def subtract_op(vol1,
vol2,
onGrid=None,
boundingGrid=False,
subregion='all',
step=1,
gridSubregion='all',
gridStep=1,
inPlace=False,
scaleFactors=None,
minRMS=False,
modelId=None):
vol1 = filter_volumes(vol1)
vol2 = filter_volumes(vol2)
if len(vol1) != 1 or len(vol2) != 1:
raise CommandError, 'vop subtract operation requires exactly two volumes'
if minRMS and scaleFactors:
raise CommandError, 'vop subtract cannot specify both minRMS and scaleFactors options.'
if minRMS:
mult = (1, 'minrms')
elif scaleFactors:
m0, m1 = parse_floats(scaleFactors, 'scaleFactors', 2)
mult = (m0, -m1)
else:
mult = (1, -1)
add_op(vol1 + vol2, onGrid, boundingGrid, subregion, step, gridSubregion,
gridStep, inPlace, mult, modelId)
def add_op(volumes,
onGrid=None,
boundingGrid=None,
subregion='all',
step=1,
gridSubregion='all',
gridStep=1,
inPlace=False,
scaleFactors=None,
modelId=None):
volumes = filter_volumes(volumes)
if boundingGrid is None and not inPlace:
boundingGrid = (onGrid is None)
if onGrid is None:
onGrid = volumes[:1]
onGrid = filter_volumes(onGrid, 'onGrid')
subregion = parse_subregion(subregion)
step = parse_step(step)
gridSubregion = parse_subregion(gridSubregion, 'gridSubregion')
gridStep = parse_step(gridStep, 'gridStep')
if inPlace:
if boundingGrid or gridStep != 1 or gridSubregion != 'all':
raise CommandError, "Can't use inPlace option with boundingGrid or gridStep or gridSubregion options"
for gv in onGrid:
if not gv.data.writable:
raise CommandError, "Can't modify volume in place: %s" % gv.name
if not gv in volumes:
raise CommandError, "Can't change grid in place"
if isinstance(scaleFactors, basestring):
scaleFactors = parse_floats(scaleFactors, 'scaleFactors', len(volumes))
modelId = parse_model_id(modelId)
for gv in onGrid:
add_operation(volumes, subregion, step, gv, gridSubregion, gridStep,
boundingGrid, inPlace, scaleFactors, modelId)
def add_op(volumes, onGrid = None, boundingGrid = None,
subregion = 'all', step = 1,
gridSubregion = 'all', gridStep = 1,
inPlace = False, scaleFactors = None, modelId = None):
volumes = filter_volumes(volumes)
if boundingGrid is None and not inPlace:
boundingGrid = (onGrid is None)
if onGrid is None:
onGrid = volumes[:1]
onGrid = filter_volumes(onGrid, 'onGrid')
subregion = parse_subregion(subregion)
step = parse_step(step)
gridSubregion = parse_subregion(gridSubregion, 'gridSubregion')
gridStep = parse_step(gridStep, 'gridStep')
if inPlace:
if boundingGrid or gridStep != 1 or gridSubregion != 'all':
raise CommandError, "Can't use inPlace option with boundingGrid or gridStep or gridSubregion options"
for gv in onGrid:
if not gv.data.writable:
raise CommandError, "Can't modify volume in place: %s" % gv.name
if not gv in volumes:
raise CommandError, "Can't change grid in place"
if isinstance(scaleFactors, basestring):
scaleFactors = parse_floats(scaleFactors, 'scaleFactors', len(volumes))
modelId = parse_model_id(modelId)
for gv in onGrid:
add_operation(volumes, subregion, step,
gv, gridSubregion, gridStep,
boundingGrid, inPlace, scaleFactors, modelId)
def cover_op(volumes, atomBox = None, pad = 5.0,
box = None, x = None, y = None, z = None,
fBox = None, fx = None, fy = None, fz = None,
iBox = None, ix = None, iy = None, iz = None,
step = 1, modelId = None):
volumes = filter_volumes(volumes)
check_number(pad, 'pad')
if not atomBox is None and len(atomBox) == 0:
