From f0053e38785f1c4d35f1fa0739e18c1cc07b0953 Mon Sep 17 00:00:00 2001
From: raul-silva <40128918+raul-silva@users.noreply.github.com>
Date: Mon, 28 Apr 2025 16:03:59 +0200
Subject: [PATCH] v250428: Removing Cache where it is not needed
For single event scripts it is not necessary.
Also adding a close call for sqlite connections (for safety).
Minor changes of homogeneity.
---
.../Rebuild_All_Events_LMT.ipynb | 14 +---
.../Rebuild_Huddling_events.ipynb | 64 +++++++----------
.../Rebuild_InterestZone_events.ipynb | 35 ++++-----
EMT/EMT_notebooks/Rebuild_SAP_events.ipynb | 63 +++++++---------
.../Rebuild_WallJump_events.ipynb | 64 +++++++----------
.../Rebuild_WaterZone_events.ipynb | 28 +++-----
.../Rebuild_All_Events_LMT_script.py | 6 +-
.../Rebuild_Huddling_events_script.py | 72 ++++++++-----------
EMT/EMT_scripts/Rebuild_SAP_events_script.py | 67 ++++++++---------
.../Rebuild_WallJump_events_script.py | 68 ++++++++----------
EMT/lmtanalysis/Animal.py | 42 +++++------
EMT/lmtanalysis/BuildEventHuddling.py | 9 ++-
.../BuildEventHuddling_parallel.py | 8 ++-
EMT/lmtanalysis/BuildEventSAP.py | 10 +--
EMT/lmtanalysis/BuildEventSAP_parallel.py | 3 +-
EMT/lmtanalysis/BuildEventWallJump.py | 2 +-
.../BuildEventWallJump_parallel.py | 11 ++-
EMT/lmtanalysis/BuildEventWaterPoint.py | 8 +--
EMT/lmtanalysis/Event.py | 8 +--
EMT/lmtanalysis/Util.py | 2 +-
EMT/setup.py | 2 +-
21 files changed, 244 insertions(+), 342 deletions(-)
diff --git a/EMT/EMT_notebooks/Rebuild_All_Events_LMT.ipynb b/EMT/EMT_notebooks/Rebuild_All_Events_LMT.ipynb
index f04ab8f..d596977 100644
--- a/EMT/EMT_notebooks/Rebuild_All_Events_LMT.ipynb
+++ b/EMT/EMT_notebooks/Rebuild_All_Events_LMT.ipynb
@@ -35,13 +35,12 @@
" BuildEventFloorSniffing, BuildEventSocialApproach, BuildEventSocialEscape, BuildEventApproachContact, \\\n",
" BuildEventOralOralContact, BuildEventApproachRear, BuildEventGroup2, BuildEventGroup3, BuildEventGroup4, \\\n",
" BuildEventOralGenitalContact, BuildEventStop, BuildEventMove, BuildEventGroup3MakeBreak, BuildEventGroup4MakeBreak, \\\n",
- " BuildEventSideBySide, BuildEventSideBySideOpposite, BuildDataBaseIndex, BuildEventWallJump, BuildEventSAP, \\\n",
+ " BuildEventSideBySide, BuildEventSideBySideOpposite, BuildEventWallJump, BuildEventSAP, \\\n",
" BuildEventOralSideSequence, CheckWrongAnimal, BuildEventDetection, BuildEventCenterPeripheryLocation, BuildEventNest4, \\\n",
" BuildEventNest3, BuildEventGetAway, BuildEventOtherContact, BuildEventPassiveAnogenitalSniff, BuildEventRearCenterPeriphery\n",
"from lmtanalysis.TaskLogger import TaskLogger\n",
"from lmtanalysis.FileUtil import getFilesToProcess\n",
"from lmtanalysis.EventTimeLineCache import flushEventTimeLineCache, disableEventTimeLineCache\n",
- "from lmtanalysis.EventTimeLineCache import EventTimeLineCached\n",
"from lmtanalysis.AnimalType import AnimalType\n"
]
},
@@ -192,17 +191,6 @@
" except:\n",
" print( \"METADATA field already exists\" , file )\n",
"\n",
- " #build index\n",
- "\n",
- " BuildDataBaseIndex.buildDataBaseIndex( connection, force=False )\n",
- "\n",
- " '''\n",
- " # build sensor data\n",
- " animalPool = AnimalPool( )\n",
- " animalPool.loadAnimals( connection )\n",
- " animalPool.buildSensorData(file)\n",
- " '''\n",
- "\n",
" currentT = minT\n",
"\n",
" try:\n",
diff --git a/EMT/EMT_notebooks/Rebuild_Huddling_events.ipynb b/EMT/EMT_notebooks/Rebuild_Huddling_events.ipynb
index 9bc5997..7f160dc 100644
--- a/EMT/EMT_notebooks/Rebuild_Huddling_events.ipynb
+++ b/EMT/EMT_notebooks/Rebuild_Huddling_events.ipynb
@@ -47,9 +47,7 @@
"minT = 0\n",
"maxT = 1*oneDay\n",
"''' time window to compute the events (in frame). '''\n",
- "windowT = 1*oneDay\n",
- "''' speed up process '''\n",
- "USE_CACHE_LOAD_DETECTION_CACHE = True"
+ "windowT = 1*oneDay\n"
]
},
{
@@ -79,7 +77,7 @@
"from lmtanalysis.Animal import *\n",
"from lmtanalysis.Event import *\n",
"from lmtanalysis.Measure import *\n",
- "from lmtanalysis import BuildEventHuddling, BuildEventHuddling_oldv, BuildEventHuddling_parallel, BuildDataBaseIndex\n",
+ "from lmtanalysis import BuildEventHuddling, BuildEventHuddling_oldv, BuildEventHuddling_parallel\n",
"from lmtanalysis.FileUtil import getFilesToProcess\n",
"from lmtanalysis.EventTimeLineCache import flushEventTimeLineCache, disableEventTimeLineCache\n",
"from lmtanalysis.AnimalType import AnimalType\n",
@@ -99,39 +97,31 @@
"\n",
"\n",
"def processTimeWindow(file, connection, currentMinT , currentMaxT, mode=\"new\"):\n",
- "\n",
" animalPool = None\n",
" flushEventTimeLineCache()\n",
"\n",
- " if (USE_CACHE_LOAD_DETECTION_CACHE):\n",
- " print(\"Caching load of animal detection...\")\n",
- " animalPool = AnimalPool()\n",
- " animalPool.loadAnimals(connection)\n",
- " animalPool.loadDetection(start = currentMinT, end = currentMaxT)\n",
- " print(\"Caching load of animal detection done.\")\n",
- "\n",
- " chrono = Chronometer(str(BuildEventHuddling))\n",
- " if \"old\" in mode.lower():\n",
- " BuildEventHuddling_oldv.reBuildEvent(connection, file,\n",
- " tmin=currentMinT,\n",
- " tmax=currentMaxT,\n",
- " pool = animalPool,\n",
- " animalType = AnimalType.MOUSE)\n",
- " elif \"new\" in mode.lower():\n",
- " BuildEventHuddling.reBuildEvent(connection, file,\n",
- " tmin=currentMinT,\n",
- " tmax=currentMaxT,\n",
- " pool = animalPool,\n",
- " animalType = AnimalType.MOUSE)\n",
- " elif \"parallel\" in mode.lower():\n",
