (4.20,4.59) |\n",
"| 17 | 16 | 0.00 | -0.17 | -0.52 | (4.20,4.59) |\n",
"| 18 | 17 | -45.00 | 0.06 | 0.32 | (4.20,4.59) |\n",
"| 19 | 18 | -3.50 | 0.04 | 0.28 | (4.20,4.59) |\n",
"| 20 | 19 | 45.00 | -0.42 | -0.17 | (4.20,4.59) |\n",
"| 21 | 20 | -11.60 | -0.29 | -0.06 | (4.20,4.59) |\n",
"| 22 | 21 | 45.00 | -0.72 | -0.15 | (4.20,4.59) |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"⚠️\tHole detected! Attempting to fix using Geometry::insert_frame(...) (baseline spacing = 0.569)\n",
"✅ Fixed one-frame hole between Frame 30 and Frame 31 (dz = 0.876, ratio = 1.539)\n",
"\n",
"+-------------------------------------------------------------------+\n",
"| ✅ Finished aligning 'ivus_poststent' (anomalous: true) |\n",
"+---------+------------+---------------+------+-------+-------------+\n",
"| Contour | Matched To | Rotation (°) | Tx | Ty | Centroid |\n",
"+---------+------------+---------------+------+-------+-------------+\n",
"| 1 | 0 | 3.90 | 0.16 | 0.16 | (4.84,3.84) |\n",
"| 2 | 1 | -10.70 | 0.08 | 0.12 | (4.84,3.84) |\n",
"| 3 | 2 | 17.50 | 0.40 | 0.34 | (4.84,3.84) |\n",
"| 4 | 3 | -12.70 | 0.19 | 0.38 | (4.84,3.84) |\n",
"| 5 | 4 | 3.90 | 0.34 | 0.38 | (4.84,3.84) |\n",
"| 6 | 5 | 6.00 | 0.47 | 0.39 | (4.84,3.84) |\n",
"| 7 | 6 | 13.90 | 0.65 | 0.30 | (4.84,3.84) |\n",
"| 8 | 7 | -18.00 | 0.37 | 0.43 | (4.84,3.84) |\n",
"| 9 | 8 | 15.80 | 0.57 | 0.20 | (4.84,3.84) |\n",
"| 10 | 9 | 3.00 | 0.57 | 0.18 | (4.84,3.84) |\n",
"| 11 | 10 | 0.30 | 0.68 | 0.18 | (4.84,3.84) |\n",
"| 12 | 11 | 8.80 | 0.72 | 0.02 | (4.84,3.84) |\n",
"| 13 | 12 | 7.10 | 0.81 | -0.06 | (4.84,3.84) |\n",
"| 14 | 13 | 0.00 | 0.76 | -0.14 | (4.84,3.84) |\n",
"| 15 | 14 | 5.40 | 0.78 | -0.23 | (4.84,3.84) |\n",
"| 16 | 15 | -0.80 | 0.85 | -0.25 | (4.84,3.84) |\n",
"| 17 | 16 | 10.50 | 0.88 | -0.35 | (4.84,3.84) |\n",
"| 18 | 17 | 13.70 | 0.94 | -0.43 | (4.84,3.84) |\n",
"| 19 | 18 | 0.20 | 0.92 | -0.50 | (4.84,3.84) |\n",
"| 20 | 19 | 23.30 | 0.92 | -0.72 | (4.84,3.84) |\n",
"| 21 | 20 | -12.40 | 0.86 | -0.68 | (4.84,3.84) |\n",
"| 22 | 21 | 32.40 | 0.82 | -0.85 | (4.84,3.84) |\n",
"| 23 | 22 | 18.10 | 0.78 | -0.89 | (4.84,3.84) |\n",
"| 24 | 23 | -18.00 | 0.74 | -0.75 | (4.84,3.84) |\n",
"| 25 | 24 | 18.00 | 0.79 | -0.94 | (4.84,3.84) |\n",
"| 26 | 25 | 11.30 | 0.70 | -0.95 | (4.84,3.84) |\n",
"| 27 | 26 | 0.00 | 0.77 | -0.91 | (4.84,3.84) |\n",
"| 28 | 27 | 0.00 | 0.70 | -0.88 | (4.84,3.84) |\n",
"| 29 | 28 | 12.70 | 0.74 | -0.64 | (4.84,3.84) |\n",
"| 30 | 29 | 0.00 | 1.10 | -0.63 | (4.84,3.84) |\n",
"| 31 | 30 | 11.40 | 0.82 | -0.72 | (4.84,3.84) |\n",
"| 32 | 31 | -9.60 | 1.10 | -0.64 | (4.84,3.84) |\n",
"| 33 | 32 | 4.70 | 1.09 | -0.64 | (4.84,3.84) |\n",
"+---------+------------+---------------+------+-------+-------------+\n",
"\n",
"✅ Aligned geometry 'ivus_poststent' to 'ivus_poststent'\n",
"-----------------------------------------\n",
"Applied initial translation: (-0.16, -0.05, 0.00) mm\n",
"Found best rotation of -34.90° with parameters: \n",
"range: 45.00° \n",
"step size: 0.1°\n",
"Applied final translation: ( 0, 0.00, 0.00) mm\n",
"-----------------------------------------\n",
"\n",
"✅ Aligned geometry 'ivus_prestent' to 'ivus_prestent'\n",
"-----------------------------------------\n",
"Applied initial translation: (0.12, 0.70, 0.00) mm\n",
"Found best rotation of -0.50° with parameters: \n",
"range: 45.00° \n",
"step size: 0.1°\n",
"Applied final translation: ( 0, 0.00, 0.00) mm\n",
"-----------------------------------------\n",
"\n",
"✅ Aligned geometry 'ivus_poststent' to 'ivus_prestent'\n",
"-----------------------------------------\n",
"Applied initial translation: (-0.37, 1.50, 0.00) mm\n",
"Found best rotation of 30.20° with parameters: \n",
"range: 45.00° \n",
"step size: 0.1°\n",
"Applied final translation: ( 0, 0.00, 0.00) mm\n",
"-----------------------------------------\n",
