{
  "id": 561109,
  "title": "Help - Generating Synthetic data from polnet",
  "url": "/competitions/czii-cryo-et-object-identification/discussion/561109",
  "author_name": "Keesari Vigneshwar Reddy",
  "post_date": "2025-02-04T07:58:05.082000",
  "votes": 0,
  "comment_count": 0,
  "views": 0,
  "content": "<p><a href=\"https://copick.github.io/copick-catalog/polnet/generate-copick-project/0.1.0\" target=\"_blank\">https://copick.github.io/copick-catalog/polnet/generate-copick-project/0.1.0</a></p>\n<pre><code>Arguments\n\nPath  the Copick   ( value: PARAMETER_VALUE)\n\nNumber  Tomograms  Produce Per Specified SNR ( value: )\n\nComma-separated list  SNRs  Apply  Tomograms ( value: )\n\nComma-separated List  Min,Max  Increment  the Tilt  ( value: -,,)\n\nComma-separated List  Tomogram Dimensions ( Pixels) ( value: ,,)\n\nComma-separated list Tilt Shift Minimum, Maximum  Sigma Mis-Alignmnets ( value: ,,)\n\nVoxel Size  Simulated Tomograms ( value: )\n\nComma-separated list  protein  paths ( value: PARAMETER_VALUE)\n\nComma-separated list  membrane protein  paths ( value: )\n\nComma-separated list  membrane  paths ( value: )\n</code></pre>\n<h2>What list should I pass in proteins_list, mb_proteins_list, membranes_list?</h2>\n<p>When I tried proteins_list=['apo-ferritin',<br>\n 'beta-amylase',<br>\n 'beta-galactosidase',<br>\n 'ribosome',<br>\n 'thyroglobulin',<br>\n 'virus-like-particle'], mb_proteins_list=None, membranes_list=['membrane']</p>\n<pre><code>[Polnet - Protein Inputs]\nConfig_Path: /kaggle/working/copick.config\nProtein List: [, , , , , ]\nMembrane-Bound Protein List: []\nMembranes List: []\n\n[Polnet - Copick Write Query]\nUserID: polnet\nSessionID: \nSegmentation Name: membrane\nTomogram Name: wbp\n\n[Polnet - Tomogram Simulation Parameters]\nVoxel Size: \nTomo Dimensions (Voxels): [, , ]\nTilt-Series Misalignment: [, , ]\nSNR: [, , , , ]\nNumber of Tomos Per SNR: \nTilt Series Range (Min,Max,Delta): -, , \nTilt Angles: [-, -, -, -, -, -, -, -, -, -, -, -, -, -, -, , , , , , , , , , , , , , , , ]\n\nGENERATING TOMOGRAM NUMBER: \n    PROCESSING FILE: apo-ferritin\n---------------------------------------------------------------------------\nAssertionError                            Traceback (most recent  )\n in &lt;cell : &gt;()\n      \n              # Call the   generate features\n---&gt;          all_features2(NTOMOS, VOI_SHAPE, permanent_dir, VOI_OFFS, voxel_spacing, MMER_TRIES, PMER_TRIES,\n                          MEMBRANES_LIST, [], PROTEINS_LIST, MB_PROTEINS_LIST, SURF_DEC,\n                          TILT_ANGS, SNR, MALIGN_MIN, MALIGN_MAX, MALIGN_SIGMA ) \n\n/usr/local/lib/./dist-packages//core/all_features2. in all_features2(NTOMOS, VOI_SHAPE, OUT_DIR, VOI_OFFS, VOI_VSIZE, MMER_TRIES, PMER_TRIES, MEMBRANES_LIST, HELIX_LIST, PROTEINS_LIST, MB_PROTEINS_LIST, SURF_DEC, TILT_ANGS, DETECTOR_SNR, MALIGN_MN, MALIGN_MX, MALIGN_SG)\n     \n                 # Loading the protein\n--&gt;              protein = MmerFile(p_file)\n     \n                 # Generating the occupancy\n\n/usr/local/lib/./dist-packages/polnet/stomo. in __init__(self, in_file)\n              self.__pmer_over_tol = \n               in_file  not None:\n---&gt;              self.load_mmer_file(in_file)\n      \n          def get_mmer_id(self):\n\n/usr/local/lib/./dist-packages/polnet/stomo. in load_mmer_file(self, in_file)\n              \n      \n---&gt;          assert isinstance(in_file, str)  in_file.endswith()  in_file.endswith()\n      \n              # Reading  \n\nAssertionError: \n</code></pre>",
  "messages": [
    {
      "id": 3114843,
      "postDate": "2025-02-04T07:58:05.083Z",
