def writable_volume():
from VolumeViewer import active_volume
dr = active_volume()
if dr == None:
return None # No volume chosen in volume viewer
return dr.writable_copy()
def filter_cb(self, event = None):
from VolumeViewer import active_volume
v = active_volume()
if v is None:
return
ftype = self.filter_type.get()
uv,r,params = self.unfiltered_volume(v, ftype)
if uv:
self.update_filtered_volume(v, ftype)
else:
step, subreg = self.step_and_subregion()
try:
fv, params = self.apply_filter(v, ftype, step, subreg)
except MemoryError:
from chimera.replyobj import warning
warning('Out of memory calculating %s filter of %s' % (ftype, v.name))
return
if fv is None:
return
self.update_thresholds(fv, v)
fv.show()
r = v.subregion(step, subreg)
fv.filtered_volume = (ftype, v, r, params)
def select_atoms_outside_map():
from chimera.replyobj import status, info
from VolumeViewer import active_volume
dr = active_volume()
if dr is None:
status('No density map opened.')
return
if dr.surface_model() == None or not dr.surface_model().display:
status('No surface shown for map.')
return
levels = dr.surface_levels
if len(levels) == 0:
status('No surface shown for map.')
return
contour_level = min(levels)
from chimera import selection
atoms = selection.currentAtoms()
aolist = atoms_outside_map(atoms, dr, contour_level)
msg = ('%d of %d selected atoms outside %s at level %.5g' %
(len(aolist), len(atoms), dr.name, contour_level))
status(msg)
info(msg + '\n')
selection.setCurrent(aolist)
def split_volume_by_color_zone(v = None):
if v is None:
from VolumeViewer import active_volume
v = active_volume()
if v is None:
return
m = v.surface_model()
import ColorZone
if not ColorZone.coloring_zone(m):
return
points, colors, radius = ColorZone.zone_points_colors_and_distance(m)
grids = split_zones_by_color(v, points, colors, radius)
from VolumeViewer import volume_from_grid_data
drlist = [volume_from_grid_data(g, show_data = False) for g in grids]
n = len(v.surface_colors)
for dr in drlist:
dr.copy_settings_from(v, copy_region = False)
dr.set_parameters(surface_colors = [dr.data.zone_color]*n)
dr.show()
v.unshow()
return drlist
def select_atoms_outside_map():
from chimera.replyobj import status, info
from VolumeViewer import active_volume
dr = active_volume()
if dr is None:
status('No density map opened.')
return
if dr.surface_model() == None or not dr.surface_model().display:
status('No surface shown for map.')
return
levels = dr.surface_levels
if len(levels) == 0:
status('No surface shown for map.')
return
contour_level = min(levels)
from chimera import selection
atoms = selection.currentAtoms()
aolist = atoms_outside_map(atoms, dr, contour_level)
msg = ('%d of %d selected atoms outside %s at level %.5g' %
(len(aolist), len(atoms), dr.name, contour_level))
status(msg)
info(msg + '\n')
selection.setCurrent(aolist)
def move_selected_atoms_to_maximum(max_steps = 100, ijk_step_size_min = 0.01,
ijk_step_size_max = 0.5,
optimize_translation = True,
optimize_rotation = True,
move_whole_molecules = True,
request_stop_cb = None):
from VolumeViewer import active_volume
volume = active_volume()
if volume == None or volume.model_transform() == None:
if request_stop_cb:
request_stop_cb('No volume data set.')
return {}
from chimera import selection
atoms = selection.currentAtoms()
if len(atoms) == 0:
if request_stop_cb:
request_stop_cb('No atoms selected.')