raise CommandError, 'No atoms specified'
box = parse_box(box, x, y, z, 'box', 'x', 'y', 'z')
fBox = parse_box(fBox, fx, fy, fz, 'fBox', 'fx', 'fy', 'fz')
iBox = parse_box(iBox, ix, iy, iz, 'iBox', 'ix', 'iy', 'iz')
bc = len([b for b in (box, fBox, iBox, atomBox) if b])
if bc == 0:
raise CommandError, 'Must specify box to cover'
if bc > 1:
raise CommandError, 'Specify covering box in one way'
step = parse_step(step, require_3_tuple = True)
modelId = parse_model_id(modelId)
from VolumeViewer import volume, volume_from_grid_data
for v in volumes:
g = v.grid_data(subregion = 'all', step = step, mask_zone = False)
ijk_min, ijk_max = cover_box_bounds(v, step,
atomBox, pad, box, fBox, iBox)
cg = volume.map_from_periodic_map(g, ijk_min, ijk_max)
cv = volume_from_grid_data(cg, model_id = modelId)
cv.copy_settings_from(v, copy_region = False)
cv.show()
def scale_op(volumes,
shift=0,
factor=1,
type=None,
subregion='all',
step=1,
modelId=None):
volumes = filter_volumes(volumes)
check_number(shift, 'shift')
check_number(factor, 'factor')
if not type is None:
import numpy as n
types = {
'int8': n.int8,
'uint8': n.uint8,
'int16': n.int16,
'uint16': n.uint16,
'int32': n.int32,
'uint32': n.uint32,
'float32': n.float32,
'float64': n.float64,
}
if type in types:
type = types[type]
else:
raise CommandError, ('Unknown data value type "%s", use %s' %
(type, ', '.join(types.keys())))
subregion = parse_subregion(subregion)
step = parse_step(step)
modelId = parse_model_id(modelId)
from scale import scaled_volume
for v in volumes:
scaled_volume(v, factor, shift, type, step, subregion, modelId)
def morph_op(volumes, frames = 25, start = 0, playStep = 0.04,
playDirection = 1, playRange = None, addMode = False,
constantVolume = False, scaleFactors = None,
hideOriginalMaps = True, subregion = 'all', step = 1,
modelId = None):
volumes = filter_volumes(volumes)
check_number(frames, 'frames', int, nonnegative = True)
check_number(start, 'start')
check_number(playStep, 'playStep', nonnegative = True)
if playRange is None:
if addMode:
prange = (-1.0,1.0)
else:
prange = (0.0,1.0)
else:
prange = parse_floats(playRange, 'playRange', 2)
check_number(playDirection, 'playDirection')
sfactors = parse_floats(scaleFactors, 'scaleFactors', len(volumes))
subregion = parse_subregion(subregion)
step = parse_step(step)
modelId = parse_model_id(modelId)
vs = [tuple(v.matrix_size(step = step, subregion = subregion))
for v in volumes]
if len(set(vs)) > 1:
sizes = ' and '.join([str(s) for s in vs])
raise CommandError, "Volume grid sizes don't match: %s" % sizes
from MorphMap import morph_maps
morph_maps(volumes, frames, start, playStep, playDirection, prange,
addMode, constantVolume, sfactors,
hideOriginalMaps, subregion, step, modelId)
def scale_op(volumes, shift = 0, factor = 1, type = None,
subregion = 'all', step = 1, modelId = None):
volumes = filter_volumes(volumes)
check_number(shift, 'shift')
check_number(factor, 'factor')
if not type is None:
import numpy as n
types = {'int8': n.int8,
'uint8': n.uint8,
'int16': n.int16,
'uint16': n.uint16,
'int32': n.int32,
'uint32': n.uint32,
'float32': n.float32,
'float64': n.float64,
}
if type in types:
type = types[type]
else:
raise CommandError, ('Unknown data value type "%s", use %s'
% (type, ', '.join(types.keys())))
subregion = parse_subregion(subregion)
