def fourier_transform(v,
step=None,
subregion=None,
model_id=None,
phase=False):
m = v.matrix(step=step, subregion=subregion)
from numpy.fft import fftn
cftm = fftn(m) # Complex128 result, same array size as input
from numpy import absolute, angle, float32
if phase:
aftm = angle(cftm).astype(float32) # Radians
else:
aftm = absolute(cftm).astype(float32)
aftm *= 1.0 / aftm.size # Normalization
aftm[0, 0,
0] = 0 # Constant term often huge making histogram hard to use
cftm = None # Release memory
ftm = fftshift(aftm)
aftm = None # Release memory
# Place FT centered on data, scaled to keep same volume
xyz_min, xyz_max = v.xyz_bounds()
xyz_center = map(lambda a, b: 0.5 * (a + b), xyz_min, xyz_max)
ijk_size = list(ftm.shape)
ijk_size.reverse()
if step is None:
ijk_step = v.region[2]
elif isinstance(step, int):
ijk_step = (step, step, step)
else:
ijk_step = step
xyz_size = [a - b for a, b in zip(xyz_max, xyz_min)]
vol = xyz_size[0] * xyz_size[1] * xyz_size[2]
cell_size = [a * b for a, b in zip(v.data.step, ijk_step)]
cell_vol = cell_size[0] * cell_size[1] * cell_size[2]
scale = pow(vol * cell_vol, 1.0 / 3)
step = [scale / a for a in xyz_size]
origin = [c - 0.5 * s * z for c, s, z in zip(xyz_center, step, ijk_size)]
from chimerax.map_data import ArrayGridData
ftd = ArrayGridData(ftm, origin, step)
ftd.name = v.name + (' FT phase' if phase else ' FT')
from chimerax.map import volume_from_grid_data
ftr = volume_from_grid_data(ftd, v.session, model_id=model_id)
ftr.copy_settings_from(v,
copy_thresholds=False,
copy_colors=False,
copy_region=False)
ftr.set_parameters(show_outline_box=True)
v.display = False # Hide original map
return ftr
def tile_planes(v, axis = 'z', pstep = 1, trim = 0,
rows = None, columns = None, fill_order = 'ulh',
step = None, subregion = None, model_id = None):
vreg = v.subregion(step = step, subregion = subregion)
reg = [list(ijk) for ijk in vreg]
ac,ar,a = {'x':(1,2,0), 'y':(2,0,1), 'z':(0,1,2)}[axis]
reg[0][a] += trim
reg[1][a] -= trim
reg[2][a] = pstep
dorigin, dstep = v.region_origin_and_step(reg)
m = v.region_matrix(reg)
tcount = m.shape[2-a]
if tcount == 0:
return
if rows is None and columns is None:
# Choose columns to make square aspect ratio.
w,h = m.shape[2-ac]*dstep[ac], m.shape[2-ar]*dstep[ar]
from math import sqrt, ceil
columns = min(tcount, int(ceil(sqrt(tcount*float(h)/w))))
rows = (tcount - 1 + columns) // columns
elif rows is None:
rows = (tcount - 1 + columns) // columns
elif columns is None:
columns = (tcount - 1 + rows) // rows
s0, s1, s2 = m.shape
if axis == 'z': tshape = (1,rows*s1,columns*s2)
elif axis == 'y': tshape = (columns*s0,1,rows*s2)
elif axis == 'x': tshape = (rows*s0,columns*s1,1)
from numpy import zeros
ta = zeros(tshape, m.dtype)
for i in range(tcount):
