added strategies function, add tags tool

Stuff/Modules/cm.py

@@ -949,10 +949,10 @@ def removeReflections(self, points = None, deleteSame = True, bothframes = True)
     
 
     def countBadPoints(self, time = 20, startTime = 0):
+        start = self.findStart(startTime)
+        
         time *= 60000
         startTime *= 60000
-
-        start = self.findStart(startTime)
         
         count = 0
         bad = 0
@@ -965,9 +965,8 @@ def countBadPoints(self, time = 20, startTime = 0):
                     bad += 1
 
         proportion = (bad / count) * 100
-        
-        return round(proportion, 2)
-
+        return format(proportion, "0.2f")
+    
 
     def countOutsidePoints(self, time = 20, startTime = 0, distance = 1):
         "returns number of data points where an animal was outside the arena"
@@ -1025,6 +1024,7 @@ def findStart(self, startTime):
 
 
     def recognizeAfterShockStrategy(self, i0, i1, minAngle):
+        "characterizes strategy after a shock"
         cx, cy = self.centerX, self.centerY
         x0, y0 = self.data[i0][self.indices]
         x1, y1 = self.data[i1][self.indices]
@@ -1041,6 +1041,7 @@ def recognizeAfterShockStrategy(self, i0, i1, minAngle):
             
         
     def recognizeStrategy(self, i0, i1, minSpeed, percentSize):
+        "characterizes strategy in absence of a shock"
         x0, y0 = self.data[i0][self.indices]
         x1, y1 = self.data[i1][self.indices]
         t0, t1 = self.data[i0][1], self.data[i1][1]
@@ -1066,8 +1067,19 @@ def recognizeStrategy(self, i0, i1, minSpeed, percentSize):
         
 
     def getStrategies(self, time = 20, startTime = 0, rows = 25, minSpeed = 10, minAngle = 7,
-                      borderPercentSize = 50, indices = False):
-        i1, t1 = self.data[self.findStart(time)][0:2]
+                      borderPercentSize = 50, indices = False, summary = True):
+        """characterizes strategies in a given time interval
+            rows - number of rows in a bin
+            minSpeed - minimal speed counted as movement in absence of shock
+            minAngle - minimal angular speed counted as movement after shock
+            borderPercentSize - boundary for center area
+            indices - return indices or times
+            summary - return summary for results or dict with indices or times
+        """
+        try:
+            i1, t1 = self.data[self.findStart(time)][0:2]
+        except IndexError:
+            i1, t1 = self.data[-1][0:2]
         time = time * 60000
         start = self.findStart(startTime)
         i0, t0 = self.data[start][0:2]
@@ -1120,11 +1132,63 @@ def getStrategies(self, time = 20, startTime = 0, rows = 25, minSpeed = 10, minA
         else:
             t = self.data[i1 - 1][1]
             strategies[lastStrategy].append((beginning, t))       
+
+        if summary:
+            order = ("reaction_counterclockwise", "reaction_clockwise", "no_reaction",
+                     "counterclockwise", "clockwise", "immobile", "center")
+            times = [sum([i[1] - i[0] for i in strategies[s]]) for s in order]
+            sumOfTimes = sum(times)
+            proportions = [format(time / sumOfTimes, "0.4f") for time in times]
+            return "|".join(proportions)
+        else:
+            return strategies
+
+
+    def getProportionOfStrategies(self, time = 20, startTime = 0, numerator = [], denominator = []):
+        "returns proportion of times of strategies in nominator and denominator"
+        strategies = self.getStrategies(time, startTime)
+        num = 0
+        denom = 0
+        for strategy in numerator:
+            num += sum([i[1] - i[0] for i in strategies[strategy]])
+        for strategy in denominator:
+            denom += sum([i[1] - i[0] for i in strategies[strategy]])
+
+        return format(num / denom, "0.3f")
+
+
+    def getRotationSpeed(self, time = 20, startTime = 0, rows = 25):
+        "returns speed of arena rotation in degrees per minute"
+        start = self.findStart(startTime)
+        end = self.findStart(time)
+
+        cx, cy = self.centerX, self.centerY
+        speeds = []
+
+        ax0, ay0 = self.data[start][7:9]
+        t0, rx0, ry0 = self.data[start][1:4]        
+        for content in self.data[(start+rows):end:rows]:
+            ax1, ay1 = content[7:9]
+            t1, rx1, ry1 = content[1:4]
+        
+            arenaAngle = ((degrees(atan2(ax1 - cx, ay1 - cy + 0.0000001)) -
+                           degrees(atan2(ax0 - cx, ay0 - cy + 0.0000001)) + 180) % 360) - 180
+            roomAngle = ((degrees(atan2(rx1 - cx, ry1 - cy + 0.0000001)) -
+                          degrees(atan2(rx0 - cx, ry0 - cy + 0.0000001)) + 180) % 360) - 180
+            speeds.append(((roomAngle - arenaAngle) * 60000) / (t1 - t0))
+
+            ax0, ay0, t0, rx0, ry0 = ax1, ay1, t1, rx1, ry1
+
+        if speeds:
+            return format(sum(speeds) / len(speeds), "0.1f")
+        else:
+            return "NA"
+            
             