return {}
stats = move_atoms_to_maximum(atoms, volume, max_steps,
ijk_step_size_min, ijk_step_size_max,
optimize_translation, optimize_rotation,
move_whole_molecules,
request_stop_cb)
return stats
def test():
from Segger import SelectedRegions
rlist = SelectedRegions()
from VolumeViewer import active_volume
volume = active_volume()
make_orthoslice_images(rlist, volume)
def volume_viewer_time(self, ts):
from VolumeViewer import active_volume
dr = active_volume()
if dr == None:
t = None
else:
t = ts.data_time(dr.data)
return t
def atoms_outside_contour(atoms, volume = None):
if volume is None:
from VolumeViewer import active_volume
volume = active_volume()
points = atom_coordinates(atoms)
from chimera import Xform
poc, clevel = points_outside_contour(points, Xform(), volume)
return poc, clevel
def fourier_transform(v = None, step = None, subregion = None, model_id = None):
if v is None:
from VolumeViewer import active_volume
v = active_volume()
if v is None:
return
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, float32
aftm = absolute(cftm).astype(float32)
cftm = None # Release memory
aftm *= 1.0/aftm.size
aftm[0,0,0] = 0 # Constant term often huge making histogram hard to use
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 = map(lambda a,b: a-b, xyz_max, xyz_min)
vol = xyz_size[0]*xyz_size[1]*xyz_size[2]
cell_size = map(lambda a,b: a*b, 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 = map(lambda a: scale/a, xyz_size)
origin = map(lambda c,s,z: c-0.5*s*z, xyz_center, step, ijk_size)
from VolumeData import Array_Grid_Data
ftd = Array_Grid_Data(ftm, origin, step)
ftd.name = v.name + ' FT'
from VolumeViewer import volume_from_grid_data
ftr = volume_from_grid_data(ftd, show_data = False, model_id = model_id)
ftr.copy_settings_from(v, copy_thresholds = False, copy_colors = False,
copy_region = False)
ftr.initialize_thresholds()
ftr.set_parameters(show_outline_box = True)
ftr.show()
v.unshow() # Hide original map
return ftr
def filter_parameter_changed_cb(self, event = None):
if not self.immediate_update.get():
return
from VolumeViewer import active_volume
fv = active_volume()
if fv is None:
return
self.update_filtered_volume(fv, self.filter_type.get())
def set_scale_range(self, initial = False):
from VolumeViewer import active_volume
v = active_volume()
if v is None:
return
s = min(v.data.step)
if s > 0:
self.sdev.set_range(0.5*s, 5*s)
if initial:
self.sdev.set_value(s, invoke_callbacks = False)
def set_radius_for_volume_data(self):
dr = active_volume()
if dr == None:
return
xyz_min, xyz_max = dr.xyz_bounds()
xyz_size = map(lambda a,b: a-b, xyz_max, xyz_min)
size = max(xyz_size)
rs = self.sphere_radius_scale
rs.set_range(0, size)
rs.set_value(.1 * size)
def scaled_volume(v = None, scale = 1, shift = 0, type = None,
step = None, subregion = None, model_id = None):
if v is None:
from VolumeViewer import active_volume
v = active_volume()
if v is None:
return
sd = scaled_grid(v, scale, shift, type, subregion, step)
import VolumeViewer
sv = VolumeViewer.volume_from_grid_data(sd, model_id = model_id)
return sv
def show_volume_statistics(show_reply_log = True):
from VolumeViewer import active_volume
dr = active_volume()
if dr == None:
message('No volume data opened', show_reply_log)
return
m = dr.matrix()
mean, sd, rms = mean_sd_rms(m)
descrip = subregion_description(dr)
message('%s%s: mean = %.5g, SD = %.5g, RMS = %.5g'
% (dr.name, descrip, mean, sd, rms),
show_reply_log)
def show_volume_statistics(show_reply_log=True):
from VolumeViewer import active_volume
dr = active_volume()
if dr == None:
message('No volume data opened', show_reply_log)
return
m = dr.matrix()
mean, sd, rms = mean_sd_rms(m)
descrip = subregion_description(dr)
message(
'%s%s: mean = %.5g, SD = %.5g, RMS = %.5g' %
(dr.name, descrip, mean, sd, rms), show_reply_log)
def permute_axes(v = None, axis_order = (0,1,2),
step = None, subregion = None, model_id = None):