- " BuildEventHuddling_parallel.reBuildEvent(connection, file,\n",
- " tmin=currentMinT,\n",
- " tmax=currentMaxT,\n",
- " pool = animalPool,\n",
- " animalType = AnimalType.MOUSE)\n",
- " else:\n",
- " raise NotImplementedError(\"This mode does not exist. Use 'old', 'new' or 'parallel'\")\n",
- " chrono.printTimeInS()\n",
+ " chrono = Chronometer(str(BuildEventHuddling))\n",
+ " if \"old\" in mode.lower():\n",
+ " BuildEventHuddling_oldv.reBuildEvent(connection, file,\n",
+ " tmin=currentMinT,\n",
+ " tmax=currentMaxT,\n",
+ " pool = animalPool,\n",
+ " animalType = AnimalType.MOUSE)\n",
+ " elif \"new\" in mode.lower():\n",
+ " BuildEventHuddling.reBuildEvent(connection, file,\n",
+ " tmin=currentMinT,\n",
+ " tmax=currentMaxT,\n",
+ " pool = animalPool,\n",
+ " animalType = AnimalType.MOUSE)\n",
+ " elif \"parallel\" in mode.lower():\n",
+ " BuildEventHuddling_parallel.reBuildEvent(connection, file,\n",
+ " tmin=currentMinT,\n",
+ " tmax=currentMaxT,\n",
+ " pool = animalPool,\n",
+ " animalType = AnimalType.MOUSE)\n",
+ " else:\n",
+ " raise NotImplementedError(\"This mode does not exist. Use 'old', 'new' or 'parallel'\")\n",
+ " chrono.printTimeInS()\n",
"\n",
"def process(file, mode=\"new\"):\n",
"\n",
@@ -158,9 +148,6 @@
" except:\n",
" print(\"METADATA field already exists\" , file)\n",
"\n",
- " # Build Index\n",
- " BuildDataBaseIndex.buildDataBaseIndex(connection, force=False)\n",
- "\n",
" currentT = minT\n",
"\n",
" try:\n",
@@ -193,6 +180,9 @@
"\n",
" raise FileProcessException()\n",
"\n",
+ " connection.close()\n",
+ "\n",
+ "\n",
"print(\"Code launched.\")\n",
"\n",
"mem = virtual_memory()\n",
diff --git a/EMT/EMT_notebooks/Rebuild_InterestZone_events.ipynb b/EMT/EMT_notebooks/Rebuild_InterestZone_events.ipynb
index d96443f..019f896 100644
--- a/EMT/EMT_notebooks/Rebuild_InterestZone_events.ipynb
+++ b/EMT/EMT_notebooks/Rebuild_InterestZone_events.ipynb
@@ -39,9 +39,7 @@
"minT = 0\n",
"maxT = 3*oneDay\n",
"''' time window to compute the events (in frame). '''\n",
- "windowT = 1*oneDay\n",
- "''' speed up process '''\n",
- "USE_CACHE_LOAD_DETECTION_CACHE = True"
+ "windowT = 1*oneDay\n"
]
},
{
@@ -74,11 +72,10 @@
"from lmtanalysis.Animal import *\n",
"from lmtanalysis.TaskLogger import TaskLogger\n",
"from lmtanalysis.Event import *\n",
- "from lmtanalysis.Measure import *\n",
- "from lmtanalysis.Util import getAllEvents, getNumberOfFrames\n",
- "from lmtanalysis import BuildEventInterestZoneLocation, BuildDataBaseIndex\n",
+ "from lmtanalysis.Util import getNumberOfFrames\n",
+ "from lmtanalysis import BuildEventInterestZoneLocation\n",
"from lmtanalysis.FileUtil import getFilesToProcess\n",
- "from lmtanalysis.EventTimeLineCache import EventTimeLineCached, flushEventTimeLineCache, disableEventTimeLineCache\n",
+ "from lmtanalysis.EventTimeLineCache import flushEventTimeLineCache, disableEventTimeLineCache\n",
"from lmtanalysis.AnimalType import AnimalType\n",
"from lmtanalysis.Parameters import getAnimalTypeParameters\n",
"\n",
@@ -128,18 +125,11 @@
" animalPool = None\n",
" flushEventTimeLineCache()\n",
"\n",
- " if ( USE_CACHE_LOAD_DETECTION_CACHE ):\n",
- " print(\"Caching load of animal detection...\")\n",
- " animalPool = AnimalPool()\n",
- " animalPool.loadAnimals(connection)\n",
- " animalPool.loadDetection(start = currentMinT, end = currentMaxT)\n",
- " print(\"Caching load of animal detection done.\")\n",
- "\n",
- " chrono = Chronometer(str(BuildEventInterestZoneLocation))\n",
- " BuildEventInterestZoneLocation.reBuildEvent( connection, file, tmin=currentMinT, tmax=currentMaxT,\n",
- " pool = animalPool, animalType = AnimalType.MOUSE,\n",
- " zone_name=zone_name, zone=zone_coords )\n",
- " chrono.printTimeInS()\n",
+ " chrono = Chronometer(str(BuildEventInterestZoneLocation))\n",
+ " BuildEventInterestZoneLocation.reBuildEvent(connection, file, tmin=currentMinT, tmax=currentMaxT,\n",
+ " pool = animalPool, animalType = AnimalType.MOUSE,\n",
+ " zone_name=zone_name, zone=zone_coords )\n",
+ " chrono.printTimeInS()\n",
"\n",
"def process(file, zone_name, zone_coords):\n",
" print(file)\n",
@@ -168,9 +158,6 @@
" except:\n",
" print( \"METADATA field already exists\" , file )\n",
"\n",
- " # Build Index\n",
- " BuildDataBaseIndex.buildDataBaseIndex( connection, force=False )\n",
- "\n",
" currentT = minT\n",
"\n",
" try:\n",
@@ -200,6 +187,8 @@
"\n",
" raise FileProcessException()\n",
"\n",
+ " connection.close()\n",
+ "\n",
"def extractFrames(video_file, count):\n",
" cap = cv2.VideoCapture(video_file.absolute().__str__())\n",
" frame = None\n",
@@ -299,7 +288,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3 (ipykernel)",
+ "display_name": "LMT",
"language": "python",
"name": "python3"
},
diff --git a/EMT/EMT_notebooks/Rebuild_SAP_events.ipynb b/EMT/EMT_notebooks/Rebuild_SAP_events.ipynb
index edf086a..b63c7b6 100644
--- a/EMT/EMT_notebooks/Rebuild_SAP_events.ipynb
+++ b/EMT/EMT_notebooks/Rebuild_SAP_events.ipynb
@@ -39,9 +39,7 @@
"minT = 0\n",
"maxT = 1*oneDay\n",
"''' time window to compute the events (in frame). '''\n",
- "windowT = 1*oneDay\n",
- "''' speed up process '''\n",
- "USE_CACHE_LOAD_DETECTION_CACHE = True"
+ "windowT = 1*oneDay\n"
]
},
{
@@ -70,7 +68,7 @@
"from lmtanalysis.TaskLogger import TaskLogger\n",
"from lmtanalysis.Animal import *\n",
"from lmtanalysis.Event import *\n",
