def orient_op(orientations, m=4, positions=None, margin=0,
ret_complex=True, do_err=False, globl=False, locl=False):
"""orient_op(orientations, m=4, positions=None, margin=0,
ret_complex=True, do_err=False, globl=False, locl=False)
calculate the global m-fold particle orientational order parameter
1 N i m theta
Phi = --- SUM e j
m N j=1
"""
if not (globl or locl):
globl = True
locl = orientations.ndim == 2
np.mod(orientations, tau/m, orientations)
if margin:
if margin < ss:
margin *= ss
center = 0.5*(positions.max(0) + positions.min(0))
d = helpy.dist(positions, center) # distances to center
orientations = orientations[d < d.max() - margin]
phis = np.exp(m*orientations*1j)
if locl:
phis = np.nanmean(phis, 1)
if do_err:
err = np.nanstd(phis, ddof=1)/sqrt(np.count_nonzero(~np.isnan(phis)))
if not globl:
return (np.abs(phis), err) if do_err else np.abs(phis)
phi = np.nanmean(phis) if ret_complex else np.abs(np.nanmean(phis))
if locl:
return (np.abs(phis), phi, err) if do_err else (np.abs(phis), phi)
return (phi, err) if do_err else phi
def bulk(positions, margin=0, full_N=None, center=None, radius=None, ss=ss):
""" Filter marginal particles from bulk particles to reduce boundary effects
positions: (N, 2) array of particle positions
margin: width of margin, in units of pixels or particle sides
full_N: actual number of particles, to renormalize assuming
uniform distribution of undetected particles.
center: if known, (2,) array of center position
radius: if known, radius of system in pixels
returns
bulk_N: the number particles in the bulk
bulk_mask: a mask the shape of `positions`
"""
#raise StandardError, "not yet tested"
if center is None:
center = 0.5*(positions.max(0) + positions.min(0))
if margin < ss: margin *= ss
d = helpy.dist(positions, center) # distances to center
if radius is None:
if len(positions) > 1e5: raise ValueError, "too many points to calculate radius"
r = cdist(positions, positions) # distances between all pairs
radius = np.maximum(r.max()/2, d.max()) + ss/2
elif radius < ss:
radius *= ss
dmax = radius - margin
#print 'radius: ', radius/ss
#print 'margin: ', margin/ss
#print 'max r: ', dmax/ss
bulk_mask = d <= dmax # mask of particles in the bulk
bulk_N = np.count_nonzero(bulk_mask)
if full_N:
bulk_N *= full_N/len(positions)
return bulk_N, bulk_mask
def find_start_frame(data, estimate=None, bounds=None, plot=False):
"""Determine the time of the onset of motion
parameters
---------
data : the tracked data
estimate : an estimate, as frame index number, for start
bounds : a scalar indicating lower bound for start,
or a two-tuple of (lower, upper) bounds for the start
plot : whether or not to plot the motion vs time
returns
-------
start : frame index for onset of motion
ax : an axes object, if plot was requested
"""
estimate = estimate or 10
if bounds is None:
first = estimate // 2
last = estimate * 100
elif np.isscalar(bounds):
first = bounds
last = None
else:
first, last = bounds
if last is None:
last = first + (data['f'][-1] - first) // 3
positions = helpy.load_trackstack(data, length=last)['xy']
displacements = helpy.dist(positions, positions[0])
distances = helpy.dist(np.gradient(positions, axis=0))
ds = displacements.mean(1) * distances.mean(1)
dm = np.minimum.accumulate(ds[::-1])[::-1] == np.maximum.accumulate(ds)
dmi = np.nonzero(dm[first:last])[0] + first
start = dmi[0] - 1
if plot:
fig, ax = plt.subplots()
f = np.arange(len(ds))/args.fps
ax.plot(f, ds, '-')
ax.plot(f[dmi], ds[dmi], '*')
return start
def find_start_frame(data, estimate=None, bounds=None, plot=False):
"""Determine the time of the onset of motion
parameters
---------
data : the tracked data
estimate : an estimate, as frame index number, for start
