def import_readymade_meso_v2_membrane(**kwargs):
"""
Compute bilayer midplane structures for studying undulations.
Adapted from `undulations.py`.
"""
import ipdb
ipdb.set_trace()
#---parameters
sn = kwargs['sn']
work = kwargs['workspace']
calc = kwargs['calc']
#---import mesh points
points = import_membrane_mesh(sn=sn, calc=calc, work=work)
#---ensure there are the same number of points
points_shapes = list(set([p.shape for p in points]))
if len(points_shapes) != 1:
raise Exception('some frames have a different number of points: %s' %
points_shapes)
else:
npoints, ncols = points_shapes[0]
if ncols != 4: raise Exception('expecting 4-column input on incoming data')
#---with a consistent number of points everything is an array
points = np.array(points)[:, :, :3]
#---previously checked that the minimum points were identically zero but this was not always true
#---box vectors are just the maximum points
#---! check that this assumption makes sense
vecs = points.max(axis=1)[:, :3]
#---debug the shapes in 3D
if False:
from codes import review3d
fr = 0
review3d.pbcbox(vecs[fr])
review3d.review3d(points=[points[fr][:, :3]], radius=10)
grid_spacing = calc['specs']['grid_spacing']
nframes = len(points)
#---choose grid dimensions
grid = np.array([round(i)
for i in np.mean(vecs, axis=0) / grid_spacing])[:2]
#---compute in parallel
start = time.time()
mesh = [[]]
mesh[0] = Parallel(n_jobs=work.nprocs, verbose=0)(
delayed(makemesh_regular, has_shareable_memory)(points[fr], vecs[fr],
grid)
for fr in framelooper(nframes, start=start, text='frame'))
checktime()
#---pack
attrs, result = {}, {}
result['mesh'] = np.array(mesh)
result['grid'] = np.array(grid)
result['nframes'] = np.array(nframes)
result['vecs'] = vecs
attrs['grid_spacing'] = grid_spacing
#---introduce a dated validator string to ensure that any changes to the pipeline do not overwrite
#---...other data and are fully propagated downstream
attrs['validator'] = '2017.08.16.1930'
return result, attrs
if 'review3d' in routine:
import mayavi
from mayavi import mlab
from codes.review3d import review3d, pbcbox
sn = 'mk004'
dat = data[sn]['data']
mn, fr = 1, 10
pts = dat['%d.%d.%s' % (mn, fr, 'points')]
vec = dat['%d.%d.%s' % (mn, fr, 'vec')]
mean_curvs = dat['%d.%d.%s' % (mn, fr, 'mean')]
mean_curvs_normed = mean_curvs / np.abs(mean_curvs).max() + 0.5
review3d(points=[pts],
tube=0.02,
radius=0.2,
noshow=True,
colorset=mean_curvs_normed,
cmap='seismic')
review3d(points=data_prot[sn]['data']['points_all'][fr],
radius=0.4,
noshow=True)
pbcbox(vec)
mlab.show()
#---block: heat map of curvature from the mesh
if 'curvature' in routine:
#---settings
spacing = 0.5
mn = 0
counts, bins = np.histogram(postdat[sn], bins=hbins)
ax.plot((hbins[1:] + hbins[:-1]) / 2., counts, label=sn)
legend = ax.legend()
ax.axvline(0.0, c='k')
picturesave('fig.undulations.height_histograms',
work.plotdir,
backup=False,
version=True,
meta={},
extras=[legend])
#---block: plot the average heights
if 'debug3d' in routine:
if 'review3d' not in globals():
from codes import review3d
from codes.readymade_meso_v1 import import_membrane_mesh
#---get the calc object
data_raw, calc_raw = plotload('import_readymade_meso_v1_membrane')
sns = work.sns()
sn = sns[0]
points = import_membrane_mesh(sn=sn, calc=calc_raw, work=work)
vecs = data[sn]['data']['vecs']
fr = 0
### review3d.pbcbox(vecs[fr])
zs = points[fr][:, 2] - points[fr][:, 2].mean()
colorset = (zs - zs.min()) / (zs.max() - zs.min())
mean_zs = np.array([points[p][:, :3]
for p in range(len(points))]).mean(axis=0)
review3d.review3d(points=[mean_zs], radius=3.0, colorset=colorset)