latest changes

etrack/arena.py

@@ -5,7 +5,7 @@ import matplotlib.patches as patches
 from skimage.draw import disk
 
 from .util import RegionShape, AnalysisType, Illumination
-
+from IPython import embed
 
 class Region(object):
 
@@ -30,6 +30,14 @@ class Region(object):
 
         return mask
 
+    @property
+    def name(self):
+        return self._name
+
+    @property
+    def inverted_y(self):
+        return self._inverted_y
+
     @property
     def _max_extent(self):
         if self._shape_type == RegionShape.Rectangular:
@@ -127,7 +135,7 @@ class Region(object):
         return indices
 
     def time_in_region(self, x, y, time, analysis_type=AnalysisType.Full):
-        """_summary_
+        """Returns the entering and leaving times at which the animal entered and left a region. In case the animal was not observed after entering this region (for example when hidden in a tube) the leaving time is the maximum time entry.
 
         Parameters
         ----------
@@ -148,7 +156,7 @@ class Region(object):
         indices = self.points_in_region(x, y, analysis_type)
         if len(indices) == 0:
             return np.array([]), np.array([])
-
+  
         diffs = np.diff(indices)
         if len(diffs) == sum(diffs):
             entering = [time[indices[0]]]
@@ -199,10 +207,9 @@ class Arena(Region):
             region = Region(origin, extent, name=name, region_shape=shape_type, parent=self)
         else:
             region._parent = self
-        if self.fits(region):
+        if ~self.fits(region):
-            self.regions[name] = region
+            print(f"Warning! Region {region.name} with size {region.position} does fit into {self.name} with size {self.position}!")
-        else:
+        self.regions[name] = region
-            Warning(f"Region {region} fits not! Not added to the list of regions!")
 
     def remove_region(self, name):
         if name in self.regions:
@@ -217,9 +224,13 @@ class Arena(Region):
             axis = fig.add_subplot(111)
         axis.add_patch(self.patch())
         axis.set_xlim([self._origin[0], self._max_extent[0]])
-        axis.set_ylim([self._origin[1], self._max_extent[1]])
+
+        if self.inverted_y:
+            axis.set_ylim([self._max_extent[1], self._origin[1]])
+        else:
+            axis.set_ylim([self._origin[1], self._max_extent[1]])
         for r in self.regions:
-            axis.add_patch(r.patch())
+            axis.add_patch(self.regions[r].patch())
         return axis
 
     def region_vector(self, x, y):
@@ -250,6 +261,13 @@ class Arena(Region):
             tmp[r] = indices
         return tmp
 
+    def __getitem__(self, key):
+        if isinstance(key, (str)):
+            return self.regions[key]
+        else:
+            return self.regions[self.regions.keys()[key]]
+
+
 if __name__ == "__main__":
     a = Arena((0, 0), (1024, 768), name="arena", arena_shape=RegionShape.Rectangular)
     a.add_region("small rect1", (0, 0), (100, 300))

etrack/io/nixtrack_data.py

@@ -10,12 +10,14 @@ from IPython import embed
 
 class NixtrackData(object):
     
-    def __init__(self, results_file, crop=(0, 0)) -> None:
+    def __init__(self, filename, crop=(0, 0)) -> None:
         """
         If the video data was cropped before tracking and the tracked positions are with respect to the cropped images, we may want to correct for this to convert the data back to absolute positions in the video frame.
 
         Parameters
         ----------
+        filename : str
+            full filename
         crop : 2-tuple
             tuple of (xoffset, yoffset)
 
@@ -23,13 +25,13 @@ class NixtrackData(object):
         ------
         ValueError if crop value is not a 2-tuple
         """
-        if not os.path.exists(results_file):
+        if not os.path.exists(filename):
-            raise ValueError("File %s does not exist!" % results_file)
+            raise ValueError("File %s does not exist!" % filename)
         if not isinstance(crop, tuple) or len(crop) < 2:
             raise ValueError("Cropping info must be a 2-tuple of (x, y)")
-        self._file_name = results_file
+        self._file_name = filename
         self._crop = crop
-        self._dataset = nt.Dataset(self._file_name, nt.util.FileMode.ReadOnly)
+        self._dataset = nt.Dataset(self._file_name)
         if not self._dataset.is_open:
             raise ValueError(f"An error occurred opening file {self._file_name}! File is not open!")
 
@@ -50,14 +52,20 @@ class NixtrackData(object):
     def tracks(self):
         return self._dataset.tracks
 
-    def track(self, track=None, bodypart=0):
+    def track(self, bodypart=0, fps=None):
         if isinstance(bodypart, nb.Number):
             bp = self.bodyparts[bodypart]
-        elif isinstance(bodypart, str) and bodypart in self.bodyparts:
+        elif isinstance(bodypart, (str)) and bodypart in self.bodyparts:
             bp = bodypart
         else:
             raise ValueError(f"Body part {bodypart} is not a tracked node!")
-        positions, time, iscore, nscore = self._dataset.positions(node=bp, axis_type=nt.AxisType.Time)
+        if fps is None:
-        embed()
+            fps = self._dataset.fps
 
-        return TrackingData(positions[:, 0], positions[:, 1], time, nscore, bp, fps=self._dataset.fps)
+        positions, time, _, nscore = self._dataset.positions(node=bp, axis_type=nt.AxisType.Time)
+        valid = ~np.isnan(positions[:, 0])
+        positions = positions[valid,:]
+        time = time[valid]
+        score = nscore[valid]
+
+        return TrackingData(positions[:, 0], positions[:, 1], time, score, bp, fps=fps)