- "from lmtanalysis import BuildEventSAP, BuildEventSAP_oldv, BuildEventSAP_parallel, BuildDataBaseIndex\n",
+ "from lmtanalysis import BuildEventSAP, BuildEventSAP_oldv, BuildEventSAP_parallel\n",
"from lmtanalysis.FileUtil import getFilesToProcess\n",
"from lmtanalysis.EventTimeLineCache import flushEventTimeLineCache, disableEventTimeLineCache\n",
"from lmtanalysis.AnimalType import AnimalType\n",
@@ -94,35 +92,28 @@
" animalPool = None\n",
" flushEventTimeLineCache()\n",
"\n",
- " if (USE_CACHE_LOAD_DETECTION_CACHE):\n",
- " print(\"Caching load of animal detection...\")\n",
- " animalPool = AnimalPool()\n",
- " animalPool.loadAnimals(connection)\n",
- " animalPool.loadDetection(start = currentMinT, end = currentMaxT)\n",
- " print(\"Caching load of animal detection done.\")\n",
- "\n",
- " chrono = Chronometer(str(BuildEventSAP))\n",
- " if \"old\" in mode.lower():\n",
- " BuildEventSAP_oldv.reBuildEvent(connection, file,\n",
- " tmin=currentMinT,\n",
- " tmax=currentMaxT,\n",
- " pool = animalPool,\n",
- " animalType = AnimalType.MOUSE)\n",
- " elif \"new\" in mode.lower():\n",
- " BuildEventSAP.reBuildEvent(connection, file,\n",
- " tmin=currentMinT,\n",
- " tmax=currentMaxT,\n",
- " pool = animalPool,\n",
- " animalType = AnimalType.MOUSE)\n",
- " elif \"parallel\" in mode.lower():\n",
- " BuildEventSAP_parallel.reBuildEvent(connection, file,\n",
- " tmin=currentMinT,\n",
- " tmax=currentMaxT,\n",
- " pool = animalPool,\n",
- " animalType = AnimalType.MOUSE)\n",
- " else:\n",
- " raise NotImplementedError(\"This mode does not exist. Use 'old', 'new' or 'parallel'\")\n",
- " chrono.printTimeInS()\n",
+ " chrono = Chronometer(str(BuildEventSAP))\n",
+ " if \"old\" in mode.lower():\n",
+ " BuildEventSAP_oldv.reBuildEvent(connection, file,\n",
+ " tmin=currentMinT,\n",
+ " tmax=currentMaxT,\n",
+ " pool = animalPool,\n",
+ " animalType = AnimalType.MOUSE)\n",
+ " elif \"new\" in mode.lower():\n",
+ " BuildEventSAP.reBuildEvent(connection, file,\n",
+ " tmin=currentMinT,\n",
+ " tmax=currentMaxT,\n",
+ " pool = animalPool,\n",
+ " animalType = AnimalType.MOUSE)\n",
+ " elif \"parallel\" in mode.lower():\n",
+ " BuildEventSAP_parallel.reBuildEvent(connection, file,\n",
+ " tmin=currentMinT,\n",
+ " tmax=currentMaxT,\n",
+ " pool = animalPool,\n",
+ " animalType = AnimalType.MOUSE)\n",
+ " else:\n",
+ " raise NotImplementedError(\"This mode does not exist. Use 'old', 'new' or 'parallel'\")\n",
+ " chrono.printTimeInS()\n",
"\n",
"def process(file, mode=\"new\"):\n",
"\n",
@@ -149,9 +140,6 @@
" except:\n",
" print(\"METADATA field already exists\" , file)\n",
"\n",
- " # Build Index\n",
- " BuildDataBaseIndex.buildDataBaseIndex(connection, force=False)\n",
- "\n",
" currentT = minT\n",
"\n",
" try:\n",
@@ -183,6 +171,9 @@
"\n",
" raise FileProcessException()\n",
"\n",
+ " connection.close()\n",
+ "\n",
+ "\n",
"print(\"Code launched.\")\n",
"\n",
"mem = virtual_memory()\n",
diff --git a/EMT/EMT_notebooks/Rebuild_WallJump_events.ipynb b/EMT/EMT_notebooks/Rebuild_WallJump_events.ipynb
index f7482ea..7bd3db4 100644
--- a/EMT/EMT_notebooks/Rebuild_WallJump_events.ipynb
+++ b/EMT/EMT_notebooks/Rebuild_WallJump_events.ipynb
@@ -39,9 +39,7 @@
"minT = 0\n",
"maxT = 1*oneDay\n",
"''' time window to compute the events (in frame). '''\n",
- "windowT = 1*oneDay\n",
- "''' speed up process '''\n",
- "USE_CACHE_LOAD_DETECTION_CACHE = True"
+ "windowT = 1*oneDay\n"
]
},
{
@@ -70,8 +68,7 @@
"from lmtanalysis.TaskLogger import TaskLogger\n",
"from lmtanalysis.Animal import *\n",
"from lmtanalysis.Event import *\n",
- "from lmtanalysis.Measure import *\n",
- "from lmtanalysis import BuildEventWallJump, BuildEventWallJump_oldv, BuildEventWallJump_parallel, BuildDataBaseIndex\n",
+ "from lmtanalysis import BuildEventWallJump, BuildEventWallJump_oldv, BuildEventWallJump_parallel\n",
"from lmtanalysis.FileUtil import getFilesToProcess\n",
"from lmtanalysis.EventTimeLineCache import flushEventTimeLineCache, disableEventTimeLineCache\n",
"from lmtanalysis.AnimalType import AnimalType\n",
@@ -95,35 +92,28 @@
" animalPool = None\n",
" flushEventTimeLineCache()\n",
"\n",
- " if (USE_CACHE_LOAD_DETECTION_CACHE):\n",
- " print(\"Caching load of animal detection...\")\n",
- " animalPool = AnimalPool()\n",
- " animalPool.loadAnimals(connection)\n",
- " animalPool.loadDetection(start = currentMinT, end = currentMaxT)\n",
- " print(\"Caching load of animal detection done.\")\n",
- "\n",
- " chrono = Chronometer(str(BuildEventWallJump))\n",
- " if \"old\" in mode.lower():\n",
- " BuildEventWallJump_oldv.reBuildEvent(connection, file,\n",
- " tmin=currentMinT,\n",
- " tmax=currentMaxT,\n",
- " pool = animalPool,\n",
- " animalType = AnimalType.MOUSE)\n",
- " elif \"new\" in mode.lower():\n",
- " BuildEventWallJump.reBuildEvent(connection, file,\n",
- " tmin=currentMinT,\n",
- " tmax=currentMaxT,\n",
- " pool = animalPool,\n",
- " animalType = AnimalType.MOUSE)\n",
- " elif \"parallel\" in mode.lower():\n",
- " BuildEventWallJump_parallel.reBuildEvent(connection, file,\n",
- " tmin=currentMinT,\n",
- " tmax=currentMaxT,\n",
- " pool = animalPool,\n",
- " animalType = AnimalType.MOUSE)\n",
- " else:\n",
- " raise NotImplementedError(\"This mode does not exist. Use 'old', 'new' or 'parallel'\")\n",
- " chrono.printTimeInS()\n",
+ " chrono = Chronometer(str(BuildEventWallJump))\n",
+ " if \"old\" in mode.lower():\n",
