Import-Segments.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import datajoint as dj\n",
    "dj.config['database.user'] = 'dimitri'    #  change to your username\n",
    "dj.config['database.host'] = 'datajoint.ninai.org'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%capture\n",
    "import ta3\n",
    "import pandas as pd\n",
    "from tqdm import tqdm"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Import Segments"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The manifest list is produced as \n",
    "```shell \n",
    "gsutil -m ls gs://pinky_share/pinky40_v11/watershed_mst_trimmed_sem_remap/mesh_mip_3_err_40/*:0 > ./pinky40_v11_watershed_mst_trimmed_sem_remap_segment_list.txt\n",
    "```"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "with open(\"pinky40_v11_watershed_mst_trimmed_sem_remap_segment_list.txt\", 'rt') as f:\n",
    "    lines = f.read().splitlines()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "segment = ta3.Segment()l\n",
    "existing_segments = set(segment.fetch('segment_id'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "new_segments = set(int(line.split('/')[-1].split(':')[0]) for line in lines).difference(existing_segments)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "for segment_id in tqdm(new_segments):\n",
    "    segment.insert1(dict(segmentation=1, segment_id=segment_id))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Import meshes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
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       "[({'segment_id': 14278693, 'segmentation': 1},\n",
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       "  ValueError('Buffer size 89 is not a muliple of 4')),\n",
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       "  ValueError('Buffer size 89 is not a muliple of 4')),\n",
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       "  ValueError('Buffer size 3675 is not a muliple of 4')),\n",
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       "  ValueError('Buffer size 131 is not a muliple of 4')),\n",
       " ({'segment_id': 113430489, 'segmentation': 1},\n",
       "  ValueError('Buffer size 477 is not a muliple of 4')),\n",
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       "  ValueError('Buffer size 166 is not a muliple of 4')),\n",
       " ({'segment_id': 113973654, 'segmentation': 1},\n",
       "  ValueError('Buffer size 283 is not a muliple of 4')),\n",
       " ({'segment_id': 114841874, 'segmentation': 1},\n",
       "  ValueError('Buffer size 34721 is not a muliple of 4')),\n",
       " ({'segment_id': 117039360, 'segmentation': 1},\n",
       "  ValueError('Buffer size 363 is not a muliple of 4')),\n",
       " ({'segment_id': 117084879, 'segmentation': 1},\n",
       "  ValueError('Buffer size 3749 is not a muliple of 4')),\n",
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       "  ValueError('Buffer size 105 is not a muliple of 4')),\n",
       " ({'segment_id': 120680337, 'segmentation': 1},\n",
       "  ValueError('Buffer size 135 is not a muliple of 4')),\n",
       " ({'segment_id': 120690524, 'segmentation': 1},\n",
       "  ValueError('Buffer size 846 is not a muliple of 4')),\n",
       " ({'segment_id': 120836621, 'segmentation': 1},\n",
       "  ValueError('Buffer size 190 is not a muliple of 4')),\n",
       " ({'segment_id': 120838096, 'segmentation': 1},\n",
       "  ValueError('Buffer is to short: 176 for 559903 verticies')),\n",
       " ({'segment_id': 121254204, 'segmentation': 1},\n",
       "  ValueError('Buffer size 129 is not a muliple of 4')),\n",
       " ({'segment_id': 121325630, 'segmentation': 1},\n",
       "  ValueError('Buffer size 177 is not a muliple of 4')),\n",
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       "  ValueError('Buffer size 78 is not a muliple of 4')),\n",
       " ({'segment_id': 121401082, 'segmentation': 1},\n",
       "  ValueError('Buffer is to short: 2172 for 559903 verticies')),\n",
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       "  ValueError('Buffer size 3079 is not a muliple of 4')),\n",
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       "  ValueError('Buffer is to short: 92 for 559903 verticies'))]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ta3.Mesh.populate(display_progress=True, reserve_jobs=True, suppress_errors=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
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       "                                <p id=\"nonprimary\">pid</p>\n",
       "                                <span class=\"djtooltiptext\">system process id</span>\n",
       "                            </div></th><th><div class=\"djtooltip\">\n",
       "                                <p id=\"nonprimary\">connection_id</p>\n",
       "                                <span class=\"djtooltiptext\">connection_id()</span>\n",
       "                            </div></th><th><div class=\"djtooltip\">\n",
       "                                <p id=\"nonprimary\">timestamp</p>\n",
       "                                <span class=\"djtooltiptext\">automatic timestamp</span>\n",
       "                            </div> </th> </tr> </thead>\n",
       "                <tbody> <tr>  </tr> </tbody>\n",
       "            </table>\n",
       "            \n",
       "            <p>0 tuples</p></div>\n",
       "            "
      ],
      "text/plain": [
       "*table_name    *key_hash    status     key        error_message  error_stac user     host     pid     connection_id  timestamp    \n",
       "+------------+ +----------+ +--------+ +--------+ +------------+ +--------+ +------+ +------+ +-----+ +------------+ +-----------+\n",
       "\n",
       " (0 tuples)"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ta3.schema.jobs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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