# Start with top image in upper left corner.
p,r,c = tile_position(i, rows, columns, tcount, fill_order)
if axis == 'z':
ta[0,r*s1:(r+1)*s1,c*s2:(c+1)*s2] = m[p,:,:]
elif axis == 'y':
ta[c*s0:(c+1)*s0,0,r*s2:(r+1)*s2] = m[:,p,:]
elif axis == 'x':
ta[r*s0:(r+1)*s0,c*s1:(c+1)*s1,0] = m[:,:,p]
from chimerax.map_data import ArrayGridData
td = ArrayGridData(ta, dorigin, dstep)
td.name = v.name + ' tiled %s' % axis
from chimerax.map import volume_from_grid_data
tv = volume_from_grid_data(td, v.session, model_id = model_id)
tv.copy_settings_from(v, copy_region = False, copy_active = False,
copy_xform = open)
v.display = False # Hide original map
return tv
def flattened_grid(volume,
method='multiply linear',
step=1,
subregion=None,
region=None,
fitregion=None,
task=None):
v = volume
if region is None:
region = v.subregion(step, subregion)
m = v.region_matrix(region).copy()
if fitregion:
fregion = v.subregion(step, fitregion)
mfit = v.region_matrix(fregion)
moffset = [i - fi for i, fi in zip(region[0], fregion[0])]
else:
mfit = m
moffset = (0, 0, 0)
flatten_matrix(m, method, mfit, moffset, task=task)
from chimerax.map_data import ArrayGridData
d = v.data
if v.name.endswith('flat'): name = v.name
else: name = '%s flat' % v.name
forigin, fstep = v.region_origin_and_step(region)
fg = ArrayGridData(m, forigin, fstep, d.cell_angles, d.rotation, name=name)
return fg
def variance(session, maps):
sum = sum2 = None
for v in maps:
from numpy import float32
m = v.full_matrix().astype(float32)
if sum is None:
sum = m.copy()
sum2 = m * m
else:
if m.shape != sum.shape:
from chimerax.core.errors import UserError
raise UserError('Map %s' % v.name_with_id() +
' size (%d,%d,%d)' % tuple(v.data.size) +
' does not match map %s' %
maps[0].name_with_id() +
' size (%d,%d,%d)' % tuple(maps[0].data.size))
sum += m
sum2 += m * m
n = len(maps)
var = sum2 / n - (sum * sum) / (n * n)
d = maps[0].data
from chimerax.map_data import ArrayGridData
grid = ArrayGridData(var,
origin=d.origin,
step=d.step,
cell_angles=d.cell_angles,
rotation=d.rotation,
name='variance of %d maps' % n)
from chimerax.map import volume_from_grid_data
v = volume_from_grid_data(grid, session)
return v
def ones_volume(surfaces,
pad,
spacing,
border,
default_size=100,
value_type=None):
# Figure out array size
bounds = scene_bounds(surfaces)
bsize = [s + 2 * pad + 2 * border for s in bounds.size()]
if spacing is None:
s = max(bsize) / default_size
spacing = (s, s, s)
from math import ceil
size = [1 + int(ceil(s / sp)) for s, sp in zip(bsize, spacing)]
origin = [x - (pad + border) for x in bounds.xyz_min]
# Create ones array
from numpy import ones, int8
vtype = int8 if value_type is None else value_type
varray = ones(size[::-1], vtype)
from chimerax.map_data import ArrayGridData
g = ArrayGridData(varray, origin, spacing, name='mask')
# Create Volume model
from chimerax.map import volume_from_grid_data
v = volume_from_grid_data(g,
surfaces[0].session,
open_model=False,
show_dialog=False)
return v
def _generate_data_array(self, origin, grid_origin, dim):
data = self._data_fill_target = numpy.empty(dim, numpy.float32)
order = numpy.array([2, 1, 0], int)
from chimerax.map_data import ArrayGridData
darray = ArrayGridData(data.transpose(),
origin=origin,
step=self.voxel_size,
cell_angles=self.cell.angles_deg)
return darray
def mlp_map(session, atoms, method, spacing, max_dist, nexp, name, open_map):
data, bounds = calculatefimap(atoms, method, spacing, max_dist, nexp)
# m.pot is 1-dimensional if m.writedxfile() was called. Has indices in x,y,z order.
origin = tuple(xmin for xmin, xmax in bounds)
s = spacing
step = (s, s, s)
from chimerax.map_data import ArrayGridData
g = ArrayGridData(data, origin, step, name=name)
g.polar_values = True
from chimerax.map import volume_from_grid_data
v = volume_from_grid_data(g,
session,
open_model=open_map,
show_dialog=open_map)
if open_map:
v.update_drawings() # Compute surface levels
v.set_parameters(
surface_colors=[(0, 139 / 255, 139 / 255,
1), (184 / 255, 134 / 255, 11 / 255, 1)])
return v
def unbend_volume(volume,
path,
yaxis,
xsize,
ysize,
grid_spacing,
subregion='all',
step=1,
model_id=None):