"\n",
"✅ Aligned geometry 'ivus_poststent' to 'ivus_prestent'\n",
"-----------------------------------------\n",
"Applied initial translation: (-0.37, 1.50, 0.00) mm\n",
"Found best rotation of -27.40° with parameters: \n",
"range: 45.00° \n",
"step size: 0.1°\n",
"Applied final translation: ( 0, 0.00, 0.00) mm\n",
"-----------------------------------------\n",
"\n",
"Saving files for 'ivus_prestent - ivus_prestent' to 'output/stent_rest'\n",
"LUMEN .obj files: 2/2 written successfully\n",
"CATHETER .obj files: 2/2 written successfully\n",
"WALL .obj files: 2/2 written successfully\n",
"\n",
"Saving files for 'ivus_poststent - ivus_poststent' to 'output/stent_stress'\n",
"LUMEN .obj files: 2/2 written successfully\n",
"CATHETER .obj files: 2/2 written successfully\n",
"WALL .obj files: 2/2 written successfully\n",
"\n",
"Saving files for 'ivus_prestent - ivus_poststent' to 'output/stent_diastole'\n",
"LUMEN .obj files: 2/2 written successfully\n",
"CATHETER .obj files: 2/2 written successfully\n",
"WALL .obj files: 2/2 written successfully\n",
"\n",
"Saving files for 'ivus_prestent - ivus_poststent' to 'output/stent_systole'\n",
"LUMEN .obj files: 2/2 written successfully\n",
"CATHETER .obj files: 2/2 written successfully\n",
"WALL .obj files: 2/2 written successfully\n",
"Successfully wrote lumen to output/stent_vis/prestent_lumen.obj\n",
"Successfully wrote lumen to output/stent_vis/poststent_lumen.obj\n"
]
},
{
"data": {
"text/html": [
""
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"prestent, poststent, dia_comp, sys_comp, _ = mm.from_file_full(\n",
" input_path_ab=\"ivus_prestent\",\n",
" input_path_cd=\"ivus_poststent\",\n",
" step_rotation_deg=0.1,\n",
" range_rotation_deg=45,\n",
" watertight=False,\n",
" output_path_ab=\"output/stent_rest\",\n",
" output_path_cd=\"output/stent_stress\",\n",
" output_path_ac=\"output/stent_diastole\",\n",
" output_path_bd=\"output/stent_systole\",\n",
" interpolation_steps=0,\n",
")\n",
"# Write comparison geometries with explicit names\n",
"mm.to_obj(dia_comp.geom_a, \"output/stent_vis\", watertight=False,\n",
" contour_types=[mm.PyContourType.Lumen], filename_prefix=\"prestent\")\n",
"mm.to_obj(dia_comp.geom_b, \"output/stent_vis\", watertight=False,\n",
" contour_types=[mm.PyContourType.Lumen], filename_prefix=\"poststent\")\n",
"\n",
"mesh_pre = trimesh.load(\"output/stent_vis/prestent_lumen.obj\")\n",
"mesh_post = trimesh.load(\"output/stent_vis/poststent_lumen.obj\")\n",
"\n",
"fig = go.Figure(data=[\n",
" trimesh_to_mesh3d(mesh_pre, \"royalblue\", \"Pre-stent (diastole)\"),\n",
" trimesh_to_mesh3d(mesh_post, \"firebrick\", \"Post-stent (diastole)\"),\n",
"])\n",
"fig.update_layout(\n",
" title=\"Pre- vs. Post-stenting: diastolic lumen comparison\",\n",
" scene=dict(aspectmode=\"data\"),\n",
" margin=dict(l=0, r=0, t=40, b=0),\n",
")\n",
"fig.show()"
]
},
{
"cell_type": "markdown",
"id": "e9aa87db",
"metadata": {},
"source": [
"## 3. Workflow from numpy arrays\n",
"\n",
"The numpy workflow accepts data from **any source**: you build `PyInputData` objects manually and\n",
"then call the same alignment functions. Use this workflow when your segmentation software uses\n",
"different file formats, when you need pre-processing steps, or when embedding `multimodars` into a\n",
"larger pipeline.\n",
"\n",
"For stent comparison, both pre- and post-stent geometries are packed into `PyInputData` objects:"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "f3b436f1",
"metadata": {
"execution": {
"iopub.execute_input": "2026-05-04T15:14:37.037138Z",
"iopub.status.busy": "2026-05-04T15:14:37.036942Z",
"iopub.status.idle": "2026-05-04T15:14:42.965362Z",
"shell.execute_reply": "2026-05-04T15:14:42.964277Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"✅ Successfully built geometry from input data\n",