+ " BuildEventWallJump_oldv.reBuildEvent(connection, file,\n",
+ " tmin=currentMinT,\n",
+ " tmax=currentMaxT,\n",
+ " pool = animalPool,\n",
+ " animalType = AnimalType.MOUSE)\n",
+ " elif \"new\" in mode.lower():\n",
+ " BuildEventWallJump.reBuildEvent(connection, file,\n",
+ " tmin=currentMinT,\n",
+ " tmax=currentMaxT,\n",
+ " pool = animalPool,\n",
+ " animalType = AnimalType.MOUSE)\n",
+ " elif \"parallel\" in mode.lower():\n",
+ " BuildEventWallJump_parallel.reBuildEvent(connection, file,\n",
+ " tmin=currentMinT,\n",
+ " tmax=currentMaxT,\n",
+ " pool = animalPool,\n",
+ " animalType = AnimalType.MOUSE)\n",
+ " else:\n",
+ " raise NotImplementedError(\"This mode does not exist. Use 'old', 'new' or 'parallel'\")\n",
+ " chrono.printTimeInS()\n",
"\n",
"def process(file, mode=\"new\"):\n",
"\n",
@@ -150,9 +140,6 @@
" except:\n",
" print(\"METADATA field already exists\" , file)\n",
"\n",
- " # Build Index\n",
- " BuildDataBaseIndex.buildDataBaseIndex(connection, force=False)\n",
- "\n",
" currentT = minT\n",
"\n",
" try:\n",
@@ -184,6 +171,9 @@
"\n",
" raise FileProcessException()\n",
"\n",
+ " connection.close()\n",
+ "\n",
+ "\n",
"print(\"Code launched.\")\n",
"\n",
"mem = virtual_memory()\n",
diff --git a/EMT/EMT_notebooks/Rebuild_WaterZone_events.ipynb b/EMT/EMT_notebooks/Rebuild_WaterZone_events.ipynb
index fa6c264..1c94e5b 100644
--- a/EMT/EMT_notebooks/Rebuild_WaterZone_events.ipynb
+++ b/EMT/EMT_notebooks/Rebuild_WaterZone_events.ipynb
@@ -43,9 +43,7 @@
"minT = 0\n",
"maxT = 3*oneDay\n",
"''' time window to compute the events (in frame). '''\n",
- "windowT = 1*oneDay\n",
- "''' speed up process '''\n",
- "USE_CACHE_LOAD_DETECTION_CACHE = True"
+ "windowT = 1*oneDay\n"
]
},
{
@@ -80,10 +78,10 @@
"from lmtanalysis.TaskLogger import TaskLogger\n",
"from lmtanalysis.Event import *\n",
"from lmtanalysis.Measure import *\n",
- "from lmtanalysis.Util import getAllEvents, getNumberOfFrames\n",
- "from lmtanalysis import BuildEventWaterPoint, BuildDataBaseIndex\n",
+ "from lmtanalysis.Util import getNumberOfFrames\n",
+ "from lmtanalysis import BuildEventWaterPoint\n",
"from lmtanalysis.FileUtil import getFilesToProcess\n",
- "from lmtanalysis.EventTimeLineCache import EventTimeLineCached, flushEventTimeLineCache, disableEventTimeLineCache\n",
+ "from lmtanalysis.EventTimeLineCache import flushEventTimeLineCache, disableEventTimeLineCache\n",
"from lmtanalysis.AnimalType import AnimalType\n",
"from lmtanalysis.Parameters import getAnimalTypeParameters\n",
"\n",
@@ -133,16 +131,9 @@
" animalPool = None\n",
" flushEventTimeLineCache()\n",
"\n",
- " if ( USE_CACHE_LOAD_DETECTION_CACHE ):\n",
- " print(\"Caching load of animal detection...\")\n",
- " animalPool = AnimalPool()\n",
- " animalPool.loadAnimals(connection)\n",
- " animalPool.loadDetection(start = currentMinT, end = currentMaxT)\n",
- " print(\"Caching load of animal detection done.\")\n",
- "\n",
- " chrono = Chronometer(str(BuildEventWaterPoint))\n",
- " BuildEventWaterPoint.reBuildEvent( connection, file, tmin=currentMinT, tmax=currentMaxT, pool = animalPool, animalType = AnimalType.MOUSE, x_wp=wp[0], y_wp=wp[1] )\n",
- " chrono.printTimeInS()\n",
+ " chrono = Chronometer(str(BuildEventWaterPoint))\n",
+ " BuildEventWaterPoint.reBuildEvent(connection, file, tmin=currentMinT, tmax=currentMaxT, pool = animalPool, animalType = AnimalType.MOUSE, x_wp=wp[0], y_wp=wp[1])\n",
+ " chrono.printTimeInS()\n",
"\n",
"def process( file, wp ):\n",
" print(file)\n",
@@ -168,9 +159,6 @@
" except:\n",
" print( \"METADATA field already exists\" , file )\n",
"\n",
- " # Build Index\n",
- " BuildDataBaseIndex.buildDataBaseIndex( connection, force=False )\n",
- "\n",
" currentT = minT\n",
"\n",
" try:\n",
@@ -202,6 +190,8 @@
"\n",
" raise FileProcessException()\n",
"\n",
+ " connection.close()\n",
+ "\n",
"def extractFrames(video_file, count):\n",
" cap = cv2.VideoCapture(video_file.absolute().__str__())\n",
" frame = None\n",
diff --git a/EMT/EMT_scripts/Rebuild_All_Events_LMT_script.py b/EMT/EMT_scripts/Rebuild_All_Events_LMT_script.py
index 089786c..d8ca77e 100644
--- a/EMT/EMT_scripts/Rebuild_All_Events_LMT_script.py
+++ b/EMT/EMT_scripts/Rebuild_All_Events_LMT_script.py
@@ -16,7 +16,7 @@ from lmtanalysis import BuildEventTrain3, BuildEventTrain4, BuildEventTrain2, Bu
BuildEventFloorSniffing, BuildEventSocialApproach, BuildEventSocialEscape, BuildEventApproachContact, \
BuildEventOralOralContact, BuildEventApproachRear, BuildEventGroup2, BuildEventGroup3, BuildEventGroup4, \
BuildEventOralGenitalContact, BuildEventStop, BuildEventMove, BuildEventGroup3MakeBreak, BuildEventGroup4MakeBreak, \
- BuildEventSideBySide, BuildEventSideBySideOpposite, BuildDataBaseIndex, \
+ BuildEventSideBySide, BuildEventSideBySideOpposite, \
BuildEventOralSideSequence, CheckWrongAnimal, BuildEventDetection, BuildEventCenterPeripheryLocation, BuildEventNest4, \
BuildEventNest3, BuildEventGetAway, BuildEventOtherContact, BuildEventPassiveAnogenitalSniff, BuildEventRearCenterPeriphery
from lmtanalysis.TaskLogger import TaskLogger
@@ -136,8 +136,6 @@ def process(file, windowT=oneDay, minT=0, maxT=None, use_cache_load_detection_ca
except:
print("METADATA field already exists" , file)
- BuildDataBaseIndex.buildDataBaseIndex(connection, force=False)
-
currentT = minT
try:
@@ -172,7 +170,7 @@ def process(file, windowT=oneDay, minT=0, maxT=None, use_cache_load_detection_ca