# Compute correctly spaced cubic splined path points.
points = spline_path(path, grid_spacing)
axes = path_point_axes(points, yaxis)
nx = int(xsize / grid_spacing) + 1
ny = int(ysize / grid_spacing) + 1
nz = len(points)
# Create a rectangle of point positions to interpolate at.
from numpy import empty, float32, arange
section = empty((ny, nx, 3), float32)
x = arange(nx, dtype=float32) * grid_spacing - 0.5 * (xsize - 1.0)
y = arange(ny, dtype=float32) * grid_spacing - 0.5 * (ysize - 1.0)
for j in range(ny):
section[j, :, 0] = x
for i in range(nx):
section[:, i, 1] = y
section[:, :, 2] = 0
s = section.reshape((ny * nx, 3))
# Interpolate planes to fill straightened array.
from chimerax.geometry import translation
m = empty((nz, ny, nx), float32)
for k in range(nz):
tf = translation(points[k]) * axes[k]
m[k, :, :] = volume.interpolated_values(s,
tf,
subregion=subregion,
step=step).reshape((ny, nx))
# Create volume.
from chimerax.map_data import ArrayGridData
step = [grid_spacing] * 3
origin = [0, 0, 0]
g = ArrayGridData(m, origin, step, name='unbend')
from chimerax.map import volume_from_grid_data
v = volume_from_grid_data(g, volume.session, model_id=model_id)
v.copy_settings_from(volume,
copy_region=False,
copy_active=False,
copy_xform=open)
return v
def laplacian(v, step=None, subregion=None, model_id=None):
m = v.matrix(step=step, subregion=subregion)
from numpy import float32, multiply, add
lm = m.astype(float32) # Copy array
multiply(lm, -6.0, lm)
add(lm[:-1, :, :], m[1:, :, :], lm[:-1, :, :])
add(lm[1:, :, :], m[:-1, :, :], lm[1:, :, :])
add(lm[:, :-1, :], m[:, 1:, :], lm[:, :-1, :])
add(lm[:, 1:, :], m[:, :-1, :], lm[:, 1:, :])
add(lm[:, :, :-1], m[:, :, 1:], lm[:, :, :-1])
add(lm[:, :, 1:], m[:, :, :-1], lm[:, :, 1:])
lm[0, :, :] = 0
lm[-1, :, :] = 0
lm[:, 0, :] = 0
lm[:, -1, :] = 0
lm[:, :, 0] = 0
lm[:, :, -1] = 0
origin, step = v.data_origin_and_step(subregion=subregion, step=step)
d = v.data
from chimerax.map_data import ArrayGridData
ld = ArrayGridData(lm,
origin,
step,
d.cell_angles,
d.rotation,
name=v.name + ' Laplacian')
ld.polar_values = True
from chimerax.map import volume_from_grid_data
lv = volume_from_grid_data(ld, v.session, model_id=model_id)
lv.copy_settings_from(v, copy_thresholds=False, copy_colors=False)
lv.set_parameters(cap_faces=False)
v.display = False # Hide original map
return lv
def lattice_models(session, seg, max_surfaces=100):
# Map lattice id to dictionary mapping segment index to (descrip, color)
lattice_segs = {}
for segment in seg.segments:
v = segment.three_d_volume
if v is not None:
lseg = lattice_segs.setdefault(v.lattice_id, {})
if v.value is not None:
lseg[int(v.value)] = (segment.biological_annotation,
segment.colour)
scale, shift = guess_scale_and_shift(seg)
# Create Volume model of segment indices for each lattice.
models = []
lattices = seg.lattices
for i, lattice in enumerate(lattices):
d = lattice.data_array # Docs say number array, but emd 1547 gives bytes
name = 'region map' if len(lattices) == 1 else 'region map %d' % i
from chimerax.map_data import ArrayGridData
g = ArrayGridData(d, step=scale, origin=shift, name=name)
from chimerax.map import volume_from_grid_data
v = volume_from_grid_data(g, session, open_model=False)
v.display = False
if lattice.id in lattice_segs:
v.segments = lseg = lattice_segs[lattice.id]
set_segmentation_image_colors(v, lseg)
# Make a surface for each segment.
regions = list(lseg.items())
regions.sort()
surfs = [
segment_surface(v, sindex, descrip, color)
for sindex, (descrip, color) in regions[:max_surfaces]
]
if surfs:
ns, nr = len(surfs), len(regions)
sname = ('%d surfaces' %
ns) if ns == nr else ('%d of %d surfaces' % (ns, nr))
from chimerax.core.models import Model
surf_group = Model(sname, v.session)
surf_group.add(surfs)
models.append(surf_group)