bounds : a scalar indicating lower bound for start,
or a two-tuple of (lower, upper) bounds for the start
plot : whether or not to plot the motion vs time
returns
-------
start : frame index for onset of motion
ax : an axes object, if plot was requested
"""
estimate = estimate or 10
if bounds is None:
first = estimate // 2
last = estimate * 100
elif np.isscalar(bounds):
first = bounds
last = None
else:
first, last = bounds
if last is None:
last = first + (data['f'][-1] - first) // 3
positions = helpy.load_trackstack(data, length=last)['xy']
displacements = helpy.dist(positions, positions[0])
distances = helpy.dist(np.gradient(positions, axis=0))
ds = displacements.mean(1) * distances.mean(1)
dm = np.minimum.accumulate(ds[::-1])[::-1] == np.maximum.accumulate(ds)
dmi = np.nonzero(dm[first:last])[0] + first
start = dmi[0] - 1
if plot:
fig, ax = plt.subplots()
f = np.arange(len(ds)) / args.fps
ax.plot(f, ds, '-')
ax.plot(f[dmi], ds[dmi], '*')
return start
def pair_angles(positions, neighborhood=None, ang_type='absolute', margin=0, dub=2*ss):
""" do something with the angles a given particle makes with its neighbors
`ang_type` can be 'relative', 'delta', or 'absolute'
`neighborhood` may be:
an integer (probably 4, 6, or 8), giving that many nearest neighbors,
or None (which gives voronoi)
`margin` is the width of excluded boundary margin
`dub` is the distance upper bound (won't use pairs farther apart)
"""
if neighborhood is None or str(neighborhood).lower() in ['voronoi', 'delauney']:
#method = 'voronoi'
tess = Delaunay(positions)
neighbors = get_neighbors(tess, xrange(tess.npoints))
neighbors, nmask = helpy.pad_uneven(neighbors, 0, True, int)
elif isinstance(neighborhood, int):
#method = 'nearest'
tree = cKDTree(positions)
# tree.query(P, N) returns query particle and N-1 neighbors
distances, neighbors = tree.query(positions, 1 + neighborhood,
distance_upper_bound=dub)
assert np.allclose(distances[:,0], 0), "distance to self not zero"
distances = distances[:,1:]
assert np.allclose(neighbors[:,0], np.arange(tree.n)), "first neighbor not self"
neighbors = neighbors[:,1:]
nmask = np.isfinite(distances)
neighbors[~nmask] = np.where(~nmask)[0]
dx, dy = (positions[neighbors] - positions[:, None, :]).T
angles = np.arctan2(dy, dx).T % tau
assert angles.shape == neighbors.shape
if ang_type == 'relative':
# subtract off angle to nearest neighbor
angles -= angles[:, 0, None] # None to keep dims
elif ang_type == 'delta':
# sort by angle then take diff
angles[~nmask] = np.inf
angles.sort(-1)
angles -= np.roll(angles, 1, -1)
nmask = np.all(nmask, 1)
elif ang_type != 'absolute':
raise ValueError, "unknown ang_type {}".format(ang_type)
angles[~nmask] = np.nan
if margin:
if margin < ss: margin *= ss
center = 0.5*(positions.max(0) + positions.min(0))
d = helpy.dist(positions, center) # distances to center
dmask = d < d.max() - margin
assert np.allclose(len(dmask), map(len, [angles, nmask]))
angles = angles[dmask]
nmask = nmask[dmask]
return (angles % tau, nmask) + ((dmask,) if margin else ())
def orient_corr(positions, orientations, m=4, margin=0, bins=10):
""" orient_corr():
the orientational correlation function g_m(r)
given by mean(phi(0)*phi(r))
"""
center = 0.5*(positions.max(0) + positions.min(0))
d = helpy.dist(positions, center) # distances to center
if margin < ss: margin *= ss
loc_mask = d < d.max() - margin
r = pdist(positions[loc_mask])
ind = np.column_stack(pair_indices(np.count_nonzero(loc_mask)))
pairs = orientations[loc_mask][ind]
diffs = np.cos(m*dtheta(pairs, m=m))
return bin_average(r, diffs, bins)
def radial_distribution(positions,
dr=ss / 5,
nbins=None,
dmax=None,
rmax=None,
margin=0,
do_err=False,
ss=ss):
""" radial_distribution(positions):
