{
  "id": 551082,
  "title": "Doubt in Config_blob",
  "url": "/competitions/czii-cryo-et-object-identification/discussion/551082",
  "author_name": "",
  "post_date": "2024-12-11T05:48:47.731661600Z",
  "votes": 1,
  "comment_count": 3,
  "views": 0,
  "content": "<p>Below is the config_blob. My doubts are : </p>\n<ul>\n<li>what is this <code>map_threshold</code> ??</li>\n<li>why color is a 4D vector instead of being 3D (r,g,b)?</li>\n</ul>\n<pre><code>config_blob = namezii_cryoet_mlchallenge_2024escription CZII CryoET ML Challenge training data.pickable_objectsnameapo-ferritinis_particlepdb_idV1Wlabeloloradiusmap_thresholdnamebeta-amylaseis_particlepdb_idFA2labeloloradiusmap_thresholdnamebeta-galactosidaseis_particlepdb_idX1Qlabeloloradiusmap_thresholdnameribosomeis_particlepdb_idEK0labeloloradiusmap_thresholdnamethyroglobulinis_particlepdb_idSCJlabeloloradiusmap_thresholdnamevirus-like-particleis_particlepdb_idN4Vlabeloloradiusmap_thresholdoverlay_rootXXXXXXXXXXtrain/overlayoverlay_fs_argsauto_mkdistatic_rootXXXXXXXXXXtrain//\n</code></pre>",
  "messages": [
    {
      "id": "3069145",
      "postDate": "12/11/2024 05:48:47",
      "content": "<p>Below is the config_blob. My doubts are : </p>\n<ul>\n<li>what is this <code>map_threshold</code> ??</li>\n<li>why color is a 4D vector instead of being 3D (r,g,b)?</li>\n</ul>\n<pre><code>config_blob = namezii_cryoet_mlchallenge_2024escription CZII CryoET ML Challenge training data.pickable_objectsnameapo-ferritinis_particlepdb_idV1Wlabeloloradiusmap_thresholdnamebeta-amylaseis_particlepdb_idFA2labeloloradiusmap_thresholdnamebeta-galactosidaseis_particlepdb_idX1Qlabeloloradiusmap_thresholdnameribosomeis_particlepdb_idEK0labeloloradiusmap_thresholdnamethyroglobulinis_particlepdb_idSCJlabeloloradiusmap_thresholdnamevirus-like-particleis_particlepdb_idN4Vlabeloloradiusmap_thresholdoverlay_rootXXXXXXXXXXtrain/overlayoverlay_fs_argsauto_mkdistatic_rootXXXXXXXXXXtrain//\n</code></pre>",
      "rawMarkdown": "Below is the config_blob. My doubts are : \n-  what is this ```map_threshold``` ??\n- why color is a 4D vector instead of being 3D (r,g,b)?\n\n```\nconfig_blob = \"\"\"{\n    \"name\": \"czii_cryoet_mlchallenge_2024\",\n    \"description\": \"2024 CZII CryoET ML Challenge training data.\",\n    \"version\": \"1.0.0\",\n\n    \"pickable_objects\": [\n        {\n            \"name\": \"apo-ferritin\",\n            \"is_particle\": true,\n            \"pdb_id\": \"4V1W\",\n            \"label\": 1,\n            \"color\": [  0, 117, 220, 128],\n            \"radius\": 60,\n            \"map_threshold\": 0.0418\n        },\n        {\n            \"name\": \"beta-amylase\",\n            \"is_particle\": true,\n            \"pdb_id\": \"1FA2\",\n            \"label\": 2,\n            \"color\": [153,  63,   0, 128],\n            \"radius\": 65,\n            \"map_threshold\": 0.035\n        },\n        {\n            \"name\": \"beta-galactosidase\",\n            \"is_particle\": true,\n            \"pdb_id\": \"6X1Q\",\n            \"label\": 3,\n            \"color\": [ 76,   0,  92, 128],\n            \"radius\": 90,\n            \"map_threshold\": 0.0578\n        },\n        {\n            \"name\": \"ribosome\",\n            \"is_particle\": true,\n            \"pdb_id\": \"6EK0\",\n            \"label\": 4,\n            \"color\": [  0,  92,  49, 128],\n            \"radius\": 150,\n            \"map_threshold\": 0.0374\n        },\n        {\n            \"name\": \"thyroglobulin\",\n            \"is_particle\": true,\n            \"pdb_id\": \"6SCJ\",\n            \"label\": 5,\n            \"color\": [ 43, 206,  72, 128],\n            \"radius\": 130,\n            \"map_threshold\": 0.0278\n        },\n        {\n            \"name\": \"virus-like-particle\",\n            \"is_particle\": true,\n            \"pdb_id\": \"6N4V\",            \n            \"label\": 6,\n            \"color\": [255, 204, 153, 128],\n            \"radius\": 135,\n            \"map_threshold\": 0.201\n        }\n    ],\n\n    \"overlay_root\": \"XXXXXXXXXXtrain/overlay\",\n\n    \"overlay_fs_args\": {\n        \"auto_mkdir\": true\n    },\n\n    \"static_root\": \"XXXXXXXXXXtrain/static/\"\n}\"\"\"\n```",