# TODO: Don't see how to get the transform id for the lattice.
# EMD 1547 segmentation has two transforms, identity and the
# map transform (2.8A voxel size, shift to center) but I didn't
# find any place where transform 1 is associated with the lattice.
# Appears it should be in segment.three_d_volume.transform_id but this
# attribute is optional and is None in this case.
models.append(v)
return models
def bounding_grid(xyz, step, pad, transforms=None):
from chimerax.geometry import bounds
b = bounds.point_bounds(xyz, transforms)
origin = [x - pad for x in b.xyz_min]
from math import ceil
shape = [
int(ceil((b.xyz_max[a] - b.xyz_min[a] + 2 * pad) / step))
for a in (2, 1, 0)
]
from numpy import zeros, float32
matrix = zeros(shape, float32)
from chimerax.map_data import ArrayGridData
grid = ArrayGridData(matrix, origin, (step, step, step))
return grid
def ridge_grid(volume, level=None, step=1, subregion=None):
v = volume
region = v.subregion(step, subregion)
m = v.region_matrix(region)
rm = ridge_matrix(m, level)
from chimerax.map_data import ArrayGridData
d = v.data
name = '%s ridges' % v.name
origin, step = v.region_origin_and_step(region)
rg = ArrayGridData(rm, origin, step, d.cell_angles, d.rotation, name=name)
return rg
def falloff_grid(volume, iterations = 10, step = 1, subregion = None):
v = volume
region = v.subregion(step, subregion)
from numpy import float32
m = v.region_matrix(region).astype(float32)
falloff_matrix(m, iterations)
from chimerax.map_data import ArrayGridData
d = v.data
name = '%s falloff' % v.name
forigin, fstep = v.region_origin_and_step(region)
fg = ArrayGridData(m, forigin, fstep, d.cell_angles, d.rotation,
name = name)
return fg
def map_covering_box(v, ijk_min, ijk_max, ijk_cell_size, symmetries, step):
d = v.data
if ijk_cell_size == d.size and (symmetries is None
or len(symmetries) == 0):
# Full unit cell and no symmetries to average.
g = v.grid_data(subregion='all', step=step, mask_zone=False)
from chimerax.map import volume
cg = volume.map_from_periodic_map(g, ijk_min, ijk_max)
return cg
out_ijk_size = tuple(a - b + 1 for a, b in zip(ijk_max, ijk_min))
from chimerax.geometry import translation
out_ijk_to_vijk_transform = translation(ijk_min)
ijk_symmetries = ijk_symmetry_matrices(d, symmetries)
from numpy import empty, float32
shape = list(reversed(out_ijk_size))
m = empty(shape, float32)
from chimerax.map import extend_crystal_map
nnc, dmax = extend_crystal_map(v.full_matrix(), ijk_cell_size,
ijk_symmetries.array(), m,
out_ijk_to_vijk_transform.matrix)
log = v.session.logger
log.info(
'Extended map %s to box of size (%d, %d, %d),\n' %
((v.name, ) + out_ijk_size) +
' cell size (%d, %d, %d) grid points, %d symmetry operations,\n' %
(tuple(ijk_cell_size) + (len(ijk_symmetries), )) +
' %d points not covered by any symmetry,\n' % nnc +
' maximum value difference where symmetric map copies overlap = %.5g\n'
% dmax)
if nnc > 0:
log.status('%d grid points not covered' % nnc)
origin = d.ijk_to_xyz(ijk_min)
from chimerax.map_data import ArrayGridData
g = ArrayGridData(m,
origin,
d.step,
d.cell_angles,
name=v.name + ' extended')
return g
def sphere_volume(session, n, r, noise=1.0):
from numpy import indices, single as floatc
o = 0.5 * (n - 1)
i = indices((n, n, n), floatc) - o
a = (i[0, ...] * i[0, ...] + i[1, ...] * i[1, ...] + i[2, ...] * i[2, ...]
