def run(self):
print "Performing expensive calculation in %s..." % self.getName(),
sleep(3)
sd = self.data.scalar_data
sd += numpy.sin(numpy.random.rand(*sd.shape) * 2.0 * numpy.pi)
GUI.invoke_later(self.data.update)
print 'done.'
def run(self):
print "Performing expensive calculation in %s..." % self.getName(),
sleep(3)
sd = self.data.scalar_data
sd += numpy.sin(numpy.random.rand(*sd.shape) * 2.0 * numpy.pi)
GUI.invoke_later(self.data.update)
print "done."
def wrapper(*args, **kw):
"""Wrapper function to run given function inside the GUI event
loop.
"""
global _gui, _stop_show
tk = ETSConfig.toolkit
if is_ui_running():
# In this case we should not pop up the UI since we likely
# don't want to stop the mainloop.
return func(*args, **kw)
else:
g = GUI()
if tk == "wx":
# Create a dummy app so invoke later works on wx.
a = ApplicationWindow(size=(1, 1))
GUI.invoke_later(lambda: a.close())
a.open()
GUI.invoke_later(func, *args, **kw)
_gui = g
if stop:
# Pop up the UI to stop the mainloop.
_stop_show = StopShow()
g.start_event_loop()
def wrapper(*args, **kw):
"""Wrapper function to run given function inside the GUI event
loop.
"""
global _gui, _stop_show
tk = ETSConfig.toolkit
if is_ui_running():
# In this case we should not pop up the UI since we likely
# don't want to stop the mainloop.
return func(*args, **kw)
else:
g = GUI()
if tk == 'wx':
# Create a dummy app so invoke later works on wx.
a = ApplicationWindow(size=(1, 1))
GUI.invoke_later(lambda: a.close())
a.open()
GUI.invoke_later(func, *args, **kw)
_gui = g
if stop:
# Pop up the UI to stop the mainloop.
_stop_show = StopShow()
g.start_event_loop()
def run(self):
if ((not hasattr(self,'nonlinear_distortion_model')) or
(self.nonlinear_distortion_model is None)):
do_undistortion = False
else:
do_undistortion = True
if do_undistortion:
im,ll,ur = self.nonlinear_distortion_model.remove_distortion(
self.image_data)
else:
im = self.image_data
ll = 0,0
ur = im.shape[:2][::-1]-np.array([1,1])
ax = self.mplwidget.axes
ax.images=[]
ax.lines=[]
kwargs = {}
if self.display_transform == 'flip y':
display_im = im
kwargs['origin']='lower'
kwargs['extent']=(ll[0],ur[0],ll[1],ur[1])
elif self.display_transform == 'identity':
display_im = im
kwargs['extent']=(ll[0],ur[0],ur[1],ll[1])
elif self.display_transform == 'rotate 180':
display_im = np.rot90(np.rot90(im))
kwargs['extent']=(ur[0],ll[0],ll[1],ur[1])#(ll[0],ur[0],ur[1],ll[1])
elif self.display_transform == 'rotate 90':
display_im = np.rot90(im)
kwargs['extent']=(ll[1],ur[1],ll[0],ur[0])
elif self.display_transform == 'rotate 270':
display_im = np.rot90(np.rot90(np.rot90(im)))
kwargs['extent']=(ur[1],ll[1],ur[0],ll[0])
else:
raise ValueError("unknown transform '%s'"%self.display_transform)
ax.imshow(display_im,
aspect='equal',
cmap=cm.pink,
**kwargs)
if hasattr(self,'lines'):
if do_undistortion:
func = self.nonlinear_distortion_model.undistort
else:
func = None
draw_lines_on_ax(ax,self.lines,func=func,
display_transform=self.display_transform)
GUI.invoke_later(self.mplwidget.figure.canvas.draw)
def _loaded_changed(self, value):
if value:
n = self.dname
if ' [Active]' not in n:
self.dname = "%s [Loaded]" % n
if not self.window is None:
#from enthought.pyface.timer.api import do_later
from enthought.pyface.api import GUI
GUI.invoke_later(self.window.status_bar_manager.set, message = '')
else:
self.dname = self.dname.replace(' [Loaded]', '')
def _active_changed(self , value):
if value:
n = self.name
if ' [Active]' not in n:
self.name = "%s [Active]" % n
# XXX: do refactor with threaded loading of surfaces
# and default spring force layout for graph rendering!
# see also TraitsUI Demos: Multi thread demo
# load the surface containers data
# make a deep copy of the already loaded surface containers
import copy
self.surfaces = copy.deepcopy(self.surfaces_loaded)
for surfcont in self.surfaces:
surfcont.load_surface_container()
if self.rendermanager is None:
self._create_datasourcemanager()
self._create_renderer()
# if there are no surfaces, initialize
# network rendering, but only if dn_positions are given
if len(self.surfaces) == 0:
logger.debug('No surfaces found. Try to render graph view with dn_position information.')
self.rendermanager.datasourcemanager._compute_3DLayout(-1, -1)
self.rendermanager.visualize_graph()
else:
logger.debug('SurfaceContainer found. Try to render 3D View using %s.' % self.surfaces[0].name)
if len(self.surfaces[0].surfaces) == 0:
logger.debug('Rendering not possible because SurfaceContainer contains no surfaces.')
else:
logger.debug('Using first surface for rendering.')
self.surfaces[0].surfaces[0]._layout_3DView()
if not self._parentcfile._workbenchwin is None:
#from enthought.pyface.timer.api import do_later
from enthought.pyface.api import GUI
GUI.invoke_later(self._parentcfile._workbenchwin.status_bar_manager.set, message = '')
else:
self.name = self.name.replace(' [Active]', '')
logger.debug('Close RenderManager scenes')
self.rendermanager.close_scenes()
logger.debug('All scenes closed.')
# FIXME: what is happening in the following?
# e.g. for instances. e.g. reset traits?
# XXX: this is somehow not correct. do i need to use del
# or remove/reset traits?
self.rendermanager = None
self.datasourcemanager = None
self.surfaces = []
def _on_tree_end_label_edit(self, event):
""" Called when the user has finished editing am item's label. """
wxid = event.GetItem()
# The item data is a tuple. The first element indicates whether or not
# we have already populated the item with its children. The second
# element is the actual item data.
populated, node = self.control.GetPyData(wxid)
# Give the model a chance to veto the edit.
label = event.GetLabel()
# Making sure the new label is not an empty string
if label is not None and len(label) > 0 and \
self.model.can_set_text(node, label):
def end_label_edit():
""" Called to complete the label edit. """
# Set the node's text.
self.model.set_text(node, label)
# If a label edit callback was specified (in the call to
# 'edit_label'), then call it).
if self._label_edit_callback is not None:
self._label_edit_callback(self, node, label)
return
# We use a deffered call here, because a name change can trigger
# the structure of a node to change, and hence the actual tree
# nodes might get moved/deleted before the label edit operation has
# completed. When this happens wx gets very confused! By using
# 'invoke_later' we allow the label edit to complete.
GUI.invoke_later(end_label_edit)
else:
event.Veto()
# If a label edit callback was specified (in the call to
# 'edit_label'), then call it).
if self._label_edit_callback is not None:
self._label_edit_callback(self, node, label)
return
def _on_tree_end_label_edit(self, event):
""" Called when the user has finished editing am item's label. """
wxid = event.GetItem()
# The item data is a tuple. The first element indicates whether or not
# we have already populated the item with its children. The second
# element is the actual item data.
populated, node = self.control.GetPyData(wxid)
# Give the model a chance to veto the edit.
label = event.GetLabel()
# Making sure the new label is not an empty string
if label is not None and len(label) > 0 and \
self.model.can_set_text(node, label):
def end_label_edit():
""" Called to complete the label edit. """
# Set the node's text.
self.model.set_text(node, label)
# If a label edit callback was specified (in the call to
# 'edit_label'), then call it).
if self._label_edit_callback is not None:
self._label_edit_callback(self, node, label)
