diff --git a/EMT/EMT_notebooks/Add_markers.ipynb b/EMT/EMT_notebooks/Add_markers.ipynb index 50baa16ca3fc275db4532d7ab99a3959c9ea1554..bc0df776985b183370f8beb94fe41bf85e3f2d6f 100644 --- a/EMT/EMT_notebooks/Add_markers.ipynb +++ b/EMT/EMT_notebooks/Add_markers.ipynb @@ -28,7 +28,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "135e9aca", "metadata": {}, "outputs": [], @@ -48,19 +48,11 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "id": "287fb552", "metadata": {}, "outputs": [], "source": [ - "# Passing video paths by hand - few videos\n", - "# database = \"D:\\\\Experiments_data\\\\exp_20230519\\\\1 object\\\\Experiment 2479.sqlite\"\n", - "# video_path = [\"D:\\\\Experiments_data\\\\exp_20230519\\\\1 object\\\\video_t18011.mp4\",\n", - "# \"D:\\\\Experiments_data\\\\exp_20230519\\\\1 object\\\\video_t36009.mp4\"]\n", - "\n", - "# output_video_name = [\".\\\\video_t18011_marked.mp4\",\n", - "# \".\\\\video_t36009_marked.mp4\"]\n", - "\n", "# Automatically processing all videos\n", "from pathlib import Path\n", "from lmtanalysis.FileUtil import getVideoFilesToProcess\n", @@ -94,7 +86,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "id": "39ba84ad", "metadata": {}, "outputs": [], diff --git a/EMT/EMT_notebooks/Add_markers_social_range.ipynb b/EMT/EMT_notebooks/Add_markers_social_range.ipynb index 2a671a50066789eec8c4025d02fd219a0ce18d5d..8c73ca4896de18fdda893fc4a954b2867d0ac8e3 100644 --- a/EMT/EMT_notebooks/Add_markers_social_range.ipynb +++ b/EMT/EMT_notebooks/Add_markers_social_range.ipynb @@ -54,14 +54,6 @@ "metadata": {}, "outputs": [], "source": [ - "# Passing video paths by hand - few videos\n", - "# database = \"D:\\\\Experiments_data\\\\exp_20230519\\\\1 object\\\\Experiment 2479.sqlite\"\n", - "# video_path = [\"D:\\\\Experiments_data\\\\exp_20230519\\\\1 object\\\\video_t18011.mp4\",\n", - "# \"D:\\\\Experiments_data\\\\exp_20230519\\\\1 object\\\\video_t36009.mp4\"]\n", - "\n", - "# output_video_name = [\".\\\\video_t18011_marked.mp4\",\n", - "# \".\\\\video_t36009_marked.mp4\"]\n", - "\n", "# Automatically processing all videos\n", "from pathlib import Path\n", "from lmtanalysis.FileUtil import getVideoFilesToProcess\n", diff --git a/EMT/EMT_notebooks/Add_markers_speed.ipynb b/EMT/EMT_notebooks/Add_markers_speed.ipynb index 02f60bc158002f3b39847e262c62f9944b54ad2f..13be535250ed733eab5275ac6761e95a15d3bf4d 100644 --- a/EMT/EMT_notebooks/Add_markers_speed.ipynb +++ b/EMT/EMT_notebooks/Add_markers_speed.ipynb @@ -54,14 +54,6 @@ "metadata": {}, "outputs": [], "source": [ - "# Passing video paths by hand - few videos\n", - "# database = \"D:\\\\Experiments_data\\\\exp_20230519\\\\1 object\\\\Experiment 2479.sqlite\"\n", - "# video_path = [\"D:\\\\Experiments_data\\\\exp_20230519\\\\1 object\\\\video_t18011.mp4\",\n", - "# \"D:\\\\Experiments_data\\\\exp_20230519\\\\1 object\\\\video_t36009.mp4\"]\n", - "\n", - "# output_video_name = [\".\\\\video_t18011_marked.mp4\",\n", - "# \".\\\\video_t36009_marked.mp4\"]\n", - "\n", "# Automatically processing all videos\n", "from pathlib import Path\n", "from lmtanalysis.FileUtil import getVideoFilesToProcess\n", diff --git a/EMT/EMT_notebooks/Post-process_events.ipynb b/EMT/EMT_notebooks/Post-process_events.ipynb index 80f72669ee202926d6d11bc4036dda1985591df6..5905356ca15dd2aa1c8e2e406353191eff17006e 100644 --- a/EMT/EMT_notebooks/Post-process_events.ipynb +++ b/EMT/EMT_notebooks/Post-process_events.ipynb @@ -42,7 +42,6 @@ "import sqlite3\n", "from pathlib import Path\n", "import os\n", - "import shutil\n", "import yaml\n", "\n", "import pandas as pd\n", @@ -295,8 +294,9 @@ " connection = sqlite3.connect(file)\n", " sqlite_dir = Path(file).parent\n", " if save_sqlite_file:\n", - " filename, file_extension = os.path.splitext(file)\n", - " target_db = filename + '_filtered' + file_extension\n", + " filename = Path(file).stem\n", + " file_extension = Path(file).suffix\n", + " target_db = Path(file).parent / (filename + '_filtered' + file_extension)\n", " start = 0\n", " length = getNumberOfFrames(file)\n", " extractEventTable(connection, target_db, start, length)\n", @@ -304,7 +304,7 @@ " logs_dir = sqlite_dir / filtered_events_dir\n", " logs_dir.mkdir(exist_ok=True)\n", " nest4_TL = None\n", - " with open('actions_pproc_params.yaml', 'r') as f:\n", + " with open(Path(__file__).parent / '../lmtanalysis/actions_pproc_params.yaml', 'r') as f:\n", " actions_dictionary = yaml.load(f, Loader=yaml.SafeLoader)\n", "\n", " for name, params in actions_dictionary.items():\n", diff --git a/EMT/EMT_scripts/Post_process_events_script.py b/EMT/EMT_scripts/Post_process_events_script.py index 4ceddc95629fb95e2e43b17e3a31019c8ace5116..9a08bedf33067c79b85ab59ce9b27aafde723c7e 100644 --- a/EMT/EMT_scripts/Post_process_events_script.py +++ b/EMT/EMT_scripts/Post_process_events_script.py @@ -127,15 +127,16 @@ def process(file, minf=0, maxf=None, timestep=10*oneMinute, logs_dir = sqlite_dir / filtered_events_dir logs_dir.mkdir(exist_ok=True) nest4_TL = None - with open('actions_pproc_params.yaml', 'r') as f: + with open(Path(__file__).parent / '../lmtanalysis/actions_pproc_params.yaml', 'r') as f: actions_dictionary = yaml.load(f, Loader=yaml.SafeLoader) if maxf == None: maxf = getNumberOfFrames(file) if save_sqlite_file: - filename, file_extension = os.path.splitext(file) - target_db = filename + '_filtered' + file_extension + filename = Path(file).stem + file_extension = Path(file).suffix + target_db = Path(file).parent / (filename + '_filtered' + file_extension) extractEventTable(connection, target_db, minf, maxf) target_connection = sqlite3.connect(target_db) diff --git a/EMT/EMT_scripts/extract_actions.py b/EMT/EMT_scripts/extract_actions.py index fe6fc0ef2f9b16dafc9e02ed4061960a76eb2816..b2843d3ff21251a47d687077113097787606af9f 100644 --- a/EMT/EMT_scripts/extract_actions.py +++ b/EMT/EMT_scripts/extract_actions.py @@ -116,6 +116,7 @@ def extractActions(sqlite_file, csv_file_name, id): timeline[t] = event writeToCsv(csv_file_name, timeline) + connection.close() if __name__ == "__main__": argparser = argparse.ArgumentParser() @@ -125,6 +126,7 @@ if __name__ == "__main__": start_time = perf_counter() sqlite_file = Path(args.sqlite_file) + for id_animal in range(1, 5): dir = sqlite_file.parent / sqlite_file.stem dir.mkdir(exist_ok = True) @@ -134,8 +136,6 @@ if __name__ == "__main__": csv_writer = csv.writer(f) csv_writer.writerow(headers) - connection = sqlite3.connect(sqlite_file) - number_of_frames = getNumberOfFrames(sqlite_file) extractActions(sqlite_file, csv_file_name, id_animal) diff --git a/EMT/lmtanalysis/Animal.py b/EMT/lmtanalysis/Animal.py index 6143da80693e646c36e80743c54b0fcd789b35df..b453541114b130f697fa89321ea6e098d62f3b0b 100644 --- a/EMT/lmtanalysis/Animal.py +++ b/EMT/lmtanalysis/Animal.py @@ -19,8 +19,8 @@ import sqlite3 from time import sleep from lmtanalysis.Measure import * -from lmtanalysis.Detection import * -from lmtanalysis.Chronometer import * +from lmtanalysis.Detection import Detection +from lmtanalysis.Chronometer import Chronometer from lmtanalysis.Event import EventTimeLine from lmtanalysis.Point import Point from lmtanalysis.Mask import Mask diff --git a/EMT/lmtanalysis/BuildEventApproachContact.py b/EMT/lmtanalysis/BuildEventApproachContact.py index b646a9be8c573ababdeeb43e087402c645700828..9cb608d21840350c1c126d34de7eb05a5b0a76f2 100644 --- a/EMT/lmtanalysis/BuildEventApproachContact.py +++ b/EMT/lmtanalysis/BuildEventApproachContact.py @@ -3,17 +3,10 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.EventTimeLineCache import EventTimeLineCached +from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger def flush( connection ): diff --git a/EMT/lmtanalysis/BuildEventApproachRear.py b/EMT/lmtanalysis/BuildEventApproachRear.py index 296a076a009a56ec0a7e00a76d76f94ba390bd30..5656a3e6a8617a4b0fe89f176efea89d950f058c 100644 --- a/EMT/lmtanalysis/BuildEventApproachRear.py +++ b/EMT/lmtanalysis/BuildEventApproachRear.py @@ -3,17 +3,11 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.EventTimeLineCache import EventTimeLineCached +from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger def flush( connection ): diff --git a/EMT/lmtanalysis/BuildEventCenterPeripheryLocation.py b/EMT/lmtanalysis/BuildEventCenterPeripheryLocation.py index 2c37938393777b470196997acce91bb5a9fcfede..0ffbb9ab5cbd49702741a91b16cfbdede67a9018 100644 --- a/EMT/lmtanalysis/BuildEventCenterPeripheryLocation.py +++ b/EMT/lmtanalysis/BuildEventCenterPeripheryLocation.py @@ -3,18 +3,10 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import numpy as np -from lmtanalysis.Event import * + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * -#from affine import Affine -import matplotlib.pyplot as plt -import matplotlib.lines as mlines from lmtanalysis.TaskLogger import TaskLogger def flush( connection ): diff --git a/EMT/lmtanalysis/BuildEventDetection.py b/EMT/lmtanalysis/BuildEventDetection.py index c739d37e17fe115a36664fe4615928d0317cafcc..dac079b6e0728e4ab77a323096b0ce221df496bd 100644 --- a/EMT/lmtanalysis/BuildEventDetection.py +++ b/EMT/lmtanalysis/BuildEventDetection.py @@ -3,15 +3,9 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * from lmtanalysis.Chronometer import Chronometer from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventExclusiveCleanOralOralSideSideNoseAnogenitalContact.py b/EMT/lmtanalysis/BuildEventExclusiveCleanOralOralSideSideNoseAnogenitalContact.py index 89a238ddf6d56f25134309b7f252d93533fdd91f..4d81bd70fe832444f7212b544ce91886da6d9903 100644 --- a/EMT/lmtanalysis/BuildEventExclusiveCleanOralOralSideSideNoseAnogenitalContact.py +++ b/EMT/lmtanalysis/BuildEventExclusiveCleanOralOralSideSideNoseAnogenitalContact.py @@ -3,17 +3,10 @@ Created on 15 Feb. 2022 @author: Elodie ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.EventTimeLineCache import EventTimeLineCached +from lmtanalysis.Measure import * from lmtanalysis.BehaviouralSequencesUtil import exclusiveEventList, contactTypeList from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventExclusiveMoveStopIsolated.py b/EMT/lmtanalysis/BuildEventExclusiveMoveStopIsolated.py index 574dfd4dd35960797eeda893110b0ed78711ac25..1e1100ca5398a52217756153d28c49ad0cd20882 100644 --- a/EMT/lmtanalysis/BuildEventExclusiveMoveStopIsolated.py +++ b/EMT/lmtanalysis/BuildEventExclusiveMoveStopIsolated.py @@ -3,17 +3,10 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.EventTimeLineCache import EventTimeLineCached +from lmtanalysis.Measure import * from lmtanalysis.BehaviouralSequencesUtil import exclusiveEventList from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventExclusiveUndetected.py b/EMT/lmtanalysis/BuildEventExclusiveUndetected.py index 07c8c726255065e502b6f091f5cc9093c25c9951..c3aa447d1629d71551160e6c150def4f08011918 100644 --- a/EMT/lmtanalysis/BuildEventExclusiveUndetected.py +++ b/EMT/lmtanalysis/BuildEventExclusiveUndetected.py @@ -3,18 +3,11 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.EventTimeLineCache import EventTimeLineCached -from lmtanalysis.BehaviouralSequencesUtil import exclusiveEventList +from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger def flush( connection ): diff --git a/EMT/lmtanalysis/BuildEventFloorSniffing.py b/EMT/lmtanalysis/BuildEventFloorSniffing.py index 3143ca51719dbed13201235910a8c1f467a0d896..627b9862c1fdb3cbcbfd7b43e39829292cad67ff 100644 --- a/EMT/lmtanalysis/BuildEventFloorSniffing.py +++ b/EMT/lmtanalysis/BuildEventFloorSniffing.py @@ -3,18 +3,10 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import numpy as np -from lmtanalysis.Event import * + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * -#from affine import Affine -import matplotlib.pyplot as plt -import matplotlib.lines as