< r * r).astype(floatc)
if noise > 0:
from numpy.random import normal
a += normal(0, noise, a.shape)
from chimerax.map_data import ArrayGridData
g = ArrayGridData(a, origin=(-o, -o, -o), step=(1, 1, 1), name='sphere')
from chimerax.map import volume_from_grid_data
v = volume_from_grid_data(g, session)
return v
def _generate_data_array(self, coords, step, radius, pad=0):
import numpy
if hasattr(step, '__len__'):
step = min(step)
step = max((step, radius / 4))
step = min(step, 1.5)
step = numpy.ones(3) * step
cmin = coords.min(axis=0)
cmax = coords.max(axis=0)
mincoor = cmin - radius - pad
maxcoor = cmax + radius + pad
dim = numpy.ceil((maxcoor - mincoor) / step).astype(numpy.int)
data = numpy.zeros(dim, numpy.uint8)
self._data_fill_target = data
from chimerax.map_data import ArrayGridData
darray = ArrayGridData(data.transpose(), origin=mincoor, step=step)
return darray
def unroll_operation(v, r0, r1, h, center, axis, gsp, subregion, step,
modelId):
from math import ceil, pi
zsize = int(max(1, ceil(h / gsp))) # cylinder height
xsize = int(max(1, ceil((r1 - r0) / gsp))) # slab thickness
rmid = 0.5 * (r0 + r1)
circum = rmid * 2 * pi
ysize = int(max(1, ceil(circum / gsp))) # circumference
from chimerax.geometry import normalize_vector
axis = normalize_vector(axis)
agrid_points = annulus_grid(r0, r1, center, axis, ysize, xsize)
grid_points = agrid_points.reshape((ysize * xsize, 3))
grid_points[:] += tuple([-0.5 * h * ai for ai in axis]) # Shift annulus.
from numpy import empty
values = empty((zsize, ysize, xsize), v.data.value_type)
axis_step = tuple([h * float(ai) / (zsize - 1) for ai in axis])
for i in range(zsize):
vval = v.interpolated_values(grid_points,
subregion=subregion,
step=step)
values[i, :, :] = vval.reshape((ysize, xsize))
grid_points[:] += axis_step # Shift annulus.
from chimerax.map_data import ArrayGridData
gstep = (float(r1 - r0) / (xsize - 1), circum / (ysize - 1),
float(h) / (zsize - 1))
gorigin = (center[0] + r0, center[1] - 0.5 * circum, center[2] - 0.5 * h)
g = ArrayGridData(values, gorigin, gstep, name='unrolled %s' % v.name)
from chimerax.map import volume_from_grid_data
vu = volume_from_grid_data(g, v.session, model_id=modelId)
vu.copy_settings_from(v,
copy_region=False,
copy_active=False,
copy_colors=False)
if axis[0] != 0 or axis[1] != 0:
# Rotate so unrolled volume is tangential to cylinder
from chimerax.geometry import orthonormal_frame
vu.position = v.position * orthonormal_frame(axis)
return vu
def array_to_model(mvol, volume, ijk_origin, model_id):
# Create masked volume grid object.
from chimerax.map_data import ArrayGridData
g = volume.data
morigin = g.ijk_to_xyz_transform * ijk_origin
m = ArrayGridData(mvol,
morigin,
g.step,
cell_angles=g.cell_angles,
rotation=g.rotation,
name=g.name + ' masked')