return
# We use a deffered call here, because a name change can trigger
# the structure of a node to change, and hence the actual tree
# nodes might get moved/deleted before the label edit operation has
# completed. When this happens wx gets very confused! By using
# 'invoke_later' we allow the label edit to complete.
GUI.invoke_later(end_label_edit)
else:
event.Veto()
# If a label edit callback was specified (in the call to
# 'edit_label'), then call it).
if self._label_edit_callback is not None:
self._label_edit_callback(self, node, label)
return
def _on_editor_closed(self, editor):
""" Dynamic trait change handler. """
index = self.editors.index(editor)
del self.editors[index]
if editor is self.active_editor:
if len(self.editors) > 0:
index = min(index, len(self.editors) - 1)
# If the user closed the editor manually then this method is
# being called from a toolkit-specific event handler. Because
# of that we have to make sure that we don't change the focus
# from within this method directly hence we activate the editor
# later in the GUI thread.
GUI.invoke_later(self.activate_editor, self.editors[index])
else:
self.active_editor = None
return
def normal_right_down(self, event):
""" Right click will bring up a dialog to edit the
prefix/suffix of the selected variables.
"""
field = self._get_underlying_box_field(event.x, event.y)
if field:
selected_fields = self.input_selected_fields + self.output_selected_fields
if field in selected_fields:
for group in self.menu.groups:
for action_item in group.items:
action = action_item.action
action.container = self.component
action.selected_fields = selected_fields
menu = self.menu.create_menu(event.window.control)
if len(event._pos_stack) > 0:
real_x, real_y = event._pos_stack[0]
else:
real_x, real_y = event.x, event.y
from enthought.pyface.api import GUI
GUI.invoke_later(menu.show, real_x - 10, event.window._flip_y(real_y))
self.component.request_redraw()
event.handled = True
def run(self):
im = self.image
X, Y = indices(im.shape)
x = sum(X*im)/sum(im)
y = sum(Y*im)/sum(im)
width = sqrt(abs(sum(((X-x)**2+(Y-y)**2)*im)/sum(im)))
GUI.invoke_later(setattr, self.results, 'x', x)
GUI.invoke_later(setattr, self.results, 'y', y)
GUI.invoke_later(setattr, self.results, 'width', width)
def run(self):
logger.debug("Start Threaded Parsing of Connectome File ...")
import time
tic = time.time()
# given the full path to meta.xml, create lxml tree and
# under the precondition of having a certain file version and generator
# one can assume some content of the .cff file
# loop over the networks, for each network, the surfaces etc.
# in the form of all the attributes (name, srce filename, description etc.)
# are given to the created Network instance methods to complete
from lxml import etree
tree = etree.fromstring(self.metaxmlcontent)
nsprefix = "{%s}" % tree.nsmap[None]
t = 0
for child in tree.iterchildren():
if child.tag == (nsprefix+'viewer-network'):
t = t + 1
if t != self.data.metadata.nr_of_networks:
logger.error('The number of networks of networks in meta.xml is not correct!')
logger.error('Loading ' + str(t) + ' network(s).')
# find all the networks
for child in tree.iterchildren():
if child.tag == (nsprefix+'viewer-network'):
# load network as string from zip
# create temporary StringIO
logger.info('-----------------------------------------')
logger.info('Now loading ' + child.attrib['src'])
logger.info('-----------------------------------------')
if child.attrib.has_key('src'):
(tmpstring, pickled_graph, local_fname) = self.process_pickle(childnode = child)
tmp_network = Network(name = child.attrib['name'],
src = tmpstring,
pickled_graph = pickled_graph,
directed = child.attrib['directed'],
hierarchical = child.attrib['hierarchical'],
hypergraph = child.attrib['hypergraph'])
# store pickled version in connectome file
if not tmpstring is None and pickled_graph is None:
self.save_pickle_in_cfile(local_fname, networkref = tmp_network)
# iterate over children
for mchildren in child.iterchildren():
# handling of the metadata
# -------------------------
if mchildren.tag == (nsprefix+'network-metadata'):
tmp_network.metadata = self.process_metadata(metadata_node = mchildren, nsprefix = nsprefix)
# handling of the surfaces
# ------------------------
if mchildren.tag == (nsprefix+'network-surface'):
# load into surface
attr = mchildren.attrib
if attr.has_key('src'):
# create surface container
tmpsurfacecontainer = self.process_surface(surface_node = mchildren, nsprefix = nsprefix)
# and add it to the network
tmp_network.add_surface_container(tmpsurfacecontainer)
# adding a template atlas if stated in the meta.xml
if attr.has_key('addatlas'):
# create surface container for atlas
tmpsurfacecontainer = self.process_atlas(surface_node = mchildren, nsprefix = nsprefix)
# and add it to the network
tmp_network.add_surface_container(tmpsurfacecontainer)
# handling of the volumes
# -----------------------
elif mchildren.tag == (nsprefix+'network-volume'):