step = parse_step(step)
modelId = parse_model_id(modelId)
from scale import scaled_volume
for v in volumes:
scaled_volume(v, factor, shift, type, step, subregion, modelId)
def laplacian_op(volumes, subregion = 'all', step = 1, modelId = None):
volumes = filter_volumes(volumes)
subregion = parse_subregion(subregion)
step = parse_step(step)
modelId = parse_model_id(modelId)
from laplace import laplacian
for v in volumes:
laplacian(v, step, subregion, modelId)
def z_flip_op(volumes, subregion='all', step=1, inPlace=False, modelId=None):
volumes = filter_volumes(volumes)
subregion = parse_subregion(subregion)
step = parse_step(step)
check_in_place(inPlace, volumes[:1])
modelId = parse_model_id(modelId)
for v in volumes:
zflip_operation(v, subregion, step, inPlace, modelId)
def fourier_op(volumes, subregion='all', step=1, modelId=None):
volumes = filter_volumes(volumes)
subregion = parse_subregion(subregion)
step = parse_step(step)
modelId = parse_model_id(modelId)
from fourier import fourier_transform
for v in volumes:
fourier_transform(v, step, subregion, modelId)
def fourier_op(volumes, subregion = 'all', step = 1, modelId = None):
volumes = filter_volumes(volumes)
subregion = parse_subregion(subregion)
step = parse_step(step)
modelId = parse_model_id(modelId)
from fourier import fourier_transform
for v in volumes:
fourier_transform(v, step, subregion, modelId)
def resample_op(volumes, onGrid = None, boundingGrid = False,
subregion = 'all', step = 1,
gridSubregion = 'all', gridStep = 1,
modelId = None):
volumes = filter_volumes(volumes)
if onGrid is None:
raise CommandError, 'Resample operation must specify onGrid option'
subregion = parse_subregion(subregion)
step = parse_step(step)
gridSubregion = parse_subregion(gridSubregion, 'gridSubregion')
gridStep = parse_step(gridStep, 'gridStep')
onGrid = filter_volumes(onGrid, 'onGrid')
modelId = parse_model_id(modelId)
for v in volumes:
for gv in onGrid:
add_operation([v], subregion, step,
gv, gridSubregion, gridStep,
boundingGrid, False, None, modelId)
def laplacian_op(volumes, subregion='all', step=1, modelId=None):
volumes = filter_volumes(volumes)
subregion = parse_subregion(subregion)
step = parse_step(step)
modelId = parse_model_id(modelId)
from laplace import laplacian
for v in volumes:
laplacian(v, step, subregion, modelId)
def z_flip_op(volumes, subregion = 'all', step = 1,
inPlace = False, modelId = None):
volumes = filter_volumes(volumes)
subregion = parse_subregion(subregion)
step = parse_step(step)
check_in_place(inPlace, volumes[:1])
modelId = parse_model_id(modelId)
for v in volumes:
zflip_operation(v, subregion, step, inPlace, modelId)
def gaussian_op(volumes, sDev=1.0, subregion='all', step=1, modelId=None):
volumes = filter_volumes(volumes)
check_number(sDev, 'sDev', positive=True)
subregion = parse_subregion(subregion)
step = parse_step(step)
modelId = parse_model_id(modelId)
from gaussian import gaussian_convolve
for v in volumes:
gaussian_convolve(v, sDev, step, subregion, modelId)
def gaussian_op(volumes, sDev = 1.0,
subregion = 'all', step = 1, modelId = None):
volumes = filter_volumes(volumes)
check_number(sDev, 'sDev', positive = True)
subregion = parse_subregion(subregion)
step = parse_step(step)
modelId = parse_model_id(modelId)
from gaussian import gaussian_convolve
for v in volumes:
gaussian_convolve(v, sDev, step, subregion, modelId)
