class WorldTest(TestCase):
def setUp(self):
ev.events
self.world = World()
self.world.register_listener(ev)
def tearDown(self):
self.world.unregister_listener(ev)
ev.events
del self.world
def test_world_objects(self):
wo = WorldObject(name='o', data=1)
assert wo.name == 'o'
assert wo.data == 1
def test_world(self):
obj = self.world.add(1, 'a')
events = ev.events
self.check_events(events,
names=['world_object_changed'],
values={0: {0: self.world, 1: None, 2: obj}}
)
attribute_dict = dict(name='attr1', value=1, interface='IInt', label="Attribute 1")
final_dict = dict(name='attr1', value=1, interface='IInt', label="Attribute 1", constraints=None)
obj.set_attribute(**attribute_dict)
events = ev.events
self.check_events(events,
names=['world_object_item_changed'],
values={0: {0: self.world, 1: obj, 2: "attribute", 3: None, 4: final_dict}}
)
assert obj['attr1'] == attribute_dict['value']
def clear_namespace(self, interpreter, project):
if project is None:
return
sys.path = self.old_syspath
for k in project.ns.keys() + ['world', 'data', 'project']:
if k in interpreter.user_ns:
del interpreter.user_ns[k]
from openalea.core.world import World
world = World()
world.clear()
class WorldTest(TestCase):
def setUp(self):
ev.events
self.world = World()
self.world.register_listener(ev)
def tearDown(self):
self.world.unregister_listener(ev)
ev.events
del self.world
def test_world_objects(self):
wo = WorldObject(name='o', data=1)
assert wo.name == 'o'
assert wo.data == 1
def test_world(self):
obj = self.world.add(1, 'a')
events = ev.events
self.check_events(events,
names=['world_object_changed'],
values={0: {
0: self.world,
1: None,
2: obj
}})
attribute_dict = dict(name='attr1',
value=1,
interface='IInt',
label="Attribute 1")
final_dict = dict(name='attr1',
value=1,
interface='IInt',
label="Attribute 1",
constraints=None)
obj.set_attribute(**attribute_dict)
events = ev.events
self.check_events(events,
names=['world_object_item_changed'],
values={
0: {
0: self.world,
1: obj,
2: "attribute",
3: None,
4: final_dict
}
})
assert obj['attr1'] == attribute_dict['value']
def add_objects_with_attributes_set():
"""
Attributes are defined before adding object to world.
Results is less signals sent by world
"""
world = World()
world.clear()
obj1 = WorldObject("obj1", 1)
obj2 = WorldObject("obj2", 2)
obj1.set_attribute('a1', 1, 'IInt', constraints=c1)
obj1.set_attribute('a2', True, 'IBool')
obj2.set_attribute('b1', 2.34, 'IFloat', constraints=c2)
world["obj1"] = obj1
world["obj2"] = obj2
def add_objects_with_attributes_set():
"""
Attributes are defined before adding object to world.
Results is less signals sent by world
"""
world = World()
world.clear()
obj1 = WorldObject("obj1", 1)
obj2 = WorldObject("obj2", 2)
obj1.set_attribute('a1', 1, 'IInt', constraints=c1)
obj1.set_attribute('a2', True, 'IBool')
obj2.set_attribute('b1', 2.34, 'IFloat', constraints=c2)
world["obj1"] = obj1
world["obj2"] = obj2
def update_namespace(self, interpreter):
"""
Definition: Update namespace
"""
if self._cproject:
if self._cproject.path.exists():
os.chdir(self._cproject.path)
sys.path.insert(0, str(self._cproject.path / 'lib'))
else:
os.chdir(self.tmpdir)
sys.path.insert(0, str(self.tmpdir / 'lib'))
interpreter.user_ns.update(self._cproject.ns)
interpreter.user_ns['project'] = self._cproject
interpreter.user_ns['data'] = self._cproject.path / 'data'
from openalea.core.world import World
world = World()
world.update_namespace(interpreter)
def add_objects_then_attributes():
world = World()
world["obj1"] = 1
world["obj2"] = 2
obj1 = world["obj1"]
obj2 = world["obj2"]
obj1.set_attribute('a1', 1, 'IInt', constraints=c1)
obj1.set_attribute('a2', True, 'IBool')
obj2.set_attribute('b1', 2.34, 'IFloat', constraints=c2)
def setUp(self):
ev.events
self.world = World()
self.world.register_listener(ev)
