Neuroblocks

.ipynb_checkpoints/Untitled0-checkpoint.ipynb

@@ -0,0 +1,9 @@
+{
+ "metadata": {
+  "name": "",
+  "signature": "sha256:75ae90dd9efb8c17f74ffbcf0b84c75bf22ce3964745d68eb6461b00d14cc1b7"
+ },
+ "nbformat": 3,
+ "nbformat_minor": 0,
+ "worksheets": []
+}

Untitled0.ipynb

@@ -0,0 +1,60 @@
+{
+ "metadata": {
+  "name": "",
+  "signature": "sha256:f811fc625a7ce723c171d5490cda4d9b8501943811abe69feb9e028db8bdf7fc"
+ },
+ "nbformat": 3,
+ "nbformat_minor": 0,
+ "worksheets": [
+  {
+   "cells": [
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "data_dir = '/Users/d/Desktop/data/Alyssa/Scan1/021/000001'\n",
+      "import os\n"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 12
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "level = 0\n",
+      "for root, dirs, files in os.walk(data_dir):\n",
+      "    if 'image_coordinates.txt' in files:\n",
+      "        print level\n",
+      "    level += 1\n",
+      "    \n",
+      "    "
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [
+      {
+       "output_type": "stream",
+       "stream": "stdout",
+       "text": [
+        "0\n"
+       ]
+      }
+     ],
+     "prompt_number": 13
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    }
+   ],
+   "metadata": {}
+  }
+ ]
+}

_dojo/__init__.py

@@ -5,3 +5,4 @@
 from websockets import Websockets
 from controller import Controller
 from database import Database
+from neuroblocks import Neuroblocks

_dojo/controller.py

@@ -1,3 +1,4 @@
+import datetime
 import h5py
 import os, errno
 import json
@@ -11,7 +12,7 @@
 
 class Controller(object):
 
-  def __init__(self, mojo_dir, out_dir, tmp_dir, database):
+  def __init__(self, mojo_dir, out_dir, tmp_dir, database, neuroblocks=None, neuroblocks_project_id=None):
     '''
     '''
     self.__websocket = None
@@ -32,6 +33,10 @@ def __init__(self, mojo_dir, out_dir, tmp_dir, database):
 
     self.__database = database
 
+    self.__neuroblocks = neuroblocks
+
+    self.__neuroblocks_project_id = neuroblocks_project_id
+
     if self.__database:
       self.__largest_id = self.__database.get_largest_id()
     else:
@@ -63,7 +68,12 @@ def send_welcome(self):
     output = {}
     output['name'] = 'WELCOME'
     output['origin'] = 'SERVER'
-    output['value'] = ''
+
+    config = {}
+    config['neuroblocks'] = self.__neuroblocks != None
+    config['neuroblocks_project_id'] = self.__neuroblocks_project_id
+
+    output['value'] = config
 
     self.__websocket.send(json.dumps(output))
 
@@ -127,6 +137,19 @@ def send_problem_table(self, origin):
     self.__websocket.send(json.dumps(output))
 
 
+  def send_restore_state(self, origin, state_id):
+    '''
+    '''
+
+    output = {}
+    output['name'] = 'RESTORE_STATE'
+    output['origin'] = origin
+    output['value'] = self.__neuroblocks.get_state(state_id)
+
+    self.__websocket.send(json.dumps(output))
+
+
+
   def on_message(self, message):
     '''
     '''
@@ -137,6 +160,14 @@ def on_message(self, message):
 
       self.__users.append(input['origin'])
 
+      #
+      # let's check if we should restore a neuroblocks state
+      #
+      state_id = input['value']['neuroblocks_state_id']
+      if state_id:
+        # we do have a state restore request
+        self.send_restore_state(input['origin'], state_id)
+
     elif input['name'] == 'MERGETABLE':
       self.__merge_table = input['value']
 
@@ -178,6 +209,44 @@ def on_message(self, message):
     elif input['name'] == 'SAVE':
       self.save(input)
 
+    elif input['name'] == 'SAVE_STATE':
+      self.save_state(input)
+
+    elif input['name'] == 'SAVE_PICK2D':
+      self.save_pick2d(input)
+
+    elif input['name'] == 'SAVE_ACTION':
+      self.save_action(input)
+
+  def save_action(self, input):
+    '''
+    '''
+    values = input['value']
+    values['on'] = datetime.datetime.utcnow()
+
+    self.__neuroblocks.save_action(values)
+
+
+  def save_pick2d(self, input):
+    '''
+    '''
+    values = input['value']
+    values['on'] = datetime.datetime.utcnow()
+
+    self.__neuroblocks.save_pick2d(values)
+
+
+  def save_state(self, input):
+    '''
+    '''
+    values = input['value']
+    values['on'] = datetime.datetime.utcnow()
+
+
+    new_id = self.__neuroblocks.save_state(values)
+
+    print 'Stored state', new_id
+
 
   def adjust(self, input):
     '''

_dojo/datasource.py

@@ -124,9 +124,16 @@ def get_volume(self, zoomlevel):
     tile_files = []
 
     for d in dirs:
+      if d.startswith('.'):
+	continue
+
       files = os.listdir(os.path.join(w_path,d))
 
       for f in files:
+
+	if f.startswith('.'):
+	  continue
+
         # check if we have an updated version for this tile
         if os.path.exists(os.path.join(w_path_tmp, d, f)):
           tile_files.append(os.path.join(w_path_tmp, d, f))