def resample_op(volumes,
onGrid=None,
boundingGrid=False,
subregion='all',
step=1,
gridSubregion='all',
gridStep=1,
modelId=None):
volumes = filter_volumes(volumes)
if onGrid is None:
raise CommandError, 'Resample operation must specify onGrid option'
subregion = parse_subregion(subregion)
step = parse_step(step)
gridSubregion = parse_subregion(gridSubregion, 'gridSubregion')
gridStep = parse_step(gridStep, 'gridStep')
onGrid = filter_volumes(onGrid, 'onGrid')
modelId = parse_model_id(modelId)
for v in volumes:
for gv in onGrid:
add_operation([v], subregion, step, gv, gridSubregion, gridStep,
boundingGrid, False, None, modelId)
def subtract_op(vol1, vol2, onGrid = None, boundingGrid = False,
subregion = 'all', step = 1,
gridSubregion = 'all', gridStep = 1,
inPlace = False, scaleFactors = None, minRMS = False,
modelId = None):
vol1 = filter_volumes(vol1)
vol2 = filter_volumes(vol2)
if len(vol1) != 1 or len(vol2) != 1:
raise CommandError, 'vop subtract operation requires exactly two volumes'
if minRMS and scaleFactors:
raise CommandError, 'vop subtract cannot specify both minRMS and scaleFactors options.'
if minRMS:
mult = (1,'minrms')
elif scaleFactors:
m0,m1 = parse_floats(scaleFactors, 'scaleFactors', 2)
mult = (m0,-m1)
else:
mult = (1,-1)
add_op(vol1+vol2, onGrid, boundingGrid, subregion, step,
gridSubregion, gridStep, inPlace, mult, modelId)
def boxes_op(volumes, markers, size = 0, useMarkerSize = False,
subregion = 'all', step = 1, modelId = None):
volumes = filter_volumes(volumes)
check_number(size, 'size')
if size <= 0 and not useMarkerSize:
raise CommandError, 'Must specify size or enable useMarkerSize'
subregion = parse_subregion(subregion)
step = parse_step(step)
modelId = parse_model_id(modelId)
from boxes import boxes
for v in volumes:
boxes(v, markers, size, useMarkerSize, step, subregion, modelId)
def bin_op(volumes, subregion='all', step=1, binSize=(2, 2, 2), modelId=None):
volumes = filter_volumes(volumes)
subregion = parse_subregion(subregion)
step = parse_step(step)
if isinstance(binSize, int):
binSize = (binSize, binSize, binSize)
elif isinstance(binSize, basestring):
binSize = parse_ints(binSize, 'binSize', 3)
modelId = parse_model_id(modelId)
from bin import bin
for v in volumes:
bin(v, binSize, step, subregion, modelId)
def permute_axes_op(volumes, axisOrder = 'xyz',
subregion = 'all', step = 1, modelId = None):
volumes = filter_volumes(volumes)
ao = {'xyz':(0,1,2), 'xzy':(0,2,1), 'yxz':(1,0,2),
'yzx':(1,2,0), 'zxy':(2,0,1), 'zyx':(2,1,0)}
if not axisOrder in ao:
raise CommandError, 'Axis order must be xyz, xzy, zxy, zyx, yxz, or yzx'
subregion = parse_subregion(subregion)
step = parse_step(step)
modelId = parse_model_id(modelId)
from permute import permute_axes
for v in volumes:
permute_axes(v, ao[axisOrder], step, subregion, modelId)
def bin_op(volumes, subregion = 'all', step = 1,
binSize = (2,2,2), modelId = None):
volumes = filter_volumes(volumes)
subregion = parse_subregion(subregion)
step = parse_step(step)
if isinstance(binSize, int):
binSize = (binSize, binSize, binSize)
elif isinstance(binSize, basestring):
binSize = parse_ints(binSize, 'binSize', 3)
modelId = parse_model_id(modelId)
from bin import bin
for v in volumes:
bin(v, binSize, step, subregion, modelId)
def octant_complement_op(volumes, center = None, iCenter = None,