"-----------------------------------------\n",
"✅ Lumen\n",
"❌ Eem\n",
"❌ Calcification\n",
"❌ Sidebranch\n",
"✅ Catheter\n",
"-----------------------------------------\n",
"Label: prestent\n",
"Diastole phase: Yes\n",
"\n",
"\n",
"✅ Successfully built geometry from input data\n",
"-----------------------------------------\n",
"✅ Lumen\n",
"❌ Eem\n",
"❌ Calcification\n",
"❌ Sidebranch\n",
"✅ Catheter\n",
"-----------------------------------------\n",
"Label: poststent\n",
"Diastole phase: Yes\n",
"\n",
"\n",
"+--------------------------------------------------------------------+\n",
"| ✅ Finished aligning 'prestent' (anomalous: true) |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"| Contour | Matched To | Rotation (°) | Tx | Ty | Centroid |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"| 1 | 0 | -19.43 | 0.23 | 0.35 | (4.32,5.28) |\n",
"| 2 | 1 | 2.77 | 0.08 | 0.17 | (4.32,5.28) |\n",
"| 3 | 2 | -8.61 | 0.14 | 0.69 | (4.32,5.28) |\n",
"| 4 | 3 | 1.44 | 0.09 | 0.86 | (4.32,5.28) |\n",
"| 5 | 4 | -10.88 | -0.10 | -0.61 | (4.32,5.28) |\n",
"| 6 | 5 | 5.32 | -0.20 | -0.51 | (4.32,5.28) |\n",
"| 7 | 6 | -0.54 | -0.30 | -0.49 | (4.32,5.28) |\n",
"| 8 | 7 | -3.14 | -0.38 | -0.86 | (4.32,5.28) |\n",
"| 9 | 8 | 7.40 | -0.72 | -0.77 | (4.32,5.28) |\n",
"| 10 | 9 | -19.75 | -0.23 | -0.57 | (4.32,5.28) |\n",
"| 11 | 10 | 0.00 | -0.21 | -0.08 | (4.32,5.28) |\n",
"| 12 | 11 | 16.53 | -0.35 | 0.23 | (4.32,5.28) |\n",
"| 13 | 12 | -6.85 | -0.36 | 0.22 | (4.32,5.28) |\n",
"| 14 | 13 | 0.00 | -0.30 | 0.48 | (4.32,5.28) |\n",
"| 15 | 14 | -8.01 | -0.29 | 0.49 | (4.32,5.28) |\n",
"| 16 | 15 | -17.73 | -0.12 | 0.24 | (4.32,5.28) |\n",
"| 17 | 16 | -14.66 | 0.04 | 0.26 | (4.32,5.28) |\n",
"| 18 | 17 | -30.00 | 0.07 | 0.90 | (4.32,5.28) |\n",
"| 19 | 18 | 16.52 | -0.09 | 0.97 | (4.32,5.28) |\n",
"| 20 | 19 | -14.64 | -0.10 | 1.01 | (4.32,5.28) |\n",
"| 21 | 20 | 17.73 | -0.10 | 0.99 | (4.32,5.28) |\n",
"| 22 | 21 | -26.19 | -0.11 | 0.78 | (4.32,5.28) |\n",
"| 23 | 22 | 30.00 | 0.07 | 0.37 | (4.32,5.28) |\n",
"| 24 | 23 | -6.49 | 0.09 | 0.78 | (4.32,5.28) |\n",
"| 25 | 24 | 29.51 | -0.25 | 0.70 | (4.32,5.28) |\n",
"| 26 | 25 | -29.88 | -0.24 | 0.67 | (4.32,5.28) |\n",
"| 27 | 26 | 30.00 | -0.38 | 1.48 | (4.32,5.28) |\n",
"| 28 | 27 | 30.00 | 0.11 | 1.11 | (4.32,5.28) |\n",
"| 29 | 28 | 18.00 | 0.22 | 1.06 | (4.32,5.28) |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"⚠️\tHole detected! Attempting to fix using Geometry::insert_frame(...) (baseline spacing = 0.559)\n",
"✅ Fixed one-frame hole between Frame 24 and Frame 25 (dz = 0.909, ratio = 1.627)\n",
"✅ Fixed one-frame hole between Frame 31 and Frame 32 (dz = 0.876, ratio = 1.568)\n",
"✅ Fixed one-frame hole between Frame 33 and Frame 34 (dz = 0.842, ratio = 1.508)\n",
"\n",
"+-------------------------------------------------------------------+\n",
"| ✅ Finished aligning 'poststent' (anomalous: false) |\n",
"+---------+------------+---------------+------+-------+-------------+\n",
"| Contour | Matched To | Rotation (°) | Tx | Ty | Centroid |\n",
"+---------+------------+---------------+------+-------+-------------+\n",
"| 1 | 0 | 12.38 | 0.18 | -0.01 | (4.69,3.78) |\n",
"| 2 | 1 | 7.45 | 0.29 | 0.00 | (4.69,3.78) |\n",
"| 3 | 2 | -12.68 | 0.25 | 0.06 | (4.69,3.78) |\n",
"| 4 | 3 | -1.86 | 0.20 | 0.31 | (4.69,3.78) |\n",
"| 5 | 4 | 3.30 | 0.33 | 0.39 | (4.69,3.78) |\n",
"| 6 | 5 | 6.94 | 0.34 | 0.32 | (4.69,3.78) |\n",
"| 7 | 6 | 8.74 | 0.50 | 0.31 | (4.69,3.78) |\n",
"| 8 | 7 | -7.95 | 0.46 | 0.32 | (4.69,3.78) |\n",
"| 9 | 8 | 7.24 | 0.54 | 0.22 | (4.69,3.78) |\n",
"| 10 | 9 | 7.93 | 0.65 | 0.09 | (4.69,3.78) |\n",
"| 11 | 10 | 0.00 | 0.62 | 0.00 | (4.69,3.78) |\n",
"| 12 | 11 | 5.25 | 0.66 | -0.11 | (4.69,3.78) |\n",
"| 13 | 12 | -11.45 | 0.60 | -0.18 | (4.69,3.78) |\n",
"| 14 | 13 | -2.92 | 0.56 | -0.21 | (4.69,3.78) |\n",