if v is None:
from VolumeViewer import active_volume
v = active_volume()
if v is None:
return
d = v.grid_data(subregion, step, mask_zone = False)
pd = Permuted_Grid(d, axis_order)
import VolumeViewer
pv = VolumeViewer.volume_from_grid_data(pd, model_id = model_id)
return pv
def mask_volume_using_selected_surfaces(axis = (0,1,0), pad = None):
from VolumeViewer import active_volume
v = active_volume()
if v is None:
return
from Surface import selected_surface_pieces
plist = selected_surface_pieces()
from Matrix import xform_matrix, invert_matrix
tf = invert_matrix(xform_matrix(v.model_transform()))
surfaces = surface_geometry(plist, tf, pad)
if surfaces:
masked_volume(v, surfaces, axis)
def mask_volume_using_selected_surfaces(axis=(0, 1, 0), pad=None):
from VolumeViewer import active_volume
v = active_volume()
if v is None:
return
from Surface import selected_surface_pieces
plist = selected_surface_pieces()
from Matrix import xform_matrix, invert_matrix
tf = invert_matrix(xform_matrix(v.model_transform()))
surfaces = surface_geometry(plist, tf, pad)
if surfaces:
masked_volume(v, surfaces, axis)
def average_map_value_at_atom_positions(atoms, volume = None):
if volume is None:
from VolumeViewer import active_volume
volume = active_volume()
points = atom_coordinates(atoms)
if volume is None or len(points) == 0:
return 0, len(points)
xyz_to_ijk_transform = data_region_xyz_to_ijk_transform(volume)
data_array = volume.matrix(step = 1)
amv, npts = average_map_value(points, xyz_to_ijk_transform, data_array)
return amv, npts
def bin(v = None, bin_size = (2,2,2),
step = None, subregion = None, model_id = None):
if v is None:
from VolumeViewer import active_volume
v = active_volume()
if v is None:
return None
bd = bin_grid(v, bin_size, step, subregion)
import VolumeViewer
bv = VolumeViewer.volume_from_grid_data(bd, model_id = model_id)
bv.copy_settings_from(v, copy_region = False)
v.unshow() # Hide original map
return bv
def permute_axes(v=None,
axis_order=(0, 1, 2),
step=None,
subregion=None,
model_id=None):
if v is None:
from VolumeViewer import active_volume
v = active_volume()
if v is None:
return
d = v.grid_data(subregion, step, mask_zone=False)
pd = Permuted_Grid(d, axis_order)
import VolumeViewer
pv = VolumeViewer.volume_from_grid_data(pd, model_id=model_id)
return pv
def scaled_volume(v=None,
scale=1,
shift=0,
type=None,
step=None,
subregion=None,
model_id=None):
if v is None:
from VolumeViewer import active_volume
v = active_volume()
if v is None:
return
sd = scaled_grid(v, scale, shift, type, subregion, step)
import VolumeViewer
sv = VolumeViewer.volume_from_grid_data(sd, model_id=model_id)
return sv
def laplacian(v = None, step = None, subregion = None, model_id = None):
if v is None:
from VolumeViewer import active_volume
v = active_volume()
if v is None:
return 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 VolumeData import Array_Grid_Data
ld = Array_Grid_Data(lm, origin, step, d.cell_angles, d.rotation,
name = v.name + ' Laplacian')
ld.polar_values = True
from VolumeViewer import volume_from_grid_data
lv = volume_from_grid_data(ld, show_data = False, model_id = model_id)
lv.copy_settings_from(v, copy_thresholds = False, copy_colors = False)
lv.set_parameters(cap_faces = False)
lv.initialize_thresholds()
lv.show()
v.unshow() # Hide original map
return lv
def front_of_volume_at_screen_center():
v = active_volume()
if v == None:
return None
import chimera
wx_size, wy_size = chimera.viewer.windowSize
from VolumeViewer.slice import volume_segment
xyz_in, xyz_out, shown = volume_segment(v, wx_size/2, wy_size/2)
if xyz_in == None:
return None
xf = v.model_transform()
eye_xyz_in = xf.apply(chimera.Point(*xyz_in))
return eye_xyz_in
def set_volume_icosahedral_symmetry():
from VolumeViewer import active_volume
v = active_volume()
if v is None:
from chimera.replyobj import status
status('Set icosahedral symmetry: No active volume data.')