subregion = 'all', step = 1, inPlace = False,
fillValue = 0, modelId = None):
volumes = filter_volumes(volumes)
center = parse_floats(center, 'center', 3)
iCenter = parse_floats(iCenter, 'iCenter', 3)
subregion = parse_subregion(subregion)
step = parse_step(step)
check_in_place(inPlace, volumes)
check_number(fillValue, 'fillValue')
modelId = parse_model_id(modelId)
outside = False
for v in volumes:
octant_operation(v, outside, center, iCenter, subregion, step,
inPlace, fillValue, modelId)
def median_op(volumes, binSize = 3, iterations = 1,
subregion = 'all', step = 1, modelId = None):
volumes = filter_volumes(volumes)
check_number(iterations, 'iterations', positive = True)
binSize = parse_step(binSize, 'binSize', require_3_tuple = True)
for b in binSize:
if b <= 0 or b % 2 == 0:
raise CommandError, 'Bin size must be positive odd integer, got %d' % b
subregion = parse_subregion(subregion)
step = parse_step(step)
modelId = parse_model_id(modelId)
from median import median_filter
for v in volumes:
median_filter(v, binSize, iterations, step, subregion, modelId)
def cover_op(volumes,
atomBox=None,
pad=5.0,
box=None,
x=None,
y=None,
z=None,
fBox=None,
fx=None,
fy=None,
fz=None,
iBox=None,
ix=None,
iy=None,
iz=None,
step=1,
modelId=None):
volumes = filter_volumes(volumes)
check_number(pad, 'pad')
if not atomBox is None and len(atomBox) == 0:
raise CommandError, 'No atoms specified'
box = parse_box(box, x, y, z, 'box', 'x', 'y', 'z')
fBox = parse_box(fBox, fx, fy, fz, 'fBox', 'fx', 'fy', 'fz')
iBox = parse_box(iBox, ix, iy, iz, 'iBox', 'ix', 'iy', 'iz')
bc = len([b for b in (box, fBox, iBox, atomBox) if b])
if bc == 0:
raise CommandError, 'Must specify box to cover'
if bc > 1:
raise CommandError, 'Specify covering box in one way'
step = parse_step(step, require_3_tuple=True)
modelId = parse_model_id(modelId)
from VolumeViewer import volume, volume_from_grid_data
for v in volumes:
g = v.grid_data(subregion='all', step=step, mask_zone=False)
ijk_min, ijk_max = cover_box_bounds(v, step, atomBox, pad, box, fBox,
iBox)
cg = volume.map_from_periodic_map(g, ijk_min, ijk_max)
cv = volume_from_grid_data(cg, model_id=modelId)
cv.copy_settings_from(v, copy_region=False)
cv.show()
def boxes_op(volumes,
markers,
size=0,
useMarkerSize=False,
subregion='all',
step=1,
modelId=None):
volumes = filter_volumes(volumes)
check_number(size, 'size')
if size <= 0 and not useMarkerSize:
raise CommandError, 'Must specify size or enable useMarkerSize'
subregion = parse_subregion(subregion)
step = parse_step(step)
modelId = parse_model_id(modelId)
from boxes import boxes
for v in volumes:
boxes(v, markers, size, useMarkerSize, step, subregion, modelId)
def median_op(volumes,
binSize=3,
iterations=1,
subregion='all',
step=1,
modelId=None):
volumes = filter_volumes(volumes)
check_number(iterations, 'iterations', positive=True)
binSize = parse_step(binSize, 'binSize', require_3_tuple=True)
for b in binSize:
if b <= 0 or b % 2 == 0:
raise CommandError, 'Bin size must be positive odd integer, got %d' % b
subregion = parse_subregion(subregion)
step = parse_step(step)
modelId = parse_model_id(modelId)
from median import median_filter
for v in volumes:
median_filter(v, binSize, iterations, step, subregion, modelId)
def octant_complement_op(volumes,
center=None,
iCenter=None,
subregion='all',
step=1,
inPlace=False,