-        return strategies
 
 
 def main():
+    return
     start = 9
     end = 12
     diff = end - start

Stuff/Modules/controller.py

@@ -553,6 +553,7 @@ def assessImportance(self, cm, control, file):
             value = results
 
         elif method == "Bad Points":
+            results = float(results)
             if results > 10:
                 importance = "Problem"
             elif results > 5:

Stuff/Modules/explorer.py

@@ -27,6 +27,7 @@
 import os.path
 
 
+from showtracks import ShowTracks
 from filestorage import FileStorageFrame
 from commonframes import TimeFrame, returnName
 from image import SVG
@@ -995,13 +996,15 @@ def graphPopUp(self, event):
     def parametersPopUp(self, event):
         "shows menu for selection of parameters to be shown in parameters frame"      
         menu = Menu(self, tearoff = 0)
-        notAvailable = ["Total distance", "Entrances", "Time in sectors", "Time in quadrants"]
+        notAvailable = ["Total distance", "Entrances", "Time in sectors", "Time in quadrants",
+                        "Strategies"]
+        available = ["Bad points", "Outside points", "Reflections"]
         menu.add_radiobutton(label = "Don't show anything",
                              variable = self.selectedParameter, value = "nothing",
                              command = self._changedSelectedParameter)
         menu.add_separator()
         for name, par in m.parameters.items():
-            if par.group not in ["info", "custom"] and name not in notAvailable:
+            if par.group not in ["info", "custom"] and name not in notAvailable or name in available:
                 menu.add_radiobutton(label = 'Show {}'.format(name.lower()),
                                      variable = self.selectedParameter, value = name,
                                      command = self._changedSelectedParameter)
@@ -1024,7 +1027,8 @@ def _changedSelectedParameter(self):
                            "Time": "t.",
                            "time": "t.",
                            "Circular": "Circ.",
-                           "variance": "var."
+                           "variance": "var.",
+                           "points": "pts."
                            }
                 for key, value in mapping.items():
                     name = name.replace(key, value)
@@ -1324,6 +1328,11 @@ def refresh(self):
         "refreshes the tree after adding a comment"
         self.root._showComment(self.selected)
         self.drawTree(selected = self.selected)
+
+
+    def _showTrack(self, file):
+        "opens ShowTracks; accessed by right click on file"
+        ShowTracks(self, self.fileStorage.arenafiles, file)
             
 
     def popUp(self, event):
@@ -1340,6 +1349,7 @@ def popUp(self, event):
             else:
                 menu.add_command(label = "Add tag", command = lambda: self.tagFun(index =
                                                                                   int(item)))
+            menu.add_command(label = "Show track", command = lambda: self._showTrack(file))
 
             menu.post(event.x_root, event.y_root)
 

Stuff/Modules/graphs.py

@@ -260,7 +260,7 @@ def distance(line):
             strategies = cm.getStrategies(time = self.maxTime / 60000,
                                           startTime = self.minTime / 60000,
                                           rows = rows, minSpeed = minSpeed, minAngle = minAngle,
-                                          borderPercentSize = borderPercentSize)
+                                          borderPercentSize = borderPercentSize, summary = False)
             colors = {"counterclockwise": "green",
                       "clockwise": "dodger blue",
                       "no_reaction": "deep pink",

Stuff/Modules/menu.py

@@ -31,7 +31,7 @@
 from optionwrite import optionWrite
 from optionget import optionGet
 from helpcmm import HelpCM
-from tools import saveFileStorage, loadFileStorage
+from tools import saveFileStorage, loadFileStorage, addTags
 from window import placeWindow
 from filestorage import FileStorage
 import version
@@ -50,14 +50,14 @@ def __init__(self, root):
 
         self.menu_file = Menu(self)
         self.menu_options = Menu(self)
-        #self.menu_tools = Menu(self) # for future
+        self.menu_tools = Menu(self)
         self.menu_task = Menu(self)
         self.menu_help = Menu(self)
         
         menuWidth = 8
         self.add_cascade(menu = self.menu_file, label = "{:^{}}".format("File", menuWidth))
         self.add_cascade(menu = self.menu_options, label = "{:^{}}".format("Options", menuWidth))
-        #self.add_cascade(menu = self.menu_tools, label = "{:^{}}".format("Tools", menuWidth))
+        self.add_cascade(menu = self.menu_tools, label = "{:^{}}".format("Tools", menuWidth))
         self.add_cascade(menu = self.menu_task, label = "{:^{}}".format("Task", menuWidth))
         self.add_cascade(menu = self.menu_help, label = "{:^{}}".format("Help", menuWidth))
 