def initialize(self):
self.world = World()
self.world.register_listener(self)
class ImageStackViewer(QtGui.QTabWidget, AbstractListener):
def __init__(self):
QtGui.QTabWidget.__init__(self)
AbstractListener.__init__(self)
self.setAcceptDrops(True)
self._image = {}
self._viewer = {}
self._create_connections()
def initialize(self):
self.world = World()
self.world.register_listener(self)
def notify(self, sender, event=None):
signal, data = event
if signal == 'world_sync':
self.set_world(data)
elif signal == 'world_object_removed':
world, old = data
self.remove_world_object(world, old)
elif signal == 'world_object_changed':
world, old, new = data
self.set_world_object(world, new)
elif signal == 'world_object_item_changed':
world, obj, item, old, new = data
if item == 'attribute':
self.update_world_object(world, obj, item, old, new)
def set_image(self, name, image):
if name in self._viewer:
viewer = self._viewer[name]
else:
viewer = ImageStackViewerWidget()
viewer.setAttribute(QtCore.Qt.WA_DeleteOnClose)
connect(viewer, viewer.stackChanged, self._on_stack_changed)
self._viewer[name] = viewer
self._image[viewer] = name
self.addTab(viewer, name)
viewer.setValue(image)
def remove_image(self, name):
if name in self._viewer:
viewer = self._viewer[name]
disconnect(viewer, viewer.stackChanged, self._on_stack_changed)
self.removeTab(self.indexOf(viewer))
viewer.close()
del self._image[viewer]
del self._viewer[name]
def set_world_object(self, world, world_object):
if not isinstance(world_object.data, SpatialImage):
return
self.set_image(world_object.name, world_object.data)
def remove_world_object(self, world, world_object):
if not isinstance(world_object.data, SpatialImage):
return
self.set_image(world_object.name, world_object.data)
def set_world(self, world):
# Clear viewer
for image in self._viewer.keys():
self.remove_image(image)
# Set object in viewer
for obj_name, world_object in world.items():
self.set_world_object(world, world_object)
def update_world_object(self, world, obj, item, old, new):
attr_name = new['name']
if attr_name.endswith('plane_position'):
axis = list('xyz').index(attr_name[0])
position = new['value']
if obj.name in self._viewer:
viewer = self._viewer[obj.name]
viewer.change_axis(axis)
viewer.slice_changed(position)
def _create_connections(self):
self.currentChanged.connect(self._on_current_image_changed)
def _on_current_image_changed(self, idx):
pass
def _on_stack_changed(self, stack):
name = self._image[self.sender()]
if stack:
world_object = self.world[name]
cut_plane = '%s_plane_position' % ('xyz'[stack['axis']])
world_object.set_attribute(cut_plane, stack['slice'])
def setUp(self):
ev.events
self.world = World()
self.world.register_listener(ev)
def __init__(self, parent=None):
# super(Viewer, self).__init__()
AbstractListener.__init__(self)
view3D.__init__(self, parent=parent)
self.setAccessibleName("3DViewer")
self.setMinimumSize(100, 100)
self.autofocus = True
self._fps = False
self.axis = False
self.grid = True
actionResetZoom = QtGui.QAction(QtGui.QIcon(":/images/resources/resetzoom.png"), "Home", self)
self.actionAutoFocus = QtGui.QAction(QtGui.QIcon(":/images/resources/resetzoom.png"), "Auto Focus", self)
self.actionAutoFocus.setCheckable(True)
self.actionAutoFocus.setChecked(self.autofocus)
self.actionAutoFocus.changed.connect(self._on_autofocus_changed)
actionZoomOut = QtGui.QAction(QtGui.QIcon(":/images/resources/zoomout.png"), "Zoom Out", self)
actionZoomIn = QtGui.QAction(QtGui.QIcon(":/images/resources/zoomin.png"), "Zoom In", self)
actionShowAxis = QtGui.QAction(QtGui.QIcon(":/images/resources/axis.png"), "Show Axis", self)
actionShowGrid = QtGui.QAction(QtGui.QIcon(":/images/resources/grid.png"), "Show Grid", self)
actionRadius = QtGui.QAction(QtGui.QIcon(":/images/resources/growth2.png"), "Focus", self)
