import tweezer.plotting as plt
import tweezer.force_calc as forcecalc
import tweezer.calibration as cal
# Example of unpacking the data, and plotting all plot functios
# Get data from drive (under Vzorci/1 static particle) and save it in examples folder
#script_dir = os.path.dirname(__file__) # absolute dir the script is in
file_name = 'test.dat' # name of the dat file
#path = os.path.join(script_dir, file_name)
path = file_name
particles = 1
time, traps, trajectories = plt.read_file(path, particles)
averaging_time = 0.1
for i in range(particles):
data = trajectories[:, i * 2:(i + 1) * 2]
trap = traps[:, i * 3:(i + 1) * 3]
# Example of using trajectory plot
plt.trajectory_plot(time, data, averaging_time)
# Example of using calibration plots
plt.calibration_plots(time, data, averaging_time)
# Example of using potential plot
plt.potential_plot(time, data, averaging_time)
# Calculate forces
k_estimated, phi_estimated, center_estimated = cal.calibrate(
time, data, averaging_time)
f, m = forcecalc.force_calculation(time, data, trap, k_estimated, 300)
# Plot force
plt.force_plot(time, f)
images = pims.ImageSequence(output_folder + "/*.png")
features = trackpy.batch(images, 7, minmass=50, invert=False)
tracks = trackpy.link_df(features, 15, memory=10)
all_traps = [trap_data,[0,0,-1],[0,0,-1],[0,0,-1]]
traps = [[all_traps[i][:] for j in range(num_points)]for i in range(4)]
tracking.save_tracked_data_pandas(output_folder + "/tracked_data.dat",images, tracks, times, laser_powers, traps)
#4: Read .dat file back into the program
times,traps,trajectory = plotting.read_file(output_folder + "/tracked_data.dat",1)
#5: Calibration, removing offset etc.
trap_offsets = offset.single_particle_offset(traps[:,0:2],trajectory[:,::-1]) #should be close to 0 since trap isn't shifted
coeffs_estimate,rotation_angle,_ = calibration.calibrate(times,trajectory,0.005)
#6: Force analysis
print("Trap offsets:", trap_offsets)
print("Estimate of trap coefficients:", coeffs_estimate)
print("Trap rotation angle", rotation_angle)
forces,mean_forces = force_calc.calculate(times,trajectory[:,1::-1],traps[:,0:2],coeffs_estimate,rotation_angle)
#7: Create graphs
plotting.trajectory_plot(times,trajectory[:,1::-1],0.005)
plotting.force_plot(times,forces,mean_forces)
def test_calibrate(self):
trajectory = gen.generate([self.kx, self.ky], phi = self.phi)
t = gen.generate_time()
result = cal.calibrate(t, trajectory)
self.assertTrue(np.allclose(result[0], self.expected_result[0], atol=1e-6) and
np.allclose(-result[1], self.expected_result[1], atol=0.1))