      "content": "<p><a href=\"https://copick.github.io/copick-catalog/polnet/generate-copick-project/0.1.0\" target=\"_blank\">https://copick.github.io/copick-catalog/polnet/generate-copick-project/0.1.0</a></p>\n<pre><code>Arguments\n\nPath  the Copick   ( value: PARAMETER_VALUE)\n\nNumber  Tomograms  Produce Per Specified SNR ( value: )\n\nComma-separated list  SNRs  Apply  Tomograms ( value: )\n\nComma-separated List  Min,Max  Increment  the Tilt  ( value: -,,)\n\nComma-separated List  Tomogram Dimensions ( Pixels) ( value: ,,)\n\nComma-separated list Tilt Shift Minimum, Maximum  Sigma Mis-Alignmnets ( value: ,,)\n\nVoxel Size  Simulated Tomograms ( value: )\n\nComma-separated list  protein  paths ( value: PARAMETER_VALUE)\n\nComma-separated list  membrane protein  paths ( value: )\n\nComma-separated list  membrane  paths ( value: )\n</code></pre>\n<h2>What list should I pass in proteins_list, mb_proteins_list, membranes_list?</h2>\n<p>When I tried proteins_list=['apo-ferritin',<br>\n 'beta-amylase',<br>\n 'beta-galactosidase',<br>\n 'ribosome',<br>\n 'thyroglobulin',<br>\n 'virus-like-particle'], mb_proteins_list=None, membranes_list=['membrane']</p>\n<pre><code>[Polnet - Protein Inputs]\nConfig_Path: /kaggle/working/copick.config\nProtein List: [, , , , , ]\nMembrane-Bound Protein List: []\nMembranes List: []\n\n[Polnet - Copick Write Query]\nUserID: polnet\nSessionID: \nSegmentation Name: membrane\nTomogram Name: wbp\n\n[Polnet - Tomogram Simulation Parameters]\nVoxel Size: \nTomo Dimensions (Voxels): [, , ]\nTilt-Series Misalignment: [, , ]\nSNR: [, , , , ]\nNumber of Tomos Per SNR: \nTilt Series Range (Min,Max,Delta): -, , \nTilt Angles: [-, -, -, -, -, -, -, -, -, -, -, -, -, -, -, , , , , , , , , , , , , , , , ]\n\nGENERATING TOMOGRAM NUMBER: \n    PROCESSING FILE: apo-ferritin\n---------------------------------------------------------------------------\nAssertionError                            Traceback (most recent  )\n in &lt;cell : &gt;()\n      \n              # Call the   generate features\n---&gt;          all_features2(NTOMOS, VOI_SHAPE, permanent_dir, VOI_OFFS, voxel_spacing, MMER_TRIES, PMER_TRIES,\n                          MEMBRANES_LIST, [], PROTEINS_LIST, MB_PROTEINS_LIST, SURF_DEC,\n                          TILT_ANGS, SNR, MALIGN_MIN, MALIGN_MAX, MALIGN_SIGMA ) \n\n/usr/local/lib/./dist-packages//core/all_features2. in all_features2(NTOMOS, VOI_SHAPE, OUT_DIR, VOI_OFFS, VOI_VSIZE, MMER_TRIES, PMER_TRIES, MEMBRANES_LIST, HELIX_LIST, PROTEINS_LIST, MB_PROTEINS_LIST, SURF_DEC, TILT_ANGS, DETECTOR_SNR, MALIGN_MN, MALIGN_MX, MALIGN_SG)\n     \n                 # Loading the protein\n--&gt;              protein = MmerFile(p_file)\n     \n                 # Generating the occupancy\n\n/usr/local/lib/./dist-packages/polnet/stomo. in __init__(self, in_file)\n              self.__pmer_over_tol = \n               in_file  not None:\n---&gt;              self.load_mmer_file(in_file)\n      \n          def get_mmer_id(self):\n\n/usr/local/lib/./dist-packages/polnet/stomo. in load_mmer_file(self, in_file)\n              \n      \n---&gt;          assert isinstance(in_file, str)  in_file.endswith()  in_file.endswith()\n      \n              # Reading  \n\nAssertionError: \n</code></pre>",
