{"id":34701787,"url":"https://github.com/hubmapconsortium/hra-glb-mesh-collisions","last_synced_at":"2026-05-27T09:34:37.820Z","repository":{"id":218529044,"uuid":"684172451","full_name":"hubmapconsortium/hra-glb-mesh-collisions","owner":"hubmapconsortium","description":"hra-glb-mesh-collisions: Extract mesh-mesh collision information in a GLB file","archived":false,"fork":false,"pushed_at":"2024-09-11T14:28:42.000Z","size":1522,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-09-28T05:02:50.742Z","etag":null,"topics":["human-reference-atlas","ot2od030545"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/hubmapconsortium.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-08-28T15:50:14.000Z","updated_at":"2025-06-24T13:27:41.000Z","dependencies_parsed_at":null,"dependency_job_id":"a59fecea-7ab9-40e8-801d-d9294d318495","html_url":"https://github.com/hubmapconsortium/hra-glb-mesh-collisions","commit_stats":null,"previous_names":["hubmapconsortium/hra-glb-mesh-collisions"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/hubmapconsortium/hra-glb-mesh-collisions","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hubmapconsortium%2Fhra-glb-mesh-collisions","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hubmapconsortium%2Fhra-glb-mesh-collisions/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hubmapconsortium%2Fhra-glb-mesh-collisions/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hubmapconsortium%2Fhra-glb-mesh-collisions/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/hubmapconsortium","download_url":"https://codeload.github.com/hubmapconsortium/hra-glb-mesh-collisions/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hubmapconsortium%2Fhra-glb-mesh-collisions/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33560727,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-05-27T02:00:06.184Z","response_time":53,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["human-reference-atlas","ot2od030545"],"created_at":"2025-12-24T22:53:01.685Z","updated_at":"2026-05-27T09:34:37.814Z","avatar_url":"https://github.com/hubmapconsortium.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# hra_glb_mesh_collisions\n\n[![PyPI - Version](https://img.shields.io/pypi/v/hra-glb-mesh-collisions.svg)](https://pypi.org/project/hra-glb-mesh-collisions)\n[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/hra-glb-mesh-collisions.svg)](https://pypi.org/project/hra-glb-mesh-collisions)\n\n-----\n\n## Table of Contents\n\n- [hra\\_glb\\_mesh\\_collisions](#hra_glb_mesh_collisions)\n  - [Table of Contents](#table-of-contents)\n  - [Installation](#installation)\n  - [License](#license)\n  - [Dependencies](#dependencies)\n  - [Usage](#usage)\n\n## Installation\n\n```console\npip install hra-glb-mesh-collisions\n```\n\n## License\n\n`hra-glb-mesh-collisions` is distributed under the terms of the [MIT](https://spdx.org/licenses/MIT.html) license.\n\n## Dependencies\n\nSystem packages:\n\nYou may need to install libfcl liboctomap if the program does not work right away using this command (on Ubuntu):\n\n```bash\n$ sudo apt install liboctomap-dev libfcl-dev\n```\n\nFor Python library:\n\n1. pygltflib\n2. trimesh\n\nInstall python dependencies with:\n\n```bash\npip install -r requirements.txt\n```\n\n## Usage\n\nExample usage:\n\n```bash\npython3 mesh-mesh-collisions.py ./examples/VH_F_Kidney_Left.glb collision_result.csv\n```\n\nFor help documentation:\n\n```bash\n$ python3 mesh-mesh-collisions.py --help\n\nusage: mesh-mesh-collisions.py [-h] [--include-distances] [-v] input_glb output_csv\n\npositional arguments:\n  input_glb            path to input glb file\n  output_csv           path to output collisions csv file\n\noptions:\n  -h, --help           show this help message and exit\n  --include-distances  include distances even if they dont' colide\n  -v, --verbose\n```\n\nSample result ouptut csv:\n\nNotes about the distance colum:\n- distance is in meters\n- -1 = intersection\n- distance measured between two closest points\n\n```csv\nsource,target,distance\nVHF_hilum_of_kidney_L,VHF_kidney_capsule_L,-1\nVHF_hilum_of_kidney_L,VHF_major_calyx_L_a,-1\nVHF_hilum_of_kidney_L,VHF_major_calyx_L_b,0.0014157565638410548\nVHF_hilum_of_kidney_L,VHF_major_calyx_L_c,-1\nVHF_hilum_of_kidney_L,VHF_major_calyx_L_d,-1\nVHF_hilum_of_kidney_L,VHF_minor_calyx_L_a,0.011878771067593177\nVHF_hilum_of_kidney_L,VHF_minor_calyx_L_b,0.014892350577084101\nVHF_hilum_of_kidney_L,VHF_minor_calyx_L_c,0.01049842653752553\nVHF_hilum_of_kidney_L,VHF_minor_calyx_L_d,0.013852964218697942\nVHF_hilum_of_kidney_L,VHF_minor_calyx_L_e,-1\nVHF_hilum_of_kidney_L,VHF_minor_calyx_L_f,0.0003293750826728972\nVHF_hilum_of_kidney_L,VHF_minor_calyx_L_g,0.0013917394770369632\nVHF_hilum_of_kidney_L,VHF_minor_calyx_L_h,0.002076302121193277\nVHF_hilum_of_kidney_L,VHF_minor_calyx_L_i,0.0001650410537290576\nVHF_hilum_of_kidney_L,VHF_minor_calyx_L_j,0.0026597163618629024\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhubmapconsortium%2Fhra-glb-mesh-collisions","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhubmapconsortium%2Fhra-glb-mesh-collisions","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhubmapconsortium%2Fhra-glb-mesh-collisions/lists"}