def marker_set(self, create = False):
import VolumePath as vp
marker_set = vp.find_marker_set_by_name('Volume eraser')
if marker_set == None and create:
marker_set = vp.Marker_Set('Volume eraser')
return marker_set
def active_marker_set():
import VolumePath
d = VolumePath.volume_path_dialog()
if d:
return d.active_marker_set
return None
def marker_set(self):
import VolumePath
d = VolumePath.volume_path_dialog(create = False)
if d == None:
return None
return d.active_marker_set
def transform_coord(self, from_xyz, from_xform, to_xform):
import VolumePath
to_xyz = VolumePath.transform_coordinates(from_xyz,
from_xform, to_xform)
return to_xyz
def open_skeleton_file ( open, dialog, smod ) :
if not open:
return
paths = dialog.getPaths()
path = paths[0]
import VolumePath
g = VolumePath.open_marker_set(path)
mlist = g.markers()
for m in mlist:
m.region = None
rid = int(m.extra_attributes['region_id'])
if rid in smod.id_to_region:
r = smod.id_to_region[rid]
rsize = int(m.extra_attributes['region_size'])
if r.point_count() == rsize:
m.region = r
#TODO: The regions file format renumbers the regions consecutively. So
# matching based on region id won't work. Should change file format to
# hdf5 and include region ids, colors, and any other useful per-region info.
nomatch = [m for m in mlist if m.region is None]
if nomatch:
umsg('%d of %d skeleton nodes did not match a region' %
(len(nomatch), len(mlist)))
if smod.adj_graph:
smod.adj_graph.close()
smod.adj_graph = g
def open_marker_set(path): import VolumePath d = VolumePath.show_volume_path_dialog() d.open_marker_set(path) models = [] return models
def marker_refresh_cb(self):
"""marker_refresh_cb()
Refresh markers list whenever models are opened or closed in
Chimera.
"""
# @ Need to update menu with Listbox in VolumePath
# whenever that listbox changes. Any better ways?
if self.marker_dialog == None:
import VolumePath
vpd = VolumePath.volume_path_dialog()
if vpd == None:
return
self.marker_dialog = vpd
# flush out all entries, get open models list, populate menu
self.marker_menu.remove_all_entries()
open_models = chimera.openModels.list()
for ms in self.marker_sets():
self.marker_menu.add_entry(ms.name)
# if previous entry still in current marker sets list,
# then reset else, set to top most entry
ms = self.marker_set
if ms and self.find_marker_set_by_name(ms.name):
self.marker_menu.variable.set(ms.name)
elif len(self.marker_sets()) > 0:
ms = self.marker_sets()[-1]
self.marker_menu.variable.set(ms.name)
else:
self.marker_menu.variable.set('')
def Compute(self):
"""Compute parameters
"""
if self.volume_path_dialog == None:
import VolumePath
self.volume_path_dialog = VolumePath.volume_path_dialog()
self.update_parameters_value()
def marker_set(self):
return None
import VolumePath
d = VolumePath.volume_path_dialog(create = False)
if d is None:
return None
return d.active_marker_set
def place_marker(xyz, msys, color, radius, model_name=None, model_id=None):
# Locate specified marker model
mset = None
import VolumePath as VP
if not model_id is None:
msets = VP.marker_sets(model_id)
if len(msets) >= 1:
mset = msets[0]
if mset is None:
# Create a new marker model
mname = msys.name + ' center' if model_name is None else model_name
mset = VP.Marker_Set(mname)
mset.marker_molecule(model_id)
mos = mset.marker_molecule().openState
if mos != msys.openState:
# Transform from volume to marker model coordinates.
import Matrix
xyz = Matrix.xform_xyz(xyz, msys.openState.xform, mos.xform)
# Place marker at center position.
mset.place_marker(xyz, color, radius)
def marker_open_cb(self):
"""marker_open_cb() - callback for marker set open buton
Calls the Volume Path Dialog and its open dialog.
"""
# @ Better way?
if self.marker_dialog == None:
import VolumePath
self.marker_dialog = VolumePath.volume_path_dialog(1)
self.marker_dialog.ImportXML()
self.marker_dialog.enter()
self.marker_dialog.open_dialog.enter()
return
def restore_path_tracer_state(path_tracer_dialog_basic_state):
from SessionUtil.stateclasses import Model_State, Xform_State
classes = (Path_Tracer_Dialog_State, Marker_Set_State, Marker_State, Link_State, Model_State, Xform_State)
name_to_class = {}
for c in classes:
name_to_class[c.__name__] = c
from SessionUtil import objecttree
s = objecttree.basic_tree_to_instance_tree(path_tracer_dialog_basic_state, name_to_class)
import VolumePath
d = VolumePath.volume_path_dialog(create=1)
set_dialog_state(s, d)
def transform_coord(self, from_xyz, from_xform, to_xform):
"""transform_coord(from_xyz, from_xform, to_xform)
Input:
from_xyz from object coordinates
from_xform from object's transform
to_xform to objcet's transform
Output:
to_xyz to object coordinates
Convert coordinates from 'from object' to 'to object'
"""
import VolumePath
to_xyz = VolumePath.transform_coordinates(from_xyz,
from_xform,to_xform)
return to_xyz
def place_marker_at_mouse():
import VolumePath
VolumePath.place_marker_at_mouse()
def show_path_tracer_dialog(self):
import VolumePath
VolumePath.show_volume_path_dialog()
if self.marker_set() == None and self.series:
VolumePath.Marker_Set(self.series[0].menu_name + ' markers')
def open_marker_set(path): import VolumePath VolumePath.open_marker_set(path) models = [] return models
def place_marker_at_mouse(): import VolumePath VolumePath.place_marker_at_mouse()
def volume_path_dialog():
import VolumePath
return VolumePath.volume_path_dialog(create=1)
def Markers(self):
import VolumePath
VolumePath.show_volume_path_dialog()
def place_markers_on_atoms(): import VolumePath VolumePath.place_markers_on_atoms()
def Markers(self):
import VolumePath
VolumePath.show_volume_path_dialog()
def volume_path_dialog(): import VolumePath return VolumePath.volume_path_dialog(create = 1)
def open_marker_set(path):
import VolumePath
VolumePath.open_marker_set(path)
models = []
return models
def show_volume_path_tracer_dialog():
'Show volume path tracer viewer dialog'
import VolumePath
VolumePath.show_volume_path_dialog()
def place_markers_on_atoms():
import VolumePath
VolumePath.place_markers_on_atoms()
def volume_path_dialog(): import VolumePath d = VolumePath.volume_path_dialog(create = True) return d