      "votes": null
    },
    {
      "id": "3069165",
      "postDate": "12/11/2024 06:18:50",
      "content": "<p>Color is not important, but itsp format is RGBA, where A is alpha or transparency.</p>",
      "rawMarkdown": "Color is not important, but itsp format is RGBA, where A is alpha or transparency.",
      "votes": null
    },
    {
      "id": "3069168",
      "postDate": "12/11/2024 06:26:35",
      "content": "<p>Yeah, I'm not sure anything except name, radius, and label really matters in there for our purposes.</p>",
      "rawMarkdown": "Yeah, I'm not sure anything except name, radius, and label really matters in there for our purposes.",
      "votes": null
    },
    {
      "id": "3069171",
      "postDate": "12/11/2024 06:31:35",
      "content": "<p>Field definitions are here:<br>\n<a href=\"https://github.com/copick/copick/blob/0a13aeccb2ea5fef827efb5fbb2395eb43e4dfff/docs/datamodel.md?plain=1#L50\" target=\"_blank\">https://github.com/copick/copick/blob/0a13aeccb2ea5fef827efb5fbb2395eb43e4dfff/docs/datamodel.md?plain=1#L50</a></p>\n<ul>\n<li><strong>color</strong>: An array of four integers that represent the RGBA color of the object when rendered in a 3D viewer.</li>\n<li><strong>map_threshold</strong>: A float that represents the threshold value to use when a density map is used to represent the object. This is used to determine the isosurface level to use when rendering the object as a mesh. Density maps are discovered by the copick API by looking for files with the same name as the object in the <code>Objects</code> directory of the project's root.</li>\n</ul>",
      "rawMarkdown": "Field definitions are here:\n[https://github.com/copick/copick/blob/0a13aeccb2ea5fef827efb5fbb2395eb43e4dfff/docs/datamodel.md?plain=1#L50](https://github.com/copick/copick/blob/0a13aeccb2ea5fef827efb5fbb2395eb43e4dfff/docs/datamodel.md?plain=1#L50)\n\n- **color**: An array of four integers that represent the RGBA color of the object when rendered in a 3D viewer.\n- **map_threshold**: A float that represents the threshold value to use when a density map is used to represent the object. This is used to determine the isosurface level to use when rendering the object as a mesh. Density maps are discovered by the copick API by looking for files with the same name as the object in the `Objects` directory of the project's root.",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 3069165,
      "author_name": "sakvaua",
      "author_url": "",
      "post_date": "12/11/2024 06:18:50",
      "content": "<p>Color is not important, but itsp format is RGBA, where A is alpha or transparency.</p>",
      "votes": null,
      "replies": [
        {
          "id": 3069168,
          "author_name": "davidlist",
          "author_url": "",
          "post_date": "12/11/2024 06:26:35",
          "content": "<p>Yeah, I'm not sure anything except name, radius, and label really matters in there for our purposes.</p>",
          "votes": null,
          "replies": []
        }
      ]
    },
    {
      "id": 3069171,
      "author_name": "davidlist",
      "author_url": "",
      "post_date": "12/11/2024 06:31:35",