actionShowFps = QtGui.QAction(QtGui.QIcon(":/images/resources/fps.png"), "Show FPS", self)
actionBlack = QtGui.QAction(QtGui.QIcon(""), "Bg Black", self)
actionWhite = QtGui.QAction(QtGui.QIcon(""), "Bg White", self)
actionShowAxis.setShortcut(
QtGui.QApplication.translate("MainWindow", "Ctrl+A", None, QtGui.QApplication.UnicodeUTF8))
actionShowGrid.setShortcut(
QtGui.QApplication.translate("MainWindow", "Ctrl+I", None, QtGui.QApplication.UnicodeUTF8))
actionRadius.setShortcut(
QtGui.QApplication.translate("MainWindow", "Ctrl+M", None, QtGui.QApplication.UnicodeUTF8))
actionResetZoom.setShortcut(
QtGui.QApplication.translate("MainWindow", "Ctrl+0", None, QtGui.QApplication.UnicodeUTF8))
actionZoomOut.setShortcut(
QtGui.QApplication.translate("MainWindow", "Ctrl+-", None, QtGui.QApplication.UnicodeUTF8))
actionZoomIn.setShortcut(
QtGui.QApplication.translate("MainWindow", "Ctrl++", None, QtGui.QApplication.UnicodeUTF8))
QtCore.QObject.connect(actionResetZoom, QtCore.SIGNAL('triggered(bool)'), self.resetzoom)
QtCore.QObject.connect(actionZoomOut, QtCore.SIGNAL('triggered(bool)'), self.zoomout)
QtCore.QObject.connect(actionZoomIn, QtCore.SIGNAL('triggered(bool)'), self.zoomin)
QtCore.QObject.connect(actionShowAxis, QtCore.SIGNAL('triggered(bool)'), self.show_hide_axis)
QtCore.QObject.connect(actionShowGrid, QtCore.SIGNAL('triggered(bool)'), self.show_hide_grid)
QtCore.QObject.connect(actionRadius, QtCore.SIGNAL('triggered(bool)'), self.update_radius)
QtCore.QObject.connect(actionShowFps, QtCore.SIGNAL('triggered(bool)'), self.show_fps)
QtCore.QObject.connect(actionBlack, QtCore.SIGNAL('triggered(bool)'), self.set_bg_black)
QtCore.QObject.connect(actionWhite, QtCore.SIGNAL('triggered(bool)'), self.set_bg_white)
world = World()
world.register_listener(self)
self.object_repr = {}
self.object_scene = {}
self.property = {}
self._actions = [["Viewer", "Zoom", actionResetZoom, 0],
["Viewer", "Zoom", actionZoomOut, 0],
["Viewer", "Zoom", actionZoomIn, 0],
["Viewer", "Zoom", self.actionAutoFocus, 0],
["Viewer", "Camera", actionShowAxis, 0],
["Viewer", "Camera", actionShowGrid, 0],
["Viewer", "Camera", actionRadius, 0],
["Viewer", "Camera", actionBlack, 0],
["Viewer", "Camera", actionWhite, 0],
#["Viewer", "Informations", actionShowFps, 1]
]
def nuclei_active_region_segmentation(input_img,
positions,
omega_energies=dict(intensity=1.0,
gradient=1.5,
smoothness=10000.0),
intensity_min=20000.,
iterations=10,
display=False):
"""
3D extension of the multiple region extension of the binary level set implementation
"""
segmentation_start_time = time()
print "--> Active region segmentation (", len(positions), " regions )"
from copy import deepcopy
reference_img = deepcopy(input_img)
size = np.array(reference_img.shape)
voxelsize = np.array(reference_img.voxelsize)
if display:
from openalea.core.world import World
world = World()
if omega_energies.has_key('gradient'):
from scipy.ndimage.filters import gaussian_gradient_magnitude
start_time = time()
print " --> Computing image gradient"
gradient = gaussian_gradient_magnitude(
np.array(reference_img, np.float64),
sigma=0.5 / np.array(reference_img.voxelsize))
gradient_img = SpatialImage(np.array(gradient, np.uint16),
voxelsize=reference_img.voxelsize)
end_time = time()
print " <-- Computing image gradient [", end_time - start_time, " s]"
start_time = time()
print " --> Creating seed image"
print positions.keys()
seed_img = seed_image_from_points(size,
voxelsize,
positions,
point_radius=1.0)
regions_img = np.copy(seed_img)
end_time = time()
print " <-- Creating seed image (", len(np.unique(
regions_img)) - 1, " regions ) [", end_time - start_time, " s]"
if display:
world.add(seed_img,
'active_regions_seeds',
colormap='glasbey',
voxelsize=voxelsize,
alphamap='constant',
volume=False,
cut_planes=True)
raw_input()