"| 15 | 14 | 0.00 | 0.53 | -0.35 | (4.69,3.78) |\n",
"| 16 | 15 | 18.00 | 0.55 | -0.46 | (4.69,3.78) |\n",
"| 17 | 16 | 12.37 | 0.59 | -0.58 | (4.69,3.78) |\n",
"| 18 | 17 | 5.81 | 0.61 | -0.61 | (4.69,3.78) |\n",
"| 19 | 18 | 13.24 | 0.63 | -0.72 | (4.69,3.78) |\n",
"| 20 | 19 | 0.67 | 0.61 | -0.73 | (4.69,3.78) |\n",
"| 21 | 20 | -18.00 | 0.83 | -0.50 | (4.69,3.78) |\n",
"| 22 | 21 | 18.00 | 0.57 | -0.75 | (4.69,3.78) |\n",
"| 23 | 22 | -23.65 | 0.83 | -0.49 | (4.69,3.78) |\n",
"| 24 | 23 | 15.70 | 0.90 | -0.63 | (4.69,3.78) |\n",
"| 25 | 24 | -3.16 | 0.89 | -0.63 | (4.69,3.78) |\n",
"| 26 | 25 | -0.74 | 0.85 | -0.69 | (4.69,3.78) |\n",
"| 27 | 26 | 0.00 | 0.89 | -0.73 | (4.69,3.78) |\n",
"| 28 | 27 | -6.41 | 0.91 | -0.70 | (4.69,3.78) |\n",
"| 29 | 28 | 5.45 | 0.85 | -0.78 | (4.69,3.78) |\n",
"| 30 | 29 | -0.54 | 0.72 | -0.91 | (4.69,3.78) |\n",
"| 31 | 30 | 19.47 | 0.65 | -0.94 | (4.69,3.78) |\n",
"| 32 | 31 | 6.12 | 0.74 | -1.06 | (4.69,3.78) |\n",
"| 33 | 32 | -9.93 | 0.86 | -1.01 | (4.69,3.78) |\n",
"| 34 | 33 | -1.94 | 0.78 | -0.99 | (4.69,3.78) |\n",
"+---------+------------+---------------+------+-------+-------------+\n",
"\n",
"✅ Aligned geometry 'poststent' to 'prestent'\n",
"-----------------------------------------\n",
"Applied initial translation: (-0.37, 1.50, 0.00) mm\n",
"Found best rotation of 18.55° with parameters: \n",
"range: 30.00° \n",
"step size: 0.01°\n",
"Applied final translation: ( 0, 0.00, 0.00) mm\n",
"-----------------------------------------\n",
"\n",
"Saving files for 'prestent - poststent' to 'output/stent_comparison'\n",
"LUMEN .obj files: 2/2 written successfully\n",
"CATHETER .obj files: 2/2 written successfully\n",
"WALL .obj files: 2/2 written successfully\n"
]
}
],
"source": [
"before_arr = np.genfromtxt(\"ivus_prestent/diastolic_contours.csv\", delimiter='\\t')\n",
"before_ref = np.genfromtxt(\"ivus_prestent/diastolic_reference_points.csv\", delimiter='\\t')\n",
"after_arr = np.genfromtxt(\"ivus_poststent/diastolic_contours.csv\", delimiter='\\t')\n",
"after_ref = np.genfromtxt(\"ivus_poststent/diastolic_reference_points.csv\", delimiter='\\t')\n",
"\n",
"before_input = mm.numpy_to_inputdata(\n",
" lumen_arr=before_arr, ref_point=before_ref,\n",
" record=None, diastole=True, label=\"prestent\",\n",
")\n",
"after_input = mm.numpy_to_inputdata(\n",
" lumen_arr=after_arr, ref_point=after_ref,\n",
" record=None, diastole=True, label=\"poststent\",\n",
")\n",
"\n",
"pair, _ = mm.from_array_singlepair(\n",
" input_data_a=before_input,\n",
" input_data_b=after_input,\n",
" step_rotation_deg=0.01,\n",
" range_rotation_deg=30,\n",
" output_path=\"output/stent_comparison\",\n",
")"
]
},
{
"cell_type": "markdown",
"id": "ba9600ea",
"metadata": {},
"source": [
"A single 3D geometry can also be reconstructed from OCT. `from_array_single` returns a\n",
"`PyGeometry` from a single-state contour array. The `replace_frame` method demonstrates\n",
"in-place editing before writing:"
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "3aa0c3f9",
"metadata": {
"execution": {
"iopub.execute_input": "2026-05-04T15:14:42.967777Z",
"iopub.status.busy": "2026-05-04T15:14:42.967568Z",
"iopub.status.idle": "2026-05-04T15:15:20.571263Z",
"shell.execute_reply": "2026-05-04T15:15:20.570480Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"✅ Successfully built geometry from input data\n",
"-----------------------------------------\n",
"✅ Lumen\n",
"❌ Eem\n",
"❌ Calcification\n",
"❌ Sidebranch\n",
"✅ Catheter\n",
"-----------------------------------------\n",
"Label: oct\n",
"Diastole phase: Yes\n",
"\n",
"\n",
"+--------------------------------------------------------------------+\n",
"| ✅ Finished aligning 'oct' (anomalous: false) |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"| Contour | Matched To | Rotation (°) | Tx | Ty | Centroid |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"| 1 | 0 | -1.75 | 0.00 | 0.05 | (6.30,5.97) |\n",
