# scn.set_frame_range((param.first, param.last))
## Hitao linking criteria -----------------------------------------------------
#distThresh=0.005;
#maxDt=1;
#minLength=3;
distThresh = 0.003
maxDt = 0.025
minLength = 3
# length of elemnts in the trajs
# Though this won't be necessary if you don't save the short ones at all in the
# HDF conversion.
long_trajects = it.ifilter(lambda trj: len(trj) > minLength,
scn.iter_trajectories())
# Keyed by trajid, value is a tuple (id, dist) where id is the best candidate
# trajectory for linking, and dist is the average-distance measure for this
# pair (the measure to beat)
links = {}
back_links = {}
for trj1, trj2 in it.combinations(long_trajects, 2):
dt = (trj2.time(0) - trj1.time(-1)) / frate
if not (0 < dt <= maxDt):
continue
master_id = trj1.trajid()
slave_id = trj2.trajid()
links.setdefault(master_id, (None, distThresh))
class TestScene(unittest.TestCase):
def setUp(self):
"""
There are 3 trajectories of 4 frames each, each going along a separate
axis.
"""
tmpl = "tests/testing_fodder/three_trajects_simple.h5"
self.scene = Scene(tmpl)
# ptv_is files are in [mm], [mm/s], etc.
correct_pos = np.r_[0.1, 0.2, 0.3, 0.5] / 1000.
correct_vel = np.r_[0.1, 0.1, 0.2, 0.] / 1000.
correct_accel = np.r_[0., 0.1, 0., 0.] / 1000.
t = np.r_[1:5] + 10000
self.correct = []
for axis in [0, 1, 2]:
pos = np.zeros((4, 3))
pos[:, axis] = correct_pos
vel = np.zeros((4, 3))
vel[:, axis] = correct_vel
accel = np.zeros((4, 3))
accel[:, axis] = correct_accel
self.correct.append(
Trajectory(pos, vel, t, len(self.correct), accel=accel))
def test_keys(self):
"""Reading known available keys with the needed exclusions"""
correct_keys = ['velocity', 'pos', 'accel']
self.failUnlessEqual(self.scene.keys(), correct_keys)
def test_iter_trajectories(self):
"""Iterating trajectories and getting correct Trajectory objects"""
trjs = [tr for tr in self.scene.iter_trajectories()]
self.failUnlessEqual(len(trjs), len(self.correct))
for trj, correct in zip(trjs, self.correct):
nptest.assert_array_almost_equal(trj.pos(), correct.pos())
nptest.assert_array_almost_equal(trj.velocity(),
correct.velocity())
nptest.assert_array_almost_equal(trj.accel(), correct.accel())
nptest.assert_array_almost_equal(trj.time(), correct.time())
self.failUnlessEqual(trj.trajid(), correct.trajid())
def test_iter_trajectories_subrange(self):
"""Iterating trajectories in part of the frame range."""
self.scene.set_frame_range((10002, 10004))
trjs = [tr for tr in self.scene.iter_trajectories()]
self.failUnlessEqual(len(trjs), len(self.correct))
for trj, correct in zip(trjs, self.correct):
nptest.assert_array_almost_equal(trj.pos(), correct.pos()[1:-1])
nptest.assert_array_almost_equal(trj.velocity(),
correct.velocity()[1:-1])
nptest.assert_array_almost_equal(trj.accel(),
correct.accel()[1:-1])
nptest.assert_array_almost_equal(trj.time(), correct.time()[1:-1])
self.failUnlessEqual(trj.trajid(), correct.trajid())
def test_iter_frames(self):
"""Iterating the HDF files by frames, and getting correct ParticleSnapshot objects"""
schm = self.correct[0].schema()
correct_frames = [take_snapshot(self.correct, frm, schm) \
for frm in xrange(10001, 10005)]
frames = [frm for frm in self.scene.iter_frames()]
self.failUnlessEqual(len(frames), len(correct_frames))
for frm, correct in zip(frames, correct_frames):
nptest.assert_array_almost_equal(frm.pos(), correct.pos())
nptest.assert_array_almost_equal(frm.velocity(),
correct.velocity())
nptest.assert_array_almost_equal(frm.accel(), correct.accel())
nptest.assert_array_almost_equal(frm.trajid(), correct.trajid())
self.failUnlessEqual(frm.time(), correct.time())
def test_iter_frames_subrange(self):
"""Iterating frames subrange"""
self.scene.set_frame_range((10002, 10004))
schm = self.correct[0].schema()
correct_frames = [take_snapshot(self.correct, frm, schm) \
for frm in xrange(10002, 10004)]
frames = [frm for frm in self.scene.iter_frames()]
self.failUnlessEqual(len(frames), len(correct_frames))
for frm, correct in zip(frames, correct_frames):
nptest.assert_array_almost_equal(frm.pos(), correct.pos())
nptest.assert_array_almost_equal(frm.velocity(),
correct.velocity())
nptest.assert_array_almost_equal(frm.accel(), correct.accel())
nptest.assert_array_almost_equal(frm.trajid(), correct.trajid())
self.failUnlessEqual(frm.time(), correct.time())
def test_collect(self):
"""Slicing the file by keys or expressions"""
v = self.scene.collect(['velocity'])[0]
self.failUnlessEqual(v.shape, (12, 3))
v = v.reshape(3, 4, 3)
nptest.assert_array_almost_equal(v[0, :, 0], v[1, :, 1])
nptest.assert_array_almost_equal(v[0, :, 0], v[2, :, 2])
class TestScene(unittest.TestCase):
def setUp(self):
"""
There are 3 trajectories of 4 frames each, each going along a separate
axis.