# Create masked volume object.
from chimerax.map import volume_from_grid_data
v = volume_from_grid_data(m, volume.session, model_id=model_id)
v.copy_settings_from(volume, copy_region=False)
v.show()
return v
def threshold_grid(volume,
minimum=None,
set_minimum=None,
maximum=None,
set_maximum=None,
step=1,
subregion=None,
region=None):
v = volume
if region is None:
region = v.subregion(step, subregion)
origin, step = v.region_origin_and_step(region)
m = v.region_matrix(region).copy()
import numpy
from numpy import array, putmask
if not minimum is None:
t = array(minimum, m.dtype)
if set_minimum is None or set_minimum == minimum:
numpy.maximum(m, t, m)
else:
putmask(m, m < t, array(set_minimum, m.dtype))
if not maximum is None:
t = array(maximum, m.dtype)
if set_maximum is None or set_maximum == maximum:
numpy.minimum(m, t, m)
else:
putmask(m, m > t, array(set_maximum, m.dtype))
from chimerax.map_data import ArrayGridData
d = v.data
if v.name.endswith('thresholded'): name = v.name
else: name = '%s thresholded' % v.name
tg = ArrayGridData(m, origin, step, d.cell_angles, d.rotation, name=name)
return tg
def local_correlation(map1, map2, window_size, subtract_mean, model_id=None):
d1 = map1.data
m1 = map1.full_matrix()
d2 = map2.data
m2, same = map2.interpolate_on_grid(map1)
mc = local_correlation_matrix(m1, m2, window_size, subtract_mean)
hs = 0.5 * (window_size - 1)
origin = tuple(o + hs * s for o, s in zip(d1.origin, d1.step))
from chimerax.map_data import ArrayGridData
g = ArrayGridData(mc,
origin,
d1.step,
d1.cell_angles,
d2.rotation,
name='local correlation')
from chimerax.map import volume_from_grid_data
mapc = volume_from_grid_data(g, map1.session, model_id=model_id)
mapc.position = map1.position
return mapc
def gaussian_grid(volume, sdev, step = 1, subregion = None, region = None,
value_type = None, invert = False, task = None):
v = volume
if region is None:
region = v.subregion(step, subregion)
origin, step = v.region_origin_and_step(region)
sdev3 = (sdev,sdev,sdev) if isinstance(sdev,(float,int)) else sdev
ijk_sdev = [float(sd)/s for sd,s in zip(sdev3,step)]
m = v.region_matrix(region)
gm = gaussian_convolution(m, ijk_sdev, value_type = value_type,
invert = invert, task = task)
from chimerax.map_data import ArrayGridData
d = v.data
if v.name.endswith('gaussian'): name = v.name
else: name = '%s gaussian' % v.name
gg = ArrayGridData(gm, origin, step, d.cell_angles, d.rotation,
name = name)
return gg
def median_grid(volume,
bin_size=3,
iterations=1,
step=1,
subregion=None,
region=None):
v = volume
if region is None:
region = v.subregion(step, subregion)
origin, step = v.region_origin_and_step(region)
vm = v.region_matrix(region)
m = vm
for i in range(iterations):
m = median_array(m, bin_size)
from chimerax.map_data import ArrayGridData
d = v.data
if v.name.endswith('median'): name = v.name
else: name = '%s median' % v.name
mg = ArrayGridData(m, origin, step, d.cell_angles, d.rotation, name=name)
return mg
def processed_volume(v, subregion = None, step = None, value_type = None, threshold = None,
zero_mean = False, scale_factor = None, match_scale = None,
enclose_volume = None, fast_enclose_volume = None, normalize_level = None,
align_to = None, on_grid = None, mask = None, final_value_type = None):
d = v.data
region = None
if not subregion is None or not step is None:
from chimerax.map.volume import full_region
ijk_min, ijk_max = full_region(d.size)[:2] if subregion is None else subregion
ijk_step = (1,1,1) if step is None else step
region = (ijk_min, ijk_max, ijk_step)
from chimerax.map_data import GridSubregion
d = GridSubregion(d, ijk_min, ijk_max, ijk_step)
if (value_type is None and threshold is None and not zero_mean and
scale_factor is None and match_scale is None and align_to is None and
mask is None and final_value_type is None):
return d
m = d.full_matrix()
if not value_type is None:
m = m.astype(value_type)
if not threshold is None:
from numpy import array, putmask
t = array(threshold, m.dtype)
putmask(m, m < t, 0)