"| 2 | 1 | 1.40 | 0.02 | 0.12 | (6.30,5.97) |\n",
"| 3 | 2 | 0.47 | -0.03 | 0.17 | (6.30,5.97) |\n",
"| 4 | 3 | 3.10 | -0.04 | 0.25 | (6.30,5.97) |\n",
"| 5 | 4 | -1.86 | -0.06 | 0.29 | (6.30,5.97) |\n",
"| 6 | 5 | 4.01 | -0.10 | 0.42 | (6.30,5.97) |\n",
"| 7 | 6 | 5.88 | -0.13 | 0.59 | (6.30,5.97) |\n",
"| 8 | 7 | 5.99 | -0.14 | 0.78 | (6.30,5.97) |\n",
"| 9 | 8 | 0.71 | -0.13 | 0.90 | (6.30,5.97) |\n",
"| 10 | 9 | 2.19 | -0.10 | 1.04 | (6.30,5.97) |\n",
"| 11 | 10 | 2.24 | -0.09 | 1.14 | (6.30,5.97) |\n",
"| 12 | 11 | 2.62 | -0.05 | 1.27 | (6.30,5.97) |\n",
"| 13 | 12 | 0.92 | 0.00 | 1.37 | (6.30,5.97) |\n",
"| 14 | 13 | 5.28 | 0.05 | 1.50 | (6.30,5.97) |\n",
"| 15 | 14 | 1.82 | 0.09 | 1.59 | (6.30,5.97) |\n",
"| 16 | 15 | 2.20 | 0.15 | 1.68 | (6.30,5.97) |\n",
"| 17 | 16 | 0.01 | 0.22 | 1.78 | (6.30,5.97) |\n",
"| 18 | 17 | -0.59 | 0.29 | 1.83 | (6.30,5.97) |\n",
"| 19 | 18 | 4.33 | 0.36 | 1.91 | (6.30,5.97) |\n",
"| 20 | 19 | 2.80 | 0.42 | 1.95 | (6.30,5.97) |\n",
"| 21 | 20 | -0.80 | 0.51 | 1.97 | (6.30,5.97) |\n",
"| 22 | 21 | -6.00 | 0.67 | 1.95 | (6.30,5.97) |\n",
"| 23 | 22 | 2.37 | 0.76 | 1.90 | (6.30,5.97) |\n",
"| 24 | 23 | 0.83 | 0.82 | 1.88 | (6.30,5.97) |\n",
"| 25 | 24 | -0.62 | 0.78 | 1.86 | (6.30,5.97) |\n",
"| 26 | 25 | -0.87 | 0.82 | 1.84 | (6.30,5.97) |\n",
"| 27 | 26 | 3.52 | 0.82 | 1.84 | (6.30,5.97) |\n",
"| 28 | 27 | 4.63 | 0.86 | 1.87 | (6.30,5.97) |\n",
"| 29 | 28 | 5.46 | 0.88 | 1.92 | (6.30,5.97) |\n",
"| 30 | 29 | 1.04 | 0.90 | 1.95 | (6.30,5.97) |\n",
"| 31 | 30 | 1.64 | 0.91 | 2.00 | (6.30,5.97) |\n",
"| 32 | 31 | 0.20 | 0.90 | 2.06 | (6.30,5.97) |\n",
"| 33 | 32 | 0.88 | 0.93 | 2.13 | (6.30,5.97) |\n",
"| 34 | 33 | 1.35 | 0.96 | 2.22 | (6.30,5.97) |\n",
"| 35 | 34 | 3.43 | 0.99 | 2.28 | (6.30,5.97) |\n",
"| 36 | 35 | 3.22 | 1.04 | 2.32 | (6.30,5.97) |\n",
"| 37 | 36 | 5.27 | 1.14 | 2.39 | (6.30,5.97) |\n",
"| 38 | 37 | 5.99 | 1.25 | 2.48 | (6.30,5.97) |\n",
"| 39 | 38 | 5.99 | 1.43 | 2.53 | (6.30,5.97) |\n",
"| 40 | 39 | 4.19 | 1.56 | 2.58 | (6.30,5.97) |\n",
"| 41 | 40 | 4.06 | 1.69 | 2.59 | (6.30,5.97) |\n",
"| 42 | 41 | 3.93 | 1.79 | 2.60 | (6.30,5.97) |\n",
"| 43 | 42 | 0.38 | 1.84 | 2.61 | (6.30,5.97) |\n",
"| 44 | 43 | 3.33 | 1.92 | 2.61 | (6.30,5.97) |\n",
"| 45 | 44 | 2.85 | 1.97 | 2.61 | (6.30,5.97) |\n",
"| 46 | 45 | -0.62 | 2.00 | 2.59 | (6.30,5.97) |\n",
"| 47 | 46 | 0.62 | 2.02 | 2.57 | (6.30,5.97) |\n",
"| 48 | 47 | 2.22 | 2.05 | 2.52 | (6.30,5.97) |\n",
"| 49 | 48 | 0.99 | 2.04 | 2.53 | (6.30,5.97) |\n",
"| 50 | 49 | 5.96 | 2.09 | 2.51 | (6.30,5.97) |\n",
"| 51 | 50 | -4.71 | 2.08 | 2.54 | (6.30,5.97) |\n",
"| 52 | 51 | 1.17 | 2.09 | 2.52 | (6.30,5.97) |\n",
"| 53 | 52 | 0.70 | 2.14 | 2.51 | (6.30,5.97) |\n",
"| 54 | 53 | -0.97 | 2.19 | 2.45 | (6.30,5.97) |\n",
"| 55 | 54 | 2.69 | 2.23 | 2.40 | (6.30,5.97) |\n",
"| 56 | 55 | -4.29 | 2.19 | 2.38 | (6.30,5.97) |\n",
"| 57 | 56 | 2.00 | 2.22 | 2.29 | (6.30,5.97) |\n",
"| 58 | 57 | 1.90 | 2.25 | 2.22 | (6.30,5.97) |\n",
"| 59 | 58 | -1.62 | 2.28 | 2.14 | (6.30,5.97) |\n",
"| 60 | 59 | 1.61 | 2.26 | 2.08 | (6.30,5.97) |\n",
"| 61 | 60 | 1.23 | 2.23 | 2.03 | (6.30,5.97) |\n",
"| 62 | 61 | 1.38 | 2.18 | 1.99 | (6.30,5.97) |\n",
"| 63 | 62 | 2.23 | 2.16 | 1.96 | (6.30,5.97) |\n",
"| 64 | 63 | 1.43 | 2.16 | 1.91 | (6.30,5.97) |\n",
"| 65 | 64 | -0.70 | 2.14 | 1.88 | (6.30,5.97) |\n",
"| 66 | 65 | 2.59 | 2.14 | 1.85 | (6.30,5.97) |\n",
"| 67 | 66 | 0.93 | 2.13 | 1.83 | (6.30,5.97) |\n",
"| 68 | 67 | 1.79 | 2.13 | 1.81 | (6.30,5.97) |\n",
"| 69 | 68 | 1.58 | 2.12 | 1.80 | (6.30,5.97) |\n",
"| 70 | 69 | 0.97 | 2.10 | 1.82 | (6.30,5.97) |\n",
"| 71 | 70 | 1.95 | 2.07 | 1.81 | (6.30,5.97) |\n",
"| 72 | 71 | 0.56 | 2.04 | 1.80 | (6.30,5.97) |\n",
