def test_length_one_msd_nd():
N = 1
ND = 4
data = np.ones((N, ND))
reference_msd = np.zeros_like(data[:, 0])
computed_msd = tidynamics.msd(data)
assert np.allclose(reference_msd, computed_msd)
def MSD(df, conversion="x"):
"""
Computes the Mean Square Displacement (MSD)
which is the mean squared difference between the x or y coordinates of the fronts
--------------------------
Parameters:
--------------------------
df : pandas dataframe which contains x or y coordinates for different frames
conversion : string variable to convert pixels in micrometers, because the conversion is different for
the x and y axes
----------------------------
Returns a dataframe with the MSD
References:
-----------------
[1]http://lab.pdebuyl.be/tidynamics/
"""
#conversion from pixels to micrometers
if conversion == "y":
df = df / 1200 * 633
else:
df = df / 1600 * 844
msd = []
for i in range(len(df)):
#computes the msd for the x or y coordinates between the different frames
msd.append(tidynamics.msd(df.T[i]))
msd = pd.DataFrame(msd)
return msd
def test_random_walk_msd():
def brute_force_msd(pos):
"""
Compute the mean-square displacement with an explicit loop over all
time intervals.
"""
pos = np.asarray(pos)
if pos.ndim == 1:
pos = pos.reshape((-1, 1))
trajectory_length = len(pos)
msd = np.zeros(trajectory_length)
msd_count = np.zeros(trajectory_length)
for i in range(trajectory_length):
for j in range(i, trajectory_length):
msd[j - i] += np.sum((pos[i] - pos[j])**2)
msd_count[j - i] += 1
msd = msd / msd_count
return msd
N = 200
N_dim = 2
time = np.arange(N)
# Generate steps of value +/- 1
steps = -1 + 2 * np.random.randint(0, 2, size=(N, N_dim))
# Compute random walk position
walk = np.cumsum(steps, axis=0)
tidynamics_msd = tidynamics.msd(walk)
comparison_msd = brute_force_msd(walk)
assert np.allclose(tidynamics_msd, comparison_msd)
def test_cross_disp_1():
N = 100
D = 4
data = np.random.random(size=(N, D))
cross_disp = tidynamics.cross_displacement(data)
for i in range(D):
assert np.allclose(cross_disp[i][i], tidynamics.msd(data[:,i]))
def _conclude(self):
self.lagtimes = self.frames * self.dt
for lipid_index in range(self.membrane.n_residues):
self.msd[lipid_index] = tidynamics.msd(self.lipid_com_pos[lipid_index])
# MSD must start at 0
self.msd[:, 0] = 0.0
# Convert A^2 to nm^2
self.msd /= 100
return None
def _conclude_fft(self): # with FFT, np.float64 bit prescision required.
r""" Calculates the MSD via the FCA fast correlation algorithm.
"""
try:
import tidynamics
except ImportError:
raise ImportError("""ERROR --- tidynamics was not found!
tidynamics is required to compute an FFT based MSD (default)
try installing it using pip eg:
pip install tidynamics
or set fft=False""")
positions = self._position_array.astype(np.float64)
for n in range(self.n_particles):
self.msds_by_particle[:, n] = tidynamics.msd(positions[:, n, :])
self.timeseries = self.msds_by_particle.mean(axis=1)
def diffusion(u, t, block):
'''Computes mean squared displacement of water molecules within specified
layers parallel to a surface.
Args:
u: MDAnalysis Universe object containing trajectory.
t: Thresholds specifying layer boundaries.
block: Range of frames composing block.
Returns:
Parallel (xy) mean squared displacement.