"""
tmpl = "tests/testing_fodder/three_trajects_simple.h5"
self.scene = Scene(tmpl)
# ptv_is files are in [mm], [mm/s], etc.
correct_pos = np.r_[0.1, 0.2, 0.3, 0.5] / 1000.
correct_vel = np.r_[0.1, 0.1, 0.2, 0.] / 1000.
correct_accel = np.r_[0., 0.1, 0., 0.] / 1000.
t = np.r_[1:5] + 10000
self.correct = []
for axis in [0, 1, 2]:
pos = np.zeros((4, 3))
pos[:,axis] = correct_pos
vel = np.zeros((4, 3))
vel[:,axis] = correct_vel
accel = np.zeros((4, 3))
accel[:,axis] = correct_accel
self.correct.append(Trajectory(pos, vel, t, len(self.correct),
accel=accel))
def test_keys(self):
"""Reading known available keys with the needed exclusions"""
correct_keys = ['velocity', 'pos', 'accel']
self.failUnlessEqual(self.scene.keys(), correct_keys)
def test_iter_trajectories(self):
"""Iterating trajectories and getting correct Trajectory objects"""
trjs = [tr for tr in self.scene.iter_trajectories()]
self.failUnlessEqual(len(trjs), len(self.correct))
for trj, correct in zip(trjs, self.correct):
nptest.assert_array_almost_equal(trj.pos(), correct.pos())
nptest.assert_array_almost_equal(trj.velocity(), correct.velocity())
nptest.assert_array_almost_equal(trj.accel(), correct.accel())
nptest.assert_array_almost_equal(trj.time(), correct.time())
self.failUnlessEqual(trj.trajid(), correct.trajid())
def test_iter_trajectories_subrange(self):
"""Iterating trajectories in part of the frame range."""
self.scene.set_frame_range((10002, 10004))
trjs = [tr for tr in self.scene.iter_trajectories()]
self.failUnlessEqual(len(trjs), len(self.correct))
for trj, correct in zip(trjs, self.correct):
nptest.assert_array_almost_equal(trj.pos(), correct.pos()[1:-1])
nptest.assert_array_almost_equal(trj.velocity(), correct.velocity()[1:-1])
nptest.assert_array_almost_equal(trj.accel(), correct.accel()[1:-1])
nptest.assert_array_almost_equal(trj.time(), correct.time()[1:-1])
self.failUnlessEqual(trj.trajid(), correct.trajid())
def test_iter_frames(self):
"""Iterating the HDF files by frames, and getting correct ParticleSnapshot objects"""
schm = self.correct[0].schema()
correct_frames = [take_snapshot(self.correct, frm, schm) \
for frm in xrange(10001, 10005)]
frames = [frm for frm in self.scene.iter_frames()]
self.failUnlessEqual(len(frames), len(correct_frames))
for frm, correct in zip(frames, correct_frames):
nptest.assert_array_almost_equal(frm.pos(), correct.pos())
nptest.assert_array_almost_equal(frm.velocity(), correct.velocity())
nptest.assert_array_almost_equal(frm.accel(), correct.accel())
nptest.assert_array_almost_equal(frm.trajid(), correct.trajid())
self.failUnlessEqual(frm.time(), correct.time())
def test_iter_frames_subrange(self):
"""Iterating frames subrange"""
self.scene.set_frame_range((10002, 10004))
schm = self.correct[0].schema()
correct_frames = [take_snapshot(self.correct, frm, schm) \
for frm in xrange(10002, 10004)]
frames = [frm for frm in self.scene.iter_frames()]
self.failUnlessEqual(len(frames), len(correct_frames))
for frm, correct in zip(frames, correct_frames):
nptest.assert_array_almost_equal(frm.pos(), correct.pos())
nptest.assert_array_almost_equal(frm.velocity(), correct.velocity())
nptest.assert_array_almost_equal(frm.accel(), correct.accel())
nptest.assert_array_almost_equal(frm.trajid(), correct.trajid())
self.failUnlessEqual(frm.time(), correct.time())