Merge pull request #17 from fdechaumont/dev

Merge dev to master

LMT/experimental/Animal_LMTtoolkit.py

@@ -0,0 +1,105 @@
+'''
+Created by Nicolas Torquet at 16/02/2024
+[email protected]
+Copyright: CNRS - INSERM - UNISTRA - ICS - IGBMC
+CNRS - Mouse Clinical Institute
+PHENOMIN, CNRS UMR7104, INSERM U964, Université de Strasbourg
+Code under GPL v3.0 licence
+
+Code derived from Animal code
+Compatible with LMT-toolkit
+'''
+
+
+from lmtanalysis.Animal import *
+
+
+
+
+class AnimalToolkit(Animal):
+
+    def __init__(self, ID, RFID, NAME=None, GENOTYPE=None, TREATMENT=None, AGE=None, SEX=None, STRAIN=None, SETUP=None,
+                 conn=None, animalType=AnimalType.MOUSE):
+        self.baseId = ID
+        self.RFID = RFID
+        self.genotype = GENOTYPE
+        self.name = NAME
+        self.age = AGE
+        self.sex = SEX
+        self.strain = STRAIN
+        self.setup = SETUP
+        self.treatment = TREATMENT
+        self.conn = conn
+        self.detectionDictionary = {}
+        self.parameters = None
+        self.setAnimalType(animalType)
+
+
+    def getTrajectory(self, maskingEventTimeLine=None):
+        keyList = sorted(self.detectionDictionary.keys())
+
+        if maskingEventTimeLine != None:
+            keyList = maskingEventTimeLine.getDictionary()
+
+        trajectory = {}
+
+        for key in keyList:
+            coordinates = self.detectionDictionary.get(key)
+            trajectory[key] = (coordinates.massX, -coordinates.massY)
+
+        return trajectory
+
+
+
+class AnimalPoolToolkit(AnimalPool):
+    """
+    Manages an experiment.
+    """
+
+    def __init__(self):
+        AnimalPool.__init__(self)
+
+
+
+    def loadAnimals(self, conn):
+
+        print("Loading animals.")
+        cursor = conn.cursor()
+        self.conn = conn
+
+        # check experiment parameters
+
+        # Check the number of row available in base
+        query = "SELECT * FROM ANIMAL"
+        cursor.execute(query)
+        field_names = [i[0] for i in cursor.description]
+        # print("Fields available in lmtanalysis: ", field_names)
+
+        rows = cursor.fetchall()
+
+        cursor.close()
+
+        self.animalDictionary.clear()
+        print("----------------")
+        print(type(field_names))
+        for row in rows:
+            animal = None
+            animalPrep = {}
+            for index, field in enumerate(field_names):
+                animalPrep[field] = row[index]
+            animal = AnimalToolkit(**animalPrep, conn=conn)
+
+            if (animal != None):
+                self.animalDictionary[animal.baseId] = animal
+                print(animal)
+            else:
+                print("Animal loader : error while loading animal.")
+
+    def getSexList(self):
+        sexes = {}
+
+        for k in self.animalDictionary:
+            animal = self.animalDictionary[k]
+            sexes[animal.sex] = True
+
+        return sexes.keys()

LMT/lmtanalysis/ParametersMouse.py

@@ -102,3 +102,6 @@ class ParametersMouse():
                             (114,353)
                             ]
 
+    ''' Margin to define whole cage area without a border in cm '''
+    CAGE_MARGIN = 3
+

LMT/lmtanalysis/ParametersRat.py

@@ -125,3 +125,8 @@ class ParametersRat():
                             (114,353)
                             ]
 
+    ''' Margin to define whole cage area without a border in cm '''
+    # TODO check value for the rat
+    CAGE_MARGIN = 6
+
+

