Aspect angle feature

detection_list.py

@@ -39,7 +39,7 @@ def rowCount(self, index=None):
         return self.row_count
 
     def columnCount(self, index=None):
-        return 3
+        return 4
 
     def data(self, index, role):
         if role == QtCore.Qt.DisplayRole:
@@ -59,6 +59,8 @@ def data(self, index, role):
                 return round(d.angle, 1)
             elif col == 2:
                 return round(d.length, 3)
+            elif col == 3:
+                return round(d.aspect, 1)
             else:
                 return ""
 
@@ -68,9 +70,11 @@ def headerData(self, section, orientation, role=QtCore.Qt.DisplayRole):
                 if section == 0:
                     return "Distance (m)"
                 elif section == 1:
-                    return "Angle (deg)"
+                    return "Angle (°)"
                 elif section == 2:
                     return "Length (m)"
+                elif section == 3:
+                    return "Aspect (°)"
             else:
                 return '{: >4}'.format(section)
 

detector.py

@@ -348,12 +348,12 @@ def saveDetectionsToFile(self, path):
 
 		try:
 			with open(path, "w") as file:
-				file.write("frame;length;distance;angle;corner1 x;corner1 y;corner2 x;corner2 y;corner3 x;corner3 y;corner4 x;corner4 y\n")
+				file.write("frame;length;distance;angle;aspect;corner1 x;corner1 y;corner2 x;corner2 y;corner3 x;corner3 y;corner4 x;corner4 y\n")
 				for frame, dets in enumerate(self.detections):
 					if dets is not None:
 						for d in dets:
 							if d.corners is not None:
-								file.write(lineBase1.format(frame, d.length, d.distance, d.angle))
+								file.write(lineBase1.format(frame, d.length, d.distance, d.angle, d.aspect))
 								file.write(d.cornersToString(";"))
 								file.write("\n")
 				LogObject().print("Detections saved to path:", path)
@@ -384,15 +384,16 @@ def loadDetectionsFromFile(self, path):
 					length = float(split_line[1])
 					distance = float(split_line[2])
 					angle = float(split_line[3])
+					aspect = float(split_line[4])
 
-					c1 = [float(split_line[5]), float(split_line[4])]
-					c2 = [float(split_line[7]), float(split_line[6])]
-					c3 = [float(split_line[9]), float(split_line[8])]
-					c4 = [float(split_line[11]), float(split_line[10])]
+					c1 = [float(split_line[6]), float(split_line[5])]
+					c2 = [float(split_line[8]), float(split_line[7])]
+					c3 = [float(split_line[10]), float(split_line[9])]
+					c4 = [float(split_line[12]), float(split_line[11])]
 					corners = np.array([c1, c2, c3, c4])
 
 					det = Detection(0)
-					det.init_from_file(corners, length, distance, angle)
+					det.init_from_file(corners, length, distance, angle, aspect)
 
 					if self.detections[frame] is None:
 						self.detections[frame] = [det]
@@ -470,9 +471,10 @@ def __init__(self, label):
 		self.length = 0
 		self.distance = 0
 		self.angle = 0
+		self.aspect = 0
 
 	def __repr__(self):
-		return "Detection \"{}\" d:{:.1f}, a:{:.1f}".format(self.label, self.distance, self.angle)
+		return "Detection \"{}\" d:{:.1f}, a:{:.1f}".format(self.label, self.distance, self.angle, self.aspect)
 
 	def init_from_data(self, data, detection_size, polar_transform):
 		"""
@@ -514,8 +516,9 @@ def init_from_data(self, data, detection_size, polar_transform):
 				self.distance, self.angle = polar_transform.cart2polMetric(self.center[0], self.center[1], True)
 				self.distance = float(self.distance)
 				self.angle = float(self.angle / np.pi * 180 + 90)
+				self.aspect = float(np.arcsin(tvect[0,0]) / np.pi * 180 + 90) # aspect angle in degrees, 0 means that the length axis of the fish is perpendicular to the sound axis.  
 
-	def init_from_file(self, corners, length, distance, angle):
+	def init_from_file(self, corners, length, distance, angle, aspect):
 		"""
 		Initialize detection parameters from a csv file. Data is not stored when exporting a csv file,
 		which means it cannot be recovered here. This mainly affects the visualization of the detection.
@@ -526,6 +529,7 @@ def init_from_file(self, corners, length, distance, angle):
 		self.length = length
 		self.distance = distance
 		self.angle = angle
+		self.aspect = aspect
 
 	def visualize(self, image, color, show_text, show_detection=True):
 		if self.corners is None:

file_handlers/beamLookUp.py

@@ -94,10 +94,10 @@ def BeamLookUp(BeamCount,largeLens, beam_angle =False):
     if BeamCount == 64:
         breakpoints = breakpoints64
     if BeamCount == 48:
-        if largeLens == 1:
-            breakpoints = telephoto48
-        else:
+        if largeLens == 0:
             breakpoints = breakpoints48
+        else:
+            breakpoints = telephoto48
     if BeamCount == 135: 
         breakpoints = mp4135
     if BeamCount == 18:

file_handlers/v3/v3_file_info.py

@@ -343,7 +343,7 @@ def setWindowLength(configFlags, index, cls):
     return
 
 def setFirstBeamAngle(highResolution, cls):
-    cls.firstBeamAngle = beamLookUp.BeamLookUp(cls.BEAM_COUNT, highResolution)[-1]
+    cls.firstBeamAngle = beamLookUp.BeamLookUp(cls.BEAM_COUNT, 0)[-1]
 
     return    
 
@@ -458,4 +458,4 @@ def v3_getAllFramesData(fhand, version, cls):
     cls.DATA_SHAPE = cls.FRAMES.shape
 
     cls.FRAMES = cls.constructImages(cls.FRAMES)
-    return
+    return

file_handlers/v3/v3_frame_info.py

@@ -575,7 +575,7 @@ def getTransformationMatrix(self):
     def constructImage(self):
         I = self.FRAME_DATA.astype(np.uint8)
         I = cv2.flip( I, 0 )
-        allAngles = bl.BeamLookUp(self.BEAM_COUNT, self.largeLens)
+        allAngles = bl.BeamLookUp(self.BEAM_COUNT, 0)
 
         d0 = self.sampleStartDelay * 0.000001 * self.soundSpeed/2
         dm = d0 + self.samplePeriod * self.samplesPerBeam * 0.000001 * self.soundSpeed/2
@@ -645,4 +645,4 @@ def getBool(x):
             return False
 
 
-
+

fish_manager.py

@@ -633,7 +633,7 @@ def saveToFile(self, path):
 
         try:
             with open(path, "w") as file:
-                file.write("id;frame;length;distance;angle;direction;corner1 x;corner1 y;corner2 x;corner2 y;corner3 x;corner3 y;corner4 x;corner4 y; detection\n")
+                file.write("id;frame;length;distance;angle;aspect;direction;corner1 x;corner1 y;corner2 x;corner2 y;corner3 x;corner3 y;corner4 x;corner4 y; detection\n")
 
                 lines = self.getSaveLines()
                 lines.sort(key = lambda l: (l[0].id, l[1]))
@@ -647,7 +647,7 @@ def saveToFile(self, path):
     def getSaveLines(self):
         """
         Iterates through all the fish and returns a list containing the fish objects, frames the fish appear in, and the following information:
-        ID, Frame, Length, Angle, Direction, Corner coordinates and wether the values are from a detection or a track.
+        ID, Frame, Length, Angle, Aspect, Direction, Corner coordinates and wether the values are from a detection or a track.
         Detection information are preferred over tracks.
         """
         lines = []
@@ -664,7 +664,7 @@ def getSaveLines(self):
                 # Values calculated from detection
                 if detection is not None:
                     length = fish.length if fish.length_overwritten else detection.length
-                    line = lineBase1.format(fish.id, frame, length, detection.distance, detection.angle, fish.direction.name)
+                    line = lineBase1.format(fish.id, frame, length, detection.distance, detection.angle, detection.aspect, fish.direction.name)
                     if detection.corners is not None:
                         line += self.cornersToString(detection.corners, ";")
                     else:
@@ -681,8 +681,9 @@ def getSaveLines(self):
                     center = FishEntry.trackCenter(track)
                     distance, angle = polar_transform.cart2polMetric(center[0], center[1], True)
                     angle = float(angle / np.pi * 180 + 90)
+                    aspect = np.nan # not possible to extract this from track or detection files if not stored in the files
 
-                    line = lineBase1.format(fish.id, frame, length, distance, angle, fish.direction.name)
+                    line = lineBase1.format(fish.id, frame, length, distance, angle, aspect, fish.direction.name)
                     line += self.cornersToString([[track[0], track[1]], [track[2], track[1]], [track[2], track[3]], [track[0], track[3]]], ";")
                     line += ";0"
 
@@ -708,8 +709,9 @@ def loadFromFile(self, path):
                     id = int(split_line[0])
                     frame = int(split_line[1])
                     length = float(split_line[2])
-                    direction = SwimDirection[split_line[5]]
-                    track = [float(split_line[7]), float(split_line[6]), float(split_line[11]), float(split_line[10]), id]
+                    aspect = float(split_line[5])
+                    direction = SwimDirection[split_line[6]]
+                    track = [float(split_line[8]), float(split_line[7]), float(split_line[12]), float(split_line[11]), id]
 
                     if id in self.all_fish:
                         f = self.all_fish[id]
@@ -804,6 +806,7 @@ class FishEntry():
     def __init__(self, id, frame_in=0, frame_out=0):
         self.id = int(id)
         self.length = 0
+        self.aspect = 0
         self.direction = SwimDirection.NONE
         self.frame_in = frame_in
         self.frame_out = frame_out
@@ -823,11 +826,19 @@ def __init__(self, id, frame_in=0, frame_out=0):
         self.color_ind = 0
 
     def __repr__(self):
-        return "FishEntry {}: {:.1f} {}".format(self.id, self.length, self.direction.name)
+        return "FishEntry {}: {:.1f} {}".format(self.id, self.length, self.aspect, self.direction.name)
 
     def dirSortValue(self):
         return self.direction.value * 10**8 + self.id
 
+    def setAspect(self, value):
+        self.aspect = value
+
+    def setMeanAspect(self):
+        if not self.length_overwritten:
+            if len(self.aspects) > 0:
+                self.aspect = round(float(np.mean(self.lengths)),1)
+
     def setLength(self, value):
         self.length = value
         self.length_overwritten = True
@@ -853,6 +864,7 @@ def addTrack(self, track, detection, frame):
     def copy(self):
         f = FishEntry(self.id, self.frame_in, self.frame_out)
         f.length = self.length
+        f.aspect = self.aspect
         f.direction = self.direction
         f.tracks = self.tracks.copy()
         f.lengths = self.lengths.copy()
@@ -940,6 +952,7 @@ def setPathVariables(self, inverted, frame_time, meters_per_pixel):
             else:
                 self.direction = SwimDirection.UP if end_point_distance[1] > 0 else SwimDirection.DOWN
 
+            self.aspect = float(np.mean(valid_dets.aspect))
             self.mad = abs(valid_dets[-1].angle - valid_dets[0].angle)
             path_length = self.calculatePathLength(valid_dets)
             norm_dist = np.linalg.norm(end_point_distance)
@@ -962,6 +975,9 @@ def calculatePathLength(self, dets):
     def setLengths(self):
         self.lengths = sorted([det.length for _, det in self.tracks.values() if det is not None])
 
+    def setAspects(self):
+        self.aspects = sorted([det.aspects for _, det in self.tracks.values() if det is not None])
+
     @staticmethod
     def trackCenter(track):
         return [(track[2]+track[0])/2, (track[3]+track[1])/2]