flushEventTimeLineCache()
-
+ connection.close()
chronoFullBatch.printTimeInS()
print("*** ALL JOBS DONE ***")
diff --git a/EMT/EMT_scripts/Rebuild_Huddling_events_script.py b/EMT/EMT_scripts/Rebuild_Huddling_events_script.py
index da59cec..c4a6cd4 100644
--- a/EMT/EMT_scripts/Rebuild_Huddling_events_script.py
+++ b/EMT/EMT_scripts/Rebuild_Huddling_events_script.py
@@ -6,24 +6,19 @@
###################################################################################################
import argparse
import sqlite3
-from pathlib import Path
from psutil import virtual_memory
-
import traceback
from lmtanalysis.Animal import *
from lmtanalysis.Event import *
from lmtanalysis.Measure import *
from lmtanalysis.Util import getNumberOfFrames
-from lmtanalysis import BuildEventHuddling, BuildEventHuddling_oldv, BuildEventHuddling_parallel, BuildDataBaseIndex
+from lmtanalysis import BuildEventHuddling, BuildEventHuddling_oldv, BuildEventHuddling_parallel
from lmtanalysis.TaskLogger import TaskLogger
-from lmtanalysis.EventTimeLineCache import flushEventTimeLineCache,\
- disableEventTimeLineCache
+from lmtanalysis.EventTimeLineCache import flushEventTimeLineCache, disableEventTimeLineCache
from lmtanalysis.AnimalType import AnimalType
-USE_CACHE_LOAD_DETECTION_CACHE = True
-
class FileProcessException(Exception):
pass
@@ -41,35 +36,29 @@ def processTimeWindow(file, connection, currentMinT , currentMaxT, mode="new"):
animalPool = None
flushEventTimeLineCache()
- if (USE_CACHE_LOAD_DETECTION_CACHE):
- print("Caching load of animal detection...")
- animalPool = AnimalPool()
- animalPool.loadAnimals(connection)
- animalPool.loadDetection(start = currentMinT, end = currentMaxT)
- print("Caching load of animal detection done.")
-
- chrono = Chronometer(str(BuildEventHuddling))
- if "old" in mode.lower():
- BuildEventHuddling_oldv.reBuildEvent(connection, file,
- tmin=currentMinT,
- tmax=currentMaxT,
- pool = animalPool,
- animalType = AnimalType.MOUSE)
- elif "new" in mode.lower():
- BuildEventHuddling.reBuildEvent(connection, file,
- tmin=currentMinT,
- tmax=currentMaxT,
- pool = animalPool,
- animalType = AnimalType.MOUSE)
- elif "parallel" in mode.lower():
- BuildEventHuddling_parallel.reBuildEvent(connection, file,
- tmin=currentMinT,
- tmax=currentMaxT,
- pool = animalPool,
- animalType = AnimalType.MOUSE)
- else:
- raise NotImplementedError("This mode does not exist. Use 'old', 'new' or 'parallel'")
- chrono.printTimeInS()
+
+ chrono = Chronometer(str(BuildEventHuddling))
+ if "old" in mode.lower():
+ BuildEventHuddling_oldv.reBuildEvent(connection, file,
+ tmin=currentMinT,
+ tmax=currentMaxT,
+ pool = animalPool,
+ animalType = AnimalType.MOUSE)
+ elif "new" in mode.lower():
+ BuildEventHuddling.reBuildEvent(connection, file,
+ tmin=currentMinT,
+ tmax=currentMaxT,
+ pool = animalPool,
+ animalType = AnimalType.MOUSE)
+ elif "parallel" in mode.lower():
+ BuildEventHuddling_parallel.reBuildEvent(connection, file,
+ tmin=currentMinT,
+ tmax=currentMaxT,
+ pool = animalPool,
+ animalType = AnimalType.MOUSE)
+ else:
+ raise NotImplementedError("This mode does not exist. Use 'old', 'new' or 'parallel'")
+ chrono.printTimeInS()
def process(file, mode="new", windowT=oneDay, minT=0, maxT=None):
@@ -89,9 +78,6 @@ def process(file, mode="new", windowT=oneDay, minT=0, maxT=None):
except:
print("METADATA field already exists" , file)
- # Build Index
- BuildDataBaseIndex.buildDataBaseIndex(connection, force=False)
-
currentT = minT
try:
@@ -124,6 +110,10 @@ def process(file, mode="new", windowT=oneDay, minT=0, maxT=None):
raise FileProcessException()
+ flushEventTimeLineCache()
+ connection.close()
+ print("*** ALL JOBS DONE ***")
+
if __name__ == "__main__":
@@ -160,6 +150,4 @@ if __name__ == "__main__":
except FileProcessException:
print ("STOP PROCESSING FILE ", file , file=sys.stderr)
- flushEventTimeLineCache()
- chronoFullBatch.printTimeInS()
- print("*** ALL JOBS DONE ***")
\ No newline at end of file
+ chronoFullBatch.printTimeInS()
\ No newline at end of file
diff --git a/EMT/EMT_scripts/Rebuild_SAP_events_script.py b/EMT/EMT_scripts/Rebuild_SAP_events_script.py
index acedfca..3fb5b73 100644
--- a/EMT/EMT_scripts/Rebuild_SAP_events_script.py
+++ b/EMT/EMT_scripts/Rebuild_SAP_events_script.py
@@ -6,19 +6,16 @@
###################################################################################################
import argparse
import sqlite3
-from pathlib import Path
from psutil import virtual_memory
-
import traceback
from lmtanalysis.Animal import *
from lmtanalysis.Event import *
from lmtanalysis.Measure import *
from lmtanalysis.Util import getNumberOfFrames
-from lmtanalysis import BuildEventSAP, BuildEventSAP_oldv, BuildEventSAP_parallel, BuildDataBaseIndex
+from lmtanalysis import BuildEventSAP, BuildEventSAP_oldv, BuildEventSAP_parallel
from lmtanalysis.TaskLogger import TaskLogger
-from lmtanalysis.EventTimeLineCache import flushEventTimeLineCache,\
- disableEventTimeLineCache
+from lmtanalysis.EventTimeLineCache import flushEventTimeLineCache, disableEventTimeLineCache
from lmtanalysis.AnimalType import AnimalType
@@ -41,35 +38,28 @@ def processTimeWindow(file, connection, currentMinT , currentMaxT, mode="new"):
animalPool = None
flushEventTimeLineCache()
- if (USE_CACHE_LOAD_DETECTION_CACHE):
- print("Caching load of animal detection...")