LMT/lmtanalysis/ZoneArena.py

@@ -0,0 +1,69 @@
+'''
+Created by Nicolas Torquet at 14/02/2024
+[email protected]
+Copyright: CNRS - INSERM - UNISTRA - ICS - IGBMC
+CNRS - Mouse Clinical Institute
+PHENOMIN, CNRS UMR7104, INSERM U964, Université de Strasbourg
+Code under GPL v3.0 licence
+'''
+
+
+from Parameters import getAnimalTypeParameters
+
+
+def getZoneCoordinatesFromCornerCoordinatesOpenfieldArea(animalType = None):
+    parameters = getAnimalTypeParameters(animalType)
+    '''
+    parameters contains cornerCoordinatesOpenFieldArea attribute like:
+        cornerCoordinatesOpenFieldArea = [
+                            (114,63),
+                            (398,63),
+                            (398,353),
+                            (114,353)
+                            ]
+    '''
+    # coordinates of the whole cage: xa = 111, xb = 400, ya = 63, yb = 353
+    zoneCoordonates = {
+        'xa': parameters.cornerCoordinatesOpenFieldArea[0][0],
+        'xb': parameters.cornerCoordinatesOpenFieldArea[2][0],
+        'ya': parameters.cornerCoordinatesOpenFieldArea[0][1],
+        'yb': parameters.cornerCoordinatesOpenFieldArea[2][1]
+    }
+
+    return zoneCoordonates
+
+
+
+def getSmallerZoneFromCornerCoordinatesAndMargin(margin, animalType = None):
+    '''
+    :param margin: in centimeters: has to be converted to pixels
+    '''
+    parameters = getAnimalTypeParameters(animalType)
+    scaleFactor = parameters.scaleFactor
+    marginInPixels = margin/scaleFactor
+    zoneCoordonates = {
+        'xa': parameters.cornerCoordinatesOpenFieldArea[0][0]+marginInPixels,
+        'xb': parameters.cornerCoordinatesOpenFieldArea[2][0]-marginInPixels,
+        'ya': parameters.cornerCoordinatesOpenFieldArea[0][1]+marginInPixels,
+        'yb': parameters.cornerCoordinatesOpenFieldArea[2][1]-marginInPixels
+    }
+    return zoneCoordonates
+
+
+def getSmallerZoneFromGivenWholeCageCoordinatesAndMargin(margin, wholeCageCoordinates, animalType = None):
+    '''
+    :param margin: in centimeters: has to be converted to pixels
+    :param wholeCageCoordinates: has to be like {xa = 111, xb = 400, ya = 63, yb = 353}
+    '''
+    parameters = getAnimalTypeParameters(animalType)
+    scaleFactor = parameters.scaleFactor
+    marginInPixels = margin/scaleFactor
+    zoneCoordonates = {
+        'xa': wholeCageCoordinates['xa']+marginInPixels,
+        'xb': wholeCageCoordinates['xb']-marginInPixels,
+        'ya': wholeCageCoordinates['ya']+marginInPixels,
+        'yb': wholeCageCoordinates['yb']-marginInPixels
+    }
+    return zoneCoordonates
+
+

LMT/scripts/ComputeMeasuresIdentityProfileOneMouseAutomatic.py

@@ -36,7 +36,7 @@
 
 import random
 from random import randint
-from scipy.stats._morestats import shapiro
+from scipy.stats.morestats import shapiro
 
 def computeProfile(file, minT, maxT, behaviouralEventList):
 
@@ -1991,7 +1991,7 @@ def plotZScoreProfileAutoHorizontal(ax, cat, koDataframe, night, eventListForTes
                     n = 0
                     extension = 'no_night_{}'.format(os.path.splitext(os.path.basename(tail))[0])
                     #Compute profile2 data and save them in a text file
-                    profileData[file][n] = computeProfilePair(file = file, minT=minT, maxT=maxT, behaviouralEventListSingle=behaviouralEventOneMouse, behaviouralEventListSocial=behaviouralEventOneMouse)
+                    profileData[file][n] = computeProfilePair(file = file, minT=minT, maxT=maxT, behaviouralEventListSingle=behaviouralEventOneMouseSingle, behaviouralEventListSocial=behaviouralEventOneMouseSocial)
 
 
                 else:
@@ -2040,8 +2040,8 @@ def plotZScoreProfileAutoHorizontal(ax, cat, koDataframe, night, eventListForTes
                 n = 0
                 # Compute profile2 data
                 profileData[file][n] = computeProfilePairFromPause(file=file, experimentDuration=experimentDuration,
-                                                                   behaviouralEventListSingle=behaviouralEventOneMouse,
-                                                                   behaviouralEventListSocial=behaviouralEventOneMouse)
+                                                                   behaviouralEventListSingle=behaviouralEventOneMouseSingle,
+                                                                   behaviouralEventListSocial=behaviouralEventOneMouseSocial)
 
                 # Create a json file to store the computation
                 with open("{}/profile_data_pair_from_pause_{}_{}.json".format(head, extension, experimentDuration), 'w') as fp: