parameters for robot avoidance

Stuff/Modules/cm.py

@@ -469,8 +469,9 @@ def getThigmotaxis(self, time = 20, startTime = 0, percentSize = 20):
         center = 0
         
         for content in self.data[start:]:
-            if content[1] <= time: 
-                distance = ((content[2] - self.centerX)**2 + (content[3] - self.centerY)**2)**0.5
+            if content[1] <= time:
+                x, y = content[self.indices]
+                distance = sqrt((x - self.centerX)**2 + (y - self.centerY)**2)
                 if distance >= border:
                     periphery += 1
                 else:
@@ -480,7 +481,7 @@ def getThigmotaxis(self, time = 20, startTime = 0, percentSize = 20):
 
 
     def getAngleBoxes(self, time = 20, startTime = 0, width = "default", results = "condensed",
-                      center = "target"):
+                      center = "target", indices = slice(2,4)):
         """returns proportion of time spent in angle boxes of width 'boxWidth' (provided in
                 degreess)
             first item is centered in center of shock zone - by default it means that
@@ -491,20 +492,23 @@ def getAngleBoxes(self, time = 20, startTime = 0, width = "default", results = "
         if width == "default":
             width = self.width
 
-        time = time * 60000
+        time *= 60000
         start = self.findStart(startTime)
 
         if center == "target":
             sectorCenterAngle = self.centerAngle
         elif center == "opposite":
             sectorCenterAngle = self.centerAngle + 180
         else:
-            sectorCenterAngle = self.centerAngle + center
+            if self.centerAngle:
+                sectorCenterAngle = self.centerAngle + center
+            else:
+                sectorCenterAngle = center
   
         angles = [0] * int(360 / width)
         for content in self.data[start:]:
             if content[1] <= time:
-                angle = (degrees(self._angle(content[2], content[3])) - sectorCenterAngle +
+                angle = (degrees(self._angle(*content[indices])) - sectorCenterAngle +
                          (width / 2) + 360) % 360
                 angles[int(angle // width)] += 1
 
@@ -542,14 +546,14 @@ def _angle(self, x, y):
         return atan2(self.centerY - y, x - self.centerX + 0.000000001)
 
 
-    def getDirectionalMean(self, time = 20, startTime = 0):
+    def getDirectionalMean(self, time = 20, startTime = 0, indices = slice(2,4)):
         "returns directional mean angle in room frame"
         time = time * 60000
         start = self.findStart(startTime)
 
-        num = sum([sin(self._angle(content[2], content[3])) for content in self.data[start:] if
+        num = sum([sin(self._angle(*content[indices])) for content in self.data[start:] if
                    content[1] < time])
-        den = sum([cos(self._angle(content[2], content[3])) for content in self.data[start:] if
+        den = sum([cos(self._angle(*content[indices])) for content in self.data[start:] if
                    content[1] < time])
 
         if den == 0:
@@ -560,14 +564,14 @@ def getDirectionalMean(self, time = 20, startTime = 0):
         return format(result, "0.2f")
 
 
-    def getCircularVariance(self, time = 20, startTime = 0):
+    def getCircularVariance(self, time = 20, startTime = 0, indices = slice(2,4)):
         "return circular variance of angle in room frame (has values between 0 and 1 inclusive)"
-        circMean = radians(float(self.getDirectionalMean(time, startTime)))
+        circMean = radians(float(self.getDirectionalMean(time, startTime, indices = indices)))
         
         time = time * 60000
         start = self.findStart(startTime)
 
-        R = sum([cos(self._angle(content[2], content[3]) - circMean) for content in
+        R = sum([cos(self._angle(*content[indices]) - circMean) for content in
                  self.data[start:] if content[1] < time])
         
         circVar = 1 - R / len([1 for content in self.data[start:] if content[1] < time])
@@ -816,8 +820,10 @@ def findReflections(self, time = 20, startTime = 0, results = "both"):
 
 
     def _computeSpeed(self, row1, row2):
-        speed = ((row1[7] - row2[7])**2 + (row1[8] - row2[8])**2)**0.5 / \
-                ((abs(row2[1] - row1[1]) / 1000) * self.trackerResolution)
+        x1, y1 = row1[self.indices]
+        x2, y2 = row2[self.indices]
+        speed = (sqrt((x1 - x2)**2 + (y1 - y2)**2) /
+                 ((abs(row2[1] - row1[1]) / 1000) * self.trackerResolution))
         return speed # cm/s
 
     def _findSame(self, indices, points):
@@ -871,7 +877,7 @@ def removeReflections(self, points = None, deleteSame = True, bothframes = True)
         # finds data points that share coordinates with more than two points with reflections      
         if deleteSame:
             missing |= self._returnSame(missing)
-                 
+
         missing = sorted(missing)
 
         if missing:

Stuff/Modules/mode.py

@@ -54,13 +54,13 @@
 fullname["RA"] = "Robot avoidance"
 
 pairing = {"CM": ("Arena", "Room"),
-           "RA": ("Rat", "Rob")} # zmenit pokud se bude menit pojmenovani !!!
+           "RA": ("Rat", "Robot")}
 
 time = {"CM": 20,
         "MWM": 1,
         "OF": 10,
         "CMSF": 20,
-        "RA": 20} # zkontrolovat
+        "RA": 20}
 
 
 def changeMode(newMode):

Stuff/Modules/parameters.py

@@ -209,14 +209,36 @@ def __init__(self):
 class ParametersRA(OrderedDict):
     def __init__(self):
         super().__init__()
+        ra = {"Total distance",
+              "Maximum time avoided",
+              "Time to first",
+              "Entrances",
+              "Shocks",
+              "Thigmotaxis",
+              "Directional mean",
+              "Circular variance",
+              "Mean distance from center",
+              "Maximum time of immobility",
+              "Proportion of time moving",
+              "Real minimum time",
+              "Real maximum time"}
         for name, parameter in ParametersCM().items():
-            self[name] = parameter
-##            if name not in ("Room frame filename",):
-##                self[name] = parameter
-
-
+            if name in ra:
+                self[name] = parameter
+        
+        self["Time in sectors"] = Par("getAngleBoxes", "advanced", {
+            "width": (Opt('WidthParTimeInSectors', 90, ['int', 'float']),
+                      "Width of sector [in degrees]"),
+            "center": (Opt('CenterParTimeInSectors', 0, ['int', 'float']),
+                       "Center of sector [in degrees]")
+            })
 
+        self["Median speed after shock"] = Par("getSpeedAfterShock", "experimental", {
+            "after": (Opt('SkipSpeedAfterShock', 25, ['int']),
+                      "Computed from every [in rows]")
+            })    
 
+        self["Robot filename"] = Par("getRoomName", "info", {})
 
 
 

Stuff/Modules/ra.py

@@ -24,6 +24,7 @@
 
 
 from cm import CM
+from funcs import median
 
 
 class RA(CM):
@@ -73,9 +74,9 @@ def _setRoomName(self, name): # ZMENIT rob na robot???
         if name == "auto":
             splitname = os.path.split(self.nameA)
             if splitname[1].count("Rat") > 0:
-                self.nameR = os.path.join(splitname[0], splitname[1].replace("Rat", "Rob"))
+                self.nameR = os.path.join(splitname[0], splitname[1].replace("Rat", "Robot"))
             elif splitname[1].count("rat") > 0:
-                self.nameR = os.path.join(splitname[0], splitname[1].replace("rat", "rob"))
+                self.nameR = os.path.join(splitname[0], splitname[1].replace("rat", "robot"))
             else:
                 raise IOError
         else:
@@ -134,3 +135,40 @@ def _removalCondition(self, row, i, before, reflection):
                     row + i in self.interpolated))
 
 
+    def getCircularVariance(self, *args, indices = slice(7,9), **kwargs):
+        return super().getCircularVariance(*args, indices = indices, **kwargs)
+
+    def getDirectionalMean(self, *args, indices = slice(7,9), **kwargs):
+        return super().getDirectionalMean(*args, indices = indices, **kwargs)
+
+
+    def getSpeedAfterShock(self, time = 20, startTime = 0, after = 25):
+        "returns median speed that the rat travelled 'after' points after shock"
+        time = time * 60000
+        start = self.findStart(startTime)
+
+        shocks = [content[0] for content in self.data[start:] if
+                  content[5] == 2 and content[1] < time]
+        if shocks:
+            selected = [shocks[0]]
+            prev = shocks[0]
+            for shock in shocks[1:]:
+                if shock - prev > after:
+                    selected.append(shock)
+                prev = shock
+        else:
+            return "NA"
+
+        speeds = []
+        for shock in selected:
+            if len(self.data) <= shock + after:
+                break
+            speeds.append(self._computeSpeed(self.data[shock], self.data[shock + after]))
+
+        return format(median(speeds), "0.2f")
+
+    def getAngleBoxes(self, *args, indices = slice(7,9), **kwargs):
+        return super().getAngleBoxes(*args, indices = indices, **kwargs)
+
+
+        

Stuff/Modules/version.py

@@ -21,7 +21,7 @@ def version():
     return ['0', '4', '0']
 
 def date():
-    return "26 April 2014"
+    return "27 April 2014"
 
 def copyleft():
     return "2013, 2014"