mlines from lmtanalysis.TaskLogger import TaskLogger def flush( connection ): diff --git a/EMT/lmtanalysis/BuildEventFollowZone.py b/EMT/lmtanalysis/BuildEventFollowZone.py index b923711fbc3cf18708008ac69a116e0038ac8d34..43234651e5a5b20392c2e9f23c1960c8fb52eb5c 100644 --- a/EMT/lmtanalysis/BuildEventFollowZone.py +++ b/EMT/lmtanalysis/BuildEventFollowZone.py @@ -3,24 +3,11 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * - -from affine import Affine - -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -#from lmtanalysis.Measure import SPEED_THRESHOLD_LOW -import numpy as np -from lmtanalysis.Event import * +import math +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * - -import matplotlib.pyplot as plt -import matplotlib.lines as mlines from lmtanalysis.EventTimeLineCache import EventTimeLineCached -import copy -from copy import deepcopy from lmtanalysis.Parameters import getAnimalTypeParameters from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventGetAway.py b/EMT/lmtanalysis/BuildEventGetAway.py index b03f89f9594085899515adbc2c386fbe59be4d13..4f3839a6e06c01d9b5e066a9b60d654a5e1c82cc 100644 --- a/EMT/lmtanalysis/BuildEventGetAway.py +++ b/EMT/lmtanalysis/BuildEventGetAway.py @@ -3,15 +3,8 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * from lmtanalysis.EventTimeLineCache import EventTimeLineCached from lmtanalysis.Parameters import getAnimalTypeParameters diff --git a/EMT/lmtanalysis/BuildEventGroup2.py b/EMT/lmtanalysis/BuildEventGroup2.py index 4e41c745e606646a6cc8216fcf1ed65d37fefded..555560a641a14e86a6958cf8ef7d7761f98920f5 100644 --- a/EMT/lmtanalysis/BuildEventGroup2.py +++ b/EMT/lmtanalysis/BuildEventGroup2.py @@ -3,15 +3,9 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * from lmtanalysis.EventTimeLineCache import EventTimeLineCached from lmtanalysis.TaskLogger import TaskLogger @@ -34,7 +28,7 @@ def reBuildEvent( connection, file, tmin=None, tmax=None, pool = None, animalTyp for idAnimalB in range( 1 , 5 ): if ( animal == idAnimalB ): continue - contact[animal, idAnimalB] = EventTimeLineCached( connection, file, "Contact", animal, idAnimalB, minFrame=tmin, maxFrame=tmax ) #fait une matrice de tous les contacts à deux possibles + contact[animal, idAnimalB] = EventTimeLineCached( connection, file, "Contact", animal, idAnimalB, minFrame=tmin, maxFrame=tmax ) for animal in range( 1 , 5 ): diff --git a/EMT/lmtanalysis/BuildEventGroup3.py b/EMT/lmtanalysis/BuildEventGroup3.py index f138dc0158e6735ec1017e6c4c82be9b68f7d26d..f65af58c94f06d5a79e0f97557f0613bd029aa4a 100644 --- a/EMT/lmtanalysis/BuildEventGroup3.py +++ b/EMT/lmtanalysis/BuildEventGroup3.py @@ -3,17 +3,11 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.EventTimeLineCache import EventTimeLineCached +from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger def flush( connection ): diff --git a/EMT/lmtanalysis/BuildEventGroup3MakeBreak.py b/EMT/lmtanalysis/BuildEventGroup3MakeBreak.py index 24dc9919d8bc29952571cbc58e9ca2f2c085510a..00996ab1e8101ba58c40dd4f56688e825118a5fd 100644 --- a/EMT/lmtanalysis/BuildEventGroup3MakeBreak.py +++ b/EMT/lmtanalysis/BuildEventGroup3MakeBreak.py @@ -3,18 +3,12 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * +from pathlib import Path import yaml -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.EventTimeLineCache import EventTimeLineCached +from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger def flush( connection ): @@ -60,7 +54,7 @@ def reBuildEvent( connection, file, tmin=None, tmax=None, pool = None, animalTyp ''' process group ''' group3 = EventTimeLineCached( connection, file, "Group3", animal, idAnimalB, idAnimalC, minFrame=tmin, maxFrame=tmax ) - with open('actions_pproc_params.yaml', 'r') as f: + with open(Path(__file__).parent / 'actions_pproc_params.yaml', 'r') as f: actions_dictionary = yaml.load(f, Loader=yaml.SafeLoader) # Preprocess group3 - Break is only considered where there is a "valid" group merge_events_length= actions_dictionary["Group3"].get("merge_events_lenght", 5) diff --git a/EMT/lmtanalysis/BuildEventGroup4.py b/EMT/lmtanalysis/BuildEventGroup4.py index fa07c793cc9c288d452fc7086e9f877db4d6469c..af64754079e76759248d88eebc044f8c92f8dafb 100644 --- a/EMT/lmtanalysis/BuildEventGroup4.py +++ b/EMT/lmtanalysis/BuildEventGroup4.py @@ -3,17 +3,11 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.EventTimeLineCache import EventTimeLineCached +from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger def flush( connection ): diff --git a/EMT/lmtanalysis/BuildEventGroup4MakeBreak.py b/EMT/lmtanalysis/BuildEventGroup4MakeBreak.py index 91b3815dd70d4521b56c522197c676da047a0b01..00c96fd1ab076cd6e33ede112c02585ead29c3e8 100644 --- a/EMT/lmtanalysis/BuildEventGroup4MakeBreak.py +++ b/EMT/lmtanalysis/BuildEventGroup4MakeBreak.py @@ -3,18 +3,12 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * +from pathlib import Path import yaml -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.EventTimeLineCache import EventTimeLineCached +from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger def flush( connection ): @@ -62,7 +56,7 @@ def reBuildEvent( connection, file, tmin=None, tmax=None , pool = None, animalTy ''' process group ''' group4 = EventTimeLineCached( connection, file, "Group4", animal, idAnimalB, idAnimalC, minFrame=tmin, maxFrame=tmax ) - with open('actions_pproc_params.yaml', 'r') as f: + with open(Path(__file__).parent / 'actions_pproc_params.yaml', 'r') as f: actions_dictionary = yaml.load(f, Loader=yaml.SafeLoader) # Preprocess group4 - Break is only considered where there is a "valid" group merge_events_length= actions_dictionary["Group4"].get("merge_events_lenght", 5) diff --git a/EMT/lmtanalysis/BuildEventHuddling.py b/EMT/lmtanalysis/BuildEventHuddling.py index 43cf48b89675b868d34395fb44d3e0699ab55cd5..9cee635c839f36d4372fd544ad7d53c2a1369138 100644 --- a/EMT/lmtanalysis/BuildEventHuddling.py +++ b/EMT/lmtanalysis/BuildEventHuddling.py @@ -6,15 +6,9 @@ Created on 6 sept. 2017 Adapted on 18 sept. 2023 @author: Raul ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger from lmtanalysis.ParametersMouse import ParametersMouse diff --git a/EMT/lmtanalysis/BuildEventHuddling_oldv.py b/EMT/lmtanalysis/BuildEventHuddling_oldv.py index c5bcf87e0aeb8e73fd0b982c90503eea2d531233..c2d89dd020e902c7e358b537fad1b3727b0151c4 100644 --- a/EMT/lmtanalysis/BuildEventHuddling_oldv.py +++ b/EMT/lmtanalysis/BuildEventHuddling_oldv.py @@ -3,15 +3,9 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventHuddling_parallel.py b/EMT/lmtanalysis/BuildEventHuddling_parallel.py index ea6d6738b9d5ca60c2d52318841cd860390f8545..69c7ff182a6df4f54180b27ca9c1dad64472d07c 100644 --- a/EMT/lmtanalysis/BuildEventHuddling_parallel.py +++ b/EMT/lmtanalysis/BuildEventHuddling_parallel.py @@ -10,7 +10,8 @@ import sqlite3 from multiprocessing import Process from lmtanalysis.Animal import AnimalPool -from lmtanalysis.Event import * +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase +from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger from lmtanalysis.ParametersMouse import ParametersMouse from lmtanalysis.Util import getNumberOfFrames diff --git a/EMT/lmtanalysis/BuildEventInterestZoneLocation.py b/EMT/lmtanalysis/BuildEventInterestZoneLocation.py index 19e058b6e36748438b5f69e1895ce11e9a5f4beb..6da4c7900985c9fc8a7ba1ce97b244b40773fb13 100644 --- a/EMT/lmtanalysis/BuildEventInterestZoneLocation.py +++ b/EMT/lmtanalysis/BuildEventInterestZoneLocation.py @@ -3,19 +3,10 @@ Created on 01 may 2024 @author: Raul ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * -#from affine import Affine -import matplotlib.pyplot as plt -import matplotlib.lines as mlines +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.TaskLogger import TaskLogger +from lmtanalysis.Measure import * from lmtanalysis.ParametersMouse import ParametersMouse def flush( connection, zone_name ): diff --git a/EMT/lmtanalysis/BuildEventMove.py b/EMT/lmtanalysis/BuildEventMove.py index 6942e03b5210935148c3775fd72e6eaabd060188..e45e0f39c994505870ffcf66f5f0f5a1949e5848 100644 --- a/EMT/lmtanalysis/BuildEventMove.py +++ b/EMT/lmtanalysis/BuildEventMove.py @@ -3,15 +3,8 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * from lmtanalysis.EventTimeLineCache import EventTimeLineCached from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventNest3.py b/EMT/lmtanalysis/BuildEventNest3.py index 4f14c622ac701e7e032ce23bf86db44b8cc717de..147937fe27a6dd9b269302627f333a1b9b6d197f 100644 --- a/EMT/lmtanalysis/BuildEventNest3.py +++ b/EMT/lmtanalysis/BuildEventNest3.py @@ -3,18 +3,11 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * +from lmtanalysis.Animal import Animal, AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.EventTimeLineCache import EventTimeLineCached +from lmtanalysis.Measure import * import networkx as nx from lmtanalysis.Parameters import getAnimalTypeParameters from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventNest4.py b/EMT/lmtanalysis/BuildEventNest4.py index 5b6391cf8e31dfa10699d30e4376e8c1de391744..b54882427221baee5ebcc9ad5a1424eb3a1e9436 100644 --- a/EMT/lmtanalysis/BuildEventNest4.py +++ b/EMT/lmtanalysis/BuildEventNest4.py @@ -3,15 +3,9 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * + +from lmtanalysis.Animal import Animal, AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * from lmtanalysis.EventTimeLineCache import EventTimeLineCached import networkx as nx diff --git a/EMT/lmtanalysis/BuildEventNight.py b/EMT/lmtanalysis/BuildEventNight.py index 7852dc1e6f0c606d37a059a09b8804ee5632c794..1ad71efd5ff59cbde9614d26dd45308de2bde1d2 100644 --- a/EMT/lmtanalysis/BuildEventNight.py +++ b/EMT/lmtanalysis/BuildEventNight.py @@ -7,19 +7,13 @@ Created on 21 mars 2019 import sqlite3 from time import * import datetime -from lmtanalysis.Util import * +import sys -from lmtanalysis.Animal import * -import matplotlib.pyplot as plt -from lmtanalysis.Event import * +from lmtanalysis.Chronometer import Chronometer +from lmtanalysis.Event import Event, EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * from lmtanalysis.FileUtil import getFilesToProcess - -from psutil import virtual_memory - -from tkinter.filedialog import askopenfilename -from lmtanalysis.TaskLogger import TaskLogger -import sys +from lmtanalysis.Util import * class FileProcessException(Exception): pass diff --git a/EMT/lmtanalysis/BuildEventObjectSniffingNor.py b/EMT/lmtanalysis/BuildEventObjectSniffingNor.py index 724a3bbb6680537b633cead1e56eaf49e23bd822..dc69aea7d961d18a3764b21a7514956be033aa6a 100644 --- a/EMT/lmtanalysis/BuildEventObjectSniffingNor.py +++ b/EMT/lmtanalysis/BuildEventObjectSniffingNor.py @@ -3,18 +3,10 @@ Created on 2. February 2021 @author: Elodie ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import numpy as np -from lmtanalysis.Event import * + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * -#from affine import Affine -import matplotlib.pyplot as plt -import matplotlib.lines as mlines from lmtanalysis.Parameters import getAnimalTypeParameters from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventObjectSniffingNorAcquisitionWithConfig.py b/EMT/lmtanalysis/BuildEventObjectSniffingNorAcquisitionWithConfig.py index ca461a633a5d7fd561219e1364e26eb15f7fd461..47f2c2fed6cd139970baed230f3a5f12dcc3afd7 100644 --- a/EMT/lmtanalysis/BuildEventObjectSniffingNorAcquisitionWithConfig.py +++ b/EMT/lmtanalysis/BuildEventObjectSniffingNorAcquisitionWithConfig.py @@ -3,19 +3,10 @@ Created on 2. February 2021 @author: Elodie ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * -#from affine import Affine -import matplotlib.pyplot as plt -import matplotlib.lines as mlines +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Parameters