@@ -73,6 +73,7 @@ def __init__(self, root):
         self.menu_options.add_command(label = "General options", command = self.generalOptions)
         self.menu_options.add_separator()
         self.menu_options.add_command(label = "Reset all options", command = self.resetOptions)
+        self.menu_tools.add_command(label = "Add tags", command = self.addTagsHelper)
         for task, name in m.fullname.items():
             self.menu_task.add_radiobutton(label = name, variable = self.task, value = task,
                                            command = self.changedTask)
@@ -107,6 +108,13 @@ def saveLoadedFiles(self):
     def loadSavedFiles(self):
         loadFileStorage(self.root)
 
+    def addTagsHelper(self):
+        try:
+            addTags(self.root)
+        except Exception as e:
+            messagebox.showinfo(message = "Sorry, something went wrong.", detail = e,
+                                title = "Error", icon = "error")
+
     def resetOptions(self):
         text = ("Are you sure that you want to reset all options (including parameter settings)"
                 " to default settings?")
@@ -278,7 +286,9 @@ def checkNewVersion(self):
         newVersion = self.returnSiteContent(url).split(".")
         for i in range(3):
             if int(newVersion[i]) > int(self.version[i]):
-                return newVersion        
+                return newVersion
+            elif int(newVersion[i]) < int(self.version[i]):
+                return None
         else:
             return None
 

Stuff/Modules/parameters.py

@@ -107,12 +107,13 @@ def __init__(self):
             "borderPercentSize": (Opt('borderPercentSizeStrategies', 50, ['int', 'float']),
                                   "Annulus width [in percents]")
             })
-        self["Bad points"] = Par("countBadPoints", "info", {})
+        self["Percent bad points"] = Par("countBadPoints", "info", {})
         self["Reflections"] = Par("countReflections", "info", {})
         self["Outside points"] = Par("countOutsidePoints", "info", {
             "distance": (Opt('OutsidePointsDistance', 1, 'int'),
                      "Distance from margin counted [in pixels]"),
             })
+        self["Rotation speed"] = Par("getRotationSpeed", "info", {})
 
 
         #self.findParameters()
@@ -223,7 +224,7 @@ class ParametersCMSF(OrderedDict):
     def __init__(self):
         super().__init__()
         for name, parameter in ParametersCM().items():
-            if name not in ("Room frame filename",):
+            if name not in ("Room frame filename", "Rotation speed"):
                 self[name] = parameter
 
 

Stuff/Modules/processor.py

@@ -172,7 +172,7 @@ def processFun(self):
                 if not self.useBatchTimeVar.get():
                     methods[name] = [methodcaller(par.method, startTime = startTime,
                                                   time = time, **options)]
-                elif par.group != "info":
+                elif par.group != "info" or name == "Rotation speed":
                     methods[name] = [methodcaller(par.method, startTime = times[0],
                                                   time = times[1], **options)
                                      for times in batchTime]

Stuff/Modules/tools.py

@@ -301,7 +301,32 @@ def _roundDecimal(self, d):
             return int(d)
         else:
             return round(float(d), 3)
+
+
+def addTags(root):
+    "adds tags to files loaded from a text file"
+    # currently is not safe to possible problems
+    infile = askopenfilename(filetypes = [("Text", "*.txt")], initialdir = os.getcwd())
+    with open(infile) as f:
+        for line in f:
+            basename = os.path.basename(line.split()[0].strip())
+            for arenafile in m.fs[m.mode]:
+                if os.path.basename(arenafile) == basename:
+                    if arenafile not in m.fs[m.mode].tagged:
+                        m.fs[m.mode].tagged.append(arenafile)
+                    break
+    root.checkProcessing()
+                    
         
+       
+
+
+
+
+
+
+
+    
 
 
 

Stuff/Modules/version.py

@@ -21,7 +21,7 @@ def version():
     return ['0', '4', '0']
 
 def date():
-    return "9 August 2014"
+    return "10 August 2014"
 
 def copyleft():
     return "2013, 2014"