"| 73 | 72 | 1.54 | 2.02 | 1.78 | (6.30,5.97) |\n",
"| 74 | 73 | -0.07 | 2.00 | 1.77 | (6.30,5.97) |\n",
"| 75 | 74 | 1.18 | 1.97 | 1.78 | (6.30,5.97) |\n",
"| 76 | 75 | 0.83 | 1.96 | 1.75 | (6.30,5.97) |\n",
"| 77 | 76 | 1.11 | 1.94 | 1.71 | (6.30,5.97) |\n",
"| 78 | 77 | 1.73 | 1.95 | 1.69 | (6.30,5.97) |\n",
"| 79 | 78 | 0.16 | 1.94 | 1.66 | (6.30,5.97) |\n",
"| 80 | 79 | 2.62 | 1.94 | 1.64 | (6.30,5.97) |\n",
"| 81 | 80 | 2.81 | 1.95 | 1.63 | (6.30,5.97) |\n",
"| 82 | 81 | -1.60 | 1.97 | 1.62 | (6.30,5.97) |\n",
"| 83 | 82 | 4.01 | 1.95 | 1.63 | (6.30,5.97) |\n",
"| 84 | 83 | 5.99 | 1.96 | 1.69 | (6.30,5.97) |\n",
"| 85 | 84 | 5.99 | 2.03 | 1.60 | (6.30,5.97) |\n",
"| 86 | 85 | 4.49 | 2.06 | 1.53 | (6.30,5.97) |\n",
"| 87 | 86 | -0.62 | 2.09 | 1.45 | (6.30,5.97) |\n",
"| 88 | 87 | 1.30 | 2.12 | 1.41 | (6.30,5.97) |\n",
"| 89 | 88 | -0.70 | 2.15 | 1.37 | (6.30,5.97) |\n",
"| 90 | 89 | 2.85 | 2.19 | 1.33 | (6.30,5.97) |\n",
"| 91 | 90 | 0.63 | 2.23 | 1.28 | (6.30,5.97) |\n",
"| 92 | 91 | -0.24 | 2.27 | 1.25 | (6.30,5.97) |\n",
"| 93 | 92 | -0.26 | 2.31 | 1.23 | (6.30,5.97) |\n",
"| 94 | 93 | 3.01 | 2.35 | 1.15 | (6.30,5.97) |\n",
"| 95 | 94 | 2.36 | 2.37 | 1.08 | (6.30,5.97) |\n",
"| 96 | 95 | 3.39 | 2.36 | 1.05 | (6.30,5.97) |\n",
"| 97 | 96 | 3.71 | 2.37 | 1.04 | (6.30,5.97) |\n",
"| 98 | 97 | 5.99 | 2.38 | 1.00 | (6.30,5.97) |\n",
"| 99 | 98 | 5.99 | 2.43 | 0.99 | (6.30,5.97) |\n",
"| 100 | 99 | 5.69 | 2.44 | 0.99 | (6.30,5.97) |\n",
"| 101 | 100 | 0.35 | 2.46 | 0.90 | (6.30,5.97) |\n",
"| 102 | 101 | 0.00 | 2.46 | 0.79 | (6.30,5.97) |\n",
"| 103 | 102 | 2.10 | 2.45 | 0.66 | (6.30,5.97) |\n",
"| 104 | 103 | 3.25 | 2.43 | 0.57 | (6.30,5.97) |\n",
"| 105 | 104 | 3.92 | 2.42 | 0.47 | (6.30,5.97) |\n",
"| 106 | 105 | 0.01 | 2.41 | 0.41 | (6.30,5.97) |\n",
"| 107 | 106 | 3.23 | 2.42 | 0.33 | (6.30,5.97) |\n",
"| 108 | 107 | 0.98 | 2.41 | 0.28 | (6.30,5.97) |\n",
"| 109 | 108 | 1.37 | 2.40 | 0.25 | (6.30,5.97) |\n",
"| 110 | 109 | -0.05 | 2.41 | 0.22 | (6.30,5.97) |\n",
"| 111 | 110 | 1.56 | 2.38 | 0.20 | (6.30,5.97) |\n",
"| 112 | 111 | 2.63 | 2.35 | 0.16 | (6.30,5.97) |\n",
"| 113 | 112 | 0.12 | 2.32 | 0.15 | (6.30,5.97) |\n",
"| 114 | 113 | -1.41 | 2.32 | 0.14 | (6.30,5.97) |\n",
"| 115 | 114 | 1.38 | 2.32 | 0.14 | (6.30,5.97) |\n",
"| 116 | 115 | 0.00 | 2.29 | 0.15 | (6.30,5.97) |\n",
"| 117 | 116 | 3.14 | 2.27 | 0.13 | (6.30,5.97) |\n",
"| 118 | 117 | -0.86 | 2.25 | 0.12 | (6.30,5.97) |\n",
"| 119 | 118 | 4.18 | 2.20 | 0.14 | (6.30,5.97) |\n",
"| 120 | 119 | -1.10 | 2.19 | 0.15 | (6.30,5.97) |\n",
"| 121 | 120 | -0.71 | 2.17 | 0.20 | (6.30,5.97) |\n",
"| 122 | 121 | 0.67 | 2.13 | 0.24 | (6.30,5.97) |\n",
"| 123 | 122 | 1.49 | 2.12 | 0.27 | (6.30,5.97) |\n",
"| 124 | 123 | 1.96 | 2.09 | 0.32 | (6.30,5.97) |\n",
"| 125 | 124 | -0.32 | 2.08 | 0.34 | (6.30,5.97) |\n",
"| 126 | 125 | 2.68 | 2.04 | 0.36 | (6.30,5.97) |\n",
"| 127 | 126 | 0.64 | 2.02 | 0.33 | (6.30,5.97) |\n",
"| 128 | 127 | -1.77 | 1.99 | 0.33 | (6.30,5.97) |\n",
"| 129 | 128 | -1.93 | 1.98 | 0.31 | (6.30,5.97) |\n",
"| 130 | 129 | -1.08 | 1.99 | 0.23 | (6.30,5.97) |\n",
"| 131 | 130 | 5.99 | 1.94 | 0.28 | (6.30,5.97) |\n",
"| 132 | 131 | -4.71 | 1.95 | 0.28 | (6.30,5.97) |\n",
"| 133 | 132 | -4.51 | 1.92 | 0.35 | (6.30,5.97) |\n",
"| 134 | 133 | 1.89 | 1.86 | 0.42 | (6.30,5.97) |\n",
"| 135 | 134 | -2.08 | 1.82 | 0.46 | (6.30,5.97) |\n",
"| 136 | 135 | -0.74 | 1.76 | 0.50 | (6.30,5.97) |\n",
"| 137 | 136 | -3.69 | 1.70 | 0.57 | (6.30,5.97) |\n",
"| 138 | 137 | 2.54 | 1.58 | 0.67 | (6.30,5.97) |\n",
"| 139 | 138 | 5.99 | 1.54 | 0.66 | (6.30,5.97) |\n",
"| 140 | 139 | 5.99 | 1.41 | 0.72 | (6.30,5.97) |\n",
"| 141 | 140 | 0.62 | 1.35 | 0.73 | (6.30,5.97) |\n",
"| 142 | 141 | 3.40 | 1.35 | 0.76 | (6.30,5.97) |\n",
"| 143 | 142 | 1.15 | 1.35 | 0.80 | (6.30,5.97) |\n",
"| 144 | 143 | 0.27 | 1.31 | 0.84 | (6.30,5.97) |\n",