if zero_mean:
from numpy import float64
mean = m.mean(dtype = float64)
m = (m - mean).astype(m.dtype)
if not scale_factor is None:
m = (m*scale_factor).astype(m.dtype)
if not match_scale is None:
ms = match_scale.region_matrix(region) if region else match_scale.full_matrix()
from numpy import float64, einsum
m1, ms1 = m.sum(dtype = float64), ms.sum(dtype = float64)
m2, ms2, mms = einsum('ijk,ijk',m,m,dtype=float64), einsum('ijk,ijk',ms,ms,dtype=float64), einsum('ijk,ijk',m,ms,dtype=float64)
n = m.size
a = (mms - m1*ms1/n) / (m2 - m1*m1/n)
b = (ms1 - a*m1) / n
am = a*m
am += b
print ('scaling #%s' % v.id_string, a, b, m1, ms1, m2, ms2, mms, am.mean(), am.std(), ms.mean(), ms.std())
m[:] = am.astype(m.dtype)
if not enclose_volume is None or not fast_enclose_volume is None:
set_enclosed_volume(v, enclose_volume, fast_enclose_volume)
if not normalize_level is None:
level = v.maximum_surface_level
if level is None:
from chimerax.core.errors import UserError
raise UserError('vseries save: normalize_level used but no level set for volume %s' % v.name)
if zero_mean:
level -= mean
scale = normalize_level / level
m = (m*scale).astype(m.dtype)
if not align_to is None:
align(v, align_to)
if not on_grid is None:
vc = v.writable_copy(value_type = m.dtype, unshow_original = False)
vc.full_matrix()[:,:,:] = m
m = on_grid.full_matrix()
m[:,:,:] = 0
on_grid.add_interpolated_values(vc)
vc.close()
d = on_grid.data
if not mask is None:
m[:,:,:] *= mask.full_matrix()
if not final_value_type is None:
m = m.astype(final_value_type)
from chimerax.map_data import ArrayGridData
d = ArrayGridData(m, d.origin, d.step, d.cell_angles, d.rotation)
return d
def matching_grid(grid):
from numpy import zeros, float32
matrix = zeros(grid.full_matrix().shape, float32)
from chimerax.map_data import ArrayGridData
g = ArrayGridData(matrix, grid.origin, grid.step)
return g
def grid_data_from_state(s, gdcache, session, file_paths):
if 'array' in s:
from numpy import frombuffer, dtype
from gzip import decompress
from base64 import b64decode
a = frombuffer(decompress(b64decode(s['array'])), dtype = dtype(s['value_type']))
if not a.flags.writeable:
a = a.copy()
array = a.reshape(s['size'][::-1])
from chimerax.map_data import ArrayGridData
dlist = [ArrayGridData(array)]
else:
dbfetch = s.get('database_fetch')
ask = (dbfetch is None)
if s.get('series_index',0) >= 1 or s.get('time',0) >= 1:
ask = False
path = absolute_path(s['path'], file_paths, ask = ask,
base_path = session.session_file_path)
empty_path = (path is None or path == '' or path == () or path == [])
if empty_path and dbfetch is None:
return None
else:
gid = s.get('grid_id','')
file_type = s['file_type']
dlist = open_data(path, gid, file_type, dbfetch, gdcache, session)
for data in dlist:
data.name = s['name']
if 'xyz_step' in s:
for data in dlist:
data.set_step(s['xyz_step'])
if 'xyz_origin' in s:
for data in dlist:
data.set_origin(s['xyz_origin'])
if 'cell_angles' in s:
for data in dlist:
data.set_cell_angles(s['cell_angles'])
if 'rotation' in s:
for data in dlist:
data.set_rotation(s['rotation'])
if 'symmetries' in s:
for data in dlist:
data.symmetries = s['symmetries']
if 'series_index' in s:
for data in dlist:
data.series_index = s['series_index']
if 'channel' in s:
for data in dlist:
data.channel = s['channel']
if 'time' in s:
for data in dlist:
data.time = s['time']
if 'available_subsamplings' in s:
# Subsamples may be from separate files or the same file.
from chimerax.map_data import SubsampledGrid
dslist = []
for data in dlist:
if not isinstance(data, SubsampledGrid):
data = SubsampledGrid(data)
dslist.append(data)
dlist = dslist
for cell_size, dstate in s['available_subsamplings'].items():
dpath = absolute_path(dstate.path, file_paths, base_path = session.session_file_path)
if dpath != path:
# TODO: This looks wrong. Don't we just recurse calling grid_data_from_state()?
ssdlist = dstate.create_object(gdcache)
for i,ssdata in enumerate(ssdlist):
dlist[i].add_subsamples(ssdata, cell_size)
return dlist