the pair correlation function g(r)
calculated using a histogram of distances between particle pairs
excludes pairs in margin of given width
"""
center = 0.5 * (positions.max(0) + positions.min(0))
d = helpy.dist(positions, center) # distances to center
# faster than squareform(distance.pdist(positions)) wtf
r = distance.cdist(positions, positions)
radius = np.maximum(r.max() / 2, d.max()) + ss / 2
if rmax is None:
rmax = 2 * radius # this will have terrible statistics at large r
if nbins is None:
nbins = rmax // dr
if dmax is None:
if margin < ss:
margin *= ss
dmax = radius - margin
ind = pair_indices(len(positions))
# for weighting, use areas of the annulus, which is:
# number * arclength * dr = N alpha r dr
# where alpha = 2 arccos( (r2 + d2 - R2) / 2 r d )
cosalpha = 0.5 * (r * r + d * d - radius * radius) / (r * d)
alpha = 2 * np.arccos(np.clip(cosalpha, -1, None))
dmask = d <= dmax
w = np.where(dmask, np.reciprocal(alpha * r * dr), 0)
w = 0.5 * (w + w.T)
assert np.all(np.isfinite(w[ind]))
# Different ways to count `n`:
# number of 'bulk' (inner) particles
n = np.count_nonzero(dmask)
# effective N from number of pairs:
# n = 0.5*(1 + sqrt(1 + 8*np.count_nonzero(w[ind])))
# total number of particles:
# n = len(w)
w *= 2 / n
assert np.allclose(positions.shape[0], map(len, [r, d, w, positions]))
ret = np.histogram(r[ind], bins=nbins, range=(0, rmax), weights=w[ind])
if do_err:
return ret, np.histogram(r[ind], bins=nbins, range=(0, rmax)), n
else:
return ret + (n, )
def bulk(positions,
margin=0,
full_N=None,
center=None,
radius=None,
ss=ss,
verbose=False):
""" Filter marginal particles from bulk particles to reduce boundary effects
positions: (N, 2) array of particle positions
margin: width of margin, in units of pixels or particle sides
full_N: actual number of particles, to renormalize assuming
uniform distribution of undetected particles.
center: if known, (2,) array of center position
radius: if known, radius of system in pixels
returns
bulk_N: the number particles in the bulk
bulk_mask: a mask the shape of `positions`
"""
if center is None:
center = 0.5 * (positions.max(0) + positions.min(0))
if margin < ss:
margin *= ss
d = helpy.dist(positions, center) # distances to center
if radius is None:
max_sep = 0
if len(positions) < 1e4:
max_sep = distance.cdist(positions, positions).max() / 2
radius = max(max_sep, d.max()) + ss / 2
elif radius < ss:
radius *= ss
dmax = radius - margin
depth = d - dmax
bulk_mask = area_overlap(depth / ss, ss=1, method='aligned_square')
bulk_N = bulk_mask.sum()
# bulk_mask = bulk_mask >= 0.5 # mask of centers within bulk
if full_N:
bulk_N *= full_N / len(positions)
if verbose:
print 'margin:', margin / ss,
print 'center:', center,
print 'radius:', radius
print 'max r: ', dmax / ss,
print 'bulk_N:', bulk_N,
print
return bulk_N, bulk_mask, center, radius
def radial_distribution(positions, dr=ss/5, nbins=None, dmax=None, rmax=None,
margin=0, do_err=False, ss=ss):
""" radial_distribution(positions):
the pair correlation function g(r)
calculated using a histogram of distances between particle pairs
excludes pairs in margin of given width
"""
center = 0.5*(positions.max(0) + positions.min(0))
d = helpy.dist(positions, center) # distances to center
# faster than squareform(distance.pdist(positions)) wtf
r = distance.cdist(positions, positions)
radius = np.maximum(r.max()/2, d.max()) + ss/2
if rmax is None:
rmax = 2*radius # this will have terrible statistics at large r
if nbins is None:
nbins = rmax//dr
if dmax is None:
if margin < ss:
margin *= ss
dmax = radius - margin
ind = pair_indices(len(positions))
# for weighting, use areas of the annulus, which is:
# number * arclength * dr = N alpha r dr
# where alpha = 2 arccos( (r2 + d2 - R2) / 2 r d )
cosalpha = 0.5 * (r*r + d*d - radius*radius) / (r * d)