"| 145 | 144 | -1.53 | 1.31 | 0.82 | (6.30,5.97) |\n",
"| 146 | 145 | -6.00 | 1.32 | 0.82 | (6.30,5.97) |\n",
"| 147 | 146 | 0.00 | 1.33 | 0.90 | (6.30,5.97) |\n",
"| 148 | 147 | 0.00 | 1.33 | 1.02 | (6.30,5.97) |\n",
"| 149 | 148 | 5.99 | 1.38 | 1.05 | (6.30,5.97) |\n",
"| 150 | 149 | -5.73 | 1.42 | 0.98 | (6.30,5.97) |\n",
"| 151 | 150 | 1.77 | 1.50 | 0.93 | (6.30,5.97) |\n",
"| 152 | 151 | -6.00 | 1.64 | 0.81 | (6.30,5.97) |\n",
"| 153 | 152 | -5.97 | 1.72 | 0.76 | (6.30,5.97) |\n",
"| 154 | 153 | 2.13 | 1.81 | 0.72 | (6.30,5.97) |\n",
"| 155 | 154 | 0.97 | 1.88 | 0.70 | (6.30,5.97) |\n",
"| 156 | 155 | -3.46 | 1.94 | 0.69 | (6.30,5.97) |\n",
"| 157 | 156 | -2.27 | 1.98 | 0.69 | (6.30,5.97) |\n",
"| 158 | 157 | 3.29 | 2.00 | 0.68 | (6.30,5.97) |\n",
"| 159 | 158 | 0.53 | 2.02 | 0.70 | (6.30,5.97) |\n",
"| 160 | 159 | -3.84 | 2.04 | 0.72 | (6.30,5.97) |\n",
"| 161 | 160 | 0.88 | 2.05 | 0.75 | (6.30,5.97) |\n",
"| 162 | 161 | 1.50 | 2.06 | 0.78 | (6.30,5.97) |\n",
"| 163 | 162 | 0.86 | 2.07 | 0.80 | (6.30,5.97) |\n",
"| 164 | 163 | -1.45 | 2.09 | 0.83 | (6.30,5.97) |\n",
"| 165 | 164 | -5.89 | 2.12 | 0.87 | (6.30,5.97) |\n",
"| 166 | 165 | 1.19 | 2.15 | 0.90 | (6.30,5.97) |\n",
"| 167 | 166 | 1.00 | 2.15 | 0.90 | (6.30,5.97) |\n",
"| 168 | 167 | 1.81 | 2.14 | 0.90 | (6.30,5.97) |\n",
"| 169 | 168 | -0.80 | 2.14 | 0.90 | (6.30,5.97) |\n",
"| 170 | 169 | 0.67 | 2.15 | 0.89 | (6.30,5.97) |\n",
"| 171 | 170 | 0.61 | 2.16 | 0.89 | (6.30,5.97) |\n",
"| 172 | 171 | 1.12 | 2.15 | 0.89 | (6.30,5.97) |\n",
"| 173 | 172 | -1.80 | 2.13 | 0.91 | (6.30,5.97) |\n",
"| 174 | 173 | -2.57 | 2.13 | 0.95 | (6.30,5.97) |\n",
"| 175 | 174 | -6.00 | 0.76 | -0.29 | (6.30,5.97) |\n",
"| 176 | 175 | 5.74 | 2.09 | 1.06 | (6.30,5.97) |\n",
"| 177 | 176 | -1.61 | 2.11 | 1.08 | (6.30,5.97) |\n",
"| 178 | 177 | -0.99 | 2.11 | 1.05 | (6.30,5.97) |\n",
"| 179 | 178 | 1.95 | 2.12 | 1.02 | (6.30,5.97) |\n",
"| 180 | 179 | 1.87 | 2.11 | 0.99 | (6.30,5.97) |\n",
"| 181 | 180 | -0.88 | 2.12 | 0.99 | (6.30,5.97) |\n",
"| 182 | 181 | 0.48 | 2.13 | 1.01 | (6.30,5.97) |\n",
"| 183 | 182 | -1.57 | 2.14 | 1.04 | (6.30,5.97) |\n",
"| 184 | 183 | -0.01 | 2.17 | 1.08 | (6.30,5.97) |\n",
"| 185 | 184 | -0.61 | 2.19 | 1.11 | (6.30,5.97) |\n",
"| 186 | 185 | -1.26 | 2.22 | 1.16 | (6.30,5.97) |\n",
"| 187 | 186 | -0.16 | 2.25 | 1.19 | (6.30,5.97) |\n",
"| 188 | 187 | -0.22 | 2.28 | 1.23 | (6.30,5.97) |\n",
"| 189 | 188 | 0.00 | 2.32 | 1.25 | (6.30,5.97) |\n",
"| 190 | 189 | -0.38 | 2.38 | 1.32 | (6.30,5.97) |\n",
"| 191 | 190 | 0.00 | 2.44 | 1.35 | (6.30,5.97) |\n",
"| 192 | 191 | 0.00 | 2.50 | 1.38 | (6.30,5.97) |\n",
"| 193 | 192 | 0.00 | 2.54 | 1.41 | (6.30,5.97) |\n",
"| 194 | 193 | -0.44 | 2.59 | 1.47 | (6.30,5.97) |\n",
"| 195 | 194 | -0.67 | 2.63 | 1.53 | (6.30,5.97) |\n",
"| 196 | 195 | 0.69 | 2.67 | 1.60 | (6.30,5.97) |\n",
"| 197 | 196 | -0.31 | 2.72 | 1.66 | (6.30,5.97) |\n",
"| 198 | 197 | -0.27 | 2.76 | 1.72 | (6.30,5.97) |\n",
"| 199 | 198 | -0.46 | 2.79 | 1.77 | (6.30,5.97) |\n",
"| 200 | 199 | -1.27 | 2.82 | 1.84 | (6.30,5.97) |\n",
"| 201 | 200 | 0.03 | 2.84 | 1.89 | (6.30,5.97) |\n",
"| 202 | 201 | 0.24 | 2.86 | 1.92 | (6.30,5.97) |\n",
"| 203 | 202 | 0.47 | 2.87 | 1.94 | (6.30,5.97) |\n",
"| 204 | 203 | 0.76 | 2.88 | 1.95 | (6.30,5.97) |\n",
"| 205 | 204 | -2.53 | 2.85 | 1.96 | (6.30,5.97) |\n",
"| 206 | 205 | -3.82 | 2.78 | 1.92 | (6.30,5.97) |\n",
"| 207 | 206 | -2.64 | 2.66 | 1.87 | (6.30,5.97) |\n",
"| 208 | 207 | 1.72 | 2.54 | 1.79 | (6.30,5.97) |\n",
"| 209 | 208 | 5.02 | 2.37 | 1.71 | (6.30,5.97) |\n",
"| 210 | 209 | -0.41 | 2.27 | 1.68 | (6.30,5.97) |\n",
"| 211 | 210 | 1.44 | 2.15 | 1.67 | (6.30,5.97) |\n",
"| 212 | 211 | -5.68 | 1.99 | 1.62 | (6.30,5.97) |\n",
"| 213 | 212 | 0.00 | 1.91 | 1.59 | (6.30,5.97) |\n",
"| 214 | 213 | -2.03 | 1.84 | 1.60 | (6.30,5.97) |\n",