import getAnimalTypeParameters +from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger def flush( connection ): diff --git a/EMT/lmtanalysis/BuildEventObjectSniffingNorTestWithConfig.py b/EMT/lmtanalysis/BuildEventObjectSniffingNorTestWithConfig.py index 03584cd1dea7b0786cce873669a5cf135456b7c2..7e478c3bdab76909e359d1da80a5981a61fb07be 100644 --- a/EMT/lmtanalysis/BuildEventObjectSniffingNorTestWithConfig.py +++ b/EMT/lmtanalysis/BuildEventObjectSniffingNorTestWithConfig.py @@ -3,18 +3,10 @@ Created on 2. February 2021 @author: Elodie ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import numpy as np -from lmtanalysis.Event import * + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * -#from affine import Affine -import matplotlib.pyplot as plt -import matplotlib.lines as mlines from lmtanalysis.Parameters import getAnimalTypeParameters from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventOnHouse.py b/EMT/lmtanalysis/BuildEventOnHouse.py index 013d97257aed9b462e0bd1c7dbb93c4fd755c4a8..9547551c83a74ec85aba62e37ed40686b7d8a498 100644 --- a/EMT/lmtanalysis/BuildEventOnHouse.py +++ b/EMT/lmtanalysis/BuildEventOnHouse.py @@ -6,17 +6,9 @@ Created on 6 sept. 2017 import sqlite3 from time import * from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * -import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * -#from affine import Affine -import matplotlib.pyplot as plt -import matplotlib.lines as mlines -import sys -import matplotlib.pyplot as plt from lmtanalysis.FileUtil import getFilesToProcess from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventOralGenitalContact.py b/EMT/lmtanalysis/BuildEventOralGenitalContact.py index 436d55fc7b73bfe29a8dacabd91158b0765c44b7..2c600bcbc808baa567486ce9ca8dcb91800399d0 100644 --- a/EMT/lmtanalysis/BuildEventOralGenitalContact.py +++ b/EMT/lmtanalysis/BuildEventOralGenitalContact.py @@ -3,15 +3,9 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * +import math +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * from lmtanalysis.Parameters import getAnimalTypeParameters from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventOralOralContact.py b/EMT/lmtanalysis/BuildEventOralOralContact.py index 6cc060a0ff7194cc2e5d7bb331cd21f90e61d2d6..688acee41bb177ac4b46032fdd2a1b0e39cf1143 100644 --- a/EMT/lmtanalysis/BuildEventOralOralContact.py +++ b/EMT/lmtanalysis/BuildEventOralOralContact.py @@ -3,17 +3,11 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * +import math +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Parameters import getAnimalTypeParameters +from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger def distHeadHead( detA, detB ): diff --git a/EMT/lmtanalysis/BuildEventOralSideSequence.py b/EMT/lmtanalysis/BuildEventOralSideSequence.py index 0ac21884da3611bdb2a66ca5dc016f2c2655c862..57e95599a1b79770ecc2c0afbf4d90cc59fad901 100644 --- a/EMT/lmtanalysis/BuildEventOralSideSequence.py +++ b/EMT/lmtanalysis/BuildEventOralSideSequence.py @@ -3,19 +3,11 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * -#from affine import Affine -import matplotlib.pyplot as plt -import matplotlib.lines as mlines + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import Event, EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.EventTimeLineCache import EventTimeLineCached +from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger def flush( connection ): diff --git a/EMT/lmtanalysis/BuildEventOtherContact.py b/EMT/lmtanalysis/BuildEventOtherContact.py index 9c55d8172f52086f884c74261dc0b23ca3a55414..09c3966d28fef35cf1b701f2069f57a0fa6359c8 100644 --- a/EMT/lmtanalysis/BuildEventOtherContact.py +++ b/EMT/lmtanalysis/BuildEventOtherContact.py @@ -3,18 +3,12 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * +from pathlib import Path import yaml -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.EventTimeLineCache import EventTimeLineCached +from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger def flush( connection ): @@ -63,7 +57,7 @@ def reBuildEvent( connection, file, tmin=None, tmax=None , pool = None, animalTy eventDico = {} for event in ["Oral-oral Contact", "Oral-genital Contact", "Passive oral-genital Contact", "Side by side Contact", "Side by side Contact, opposite way"]: eventDico[event] = timeLine[event][animal, idAnimalB] - with open('actions_pproc_params.yaml', 'r') as f: + with open(Path(__file__).parent / 'actions_pproc_params.yaml', 'r') as f: actions_dictionary = yaml.load(f, Loader=yaml.SafeLoader) # Preprocess event - Break is only considered where there is a "valid" group merge_events_length= actions_dictionary[event].get("merge_events_lenght", 5) diff --git a/EMT/lmtanalysis/BuildEventPassiveAnogenitalSniff.py b/EMT/lmtanalysis/BuildEventPassiveAnogenitalSniff.py index cfb80ab9b4fa8943df121495be469b4ed0601c4d..e0e786dd7c326ce1af5dfc31a8436302e13324a1 100644 --- a/EMT/lmtanalysis/BuildEventPassiveAnogenitalSniff.py +++ b/EMT/lmtanalysis/BuildEventPassiveAnogenitalSniff.py @@ -3,17 +3,11 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.EventTimeLineCache import EventTimeLineCached +from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger def flush( connection ): diff --git a/EMT/lmtanalysis/BuildEventRear5.py b/EMT/lmtanalysis/BuildEventRear5.py index be6fd860422e99360792ad617d5cea9780c57e1a..e111a9c99614771e593727212726e3d4d900c724 100644 --- a/EMT/lmtanalysis/BuildEventRear5.py +++ b/EMT/lmtanalysis/BuildEventRear5.py @@ -3,19 +3,10 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * -#from affine import Affine -import matplotlib.pyplot as plt -import matplotlib.lines as mlines +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.EventTimeLineCache import EventTimeLineCached +from lmtanalysis.Measure import * from lmtanalysis.Parameters import getAnimalTypeParameters from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventRearCenterPeriphery.py