_dojo/neuroblocks.py

@@ -0,0 +1,98 @@
+import pymongo
+from bson.objectid import ObjectId
+
+class Neuroblocks(object):
+
+  DATABASE = 'meteor'
+
+  def __init__(self, server):
+    '''
+    '''
+    if server:
+      try:
+        self._connection = pymongo.Connection('mongodb://'+server+'/meteor')
+        self._db = self._connection[Neuroblocks.DATABASE]
+        print 'Connected to Neuroblocks.'
+      except:
+        print 'Connection to Neuroblocks failed.'
+
+
+    else:
+      self._connection = None
+
+  def get_segmentation(self, id):
+    '''
+    '''
+
+    return self._db.segmentation.find_one({"_id": id})
+
+  def get_segmentation_log(self, id):
+    '''
+    '''
+    return self._db.segmentationLog.find_one({"_id": id})
+
+  def save_state(self, state):
+    '''
+    '''
+
+    # first store the screenshot
+    screenshot = state['screenshot']
+    # delete state['screenshot'];
+    state.pop('screenshot', 0)
+
+    screenshot_id = self._db.screenshotsApps.insert({'img':screenshot, 'type':''})
+
+    state['img_id'] = screenshot_id
+
+    return self._db.appStates.insert(state)
+
+  def save_pick2d(self, values):
+    '''
+    '''
+    return self._db.appPickSegment.insert(values)
+
+  def save_action(self, values):
+    '''
+    '''
+
+    db = self._db
+
+    project_id = values['projectId']
+    user_id = values['userId']
+    segmentId2 = values['values'][0]
+    segmentId1 = values['values'][1]
+    date = values['on']
+
+
+    segment1 = db.segmentation.find_one({"projectId":project_id, "id":segmentId1});
+
+    segment2 = db.segmentation.find_one({"projectId":project_id, "id":segmentId2});
+
+    db.segmentationLog.insert({'objId':segment1['_id'],
+                               'projectId':project_id,
+                               'operation':'merge',
+                               'by':user_id,
+                               'on': date,
+                               'obj': segment1,
+                               'objId2': segment2['_id'],
+                               'obj2':segment2 });
+
+    voxelsSum = segment1['voxels'] + segment2['voxels'];
+    db.segmentation.update({'_id':segment1['_id']},
+      {'$set':{'voxels': voxelsSum, 'merged':2, 'lastUpdateOn': date, 'lastUpdateBy':user_id}});
+    db.segmentation.update({'_id':segment2['_id']},
+      {'$set':{ 'merged':1, 'lastUpdateOn': date, 'lastUpdateBy':user_id}});
+
+    print 'stored neuroblocks action'
+
+
+  def get_state(self, state_id):
+    '''
+    '''
+
+    state = self._db.appStates.find_one({"_id": ObjectId(state_id)})
+    state['_id'] = str(state['_id'])
+    state['img_id'] = str(state['img_id'])
+    state['on'] = str(state['on'])
+
+    return state

_dojo/scripts/iframe.html

@@ -0,0 +1,8 @@
+<html>
+
+<body>
+
+<iframe width=400 height =400 src='http://140.247.106.194:8000/dojo/?userId=mJdCbW76FjejQLxQi&userName=haehn' name='test' id='testid'></iframe>
+
+</body>
+</html>

_dojo/scripts/sub.py

@@ -0,0 +1,29 @@
+import cv2
+import numpy as np
+import sys
+
+
+factor = int(sys.argv[2])
+
+out = np.zeros((16384/factor,16384/factor), dtype=np.uint8)
+
+
+img = cv2.imread(sys.argv[1], cv2.CV_LOAD_IMAGE_GRAYSCALE)
+
+k = 0
+l = 0
+
+for i in range(16384):
+  if i % factor == 0:
+
+    for j in range(16384):
+      if j % factor == 0:
+
+        out[k][l] = img[i][j]
+
+        l += 1
+
+    l = 0
+    k += 1
+
+cv2.imwrite('/tmp/subplain.jpg', out)

_dojo/scripts/subcv.py

@@ -0,0 +1,11 @@
+import cv2
+import numpy as np
+import sys
+
+
+factor = int(sys.argv[2])
+
+
+img = cv2.imread(sys.argv[1], cv2.CV_LOAD_IMAGE_GRAYSCALE)
+# img = cv2.resize(img, (16384/factor, 16384/factor))
+# cv2.imwrite('/tmp/subcv.jpg', img)

_dojo/viewer.py

@@ -9,7 +9,7 @@ def __init__(self):
     '''
     self.__query_viewer_regex = re.compile('^/dojo/.*$')
 
-    self.__web_dir = '_web/'
+    self.__web_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), '../_web/')
 
   def content_type(self, extension):
     '''
@@ -45,8 +45,6 @@ def handle(self, request):
     requested_file = self.__web_dir + url.replace('/dojo/', '')
     extension = os.path.splitext(requested_file)[1]
 
-
-
     if not os.path.exists(requested_file):
       return 'Error 404', 'text/html'