      "content": "<p>Field definitions are here:<br>\n<a href=\"https://github.com/copick/copick/blob/0a13aeccb2ea5fef827efb5fbb2395eb43e4dfff/docs/datamodel.md?plain=1#L50\" target=\"_blank\">https://github.com/copick/copick/blob/0a13aeccb2ea5fef827efb5fbb2395eb43e4dfff/docs/datamodel.md?plain=1#L50</a></p>\n<ul>\n<li><strong>color</strong>: An array of four integers that represent the RGBA color of the object when rendered in a 3D viewer.</li>\n<li><strong>map_threshold</strong>: A float that represents the threshold value to use when a density map is used to represent the object. This is used to determine the isosurface level to use when rendering the object as a mesh. Density maps are discovered by the copick API by looking for files with the same name as the object in the <code>Objects</code> directory of the project's root.</li>\n</ul>",
      "votes": null,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "3069145": "Below is the config_blob. My doubts are : \n-  what is this ```map_threshold``` ??\n- why color is a 4D vector instead of being 3D (r,g,b)?\n\n```\nconfig_blob = \"\"\"{\n    \"name\": \"czii_cryoet_mlchallenge_2024\",\n    \"description\": \"2024 CZII CryoET ML Challenge training data.\",\n    \"version\": \"1.0.0\",\n\n    \"pickable_objects\": [\n        {\n            \"name\": \"apo-ferritin\",\n            \"is_particle\": true,\n            \"pdb_id\": \"4V1W\",\n            \"label\": 1,\n            \"color\": [  0, 117, 220, 128],\n            \"radius\": 60,\n            \"map_threshold\": 0.0418\n        },\n        {\n            \"name\": \"beta-amylase\",\n            \"is_particle\": true,\n            \"pdb_id\": \"1FA2\",\n            \"label\": 2,\n            \"color\": [153,  63,   0, 128],\n            \"radius\": 65,\n            \"map_threshold\": 0.035\n        },\n        {\n            \"name\": \"beta-galactosidase\",\n            \"is_particle\": true,\n            \"pdb_id\": \"6X1Q\",\n            \"label\": 3,\n            \"color\": [ 76,   0,  92, 128],\n            \"radius\": 90,\n            \"map_threshold\": 0.0578\n        },\n        {\n            \"name\": \"ribosome\",\n            \"is_particle\": true,\n            \"pdb_id\": \"6EK0\",\n            \"label\": 4,\n            \"color\": [  0,  92,  49, 128],\n            \"radius\": 150,\n            \"map_threshold\": 0.0374\n        },\n        {\n            \"name\": \"thyroglobulin\",\n            \"is_particle\": true,\n            \"pdb_id\": \"6SCJ\",\n            \"label\": 5,\n            \"color\": [ 43, 206,  72, 128],\n            \"radius\": 130,\n            \"map_threshold\": 0.0278\n        },\n        {\n            \"name\": \"virus-like-particle\",\n            \"is_particle\": true,\n            \"pdb_id\": \"6N4V\",            \n            \"label\": 6,\n            \"color\": [255, 204, 153, 128],\n            \"radius\": 135,\n            \"map_threshold\": 0.201\n        }\n    ],\n\n    \"overlay_root\": \"XXXXXXXXXXtrain/overlay\",\n\n    \"overlay_fs_args\": {\n        \"auto_mkdir\": true\n    },\n\n    \"static_root\": \"XXXXXXXXXXtrain/static/\"\n}\"\"\"\n```",
    "3069165": "Color is not important, but itsp format is RGBA, where A is alpha or transparency.",
    "3069168": "Yeah, I'm not sure anything except name, radius, and label really matters in there for our purposes.",
    "3069171": "Field definitions are here:\n[https://github.com/copick/copick/blob/0a13aeccb2ea5fef827efb5fbb2395eb43e4dfff/docs/datamodel.md?plain=1#L50](https://github.com/copick/copick/blob/0a13aeccb2ea5fef827efb5fbb2395eb43e4dfff/docs/datamodel.md?plain=1#L50)\n\n- **color**: An array of four integers that represent the RGBA color of the object when rendered in a 3D viewer.\n- **map_threshold**: A float that represents the threshold value to use when a density map is used to represent the object. This is used to determine the isosurface level to use when rendering the object as a mesh. Density maps are discovered by the copick API by looking for files with the same name as the object in the `Objects` directory of the project's root."
  },
  "source": "meta"
}