def full_volume():
'Change volume subregion to show full data'
from volumedialog import active_volume
v = active_volume()
if v:
ijk_min = (0,0,0)
ijk_max = [n-1 for n in v.data.size]
v.new_region(ijk_min, ijk_max, show = v.shown())
def full_volume():
'Change volume subregion to show full data'
from volumedialog import active_volume
v = active_volume()
if v:
ijk_min = (0, 0, 0)
ijk_max = [n - 1 for n in v.data.size]
v.new_region(ijk_min, ijk_max, show=v.shown())
def show_volume():
'Show active volume viewer volume'
from volumedialog import active_volume
v = active_volume()
if v:
if v.representation is None:
v.set_representation('surface')
v.initialize_thresholds()
v.show()
def show_volume():
'Show active volume viewer volume'
from volumedialog import active_volume
v = active_volume()
if v:
if v.representation is None:
v.set_representation('surface')
v.initialize_thresholds()
v.show()
def clip_volume():
from volumedialog import active_volume
v = active_volume()
if v:
if v.useClipPlane:
v.useClipPlane = False
else:
from chimera import tkgui
tkgui.setClipModel(v)
def clip_volume():
from volumedialog import active_volume
v = active_volume()
if v:
if v.useClipPlane:
v.useClipPlane = False
else:
from chimera import tkgui
tkgui.setClipModel(v)
def zone_volume(outside = False):
from volumedialog import active_volume
v = active_volume()
if v is None:
from chimera.replyobj import status
status('No volume shown in volume dialog')
return
mv = v.copy_zone(outside)
if mv is None:
from chimera.replyobj import status
status('No zone for volume %s' % v.name)
def invert_map():
from volumedialog import active_volume
v = active_volume()
if v is None:
return
wv = v.writable_copy()
m = wv.data.full_matrix()
from VolumeData import invert_matrix
invert_matrix(m)
wv.data.values_changed()
wv.show()
def invert_map():
from volumedialog import active_volume
v = active_volume()
if v is None:
return
wv = v.writable_copy()
m = wv.data.full_matrix()
from VolumeData import invert_matrix
invert_matrix(m)
wv.data.values_changed()
wv.show()
def zone_volume(outside=False):
from volumedialog import active_volume
v = active_volume()
if v is None:
from chimera.replyobj import status
status('No volume shown in volume dialog')
return
mv = v.copy_zone(outside)
if mv is None:
from chimera.replyobj import status
status('No zone for volume %s' % v.name)
def bounding_map(pad=5.0):
from chimera.selection import currentAtoms
atoms = currentAtoms()
if len(atoms) == 0:
from chimera.replyobj import status
status('No atoms selected')
return
from volumedialog import active_volume
v = active_volume()
if v is None:
from chimera.replyobj import status
status('No volume shown in volume dialog')
return
from volume import map_covering_atoms
bv = map_covering_atoms(atoms, pad, v)
bv.show()
v.show(show=False)
def bounding_map(pad = 5.0):
from chimera.selection import currentAtoms
atoms = currentAtoms()
if len(atoms) == 0:
from chimera.replyobj import status
status('No atoms selected')
return
from volumedialog import active_volume
v = active_volume()
if v is None:
from chimera.replyobj import status
status('No volume shown in volume dialog')
return
from volume import map_covering_atoms
bv = map_covering_atoms(atoms, pad, v)
bv.show()
v.show(show = False)
def mrc_signed8_to_unsigned8():
from volumedialog import active_volume
v = active_volume()
if v == None:
from chimera.replyobj import status
status('No volume shown in volume viewer dialog.')
return
data = v.data
if not hasattr(data, 'signed8_to_unsigned8'):
from chimera.replyobj import status
status('Volume is not MRC format.')
return
from numpy import int8
if data.value_type != int8:
from chimera.replyobj import status
status('MRC volume is not 8-bit integers.')
return
data.signed8_to_unsigned8()
v.show()
def mrc_signed8_to_unsigned8():
from volumedialog import active_volume
v = active_volume()
if v == None:
from chimera.replyobj import status
status('No volume shown in volume viewer dialog.')
return
data = v.data
if not hasattr(data, 'signed8_to_unsigned8'):
from chimera.replyobj import status
status('Volume is not MRC format.')
return
from numpy import int8
if data.value_type != int8:
from chimera.replyobj import status
status('MRC volume is not 8-bit integers.')
return
data.signed8_to_unsigned8()
v.show()
def volume(self):
from volumedialog import active_volume
v = active_volume()
return v
def hide_volume():
'Hide active volume viewer volume'
from volumedialog import active_volume
v = active_volume()
if v:
v.unshow()
def remove_volume():
'Remove active volume viewer volume'
from volumedialog import active_volume
v = active_volume()
if v:
v.close()
def writable_volume():
from volumedialog import active_volume
v = active_volume()
if v:
v.writable_copy(require_copy=True)
def writable_volume():
from volumedialog import active_volume
v = active_volume()
if v:
v.writable_copy(require_copy = True)
def remove_volume():
'Remove active volume viewer volume'
from volumedialog import active_volume
v = active_volume()
if v:
v.close()
def hide_volume():
'Hide active volume viewer volume'
from volumedialog import active_volume
v = active_volume()
if v:
v.unshow()