return
from Icosahedron.gui import icosahedron_dialog
d = icosahedron_dialog()
if d is None:
orientation = '222'
else:
orientation = d.orientation_name()
from Icosahedron import icosahedral_symmetry_matrices
v.data.symmetries = icosahedral_symmetry_matrices(orientation)
from chimera.replyobj import status
status('Set icosahedral symmetry %s of volume %s.' % (orientation, v.name))
def set_volume_icosahedral_symmetry():
from VolumeViewer import active_volume
v = active_volume()
if v is None:
from chimera.replyobj import status
status('Set icosahedral symmetry: No active volume data.')
return
from Icosahedron.gui import icosahedron_dialog
d = icosahedron_dialog()
if d is None:
orientation = '222'
else:
orientation = d.orientation_name()
from Icosahedron import icosahedral_symmetry_matrices
v.data.symmetries = icosahedral_symmetry_matrices(orientation)
from chimera.replyobj import status
status('Set icosahedral symmetry %s of volume %s.' % (orientation, v.name))
def move_atom_to_maximum(a, max_steps = 100,
ijk_step_size_min = 0.001, ijk_step_size_max = 0.5):
from VolumeViewer import active_volume
dr = active_volume()
if dr == None or dr.model_transform() == None:
from chimera.replyobj import status
status('No data shown by volume viewer dialog')
return
points = atom_coordinates([a])
point_weights = None
move_tf, stats = motion_to_maximum(points, point_weights, dr, max_steps,
ijk_step_size_min, ijk_step_size_max,
optimize_translation = True,
optimize_rotation = False)
# Update atom position.
from Matrix import chimera_xform
xf = chimera_xform(move_tf)
mxf = a.molecule.openState.xform
p = mxf.inverse().apply(xf.apply(a.xformCoord()))
a.setCoord(p)
def fillInUI(self, parent):
self.phantom_device = None
self.cursor_model = None
self.phantom_handler = None
self.gradient_force = None
self.phantom_button_down = 0
self.last_phantom_transform = None
self.last_roll = None
self.key_callback_registered = None
self.mode = 'cursor' # 'cursor', 'move models', 'zoom',
# 'contour level', 'move marker'
self.command_list_shown = False
import Tkinter
from CGLtk import Hybrid
row = 0
po = Hybrid.Checkbutton_Row(parent, 'Enable', ('cursor', 'forces', 'key commands'))
po.frame.grid(row = row, column = 0, sticky = 'w')
row = row + 1
self.phantom_on, self.force_field, self.commands = \
[c.variable for c in po.checkbuttons]
self.phantom_on.add_callback(self.settings_changed_cb)
self.force_field.add_callback(self.settings_changed_cb)
self.commands.add_callback(self.toggle_commands_cb)
cf = Tkinter.Frame(parent)
cf.grid(row = row, column = 0, sticky = 'w')
row = row + 1
cs = Hybrid.Option_Menu(cf, 'Cursor shape ',
'cross', 'jack', 'sphere', 'volume crosshair')
cs.frame.grid(row = 0, column = 0, sticky = 'nw')
row = row + 1
cs.variable.set('jack')
cs.add_callback(self.settings_changed_cb)
self.cursor_shape = cs.variable
from VolumeViewer import active_volume
v = active_volume()
if v:
csize = '%.3g' % (10 * max(v.data.step))
else:
csize = '1'
cs = Hybrid.Entry(cf, ' size ', 5, csize)
cs.frame.grid(row = 0, column = 1, sticky = 'w')
cs.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