- animalPool = AnimalPool()
- animalPool.loadAnimals(connection)
- animalPool.loadDetection(start = currentMinT, end = currentMaxT)
- print("Caching load of animal detection done.")
-
- chrono = Chronometer(str(BuildEventSAP))
- if "old" in mode.lower():
- BuildEventSAP_oldv.reBuildEvent(connection, file,
- tmin=currentMinT,
- tmax=currentMaxT,
- pool = animalPool,
- animalType = AnimalType.MOUSE)
- elif "new" in mode.lower():
- BuildEventSAP.reBuildEvent(connection, file,
- tmin=currentMinT,
- tmax=currentMaxT,
- pool = animalPool,
- animalType = AnimalType.MOUSE)
- elif "parallel" in mode.lower():
- BuildEventSAP_parallel.reBuildEvent(connection, file,
- tmin=currentMinT,
- tmax=currentMaxT,
- pool = animalPool,
- animalType = AnimalType.MOUSE)
- else:
- raise NotImplementedError("This mode does not exist. Use 'old', 'new' or 'parallel'")
- chrono.printTimeInS()
+ chrono = Chronometer(str(BuildEventSAP))
+ if "old" in mode.lower():
+ BuildEventSAP_oldv.reBuildEvent(connection, file,
+ tmin=currentMinT,
+ tmax=currentMaxT,
+ pool = animalPool,
+ animalType = AnimalType.MOUSE)
+ elif "new" in mode.lower():
+ BuildEventSAP.reBuildEvent(connection, file,
+ tmin=currentMinT,
+ tmax=currentMaxT,
+ pool = animalPool,
+ animalType = AnimalType.MOUSE)
+ elif "parallel" in mode.lower():
+ BuildEventSAP_parallel.reBuildEvent(connection, file,
+ tmin=currentMinT,
+ tmax=currentMaxT,
+ pool = animalPool,
+ animalType = AnimalType.MOUSE)
+ else:
+ raise NotImplementedError("This mode does not exist. Use 'old', 'new' or 'parallel'")
+ chrono.printTimeInS()
def process(file, mode="new", windowT=oneDay, minT=0, maxT=None):
@@ -89,9 +79,6 @@ def process(file, mode="new", windowT=oneDay, minT=0, maxT=None):
except:
print("METADATA field already exists" , file)
- # Build Index
- BuildDataBaseIndex.buildDataBaseIndex(connection, force=False)
-
currentT = minT
try:
@@ -124,6 +111,10 @@ def process(file, mode="new", windowT=oneDay, minT=0, maxT=None):
raise FileProcessException()
+ flushEventTimeLineCache()
+ connection.close()
+ print("*** ALL JOBS DONE ***")
+
if __name__ == "__main__":
@@ -160,6 +151,4 @@ if __name__ == "__main__":
except FileProcessException:
print ("STOP PROCESSING FILE ", file , file=sys.stderr)
- flushEventTimeLineCache()
chronoFullBatch.printTimeInS()
- print("*** ALL JOBS DONE ***")
\ No newline at end of file
diff --git a/EMT/EMT_scripts/Rebuild_WallJump_events_script.py b/EMT/EMT_scripts/Rebuild_WallJump_events_script.py
index e3b13be..b3ab57d 100644
--- a/EMT/EMT_scripts/Rebuild_WallJump_events_script.py
+++ b/EMT/EMT_scripts/Rebuild_WallJump_events_script.py
@@ -6,19 +6,16 @@
###################################################################################################
import argparse
import sqlite3
-from pathlib import Path
from psutil import virtual_memory
-
import traceback
from lmtanalysis.Animal import *
from lmtanalysis.Event import *
from lmtanalysis.Measure import *
from lmtanalysis.Util import getNumberOfFrames
-from lmtanalysis import BuildEventWallJump, BuildEventWallJump_oldv, BuildEventWallJump_parallel, BuildDataBaseIndex
+from lmtanalysis import BuildEventWallJump, BuildEventWallJump_oldv, BuildEventWallJump_parallel
from lmtanalysis.TaskLogger import TaskLogger
-from lmtanalysis.EventTimeLineCache import flushEventTimeLineCache,\
- disableEventTimeLineCache
+from lmtanalysis.EventTimeLineCache import flushEventTimeLineCache, disableEventTimeLineCache
from lmtanalysis.AnimalType import AnimalType
@@ -41,35 +38,28 @@ def processTimeWindow(file, connection, currentMinT , currentMaxT, mode="new"):
animalPool = None
flushEventTimeLineCache()
- if (USE_CACHE_LOAD_DETECTION_CACHE):
- print("Caching load of animal detection...")
- animalPool = AnimalPool()
- animalPool.loadAnimals(connection)
- animalPool.loadDetection(start = currentMinT, end = currentMaxT)
- print("Caching load of animal detection done.")