alpha = 2 * np.arccos(np.clip(cosalpha, -1, None))
dmask = d <= dmax
w = np.where(dmask, np.reciprocal(alpha*r*dr), 0)
w = 0.5*(w + w.T)
assert np.all(np.isfinite(w[ind]))
# Different ways to count `n`:
# number of 'bulk' (inner) particles
n = np.count_nonzero(dmask)
# effective N from number of pairs:
# n = 0.5*(1 + sqrt(1 + 8*np.count_nonzero(w[ind])))
# total number of particles:
# n = len(w)
w *= 2/n
assert np.allclose(positions.shape[0], map(len, [r, d, w, positions]))
ret = np.histogram(r[ind], bins=nbins, range=(0, rmax), weights=w[ind])
if do_err:
return ret, np.histogram(r[ind], bins=nbins, range=(0, rmax)), n
else:
return ret + (n,)
def pair_angles(xy_or_orient, neighbors, nmask, ang_type='absolute', margin=0):
"""do something with the angles a given particle makes with its neighbors
Parameters
xy_or_orient: either (N, 2) array of positions or (N,) array of angles
neighbors: (N, k) array of k neighbors
nmask: mask for neighbors
ang_type: string, choice of 'absolute' (default), 'relative', 'delta'
margin: is the width of excluded boundary margin
Returns
angles: array of angles between neighboring pairs
dmask: margin mask, only returned if margin > 0
"""
if xy_or_orient.ndim == 2:
dx, dy = (xy_or_orient[neighbors] - xy_or_orient[:, None, :]).T
angles = np.arctan2(dy, dx).T % tau
else:
angles = xy_or_orient[neighbors] - xy_or_orient[:, None]
if ang_type == 'relative':
# subtract off angle to nearest neighbor
angles -= angles[:, :1]
elif ang_type == 'delta':
# sort by angle then take diff
angles[nmask] = np.inf
angles.sort(-1)
angles -= np.roll(angles, 1, -1)
# only keep if we have all k neighbors
nmask = np.all(nmask, 1)
elif ang_type != 'absolute':
raise ValueError("unknown ang_type {}".format(ang_type))
angles[nmask] = np.nan
if margin:
if margin < ss:
margin *= ss
center = 0.5*(xy_or_orient.max(0) + xy_or_orient.min(0))
d = helpy.dist(xy_or_orient, center)
dmask = d < d.max() - margin
angles = angles[dmask]
nmask = nmask[dmask]
return (angles % tau, nmask) + ((dmask,) if margin else ())
def pair_angles(xy_or_orient, neighbors, nmask, ang_type='absolute', margin=0):
"""do something with the angles a given particle makes with its neighbors
Parameters
xy_or_orient: either (N, 2) array of positions or (N,) array of angles
neighbors: (N, k) array of k neighbors
nmask: mask for neighbors
ang_type: string, choice of 'absolute' (default), 'relative', 'delta'
margin: is the width of excluded boundary margin
Returns
angles: array of angles between neighboring pairs
dmask: margin mask, only returned if margin > 0
"""
if xy_or_orient.ndim == 2:
dx, dy = (xy_or_orient[neighbors] - xy_or_orient[:, None, :]).T
angles = np.arctan2(dy, dx).T % tau
else:
angles = xy_or_orient[neighbors] - xy_or_orient[:, None]
if ang_type == 'relative':
# subtract off angle to nearest neighbor
angles -= angles[:, :1]
elif ang_type == 'delta':
# sort by angle then take diff
angles[nmask] = np.inf
angles.sort(-1)
angles -= np.roll(angles, 1, -1)
# only keep if we have all k neighbors
nmask = np.all(nmask, 1)
elif ang_type != 'absolute':
raise ValueError("unknown ang_type {}".format(ang_type))
angles[nmask] = np.nan
if margin:
if margin < ss:
margin *= ss
center = 0.5 * (xy_or_orient.max(0) + xy_or_orient.min(0))
d = helpy.dist(xy_or_orient, center)
dmask = d < d.max() - margin
angles = angles[dmask]
nmask = nmask[dmask]
return (angles % tau, nmask) + ((dmask, ) if margin else ())
def orient_op(orientations, positions, m=4, margin=0, ret_complex=True, do_err=False):
""" orient_op(orientations, m=4)
Returns the global m-fold particle orientational order parameter
1 N i m theta
Phi = --- SUM e j
m N j=1
"""