self.cursor_size = cs.variable
cl = Tkinter.Label(cf, text = ' color ')
cl.grid(row = 0, column = 2, sticky = 'w')
from CGLtk.color import ColorWell
cc = ColorWell.ColorWell(cf, callback = self.settings_changed_cb)
self.cursor_color = cc
cc.showColor((0,0.5,1), doCallback = 0)
cc.grid(row = 0, column = 3, sticky = 'w')
sp = Hybrid.Popup_Panel(parent)
spf = sp.frame
spf.grid(row = row, column = 0, sticky = 'news')
spf.grid_remove()
spf.columnconfigure(0, weight=1)
self.settings_panel = sp.panel_shown_variable
row += 1
srow = 0
cb = sp.make_close_button(spf)
cb.grid(row = srow, column = 1, sticky = 'e')
pr = Hybrid.Entry(spf, 'Phantom physical range (mm) ', 5, '200')
pr.frame.grid(row = srow, column = 0, sticky = 'w')
srow += 1
pr.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
self.phantom_range = pr.variable
mf = Hybrid.Entry(spf, 'Maximum force (lbs) ', 5, '.4')
mf.frame.grid(row = srow, column = 0, sticky = 'w')
srow += 1
mf.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
self.maximum_force = mf.variable
af = Hybrid.Checkbutton(spf, 'Auto-adjust force constant', 1)
af.button.grid(row = srow, column = 0, sticky = 'w')
srow += 1
self.auto_adjust_force_constant = af.variable
self.force_field.add_callback(self.settings_changed_cb)
fc = Hybrid.Logarithmic_Scale(spf, 'Force constant ',
.0001, 100, 1, '%.2g')
fc.frame.grid(row = srow, column = 0, sticky = 'ew')
srow += 1
fc.set_value(1)
fc.callback(self.force_constant_changed_cb)
fc.entry.bind('<KeyPress-Return>', self.force_constant_changed_cb)
self.force_constant = fc
vf = Tkinter.Frame(spf)
vf.grid(row = srow, column = 0, sticky = 'ew')
srow += 1
self.label_row(vf, 0, ('', 'x', 'y', 'z'))
pl = self.label_row(vf, 1, ('Phantom position', '', '', ''))
self.phantom_position_labels = pl[1:]
cpl = self.label_row(vf, 2, ('Chimera position', '', '', ''))
self.chimera_position_labels = cpl[1:]
vpl = self.label_row(vf, 3, ('Volume position', '', '', ''))
self.volume_position_labels = vpl[1:]
vil = self.label_row(vf, 4, ('Volume index', '', '', ''))
self.volume_index_labels = vil[1:]
gl = self.label_row(vf, 5, ('Gradient', '', '', ''))
self.gradient_labels = gl[1:]
fl = self.label_row(vf, 6, ('Force', '', '', ''))
self.force_labels = fl[1:]
dvl = self.label_row(vf, 7, ('Data value', ''))
self.data_value_label = dvl[1]
def data_region(self):
from VolumeViewer import active_volume
return active_volume()
def active_volume(): from VolumeViewer import active_volume return active_volume()
def fillInUI(self, parent):
self.phantom_device = None
self.cursor_model = None
self.phantom_handler = None
self.gradient_force = None
self.phantom_button_down = 0
self.last_phantom_transform = None
self.last_roll = None
self.key_callback_registered = None
self.mode = 'cursor' # 'cursor', 'move models', 'zoom',
# 'contour level', 'move marker'
self.command_list_shown = False
import Tkinter
from CGLtk import Hybrid
row = 0
po = Hybrid.Checkbutton_Row(parent, 'Enable',
('cursor', 'forces', 'key commands'))
po.frame.grid(row=row, column=0, sticky='w')
row = row + 1
self.phantom_on, self.force_field, self.commands = \