-
- chrono = Chronometer(str(BuildEventWallJump))
- if "old" in mode.lower():
- BuildEventWallJump_oldv.reBuildEvent(connection, file,
- tmin=currentMinT,
- tmax=currentMaxT,
- pool = animalPool,
- animalType = AnimalType.MOUSE)
- elif "new" in mode.lower():
- BuildEventWallJump.reBuildEvent(connection, file,
- tmin=currentMinT,
- tmax=currentMaxT,
- pool = animalPool,
- animalType = AnimalType.MOUSE)
- elif "parallel" in mode.lower():
- BuildEventWallJump_parallel.reBuildEvent(connection, file,
- tmin=currentMinT,
- tmax=currentMaxT,
- pool = animalPool,
- animalType = AnimalType.MOUSE)
- else:
- raise NotImplementedError("This mode does not exist. Use 'old', 'new' or 'parallel'")
- chrono.printTimeInS()
+ chrono = Chronometer(str(BuildEventWallJump))
+ if "old" in mode.lower():
+ BuildEventWallJump_oldv.reBuildEvent(connection, file,
+ tmin=currentMinT,
+ tmax=currentMaxT,
+ pool = animalPool,
+ animalType = AnimalType.MOUSE)
+ elif "new" in mode.lower():
+ BuildEventWallJump.reBuildEvent(connection, file,
+ tmin=currentMinT,
+ tmax=currentMaxT,
+ pool = animalPool,
+ animalType = AnimalType.MOUSE)
+ elif "parallel" in mode.lower():
+ BuildEventWallJump_parallel.reBuildEvent(connection, file,
+ tmin=currentMinT,
+ tmax=currentMaxT,
+ pool = animalPool,
+ animalType = AnimalType.MOUSE)
+ else:
+ raise NotImplementedError("This mode does not exist. Use 'old', 'new' or 'parallel'")
+ chrono.printTimeInS()
def process(file, mode="new", windowT=oneDay, minT=0, maxT=None):
@@ -89,9 +79,6 @@ def process(file, mode="new", windowT=oneDay, minT=0, maxT=None):
except:
print("METADATA field already exists" , file)
- # Build Index
- BuildDataBaseIndex.buildDataBaseIndex(connection, force=False)
-
currentT = minT
try:
@@ -124,6 +111,9 @@ def process(file, mode="new", windowT=oneDay, minT=0, maxT=None):
raise FileProcessException()
+ flushEventTimeLineCache()
+ connection.close()
+ print("*** ALL JOBS DONE ***")
if __name__ == "__main__":
@@ -160,6 +150,4 @@ if __name__ == "__main__":
except FileProcessException:
print ("STOP PROCESSING FILE ", file , file=sys.stderr)
- flushEventTimeLineCache()
- chronoFullBatch.printTimeInS()
- print("*** ALL JOBS DONE ***")
\ No newline at end of file
+ chronoFullBatch.printTimeInS()
\ No newline at end of file
diff --git a/EMT/lmtanalysis/Animal.py b/EMT/lmtanalysis/Animal.py
index 888d145..6143da8 100644
--- a/EMT/lmtanalysis/Animal.py
+++ b/EMT/lmtanalysis/Animal.py
@@ -3,37 +3,28 @@ Created on 7 sept. 2017
@author: Fab
'''
-from lmtanalysis.Detection import *
#matplotlib fix for mac (uncomment if needed)
#matplotlib.use('TkAgg' )
-
-import matplotlib.pyplot as plt
-from lmtanalysis.Chronometer import *
import matplotlib as mpl
+import matplotlib.pyplot as plt
+import matplotlib.patches as mpatches
+import matplotlib.ticker as ticker
import numpy as np
import pandas as pd
from collections import defaultdict
-from mpl_toolkits.mplot3d import *
-import matplotlib.ticker
import math
-import time
-from lmtanalysis.Measure import *
+import sqlite3
+from time import sleep
-from statistics import *
-#from scipy.spatial import distance
-#from scipy.ndimage.measurements import standard_deviation
-from statistics import mean
+from lmtanalysis.Measure import *
+from lmtanalysis.Detection import *
+from lmtanalysis.Chronometer import *
from lmtanalysis.Event import EventTimeLine
from lmtanalysis.Point import Point
from lmtanalysis.Mask import Mask
-from lmtanalysis.Util import *
-import matplotlib.patches as mpatches
-from lxml import etree
-import matplotlib.ticker as ticker
-#from lmtanalysis.Util import convert_to_d_h_m_s, getDatetimeFromFrame, mute_prints
-from pickle import NONE
+from lmtanalysis.Util import getAllEvents, getDatetimeFromFrame, mute_prints, convert_to_d_h_m_s
from lmtanalysis.AnimalType import AnimalType
from lmtanalysis.ParametersMouse import ParametersMouse
from lmtanalysis.ParametersRat import ParametersRat
@@ -41,9 +32,6 @@ from lmtanalysis.ParametersRat import ParametersRat
idAnimalColor = [ None, "red","green","blue","orange"]
-from enum import Enum
-
-
def getAnimalColor( animalId ):
return idAnimalColor[ animalId % 5 ]
@@ -124,7 +112,6 @@ class Animal():
if self.verbose:
print( query )
- print( self.conn )
cursor.execute( query )
rows = cursor.fetchall()
@@ -1047,7 +1034,16 @@ class Animal():
query = "SELECT DATA FROM DETECTION WHERE ANIMALID={} AND FRAMENUMBER={}".format( self.baseId , t )
cursor = self.conn.cursor()
- cursor.execute( query )
+
+ retry = True
+ while retry:
+ try:
+ cursor.execute( query )
+ except sqlite3.OperationalError:
+ sleep(0.1)
+ continue
+ else:
+ retry = False
rows = cursor.fetchall()
cursor.close()
diff --git a/EMT/lmtanalysis/BuildEventHuddling.py b/EMT/lmtanalysis/BuildEventHuddling.py
index 1016094..43cf48b 100644
--- a/EMT/lmtanalysis/BuildEventHuddling.py
+++ b/EMT/lmtanalysis/BuildEventHuddling.py
@@ -26,11 +26,10 @@ def flush( connection ):
def reBuildEvent( connection, file, tmin=None, tmax=None, pool = None , animalType = None, showGraph = False):
''' use the pool provided or create it'''
- if ( pool == None ):
- pool = AnimalPool( )
- pool.loadAnimals( connection )
- #pool.loadDetection( start = tmin, end = tmax )
-
+ if (pool == None):
+ pool = AnimalPool()
+ pool.loadAnimals(connection)
+ pool.loadDetection(start = tmin, end = tmax)
for idAnimalA in pool.animalDictionary:
diff --git a/EMT/lmtanalysis/BuildEventHuddling_parallel.py b/EMT/lmtanalysis/BuildEventHuddling_parallel.py
index 3697f51..ea6d673 100644
--- a/EMT/lmtanalysis/BuildEventHuddling_parallel.py
+++ b/EMT/lmtanalysis/BuildEventHuddling_parallel.py
@@ -28,6 +28,7 @@ def computeHuddling(sqlite_file, idAnimalA, tmin=None, tmax=None):
connection = sqlite3.connect(sqlite_file)
pool = AnimalPool()
pool.loadAnimals(connection)
+ pool.loadDetection(start = tmin, end = tmax, idAnimal=idAnimalA)
animal = pool.animalDictionary[idAnimalA]
huddlingTimeLine = EventTimeLine(connection, "Huddling", idAnimalA, minFrame=tmin, maxFrame=tmax, loadEvent=False)
@@ -53,14 +54,15 @@ def computeHuddling(sqlite_file, idAnimalA, tmin=None, tmax=None):
huddlingTimeLine.reBuildWithDictionary(result)
huddlingTimeLine.endRebuildEventTimeLine(connection)
+ connection.close()
return result
def reBuildEvent(connection, file, tmin=None, tmax=None, pool = None , animalType = None, showGraph = False):
