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Merge pull request #49 from MunchLab/vectorizedect
Making the ECT so much faster!
2 parents 1f85e0e + e3ce61b commit fd4605c

291 files changed

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‎.github/workflows/python-package.yml‎

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@@ -16,7 +16,7 @@ jobs:
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.9", "3.10", "3.11"]
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python-version: ["3.10", "3.11"]
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steps:
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- uses: actions/checkout@v4

doc_source/notebooks/CodingFiguresFern.ipynb renamed to Extra_Notebooks/CodingFiguresFern.ipynb

File renamed without changes.

doc_source/notebooks/Matisse/Matisse_ECT.ipynb renamed to Extra_Notebooks/Matisse_ECT.ipynb

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‎Extra_Notebooks/Mesh.ipynb‎

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"1 0\n",
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"4 5\n",
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"9 8\n",
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"10 1\n"
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]
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}
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],
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"source": [
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"from CGAL.CGAL_Kernel import Point_2\n",
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"from CGAL.CGAL_Triangulation_2 import Triangulation_2\n",
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"from CGAL.CGAL_Triangulation_2 import Triangulation_2_Vertex_circulator\n",
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"from CGAL.CGAL_Triangulation_2 import Triangulation_2_Vertex_handle\n",
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"\n",
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"points=[]\n",
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"points.append( Point_2(1,0) )\n",
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"points.append( Point_2(3,2) )\n",
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"points.append( Point_2(4,5) )\n",
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"points.append( Point_2(9,8) )\n",
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"points.append( Point_2(7,4) )\n",
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"points.append( Point_2(5,2) )\n",
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"points.append( Point_2(6,3) )\n",
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"points.append( Point_2(10,1) )\n",
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" \n",
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"t=Triangulation_2()\n",
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"t.insert(points)\n",
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"\n",
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"vc = t.incident_vertices(t.infinite_vertex())\n",
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"\n",
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"if vc.hasNext():\n",
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" done = vc.next();\n",
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" iter=Triangulation_2_Vertex_handle()\n",
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" while(1):\n",
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" iter=vc.next()\n",
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" print (iter.point())\n",
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" if iter == done:\n",
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" break\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "base",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.7"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}

‎Extra_Notebooks/Playing_with_Spirals.ipynb‎

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‎Makefile‎

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clean:
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# Running autopep8
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@autopep8 -r --in-place ect/
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@autopep8 -r --in-place src/ect/
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tests:
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# Running unittests
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@make html
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# Running unittests
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@make tests
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@make tests
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develop:
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pip install -e .

‎benchmarks/benchmark_cw.py‎

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"""Benchmarks for CW complex computations"""
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import numpy as np
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import time
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from ect import ECT, EmbeddedCW, create_example_cw
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from ect import ECT
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from ect.utils.examples import create_example_cw
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import json
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from pathlib import Path
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results = {}
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configs = [
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(8, 10), # Small
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(36, 36), # Medium
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(360, 360), # Large
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(8, 10),
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(36, 36),
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(360, 360),
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]
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for num_dir, num_thresh in configs:
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start_time = time.time()
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myect = ECT(num_dirs=num_dir, num_thresh=num_thresh)
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myect.calculateECT(K)
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myect.calculate(K)
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execution_time = time.time() - start_time
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times.append(execution_time)
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print("Running CW complex benchmarks...")
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results = benchmark_cw_ect()
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# Save results
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output_dir = Path("benchmark_results")
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output_dir.mkdir(exist_ok=True)
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‎benchmarks/benchmark_graph.py‎

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"""Benchmark ECT computation on graphs"""
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results = {}
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# Warmup run to trigger JIT compilation
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warmup_shape = create_test_shape(100, 1)
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G_warmup = EmbeddedGraph()
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G_warmup.add_cycle(warmup_shape)
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myect = ECT(num_dirs=360, num_thresh=360)
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myect.calculate(G_warmup) # Warmup run
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configs = [
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(100, 1),
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(1000, 1),
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(100, 3),
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(1000, 3),
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(10000, 3),
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(100000, 5),
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]
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for points, complexity in configs:
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for _ in range(num_runs):
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start_time = time.time()
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myect = ECT(num_dirs=360, num_thresh=360)
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myect.calculateECT(G)
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myect.calculate(G)
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times.append(time.time() - start_time)
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results[f'points_{points}_complexity_{complexity}'] = {
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'min_time': float(np.min(times)),
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'max_time': float(np.max(times))
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}
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print(results)
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return results
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def benchmark_g_omega(num_runs=5):
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"""Benchmark g_omega computation"""
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results = {}
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sizes = [100, 500, 1000]
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for size in sizes:
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shape = create_test_shape(size)
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G = EmbeddedGraph()
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G.add_cycle(shape)
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times = []
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for _ in range(num_runs):
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start_time = time.time()
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for theta in np.linspace(0, 2*np.pi, 360):
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G.g_omega(theta)
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times.append(time.time() - start_time)
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results[f'size_{size}'] = {
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'mean_time': float(np.mean(times)),
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'std_time': float(np.std(times))
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}
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return results

‎benchmarks/run_benchmarks.py‎

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import time
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from pathlib import Path
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import json
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from benchmark_graph import benchmark_graph_ect, benchmark_g_omega
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from benchmark_graph import benchmark_graph_ect
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from benchmark_cw import benchmark_cw_ect
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import platform
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print("\nRunning CW complex benchmarks...")
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results['benchmarks']['cw_ect'] = benchmark_cw_ect(num_runs=num_runs)
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print("\nRunning g_omega benchmarks...")
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results['benchmarks']['g_omega'] = benchmark_g_omega(num_runs=num_runs)
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return results
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‎doc_source/notebooks/Matisse/example_matisse.ipynb‎

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