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[trackingdata] implement a bendedness function

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This commit is contained in:
Jan Grewe 2025-02-14 10:21:03 +01:00
parent 6d288aace1
commit f62c7c43e0
1 changed files with 22 additions and 8 deletions
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fixtracks/utils/trackingdata.py
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@ -171,16 +171,30 @@ class TrackingData(QObject):
return orientations return orientations
def bendedness(self, bodyaxis=None): def bendedness(self, bodyaxis=None):
"""
Calculate the bendedness of the body axis.
Parameters
----------
bodyaxis : list of int, optional
Indices of the body axis coordinates to consider. If None, defaults to [0, 1, 2, 5].
Returns
-------
numpy.ndarray
Array of mean absolute deviations of the body axis points from the head-tail vector.
"""
if bodyaxis is None: if bodyaxis is None:
bodyaxis = [0, 1, 2, 5] bodyaxis = [0, 1, 2, 5]
bodycoords = self.coordinates()[:, bodyaxis, :] bodycoords = self.coordinates()[:, bodyaxis, :]
bodycoords = np.concat((bodycoords, np.zeros((bodycoords.shape[0], len(bodyaxis), 1))), axis=2)
head_tail_vector = bodycoords[:, -1, :] - bodycoords[:, 0, :] head_tail_vector = bodycoords[:, -1, :] - bodycoords[:, 0, :]
head_tail_vector = head_tail_vector[:, np.newaxis ,:] # cross-product only defined in space, not in 2D point_axis_vector = bodycoords[:,:,:] - bodycoords[:, 0, :][:,np.newaxis,:]
head_tail_length = np.linalg.norm(head_tail_vector, axis=1, keepdims=True) # pythagoras, length of head- tail connection htv = head_tail_vector[:,np.newaxis, :]
point_axis_vectors = bodycoords - head_tail_vector # Pythagoras, length of head- tail connection
deviations = np.cross(head_tail_vector, point_axis_vectors)/head_tail_length head_tail_length = np.linalg.norm(head_tail_vector, axis=1, keepdims=True)
deviation = np.mean(deviations, axis=1) deviations = np.cross(htv, point_axis_vector)[:,:,-1] / head_tail_length
return deviation deviations = np.mean(np.abs(deviations), axis=1)
return deviations
def __getitem__(self, key): def __getitem__(self, key):
return self._data[key] return self._data[key]
@ -236,8 +250,8 @@ def main():
lengths = data.animalLength() lengths = data.animalLength()
frames = data["frame"] frames = data["frame"]
tracks = data["track"] tracks = data["track"]
bendedness = data.bendedness()
# bendedness = data.bendedness()
embed() embed()
tracks = data["track"] tracks = data["track"]