[c.variable for c in po.checkbuttons]
self.phantom_on.add_callback(self.settings_changed_cb)
self.force_field.add_callback(self.settings_changed_cb)
self.commands.add_callback(self.toggle_commands_cb)
cf = Tkinter.Frame(parent)
cf.grid(row=row, column=0, sticky='w')
row = row + 1
cs = Hybrid.Option_Menu(cf, 'Cursor shape ', 'cross', 'jack', 'sphere',
'volume crosshair')
cs.frame.grid(row=0, column=0, sticky='nw')
row = row + 1
cs.variable.set('jack')
cs.add_callback(self.settings_changed_cb)
self.cursor_shape = cs.variable
from VolumeViewer import active_volume
v = active_volume()
if v:
csize = '%.3g' % (10 * max(v.data.step))
else:
csize = '1'
cs = Hybrid.Entry(cf, ' size ', 5, csize)
cs.frame.grid(row=0, column=1, sticky='w')
cs.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
self.cursor_size = cs.variable
cl = Tkinter.Label(cf, text=' color ')
cl.grid(row=0, column=2, sticky='w')
from CGLtk.color import ColorWell
cc = ColorWell.ColorWell(cf, callback=self.settings_changed_cb)
self.cursor_color = cc
cc.showColor((0, 0.5, 1), doCallback=0)
cc.grid(row=0, column=3, sticky='w')
sp = Hybrid.Popup_Panel(parent)
spf = sp.frame
spf.grid(row=row, column=0, sticky='news')
spf.grid_remove()
spf.columnconfigure(0, weight=1)
self.settings_panel = sp.panel_shown_variable
row += 1
srow = 0
cb = sp.make_close_button(spf)
cb.grid(row=srow, column=1, sticky='e')
pr = Hybrid.Entry(spf, 'Phantom physical range (mm) ', 5, '200')
pr.frame.grid(row=srow, column=0, sticky='w')
srow += 1
pr.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
self.phantom_range = pr.variable
mf = Hybrid.Entry(spf, 'Maximum force (lbs) ', 5, '.4')
mf.frame.grid(row=srow, column=0, sticky='w')
srow += 1
mf.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
self.maximum_force = mf.variable
af = Hybrid.Checkbutton(spf, 'Auto-adjust force constant', 1)
af.button.grid(row=srow, column=0, sticky='w')
srow += 1
self.auto_adjust_force_constant = af.variable
self.force_field.add_callback(self.settings_changed_cb)
fc = Hybrid.Logarithmic_Scale(spf, 'Force constant ', .0001, 100, 1,
'%.2g')
fc.frame.grid(row=srow, column=0, sticky='ew')
srow += 1
fc.set_value(1)
fc.callback(self.force_constant_changed_cb)
fc.entry.bind('<KeyPress-Return>', self.force_constant_changed_cb)
self.force_constant = fc
vf = Tkinter.Frame(spf)
vf.grid(row=srow, column=0, sticky='ew')
srow += 1
self.label_row(vf, 0, ('', 'x', 'y', 'z'))
pl = self.label_row(vf, 1, ('Phantom position', '', '', ''))
self.phantom_position_labels = pl[1:]
cpl = self.label_row(vf, 2, ('Chimera position', '', '', ''))
self.chimera_position_labels = cpl[1:]
vpl = self.label_row(vf, 3, ('Volume position', '', '', ''))
self.volume_position_labels = vpl[1:]
vil = self.label_row(vf, 4, ('Volume index', '', '', ''))
self.volume_index_labels = vil[1:]
gl = self.label_row(vf, 5, ('Gradient', '', '', ''))
self.gradient_labels = gl[1:]
fl = self.label_row(vf, 6, ('Force', '', '', ''))
self.force_labels = fl[1:]
dvl = self.label_row(vf, 7, ('Data value', ''))
self.data_value_label = dvl[1]
def data_region(self):
from VolumeViewer import active_volume
return active_volume()