for iteration in xrange(iterations):
start_time = time()
print " --> Active region energy gradient descent : iteration", iteration, " (", len(
np.unique(regions_img)) - 1, " regions )"
previous_regions_img = np.copy(regions_img)
regions_img = active_regions_energy_gradient_descent(
regions_img,
reference_img,
omega_energies=omega_energies,
intensity_min=intensity_min,
gradient_img=gradient)
change = ((regions_img - previous_regions_img) != 0.).sum() / float(
(regions_img > 1.).sum())
end_time = time()
print " --> Active region energy gradient descent : iteration", iteration, " (Evolution : ", int(
100 * change), " %) ", "[", end_time - start_time, " s]"
if display:
world.add(regions_img,
'active_regions',
colormap='invert_grey',
voxelsize=voxelsize,
intensity_range=(1, 2))
segmented_img = SpatialImage(regions_img,
voxelsize=reference_img.voxelsize)
if display:
world.add(segmented_img,
'active_regions',
colormap='glasbey',
voxelsize=voxelsize,
alphamap='constant')
raw_input()
segmentation_end_time = time()
print "<-- Active region segmentation (", len(
np.unique(segmented_img)
) - 1, " regions ) [", segmentation_end_time - segmentation_start_time, " s]"
return segmented_img
def initialize(self):
self.world = World()
self.world.register_listener(self)
class ImageStackViewer(QtGui.QTabWidget, AbstractListener):
def __init__(self):
QtGui.QTabWidget.__init__(self)
AbstractListener.__init__(self)
self.setAcceptDrops(True)
self._image = {}
self._viewer = {}
self._create_connections()
def initialize(self):
self.world = World()
self.world.register_listener(self)
def notify(self, sender, event=None):
signal, data = event
if signal == 'world_sync':
self.set_world(data)
elif signal == 'world_object_removed':
world, old = data
self.remove_world_object(world, old)
elif signal == 'world_object_changed':
world, old, new = data
self.set_world_object(world, new)
elif signal == 'world_object_item_changed':
world, obj, item, old, new = data
if item == 'attribute':
self.update_world_object(world, obj, item, old, new)
def set_image(self, name, image):
if name in self._viewer:
viewer = self._viewer[name]
else:
viewer = ImageStackViewerWidget()
viewer.setAttribute(QtCore.Qt.WA_DeleteOnClose)
connect(viewer, viewer.stackChanged, self._on_stack_changed)
self._viewer[name] = viewer
self._image[viewer] = name
self.addTab(viewer, name)
viewer.setValue(image)
def remove_image(self, name):
if name in self._viewer:
viewer = self._viewer[name]
disconnect(viewer, viewer.stackChanged, self._on_stack_changed)
self.removeTab(self.indexOf(viewer))
viewer.close()
del self._image[viewer]
del self._viewer[name]
def set_world_object(self, world, world_object):
if not isinstance(world_object.data, SpatialImage):
return
self.set_image(world_object.name, world_object.data)
def remove_world_object(self, world, world_object):
if not isinstance(world_object.data, SpatialImage):
return
self.set_image(world_object.name, world_object.data)
def set_world(self, world):
# Clear viewer
for image in self._viewer.keys():
self.remove_image(image)
# Set object in viewer
for obj_name, world_object in world.items():
self.set_world_object(world, world_object)
def update_world_object(self, world, obj, item, old, new):
attr_name = new['name']
if attr_name.endswith('plane_position'):
axis = list('xyz').index(attr_name[0])
position = new['value']
if obj.name in self._viewer:
viewer = self._viewer[obj.name]
viewer.change_axis(axis)
viewer.slice_changed(position)
def _create_connections(self):
self.currentChanged.connect(self._on_current_image_changed)
def _on_current_image_changed(self, idx):
pass
def _on_stack_changed(self, stack):
name = self._image[self.sender()]
if stack:
world_object = self.world[name]
cut_plane = '%s_plane_position' % ('xyz'[stack['axis']])
world_object.set_attribute(cut_plane, stack['slice'])