# ''' use the pool provided or create it'''
- if ( pool == None ):
- pool = AnimalPool( )
- pool.loadAnimals( connection )
+ if (pool == None):
+ pool = AnimalPool()
+ pool.loadAnimals(connection)
processes = []
for idAnimalA in pool.animalDictionary:
diff --git a/EMT/lmtanalysis/BuildEventSAP.py b/EMT/lmtanalysis/BuildEventSAP.py
index b349867..d895a77 100644
--- a/EMT/lmtanalysis/BuildEventSAP.py
+++ b/EMT/lmtanalysis/BuildEventSAP.py
@@ -89,13 +89,13 @@ def computeMetrics(image, r = 9, debug = False):
return [I1, eccentricity, length]
-def reBuildEvent( connection, file, tmin=None, tmax=None, pool = None , animalType = None, showGraph = False ):
+def reBuildEvent(connection, file, tmin=None, tmax=None, pool = None , animalType = None, showGraph = False):
''' use the pool provided or create it'''
- if ( pool == None ):
- pool = AnimalPool( )
- pool.loadAnimals( connection )
- pool.loadDetection( start = tmin, end = tmax, lightLoad = True )
+ if (pool == None):
+ pool = AnimalPool()
+ pool.loadAnimals(connection)
+ pool.loadDetection( start = tmin, end = tmax)
'''
Animal A is stopped (built-in event):
diff --git a/EMT/lmtanalysis/BuildEventSAP_parallel.py b/EMT/lmtanalysis/BuildEventSAP_parallel.py
index d48cd55..b572715 100644
--- a/EMT/lmtanalysis/BuildEventSAP_parallel.py
+++ b/EMT/lmtanalysis/BuildEventSAP_parallel.py
@@ -99,7 +99,7 @@ def computeSAP(sqlite_file, idAnimalA, tmin=None, tmax=None):
connection = sqlite3.connect(sqlite_file)
pool = AnimalPool()
pool.loadAnimals(connection)
- pool.loadDetection(start = tmin, end = tmax, lightLoad = True, idAnimal=idAnimalA)
+ pool.loadDetection(start = tmin, end = tmax, idAnimal=idAnimalA)
animal = pool.animalDictionary[idAnimalA]
SAPTimeLine = EventTimeLine(connection, "SAP", animal.baseId, minFrame=tmin, maxFrame=tmax, loadEvent=False)
@@ -140,6 +140,7 @@ def computeSAP(sqlite_file, idAnimalA, tmin=None, tmax=None):
SAPTimeLine.reBuildWithDictionary(result)
SAPTimeLine.endRebuildEventTimeLine(connection)
+ connection.close()
return result
def reBuildEvent(connection, file, tmin=None, tmax=None, pool = None , animalType = None, showGraph = False):
diff --git a/EMT/lmtanalysis/BuildEventWallJump.py b/EMT/lmtanalysis/BuildEventWallJump.py
index 4199c14..459a8ff 100644
--- a/EMT/lmtanalysis/BuildEventWallJump.py
+++ b/EMT/lmtanalysis/BuildEventWallJump.py
@@ -80,7 +80,7 @@ def reBuildEvent( connection, file, tmin=None, tmax=None, pool = None, animalTyp
if (pool == None):
pool = AnimalPool()
pool.loadAnimals(connection)
- # pool.loadDetection(start = tmin, end = tmax, lightLoad = True)
+ pool.loadDetection(start = tmin, end = tmax)
tmin = 0 if tmin is None else tmin
tmax = getNumberOfFrames(file) if tmax is None else tmax
diff --git a/EMT/lmtanalysis/BuildEventWallJump_parallel.py b/EMT/lmtanalysis/BuildEventWallJump_parallel.py
index 9466c26..0b63463 100644
--- a/EMT/lmtanalysis/BuildEventWallJump_parallel.py
+++ b/EMT/lmtanalysis/BuildEventWallJump_parallel.py
@@ -3,6 +3,7 @@ Created on 6 sept. 2017
@author: Fab
'''
+import sqlite3
import numpy as np
import skimage.morphology as skm
from multiprocessing import Process
@@ -83,7 +84,7 @@ def computeWallJump(sqlite_file, idAnimalA, tmin=None, tmax=None):
connection = sqlite3.connect(sqlite_file)
pool = AnimalPool()
pool.loadAnimals(connection)
- pool.loadDetection(start = tmin, end = tmax, lightLoad = True, idAnimal=idAnimalA)
+ pool.loadDetection(start = tmin, end = tmax, idAnimal=idAnimalA)
animal = pool.animalDictionary[idAnimalA]
JumpWallTimeLine = EventTimeLine(connection, "WallJump", animal.baseId, None, None, None, loadEvent=False)
result={}
@@ -122,12 +123,16 @@ def computeWallJump(sqlite_file, idAnimalA, tmin=None, tmax=None):
JumpWallTimeLine.reBuildWithDictionary(result)
JumpWallTimeLine.endRebuildEventTimeLine(connection)
+ connection.close()
+ return result
def reBuildEvent( connection, file, tmin=None, tmax=None, pool = None, animalType = None, showGraph = False ):
- pool = AnimalPool()
- pool.loadAnimals(connection)
+ ''' use the pool provided or create it'''
+ if (pool == None):
+ pool = AnimalPool()
+ pool.loadAnimals(connection)
eventName = "WallJump"
print (eventName)
diff --git a/EMT/lmtanalysis/BuildEventWaterPoint.py b/EMT/lmtanalysis/BuildEventWaterPoint.py
index 3f83f01..b9bcefa 100644
--- a/EMT/lmtanalysis/BuildEventWaterPoint.py
+++ b/EMT/lmtanalysis/BuildEventWaterPoint.py
@@ -30,10 +30,10 @@ def reBuildEvent(connection, file, tmin=None, tmax=None, pool = None, animalType
parameters = getAnimalTypeParameters( animalType )
''' use the pool provided or create it'''
- if ( pool == None ):
- pool = AnimalPool( )
- pool.loadAnimals( connection )
- pool.loadDetection( start = tmin, end = tmax, lightLoad=True )
+ if (pool == None):
+ pool = AnimalPool()
+ pool.loadAnimals(connection)
+ pool.loadDetection(start = tmin, end = tmax)
'''
Event Water Zone
- the animal is in the zone around the water source
diff --git a/EMT/lmtanalysis/Event.py b/EMT/lmtanalysis/Event.py
index c2cd08d..3b22e23 100644
--- a/EMT/lmtanalysis/Event.py
+++ b/EMT/lmtanalysis/Event.py
@@ -3,22 +3,20 @@ Created on 6 sept. 2017
@author: Fab
'''
-import sqlite3
import unittest
-from time import *
-from lmtanalysis.Chronometer import Chronometer
-import matplotlib
#matplotlib fix for mac
#matplotlib.use('TkAgg')
import matplotlib.pyplot as plt
import numpy as np
-from lmtanalysis.Measure import *
import sys
import json
from numpy import NaN
+from lmtanalysis.Chronometer import Chronometer
+from lmtanalysis.Measure import *
+
class Event:
'''
an event represent the interval of frame where the event is
diff --git a/EMT/lmtanalysis/Util.py b/EMT/lmtanalysis/Util.py
index 570ddc6..feeec5e 100644
--- a/EMT/lmtanalysis/Util.py
+++ b/EMT/lmtanalysis/Util.py
@@ -10,7 +10,7 @@ import time
import sqlite3
import datetime
import contextlib
-from random import randrange, random
+from random import random
import string
diff --git a/EMT/setup.py b/EMT/setup.py
index afed539..f8af4fc 100644
--- a/EMT/setup.py
+++ b/EMT/setup.py
@@ -3,7 +3,7 @@ from setuptools import setup
setup(
name='lmtanalysis',
- version='1.2.0',
+ version='1.2.1',
description='A new LMT package under development',
author='Raul Silva',
author_email='raul-alfredo.de-sousa-silva@lis-lab.fr',
--
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