b/EMT/lmtanalysis/BuildEventRearCenterPeriphery.py index 3aa6fd965abe75091f03de8975819dc4c9edfdee..00f66271c882b7fc1194f62b396d4e1ec15ac2ad 100644 --- a/EMT/lmtanalysis/BuildEventRearCenterPeriphery.py +++ b/EMT/lmtanalysis/BuildEventRearCenterPeriphery.py @@ -3,15 +3,9 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * from lmtanalysis.EventTimeLineCache import EventTimeLineCached from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventSAP.py b/EMT/lmtanalysis/BuildEventSAP.py index d895a77d4a13c3a00a637c0efe55d03e5d15eb13..f6b63b69922d66c1dd2451e3ba5b6cd05262cc80 100644 --- a/EMT/lmtanalysis/BuildEventSAP.py +++ b/EMT/lmtanalysis/BuildEventSAP.py @@ -3,13 +3,13 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 import matplotlib.pyplot as plt import numpy as np import skimage.morphology as skm from lmtanalysis.Animal import AnimalPool -from lmtanalysis.Event import * +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase +from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger from lmtanalysis.Util import getNumberOfFrames diff --git a/EMT/lmtanalysis/BuildEventSAP_oldv.py b/EMT/lmtanalysis/BuildEventSAP_oldv.py index fe6754c04c57d2bb8bc5928deedbf20861c199d7..afb224355aad35749c9ed8b49ea216dc03887235 100644 --- a/EMT/lmtanalysis/BuildEventSAP_oldv.py +++ b/EMT/lmtanalysis/BuildEventSAP_oldv.py @@ -3,15 +3,9 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventSAP_parallel.py b/EMT/lmtanalysis/BuildEventSAP_parallel.py index b572715f2485e27e58ac405c87d77d2ee88e7732..b7220a1d4f0f5d0481ba2aaa9daedb2e81ccfecb 100644 --- a/EMT/lmtanalysis/BuildEventSAP_parallel.py +++ b/EMT/lmtanalysis/BuildEventSAP_parallel.py @@ -10,7 +10,7 @@ from multiprocessing import Process import skimage.morphology as skm from lmtanalysis.Animal import AnimalPool -from lmtanalysis.Event import * +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.TaskLogger import TaskLogger from lmtanalysis.Util import getNumberOfFrames diff --git a/EMT/lmtanalysis/BuildEventSideBySide.py b/EMT/lmtanalysis/BuildEventSideBySide.py index 75e242a818560575e2e75a401f79b842c5786f08..c09382d9ea0c9bcdd04dabb66287859ed562f8bc 100644 --- a/EMT/lmtanalysis/BuildEventSideBySide.py +++ b/EMT/lmtanalysis/BuildEventSideBySide.py @@ -3,15 +3,9 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * +import math +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * from lmtanalysis.Parameters import getAnimalTypeParameters from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventSideBySideOpposite.py b/EMT/lmtanalysis/BuildEventSideBySideOpposite.py index f0edee56546269d1592b40995b0912371dacc993..ff189b1c5c45188daccaaca3dcaa50a2330a0cd2 100644 --- a/EMT/lmtanalysis/BuildEventSideBySideOpposite.py +++ b/EMT/lmtanalysis/BuildEventSideBySideOpposite.py @@ -3,15 +3,9 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * +import math +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * from lmtanalysis.Parameters import getAnimalTypeParameters from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventSideWalk.py b/EMT/lmtanalysis/BuildEventSideWalk.py index 3868ace74d4e2f8c9548bb53af18a0de42b290ca..f56f3f506fd07facc048f452a080d5c5cd133a71 100644 --- a/EMT/lmtanalysis/BuildEventSideWalk.py +++ b/EMT/lmtanalysis/BuildEventSideWalk.py @@ -3,18 +3,11 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import numpy as np -from lmtanalysis.Event import * + +import math +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * -#from affine import Affine -import matplotlib.pyplot as plt -import matplotlib.lines as mlines from lmtanalysis.TaskLogger import TaskLogger def flush( connection ): diff --git a/EMT/lmtanalysis/BuildEventSocialApproach.py b/EMT/lmtanalysis/BuildEventSocialApproach.py index a2c593f27c832d4a7006bc1a4401c8e43be76ec4..048a6d646c3b150b0d6d037279a6ed2f1650ddf4 100644 --- a/EMT/lmtanalysis/BuildEventSocialApproach.py +++ b/EMT/lmtanalysis/BuildEventSocialApproach.py @@ -3,15 +3,8 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * from lmtanalysis.EventTimeLineCache import EventTimeLineCached from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventSocialEscape.py b/EMT/lmtanalysis/BuildEventSocialEscape.py index b00de927da9290f100ba76f3bb08bf57439fb497..430396b5c955f50ec84fec2b3789f3ee4392f03d 100644 --- a/EMT/lmtanalysis/BuildEventSocialEscape.py +++ b/EMT/lmtanalysis/BuildEventSocialEscape.py @@ -3,15 +3,9 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * from lmtanalysis.EventTimeLineCache import EventTimeLineCached from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventStop.py b/EMT/lmtanalysis/BuildEventStop.py index 19365b6c645e320ff61fb1aafdae7a3c8de99170..fbf4f741fe83670e883d0d99adc4d9cff3d201f5 100644 --- a/EMT/lmtanalysis/BuildEventStop.py +++ b/EMT/lmtanalysis/BuildEventStop.py @@ -3,15 +3,9 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * from lmtanalysis.EventTimeLineCache import EventTimeLineCached from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventTrain2.py b/EMT/lmtanalysis/BuildEventTrain2.py index a3c051f6a8b8333b65bc83bb4b03c406b19d6bcb..ad4eb2ae2c16b684244925384d986fa8289e0eb7 100644 --- a/EMT/lmtanalysis/BuildEventTrain2.py +++ b/EMT/lmtanalysis/BuildEventTrain2.py @@ -3,14 +3,8 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np + +from lmtanalysis.Animal import AnimalPool from lmtanalysis.Event import * from lmtanalysis.EventTimeLineCache import EventTimeLineCached from lmtanalysis.Parameters import getAnimalTypeParameters diff --git a/EMT/lmtanalysis/BuildEventTrain3.py b/EMT/lmtanalysis/BuildEventTrain3.py index eb680578e289ec7a588726cc16b1772361b32282..63158037ea9235b217b127c2f16b6cf95322c50d 100644 --- a/EMT/lmtanalysis/BuildEventTrain3.py +++ b/EMT/lmtanalysis/BuildEventTrain3.py @@ -3,15 +3,10 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * from lmtanalysis.EventTimeLineCache import EventTimeLineCached from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/BuildEventTrain4.py b/EMT/lmtanalysis/BuildEventTrain4.py index c40133298feda43edc7b32910502e67358e6baed..9f737c1f5e6f1c198e27a18b12f90189d1c4af0c 100644 --- a/EMT/lmtanalysis/BuildEventTrain4.py +++ b/EMT/lmtanalysis/BuildEventTrain4.py @@ -3,16 +3,11 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.EventTimeLineCache import EventTimeLineCached +from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger class Train2(): diff --git a/EMT/lmtanalysis/BuildEventWallJump.py b/EMT/lmtanalysis/BuildEventWallJump.py index 459a8ff3dc80b456b521c84dd541dd4578d74efc..154984dfea92c988706df7c52507ed664ba5c54a 100644 --- a/EMT/lmtanalysis/BuildEventWallJump.py +++ b/EMT/lmtanalysis/BuildEventWallJump.py @@ -7,7 +7,8 @@ import numpy as np import skimage.morphology as skm from lmtanalysis.Animal import AnimalPool -from lmtanalysis.Event import * +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase +from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger from lmtanalysis.Util import getNumberOfFrames diff --git a/EMT/lmtanalysis/BuildEventWallJump_oldv.py b/EMT/lmtanalysis/BuildEventWallJump_oldv.py index 5d5dfff6ff3b12fc1106fdc9665b858de8059aa9..cccdfa6db979c39f630783e5370c2d2607c694d6 100644 --- a/EMT/lmtanalysis/BuildEventWallJump_oldv.py +++ b/EMT/lmtanalysis/BuildEventWallJump_oldv.py @@ -3,20 +3,11 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * -#from affine import Affine -import matplotlib.pyplot as plt -import matplotlib.lines as mlines -import sys import matplotlib.pyplot as plt +import math +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase +from lmtanalysis.Measure import * from lmtanalysis.TaskLogger import TaskLogger def flush( connection ): diff --git a/EMT/lmtanalysis/BuildEventWallJump_parallel.py b/EMT/lmtanalysis/BuildEventWallJump_parallel.py index 0b63463248e57bb422218443b8746b0b80317774..c0379a5bc12443c7064c27943cdbf5965ae95391 100644 --- a/EMT/lmtanalysis/BuildEventWallJump_parallel.py +++ b/EMT/lmtanalysis/BuildEventWallJump_parallel.py @@ -9,7 +9,7 @@ import skimage.morphology as skm from multiprocessing import Process from lmtanalysis.Animal import AnimalPool -from lmtanalysis.Event import * +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.TaskLogger import TaskLogger from lmtanalysis.Util import getNumberOfFrames diff --git a/EMT/lmtanalysis/BuildEventWaterPoint.py b/EMT/lmtanalysis/BuildEventWaterPoint.py index b97d3ed0c7b9fb5bc936432a5ba8a438a5342270..4cb9d58e7174e1aaf32d0dd2356121667f83b54a 100644 --- a/EMT/lmtanalysis/BuildEventWaterPoint.py +++ b/EMT/lmtanalysis/BuildEventWaterPoint.py @@ -3,19 +3,12 @@ Created on 6 sept. 2017 @author: Fab ''' -import sqlite3 -from time import * -from lmtanalysis.Chronometer import Chronometer -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * import numpy as np -from lmtanalysis.Event import * -from lmtanalysis.Measure import * -#from affine import Affine -import matplotlib.pyplot as plt -import matplotlib.lines as mlines + +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine, deleteEventTimeLineInBase from lmtanalysis.EventTimeLineCache import EventTimeLineCached +from lmtanalysis.Measure import * from lmtanalysis.Parameters import getAnimalTypeParameters from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/CheckWrongAnimal.py b/EMT/lmtanalysis/CheckWrongAnimal.py index 1e25ee5919362de576b4f014bb8535754281b6e4..a6bf3121cea767d8f11e676662a49258737b18e7 100644 --- a/EMT/lmtanalysis/CheckWrongAnimal.py +++ b/EMT/lmtanalysis/CheckWrongAnimal.py @@ -7,17 +7,11 @@ In some record, we do have an extra animal with None for all parameters. This script should be used to detect those animal in databases. ''' -import sqlite3 -from time import * from lmtanalysis.Animal import * from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np from lmtanalysis.Event import * from lmtanalysis.Measure import * -from lmtanalysis.Chronometer import Chronometer from lmtanalysis.TaskLogger import TaskLogger diff --git a/EMT/lmtanalysis/CorrectDetectionIntegrity.py b/EMT/lmtanalysis/CorrectDetectionIntegrity.py index 05c634a924371cb23c5a64e37976d96c2852aa4a..82cb5efa23cdd339b60c48d5c12ef55a7e965a0c 100644 --- a/EMT/lmtanalysis/CorrectDetectionIntegrity.py +++ b/EMT/lmtanalysis/CorrectDetectionIntegrity.py @@ -14,15 +14,11 @@ This script alters the lmtanalysis: After running this script detection at t without all identity recognized will be all switched to anonymous ! ''' -import sqlite3 + from time import * -from lmtanalysis.Animal import * -from lmtanalysis.Detection import * -from lmtanalysis.Measure import * -import matplotlib.pyplot as plt -import numpy as np -from lmtanalysis.Event import * +from lmtanalysis.Animal import AnimalPool +from lmtanalysis.Event import EventTimeLine from lmtanalysis.Measure import * from lmtanalysis.Chronometer import Chronometer diff --git a/EMT/lmtanalysis/FileUtil.py b/EMT/lmtanalysis/FileUtil.py index a7a29a1eda4f1da93c043e731e9501dc4589c711..79aba8a670a79a871824bd11fea68d999b908de6 100644 --- a/EMT/lmtanalysis/FileUtil.py +++ b/EMT/lmtanalysis/FileUtil.py @@ -10,7 +10,7 @@ from tkinter.dialog import Dialog from tkinter.filedialog import askopenfilename, askdirectory import tkinter as tk import unittest -from random import randrange, random +from random import random import json diff --git a/EMT/lmtanalysis/TaskLogger.py b/EMT/lmtanalysis/TaskLogger.py index 4bcb77a4ea37a20ff5aff3771c89abbd2d15e674..25b54397b87210bb8db06fea3ee2fea4ac39b845 100644 --- a/EMT/lmtanalysis/TaskLogger.py +++ b/EMT/lmtanalysis/TaskLogger.py @@ -110,7 +110,3 @@ class TaskLogger: cursor.close() self.loadLog() - - - - diff --git a/EMT/lmtanalysis/Util.py b/EMT/lmtanalysis/Util.py index feeec5e5b5c13679a6de108473bcfbc776907446..b36d994bb7d3a558c2fcb33b3243a202bc65e17e 100644 --- a/EMT/lmtanalysis/Util.py +++ b/EMT/lmtanalysis/Util.py @@ -14,12 +14,10 @@ from random import random import string - - - class DummyFile(object): def write(self, x): pass + @contextlib.contextmanager def mute_prints(): # https://stackoverflow.com/questions/2828953/silence-the-stdout-of-a-function-in-python-without-trashing-sys-stdout-and-resto @@ -61,7 +59,6 @@ def level( data ): dico[entry]=True return sorted( dico.keys( ) ) - def pixelToCm( nbPixel ): return nbPixel * 10 / 57 @@ -105,7 +102,6 @@ def getFrameInput( text ): print("Entry (in frame) : " + str( t ) ) return t - def getMinTMaxTAndFileNameInput(): print ("Enter time information in frame. You can also set in days, hour, minutes") @@ -121,7 +117,6 @@ def getMinTMaxTAndFileNameInput(): return tmin,tmax,text_file - def getMinTMaxTInput(): print ("Enter time information in frame. You can also set in days, hour, minutes") @@ -132,7 +127,6 @@ def getMinTMaxTInput(): return tmin,tmax - def getExperimentDurationInput(): print ("Enter time information in frame. You can also set in days, hour, minutes") @@ -142,7 +136,6 @@ def getExperimentDurationInput(): return experimentDuration - def getFileNameInput(): text_file_name = input("File name : ") @@ -283,7 +276,6 @@ def recoverFrame(file, MyDatetime): print( "Distance to target: " + str( smallestDif ) + " milliseconds") return closestFrame - def addJitter(x, jit): newX = [] for item in x: @@ -292,7 +284,6 @@ def addJitter(x, jit): return newX - def getStarsFromPvalues(pvalue=None, U=None, numberOfTests=1): stars = "NA" diff --git a/EMT/EMT_scripts/actions_pproc_params.yaml b/EMT/lmtanalysis/actions_pproc_params.yaml similarity index 100% rename from EMT/EMT_scripts/actions_pproc_params.yaml rename to EMT/lmtanalysis/actions_pproc_params.yaml diff --git a/EMT/scripts/Check_Experiment_Reliability.py b/EMT/scripts/Check_Experiment_Reliability.py index 297786814b3fa0e672686efdeb4e87643fefd2e9..7054829ba2f3a426d0af712e436039fac047a2bd 100644 --- a/EMT/scripts/Check_Experiment_Reliability.py +++ b/EMT/scripts/Check_Experiment_Reliability.py @@ -97,7 +97,7 @@ if __name__ == '__main__': text_file.write("\n") print ("##############################################################") - continue + ########################################################################## '''Number of animals detected and rate of detection''' pool = AnimalPool( ) @@ -123,10 +123,10 @@ if __name__ == '__main__': rfidMismatchTimeLine = EventTimeLine( connection, "RFID MISMATCH", idA = animal ) nbOfRfidMatch = rfidMatchTimeLine.getNumberOfEvent(minFrame=startFrame, maxFrame=endFrame) nbOfRfidMismatch = rfidMismatchTimeLine.getNumberOfEvent(minFrame=startFrame, maxFrame=endFrame) - print( "Number of RFID match for animal {}: {} (rate: {} events/min)".format( pool.animalDictionary[animal].RFID, nbOfRfidMatch, nbOfRfidMatch/(durationExp*30*60) ) ) - print( "Number of RFID mismatch for animal {}: {} (rate: {} events/min)".format( pool.animalDictionary[animal].RFID, nbOfRfidMismatch, nbOfRfidMismatch/(durationExp*30*60) ) ) - text_file.write( "Number of RFID match for animal {}: {} (rate: {} events/min)\n".format( pool.animalDictionary[animal].RFID, nbOfRfidMatch, nbOfRfidMatch/(durationExp*30*60) ) ) - text_file.write( "Number of RFID mismatch for animal {}: {} (rate: {} events/min)\n".format( pool.animalDictionary[animal].RFID, nbOfRfidMismatch, nbOfRfidMismatch/(durationExp*30*60) ) ) + print( "Number of RFID match for animal {}: {} (rate: {} events/min)".format( pool.animalDictionary[animal].RFID, nbOfRfidMatch, nbOfRfidMatch/durationExp*30*60 ) ) + print( "Number of RFID mismatch for animal {}: {} (rate: {} events/min)".format( pool.animalDictionary[animal].RFID, nbOfRfidMismatch, nbOfRfidMismatch/durationExp*30*60 ) ) + text_file.write( "Number of RFID match for animal {}: {} (rate: {} events/min)\n".format( pool.animalDictionary[animal].RFID, nbOfRfidMatch, nbOfRfidMatch/durationExp*30*60 ) ) + text_file.write( "Number of RFID mismatch for animal {}: {} (rate: {} events/min)\n".format( pool.animalDictionary[animal].RFID, nbOfRfidMismatch, nbOfRfidMismatch/durationExp*30*60 ) ) print ("##############################################################") ########################################################################## diff --git a/README.md b/README.md index 797631f8295f8ee937aad13c44a07c8383f39758..cb414062dfe48fd6ccd76bbf99d206210439fbfa 100644 --- a/README.md +++ b/README.md @@ -34,6 +34,11 @@ Although this processing is long (for a 3-day database it will take a whole day If you have feeders/drinkers in the cage, ou can detect the contact of the animals with these structures by setting up the coordinates of the contours of the structure in a file named `feeders.txt` (a model can be found at `./EMT/images/`) to be put on the same directory of the database (sqlite file). The original script expects to find the coordinates of 1 drinker and 4 feeders, but you can adapt it easily four your needs by manipulating the script. Each object can have an arbitrary number of coordinates to set up the contour. +### Event filtering + +One of the improvements brought by EMT is the event filtering. Many events are noisily detected. A single event is broken in many because of the noise in detection, segmentation or orientation of the individuals. In order to overcome this failures, we propose a chain of filters for events. +The parameters for filtering each actions can be found (and modified) at `./EMT/lmtanalysis/actions_pproc_params.yaml`. + ### Processing sequences of events Using the filtered databases (output of the post_processing_events script/notebook with save_sqlite option enabled), you can process the sequences of events. First you must run the `extract_actions.py` to extract one action per frame for each animal. You can modify the priority of the frame in the dictionary of this file.