'''
# Select oxygen atoms
oxygen = u.select_atoms('name O')
msd = []
# Initialize 3D position array (frame, atom, dimension)
position_array = np.zeros((len(block), oxygen.n_atoms, 3))
for i, ts in enumerate(u.trajectory[block.start:block.stop]):
print('Processing blocks %.1f%%' % (100*i/len(block)), end='\r')
# Store positions of all oxygens at current frame
position_array[i, :, :] = oxygen.positions
# Loop over oxygen atoms
for k in range(oxygen.n_atoms):
# Get atoms in region
z = position_array[:, k, 2]
z_bool = (z > t[0])*(z < t[1])+(z > t[2])*(z < t[3])
# Get intervals in which atom remains continuously in region
contiguous_region = find_objects(label(z_bool)[0])
# Compute mean squared displacement of atom for each interval
for reg in contiguous_region:
msd.append(tidynamics.msd(
position_array[reg[0].start:reg[0].stop, k, :2]))
# Return average of all MSDs
return tolerant.mean(msd)
def _conclude(self):
self.lagtimes = self.frames * self.dt
# lagtimes must start from zero, and should be in ns
self.lagtimes -= self.lagtimes[0]
self.lagtimes /= 1000
for lipid_index in range(self.membrane.n_residues):
self.msd[lipid_index] = tidynamics.msd(
self.lipid_com_pos[lipid_index])
# MSD must start at 0
self.msd[:, 0] = 0.0
# Convert A^2 to nm^2
self.msd /= 100
return None
def MSD_Sham(dir, side="dx", delimiter="\t"):
"""
Computes the Mean Square Displacement (MSD)
which is the mean squared difference between the y coordinates of the fronts
--------------------------
Parameters:
--------------------------
dir : the directory which contains the txt files with the coordinates
side : the side of the front which is left or right, this distinguish the txt files
delimiter : the space between the x and y coordinates in the txt file
----------------------------
Returns a numpy array with the MSD
"""
x = pd.DataFrame()
y = pd.DataFrame()
for fname in os.listdir(dir):
if side in fname:
k = fname.split('_')[-2]
k = int(k)
#df = grid(dir + fname + str(i+1) + side + ".txt", delimiter = delimiter)
dfx, dfy = necklace_points(dir + fname, N=80, sep=delimiter)
x[k] = dfx
y[k] = dfy
col = np.arange(1, len(x.T))
x = x[col]
count = 0
mean = np.zeros(len(x.T))
for i in range(len(mean)):
mean = mean + tidynamics.msd(x.T[i])
count += 1
mean /= count
return mean, x, y
def test_length_one_msd():
N = 1
pos = np.zeros(N)
reference_msd = np.zeros(N)
computed_msd = tidynamics.msd(pos)
assert np.allclose(reference_msd, computed_msd)
plt.rcParams['figure.figsize'] = 5.12, 3.84
plt.rcParams['figure.subplot.bottom'] = 0.18
plt.rcParams['figure.subplot.left'] = 0.16
# Generate 32 random walks and compute their mean-square
# displacements
N = 1000
mean = np.zeros(N)
count = 0
for i in range(32):
# Generate steps of value +/- 1
steps = -1 + 2 * np.random.randint(0, 2, size=(N, 2))
# Compute random walk position
data = np.cumsum(steps, axis=0)
mean += tidynamics.msd(data)
count += 1
mean /= count
mean = mean[1:N // 2]
time = np.arange(N)[1:N // 2]
plt.plot(time, mean, label='Random walk (num.)')
plt.plot(time, 2 * time, label='Random walk (theo.)')
time = np.arange(N // 2)
# Display the mean-square displacement for a trajectory with
# constant velocity. Here the trajectory is taken equal to the
r_dt = group['position/time'][()]
im = group['image/value'][:, slicer, :]
v = group['velocity/value'][:, slicer, :]
v_dt = group['velocity/time'][()]
edges = group['box/edges'][:].reshape((1, -1))
r += im * edges
assert abs(r_dt - v_dt) < 1e-12
if args.dimer:
assert r.shape[1] == 2
assert r.shape[2] == 3
r = r.mean(axis=1)
v_com = v.mean(axis=1)
if r.ndim == 3:
for i in range(r.shape[1]):
msd_data.append(tidynamics.msd(r[:, i, :]))
else:
msd_data.append(tidynamics.msd(r))
msd_data = np.array(msd_data)
m = msd_data.mean(axis=0)
s = msd_data.std(axis=0)
time = np.arange(r.shape[0]) * r_dt
plt.plot(time, m, 'k-')
plt.plot(time, m + s, 'k--')
plt.plot(time, m - s, 'k--')
fit = np.polyfit(time[:r.shape[0] // 4], m[:r.shape[0] // 4], 1)
D = fit[0] / 6
plt.plot(time, 6 * D * time, 'k:')
np.savetxt from NumPy.
For more information, consult the documentation of tidynamics at
http://lab.pdebuyl.be/tidynamics/
"""
from __future__ import print_function, division
import argparse
import numpy as np
import tidynamics
parser = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('action',
help='Choice of computation to perform on input file',
choices=['acf', 'msd'])
parser.add_argument('input_file', help='Filename for input data')
parser.add_argument('output_file',
help='Filename for the result of the computation')
args = parser.parse_args()
input_data = np.loadtxt(args.input_file)
if args.action == 'acf':
result = tidynamics.acf(input_data)
elif args.action == 'msd':
result = tidynamics.msd(input_data)
np.savetxt(args.output_file, result)
def test_linear_msd():
N = 100
time = np.arange(N)
reference_msd = time**2
computed_msd = tidynamics.msd(time)
assert np.allclose(reference_msd, computed_msd)
def test_cst_msd():
N = 100
data = np.ones(N)
reference_msd = np.zeros_like(data)
computed_msd = tidynamics.msd(data)
assert np.allclose(reference_msd, computed_msd)