np.mod(orientations, tau/m, orientations) # what's this for? (was tau/4 not tau/m)
if margin:
if margin < ss: margin *= ss
center = 0.5*(positions.max(0) + positions.min(0))
d = helpy.dist(positions, center) # distances to center
orientations = orientations[d < d.max() - margin]
phi = np.exp(m*orientations*1j).mean()
if do_err:
err = phi.std(ddof=1)/sqrt(phi.size)
return (phi, err) if ret_complex else (np.abs(phi), err)
else:
return phi if ret_complex else np.abs(phi)
def distribution(positions, rmax=10, bins=10, margin=0, rectang=0):
if margin < ss: margin *= ss
center = 0.5*(positions.max(0) + positions.min(0))
d = helpy.dist(positions, center) # distances to center
dmask = d < d.max() - margin
r = cdist(positions, positions[dmask])#.ravel()
radius = np.maximum(r.max()/2, d.max()) + ss/2
cosalpha = 0.5 * (r**2 + d[dmask]**2 - radius**2) / (r * d[dmask])
alpha = 2 * np.arccos(np.clip(cosalpha, -1, None))
dr = radius / bins
w = dr**-2 * tau/alpha
w[~np.isfinite(w)] = 0
if rmax < ss: rmax *= ss
rmask = r < rmax
displacements = positions[:, None] - positions[None, dmask] #origin must be within margin
if rectang:
if rectang is True:
rectang = rectify(positions, margin=margin)[0]
rotate2d(displacements, rectify(positions, margin=margin))
return np.histogramdd(displacements[rmask], bins=bins, weights=w[rmask])[0]
def bulk(positions, margin=0, full_N=None, center=None, radius=None, ss=ss,
verbose=False):
""" Filter marginal particles from bulk particles to reduce boundary effects
positions: (N, 2) array of particle positions
margin: width of margin, in units of pixels or particle sides
full_N: actual number of particles, to renormalize assuming
uniform distribution of undetected particles.
center: if known, (2,) array of center position
radius: if known, radius of system in pixels
returns
bulk_N: the number particles in the bulk
bulk_mask: a mask the shape of `positions`
"""
if center is None:
center = 0.5*(positions.max(0) + positions.min(0))
if margin < ss:
margin *= ss
d = helpy.dist(positions, center) # distances to center
if radius is None:
max_sep = 0
if len(positions) < 1e4:
max_sep = distance.cdist(positions, positions).max()/2
radius = max(max_sep, d.max()) + ss/2
elif radius < ss:
radius *= ss
dmax = radius - margin
depth = d - dmax
bulk_mask = area_overlap(depth/ss, ss=1, method='aligned_square')
bulk_N = bulk_mask.sum()
# bulk_mask = bulk_mask >= 0.5 # mask of centers within bulk
if full_N:
bulk_N *= full_N/len(positions)
if verbose:
print 'margin:', margin/ss,
print 'center:', center,
print 'radius:', radius
print 'max r: ', dmax/ss,
print 'bulk_N:', bulk_N,
print
return bulk_N, bulk_mask, center, radius
def orient_op(orientations,
m=4,
positions=None,
margin=0,
ret_complex=True,
do_err=False,
globl=False,
locl=False):
"""orient_op(orientations, m=4, positions=None, margin=0,
ret_complex=True, do_err=False, globl=False, locl=False)
calculate the global m-fold particle orientational order parameter
1 N i m theta
Phi = --- SUM e j
m N j=1
"""
if not (globl or locl):
globl = True
locl = orientations.ndim == 2
np.mod(orientations, tau / m, orientations)
if margin:
if margin < ss:
margin *= ss
center = 0.5 * (positions.max(0) + positions.min(0))
d = helpy.dist(positions, center) # distances to center
orientations = orientations[d < d.max() - margin]
phis = np.exp(m * orientations * 1j)
if locl:
phis = np.nanmean(phis, 1)
if do_err:
err = np.nanstd(phis, ddof=1) / sqrt(np.count_nonzero(~np.isnan(phis)))
if not globl:
return (np.abs(phis), err) if do_err else np.abs(phis)
phi = np.nanmean(phis) if ret_complex else np.abs(np.nanmean(phis))
if locl:
return (np.abs(phis), phi, err) if do_err else (np.abs(phis), phi)
return (phi, err) if do_err else phi