      "rawMarkdown": "https://copick.github.io/copick-catalog/polnet/generate-copick-project/0.1.0\n```\nArguments\n--copick_config_path\nPath to the Copick configuration file (default value: PARAMETER_VALUE)\n--num_tomos_per_snr\nNumber of Tomograms to Produce Per Specified SNR (default value: 1)\n--snr\nComma-separated list of SNRs to Apply to Tomograms (default value: 0.5)\n--tilt_range\nComma-separated List of Min,Max and Increment for the Tilt Range (default value: -60,60,3)\n--tomo_shape\nComma-separated List of Tomogram Dimensions (in Pixels) (default value: 630,630,200)\n--misalignment\nComma-separated list Tilt Shift Minimum, Maximum and Sigma Mis-Alignmnets (default value: 1,5,0.5)\n--voxel_size\nVoxel Size for Simulated Tomograms (default value: 10)\n--proteins_list\nComma-separated list of protein file paths (default value: PARAMETER_VALUE)\n--mb_proteins_list\nComma-separated list of membrane protein file paths (default value: )\n--membranes_list\nComma-separated list of membrane file paths (default value: )\n```\n## What list should I pass in proteins_list, mb_proteins_list, membranes_list?\n\nWhen I tried proteins_list=['apo-ferritin',\n 'beta-amylase',\n 'beta-galactosidase',\n 'ribosome',\n 'thyroglobulin',\n 'virus-like-particle'], mb_proteins_list=None, membranes_list=['membrane']\n\n```\n[Polnet - Protein Inputs]\nConfig_Path: /kaggle/working/copick.config\nProtein List: ['apo-ferritin', 'beta-amylase', 'beta-galactosidase', 'ribosome', 'thyroglobulin', 'virus-like-particle']\nMembrane-Bound Protein List: []\nMembranes List: []\n\n[Polnet - Copick Write Query]\nUserID: polnet\nSessionID: 0\nSegmentation Name: membrane\nTomogram Name: wbp\n\n[Polnet - Tomogram Simulation Parameters]\nVoxel Size: 10.0\nTomo Dimensions (Voxels): [630, 630, 630]\nTilt-Series Misalignment: [1.0, 5.0, 0.5]\nSNR: [0.3, 0.4, 0.5, 0.6, 0.7]\nNumber of Tomos Per SNR: 1\nTilt Series Range (Min,Max,Delta): -45.0, 45.0, 3\nTilt Angles: [-45.0, -42.0, -39.0, -36.0, -33.0, -30.0, -27.0, -24.0, -21.0, -18.0, -15.0, -12.0, -9.0, -6.0, -3.0, 0.0, 3.0, 6.0, 9.0, 12.0, 15.0, 18.0, 21.0, 24.0, 27.0, 30.0, 33.0, 36.0, 39.0, 42.0, 45.0]\n\nGENERATING TOMOGRAM NUMBER: 0\n\tPROCESSING FILE: apo-ferritin\n---------------------------------------------------------------------------\nAssertionError                            Traceback (most recent call last)\n<ipython-input-14-13a45bdc006c> in <cell line: 53>()\n     69 \n     70         # Call the function to generate features\n---> 71         all_features2(NTOMOS, VOI_SHAPE, permanent_dir, VOI_OFFS, voxel_spacing, MMER_TRIES, PMER_TRIES,\n     72                     MEMBRANES_LIST, [], PROTEINS_LIST, MB_PROTEINS_LIST, SURF_DEC,\n     73                     TILT_ANGS, SNR, MALIGN_MIN, MALIGN_MAX, MALIGN_SIGMA ) \n\n/usr/local/lib/python3.10/dist-packages/gui/core/all_features2.py in all_features2(NTOMOS, VOI_SHAPE, OUT_DIR, VOI_OFFS, VOI_VSIZE, MMER_TRIES, PMER_TRIES, MEMBRANES_LIST, HELIX_LIST, PROTEINS_LIST, MB_PROTEINS_LIST, SURF_DEC, TILT_ANGS, DETECTOR_SNR, MALIGN_MN, MALIGN_MX, MALIGN_SG)\n    269 \n    270             # Loading the protein\n--> 271             protein = MmerFile(p_file)\n    272 \n    273             # Generating the occupancy\n\n/usr/local/lib/python3.10/dist-packages/polnet/stomo.py in __init__(self, in_file)\n     32         self.__pmer_over_tol = 0\n     33         if in_file is not None:\n---> 34             self.load_mmer_file(in_file)\n     35 \n     36     def get_mmer_id(self):\n\n/usr/local/lib/python3.10/dist-packages/polnet/stomo.py in load_mmer_file(self, in_file)\n     65         \"\"\"\n     66 \n---> 67         assert isinstance(in_file, str) and in_file.endswith('.pms') or in_file.endswith('.pns')\n     68 \n     69         # Reading input file\n\nAssertionError: \n```"
    }
  ],
  "comments": [],
  "raw_markdown_by_id": {