"| 215 | 214 | -5.80 | 1.72 | 1.61 | (6.30,5.97) |\n",
"| 216 | 215 | -2.52 | 1.64 | 1.61 | (6.30,5.97) |\n",
"| 217 | 216 | -3.02 | 1.56 | 1.60 | (6.30,5.97) |\n",
"| 218 | 217 | -0.79 | 1.52 | 1.61 | (6.30,5.97) |\n",
"| 219 | 218 | -0.27 | 1.49 | 1.60 | (6.30,5.97) |\n",
"| 220 | 219 | -2.81 | 1.47 | 1.60 | (6.30,5.97) |\n",
"| 221 | 220 | -1.28 | 1.44 | 1.61 | (6.30,5.97) |\n",
"| 222 | 221 | -2.63 | 1.41 | 1.63 | (6.30,5.97) |\n",
"| 223 | 222 | -1.33 | 1.39 | 1.64 | (6.30,5.97) |\n",
"| 224 | 223 | -1.16 | 1.37 | 1.64 | (6.30,5.97) |\n",
"| 225 | 224 | -2.10 | 1.34 | 1.65 | (6.30,5.97) |\n",
"| 226 | 225 | -2.43 | 1.31 | 1.65 | (6.30,5.97) |\n",
"| 227 | 226 | -1.13 | 1.28 | 1.66 | (6.30,5.97) |\n",
"| 228 | 227 | -1.61 | 1.26 | 1.67 | (6.30,5.97) |\n",
"| 229 | 228 | 0.23 | 1.24 | 1.67 | (6.30,5.97) |\n",
"| 230 | 229 | -1.46 | 1.21 | 1.68 | (6.30,5.97) |\n",
"| 231 | 230 | -1.54 | 1.19 | 1.69 | (6.30,5.97) |\n",
"| 232 | 231 | 0.00 | 1.17 | 1.71 | (6.30,5.97) |\n",
"| 233 | 232 | -1.35 | 1.15 | 1.72 | (6.30,5.97) |\n",
"| 234 | 233 | 1.73 | 1.15 | 1.73 | (6.30,5.97) |\n",
"| 235 | 234 | -0.12 | 1.14 | 1.73 | (6.30,5.97) |\n",
"| 236 | 235 | -1.14 | 1.12 | 1.73 | (6.30,5.97) |\n",
"| 237 | 236 | -0.49 | 1.09 | 1.75 | (6.30,5.97) |\n",
"| 238 | 237 | -2.95 | 1.07 | 1.76 | (6.30,5.97) |\n",
"| 239 | 238 | -0.12 | 1.06 | 1.76 | (6.30,5.97) |\n",
"| 240 | 239 | -1.87 | 1.03 | 1.74 | (6.30,5.97) |\n",
"| 241 | 240 | -0.03 | 1.00 | 1.73 | (6.30,5.97) |\n",
"| 242 | 241 | -1.49 | 0.99 | 1.73 | (6.30,5.97) |\n",
"| 243 | 242 | 1.90 | 1.00 | 1.70 | (6.30,5.97) |\n",
"| 244 | 243 | 0.24 | 0.96 | 1.70 | (6.30,5.97) |\n",
"| 245 | 244 | 0.51 | 0.95 | 1.69 | (6.30,5.97) |\n",
"| 246 | 245 | -0.80 | 0.92 | 1.68 | (6.30,5.97) |\n",
"| 247 | 246 | -0.32 | 0.91 | 1.67 | (6.30,5.97) |\n",
"| 248 | 247 | -0.20 | 0.90 | 1.66 | (6.30,5.97) |\n",
"| 249 | 248 | -2.02 | 0.89 | 1.66 | (6.30,5.97) |\n",
"| 250 | 249 | -1.93 | 0.90 | 1.66 | (6.30,5.97) |\n",
"| 251 | 250 | 1.96 | 0.89 | 1.66 | (6.30,5.97) |\n",
"| 252 | 251 | 0.94 | 0.89 | 1.66 | (6.30,5.97) |\n",
"| 253 | 252 | -0.72 | 0.89 | 1.65 | (6.30,5.97) |\n",
"| 254 | 253 | -0.04 | 0.89 | 1.66 | (6.30,5.97) |\n",
"| 255 | 254 | -0.53 | 0.90 | 1.67 | (6.30,5.97) |\n",
"| 256 | 255 | 0.46 | 0.88 | 1.65 | (6.30,5.97) |\n",
"| 257 | 256 | -1.66 | 0.86 | 1.63 | (6.30,5.97) |\n",
"| 258 | 257 | -1.58 | 0.85 | 1.63 | (6.30,5.97) |\n",
"| 259 | 258 | 1.73 | 0.86 | 1.62 | (6.30,5.97) |\n",
"| 260 | 259 | -1.50 | 0.87 | 1.62 | (6.30,5.97) |\n",
"| 261 | 260 | -0.70 | 0.84 | 1.59 | (6.30,5.97) |\n",
"| 262 | 261 | -1.45 | 0.84 | 1.59 | (6.30,5.97) |\n",
"| 263 | 262 | 1.30 | 0.83 | 1.58 | (6.30,5.97) |\n",
"| 264 | 263 | -1.63 | 0.84 | 1.59 | (6.30,5.97) |\n",
"| 265 | 264 | 1.35 | 0.83 | 1.55 | (6.30,5.97) |\n",
"| 266 | 265 | -1.02 | 0.83 | 1.56 | (6.30,5.97) |\n",
"| 267 | 266 | 0.18 | 0.83 | 1.54 | (6.30,5.97) |\n",
"| 268 | 267 | 0.24 | 0.84 | 1.52 | (6.30,5.97) |\n",
"| 269 | 268 | -0.84 | 0.84 | 1.50 | (6.30,5.97) |\n",
"| 270 | 269 | -0.83 | 0.85 | 1.49 | (6.30,5.97) |\n",
"| 271 | 270 | 0.00 | 0.85 | 1.47 | (6.30,5.97) |\n",
"| 272 | 271 | 0.84 | 0.84 | 1.45 | (6.30,5.97) |\n",
"| 273 | 272 | 0.00 | 0.85 | 1.41 | (6.30,5.97) |\n",
"| 274 | 273 | 0.00 | 0.85 | 1.38 | (6.30,5.97) |\n",
"| 275 | 274 | -1.67 | 0.85 | 1.36 | (6.30,5.97) |\n",
"| 276 | 275 | -0.12 | 0.85 | 1.33 | (6.30,5.97) |\n",
"| 277 | 276 | -0.86 | 0.86 | 1.30 | (6.30,5.97) |\n",
"| 278 | 277 | -0.06 | 0.87 | 1.27 | (6.30,5.97) |\n",
"| 279 | 278 | -2.59 | 0.87 | 1.24 | (6.30,5.97) |\n",
"| 280 | 279 | -0.78 | 0.87 | 1.24 | (6.30,5.97) |\n",
"+---------+------------+---------------+-------+-------+-------------+\n",
"Successfully wrote lumen to output/oct/oct_lumen.obj\n",
"Successfully wrote lumen to output/oct/oct_replaced_lumen.obj\n"
]
},
{
"data": {
"text/html": [
"