# get the description, is there an easier way with lxml?
for desc in mchildren.iterchildren():
if desc.tag == (nsprefix+'description'):
mydescr = desc.text
attr = mchildren.attrib
if attr.has_key('src') and attr.has_key('name'):
if not attr.has_key('segmentation'):
segm = False
else:
segm = bool(attr['segmentation'])
# create an instance of the Volume class with it
tmpvolume = Volume(volumename = attr['name'], \
networkref = tmp_network, \
src = attr['src'], \
description = mydescr, \
segmentation = segm)
# add this instance to the list of its network
tmp_network.add_volume(tmpvolume)
logger.info('Added volume ' + tmpvolume.volumename + \
' to ' + tmp_network.networkname)
# handling of the trackfiles
# --------------------------
elif mchildren.tag == (nsprefix+'network-track'):
# get the description, is there an easier way with lxml?
for desc in mchildren.iterchildren():
if desc.tag == (nsprefix+'description'):
mydescr = desc.text
attr = mchildren.attrib
if attr.has_key('src') and attr.has_key('name'):
tmptrack = Trackfile(trkname = attr['name'], tmpfname = attr['src'], \
description = mydescr, networkref = tmp_network)
# add this instance to the list of its trackfiles
tmp_network.add_trackfile(tmptrack)
logger.info('Added trackfile ' + tmptrack.trkname + \
' to ' + tmp_network.networkname)
# setting the correct parent cfile
tmp_network._parentcfile = self.data
# add the created network object to this cfile
self.data.networks.append(tmp_network)
toc = time.time()
logger.info('Loading Connectome File DONE. (Time: %s)' % str(toc-tic))
logger.info('-----------------------------------------')
# setting data loaded flag
self.data._data_loaded = True
# with do_later, we the change in the statusbar is done in the gui main thread
if not self.data._workbenchwin is None:
#from enthought.pyface.timer.api import do_later
#do_later(self.data._workbenchwin.status_bar_manager.set, message = '')
# TEST
from enthought.pyface.api import GUI
GUI.invoke_later(self.data._workbenchwin.status_bar_manager.set, message = '')
def update(self):
for prim in self.primitives:
prim.update()
GUI.invoke_later(self.scene.render)
def update(self):
for prim in self.primitives:
prim.update()
GUI.invoke_later(self.scene.render)
def image_show(self, image):
""" Plots an image on the canvas in a thread safe way.
"""
self.mplwidget.axes.images=[]
self.mplwidget.axes.imshow(image, aspect='auto')
GUI.invoke_later(self.mplwidget.figure.canvas.draw)
def add_line(self, string):
""" Adds a line to the textbox display in a thread-safe way.
"""
GUI.invoke_later(setattr, self, 'results_string',
(string + "\n" + self.results_string)[0:1000] )
def object_update_changed(self, info):
if info.initialized:
def run():
info.object.fig.canvas.draw()
GUI.invoke_later(run)
def object_update_changed(self, info):
if info.initialized:
info.object.ax.mouse_init()
GUI.invoke_later(info.object.fig.canvas.draw)
def _snrs_changed(self): GUI.invoke_later(self.update_snrs)
def run(self):
new_data = self.dataset[self.dataset.time]
GUI.invoke_later(setattr, self.scalar_field.mlab_source, 'scalars',
new_data)
def add_line(self, string):
GUI.invoke_later(setattr, self, 'string', string + "\n" + self.string)