    "3114843": "https://copick.github.io/copick-catalog/polnet/generate-copick-project/0.1.0\n```\nArguments\n--copick_config_path\nPath to the Copick configuration file (default value: PARAMETER_VALUE)\n--num_tomos_per_snr\nNumber of Tomograms to Produce Per Specified SNR (default value: 1)\n--snr\nComma-separated list of SNRs to Apply to Tomograms (default value: 0.5)\n--tilt_range\nComma-separated List of Min,Max and Increment for the Tilt Range (default value: -60,60,3)\n--tomo_shape\nComma-separated List of Tomogram Dimensions (in Pixels) (default value: 630,630,200)\n--misalignment\nComma-separated list Tilt Shift Minimum, Maximum and Sigma Mis-Alignmnets (default value: 1,5,0.5)\n--voxel_size\nVoxel Size for Simulated Tomograms (default value: 10)\n--proteins_list\nComma-separated list of protein file paths (default value: PARAMETER_VALUE)\n--mb_proteins_list\nComma-separated list of membrane protein file paths (default value: )\n--membranes_list\nComma-separated list of membrane file paths (default value: )\n```\n## What list should I pass in proteins_list, mb_proteins_list, membranes_list?\n\nWhen I tried proteins_list=['apo-ferritin',\n 'beta-amylase',\n 'beta-galactosidase',\n 'ribosome',\n 'thyroglobulin',\n 'virus-like-particle'], mb_proteins_list=None, membranes_list=['membrane']\n\n```\n[Polnet - Protein Inputs]\nConfig_Path: /kaggle/working/copick.config\nProtein List: ['apo-ferritin', 'beta-amylase', 'beta-galactosidase', 'ribosome', 'thyroglobulin', 'virus-like-particle']\nMembrane-Bound Protein List: []\nMembranes List: []\n\n[Polnet - Copick Write Query]\nUserID: polnet\nSessionID: 0\nSegmentation Name: membrane\nTomogram Name: wbp\n\n[Polnet - Tomogram Simulation Parameters]\nVoxel Size: 10.0\nTomo Dimensions (Voxels): [630, 630, 630]\nTilt-Series Misalignment: [1.0, 5.0, 0.5]\nSNR: [0.3, 0.4, 0.5, 0.6, 0.7]\nNumber of Tomos Per SNR: 1\nTilt Series Range (Min,Max,Delta): -45.0, 45.0, 3\nTilt Angles: [-45.0, -42.0, -39.0, -36.0, -33.0, -30.0, -27.0, -24.0, -21.0, -18.0, -15.0, -12.0, -9.0, -6.0, -3.0, 0.0, 3.0, 6.0, 9.0, 12.0, 15.0, 18.0, 21.0, 24.0, 27.0, 30.0, 33.0, 36.0, 39.0, 42.0, 45.0]\n\nGENERATING TOMOGRAM NUMBER: 0\n\tPROCESSING FILE: apo-ferritin\n---------------------------------------------------------------------------\nAssertionError                            Traceback (most recent call last)\n<ipython-input-14-13a45bdc006c> in <cell line: 53>()\n     69 \n     70         # Call the function to generate features\n---> 71         all_features2(NTOMOS, VOI_SHAPE, permanent_dir, VOI_OFFS, voxel_spacing, MMER_TRIES, PMER_TRIES,\n     72                     MEMBRANES_LIST, [], PROTEINS_LIST, MB_PROTEINS_LIST, SURF_DEC,\n     73                     TILT_ANGS, SNR, MALIGN_MIN, MALIGN_MAX, MALIGN_SIGMA ) \n\n/usr/local/lib/python3.10/dist-packages/gui/core/all_features2.py in all_features2(NTOMOS, VOI_SHAPE, OUT_DIR, VOI_OFFS, VOI_VSIZE, MMER_TRIES, PMER_TRIES, MEMBRANES_LIST, HELIX_LIST, PROTEINS_LIST, MB_PROTEINS_LIST, SURF_DEC, TILT_ANGS, DETECTOR_SNR, MALIGN_MN, MALIGN_MX, MALIGN_SG)\n    269 \n    270             # Loading the protein\n--> 271             protein = MmerFile(p_file)\n    272 \n    273             # Generating the occupancy\n\n/usr/local/lib/python3.10/dist-packages/polnet/stomo.py in __init__(self, in_file)\n     32         self.__pmer_over_tol = 0\n     33         if in_file is not None:\n---> 34             self.load_mmer_file(in_file)\n     35 \n     36     def get_mmer_id(self):\n\n/usr/local/lib/python3.10/dist-packages/polnet/stomo.py in load_mmer_file(self, in_file)\n     65         \"\"\"\n     66 \n---> 67         assert isinstance(in_file, str) and in_file.endswith('.pms') or in_file.endswith('.pns')\n     68 \n     69         # Reading input file\n\nAssertionError: \n```"
  }
}