fillValue=0,
modelId=None):
volumes = filter_volumes(volumes)
center = parse_floats(center, 'center', 3)
iCenter = parse_floats(iCenter, 'iCenter', 3)
subregion = parse_subregion(subregion)
step = parse_step(step)
check_in_place(inPlace, volumes)
check_number(fillValue, 'fillValue')
modelId = parse_model_id(modelId)
outside = False
for v in volumes:
octant_operation(v, outside, center, iCenter, subregion, step, inPlace,
fillValue, modelId)
def morph_op(volumes,
frames=25,
start=0,
playStep=0.04,
playDirection=1,
playRange=None,
addMode=False,
constantVolume=False,
scaleFactors=None,
hideOriginalMaps=True,
subregion='all',
step=1,
modelId=None):
volumes = filter_volumes(volumes)
check_number(frames, 'frames', int, nonnegative=True)
check_number(start, 'start')
check_number(playStep, 'playStep', nonnegative=True)
if playRange is None:
if addMode:
prange = (-1.0, 1.0)
else:
prange = (0.0, 1.0)
else:
prange = parse_floats(playRange, 'playRange', 2)
check_number(playDirection, 'playDirection')
sfactors = parse_floats(scaleFactors, 'scaleFactors', len(volumes))
subregion = parse_subregion(subregion)
step = parse_step(step)
modelId = parse_model_id(modelId)
vs = [
tuple(v.matrix_size(step=step, subregion=subregion)) for v in volumes
]
if len(set(vs)) > 1:
sizes = ' and '.join([str(s) for s in vs])
raise CommandError, "Volume grid sizes don't match: %s" % sizes
from MorphMap import morph_maps
morph_maps(volumes, frames, start, playStep, playDirection, prange,
addMode, constantVolume, sfactors, hideOriginalMaps, subregion,
step, modelId)
def mask(volumes, surfaces, axis = None, fullMap = False,
pad = 0., slab = None, sandwich = True, invertMask = False):
from Commands import CommandError, filter_volumes, parse_floats
vlist = filter_volumes(volumes)
from Surface import selected_surface_pieces
glist = selected_surface_pieces(surfaces, include_outline_boxes = False)
if len(glist) == 0:
raise CommandError, 'No surfaces specified'
axis = parse_floats(axis, 'axis', 3, (0,1,0))
if not isinstance(fullMap, (bool,int)):
raise CommandError, 'fullMap option value must be true or false'
if not isinstance(invertMask, (bool,int)):
raise CommandError, 'invertMask option value must be true or false'
if not isinstance(pad, (float,int)):
raise CommandError, 'pad option value must be a number'
if isinstance(slab, (float,int)):
pad = (-0.5*slab, 0.5*slab)
elif not slab is None:
pad = parse_floats(slab, 'slab', 2)
if not isinstance(sandwich, bool):
raise CommandError, 'sandwich option value must be true or false'
from depthmask import surface_geometry, masked_volume
from Matrix import xform_matrix, invert_matrix
for v in vlist:
tf = invert_matrix(xform_matrix(v.model_transform()))
surfs = surface_geometry(glist, tf, pad)
masked_volume(v, surfs, axis, fullMap, sandwich, invertMask)
def permute_axes_op(volumes,
axisOrder='xyz',
subregion='all',
step=1,
modelId=None):
volumes = filter_volumes(volumes)
ao = {
'xyz': (0, 1, 2),
'xzy': (0, 2, 1),
'yxz': (1, 0, 2),
'yzx': (1, 2, 0),
'zxy': (2, 0, 1),
'zyx': (2, 1, 0)
}
if not axisOrder in ao:
raise CommandError, 'Axis order must be xyz, xzy, zxy, zyx, yxz, or yzx'
subregion = parse_subregion(subregion)
step = parse_step(step)
modelId = parse_model_id(modelId)
from permute import permute_axes
for v in volumes:
permute_axes(v, ao[axisOrder], step, subregion, modelId)