def mark_selected(self): # what different from scatter selection
# Change the color of the selected point
reds = get_translucent_cmap(1, 0, 0)
select_data = np.transpose(self._vol_data)
not_select = np.logical_not(self.selected)
np.place(select_data, not_select, 0)
select_data = np.transpose(select_data)
self._volume_pool.append((select_data, (1, 6), reds))
# TODO: no set_data function available in multi_volume_visual
self._volume._update_all_volumes(self._volume_pool)
print('self.volume_pool', len(self._volume_pool))
def __init__(self, keys='interactive'):
super(DemoScene, self).__init__()
# Layout and canvas creation
box = QtGui.QVBoxLayout(self)
self.resize(500,500)
self.setLayout(box)
self.canvas = scene.SceneCanvas(keys=keys)
box.addWidget(self.canvas.native)
# Camera
self.view = self.canvas.central_widget.add_view()
self.view.camera = scene.cameras.TurntableCamera(elevation = 25, azimuth=20, distance = 2.0, center=(0,0,0))
# Data
fitsdata = pyfits.open('l1448_13co.fits')
vol1 = np.nan_to_num(fitsdata[0].data)
self.vol_data = vol1
"""
The transpose here and after is for solving the coordinate mismatch between volume visual input data and its
rendering result. The rendered volume shown on 2D screen, or 'what we see', is through displaying transform
(self.tr here) of 'transposed input data', thus we use 'transpose' to enable our selection focusing on 'what
we see' on the screen rather than the real input data of volume.
"""
new_pos = np.transpose(vol1)
# TODO: replace the min&max threshold with real settings in Glue UI
min_threshold = np.min(self.vol_data)
max_threshold = np.max(self.vol_data)
self.pos_data = np.argwhere(new_pos >= min_threshold) # get voxel positions
grays = get_translucent_cmap(1, 1, 1)
self.volume_pool = [(vol1, (1, 6), grays)]
self.volume = MultiVolume(self.volume_pool)
self.trans = [-vol1.shape[2]/2., -vol1.shape[1]/2., -vol1.shape[0]/2.]
self.volume.transform = scene.STTransform(translate=self.trans)
self.view.add(self.volume)
# Add a 3D axis to keep us oriented
axis = scene.visuals.XYZAxis(parent=self.view.scene)
self.selection = SelectionCommon(canvas=self.canvas, view=self.view,
vol_data=self.vol_data, volume=self.volume,
volume_pool=self.volume_pool, pos_data=self.pos_data)
def mark_selected(self):
# Change the color of the selected point
reds = get_translucent_cmap(1, 0, 0)
select_data = np.transpose(self.vol_data)
not_select = np.logical_not(self.selected)
np.place(select_data, not_select, 0)
select_data = np.transpose(select_data)
print('select_data is', select_data, select_data.shape)
maxpos = np.unravel_index(select_data.argmax(), select_data.shape)
print('got the max pos', maxpos)
self.volume_pool.append((select_data, (1, 6), reds))
# TODO: no set_data function available in multi_volume_visual
self.volume._update_all_volumes(self.volume_pool)
print('self.volume_pool', len(self.volume_pool))
self.canvas.update()
def __init__(self, keys='interactive'):
super(DemoScene, self).__init__()
# Layout and canvas creation
box = QtGui.QVBoxLayout(self)
self.resize(800, 600)
self.setLayout(box)
self.canvas = scene.SceneCanvas(keys=keys)
box.addWidget(self.canvas.native)
# Connect events
self.canvas.events.mouse_press.connect(self.on_mouse_press)
self.canvas.events.mouse_release.connect(self.on_mouse_release)
self.canvas.events.mouse_move.connect(self.on_mouse_move)
self.canvas.events.key_press.connect(self.on_key_press)
# Setup some defaults
self.mesh = None
self.selected = []
self.white = (1.0, 1.0, 1.0, 1.0)
self.black = (0.0, 0.0, 0.0, 0.0)
# Camera
self.view = self.canvas.central_widget.add_view()
self.view.camera = scene.cameras.TurntableCamera(elevation = 25, azimuth=20, distance = 2.0, center=(0,0,0))
# Data
fitsdata = pyfits.open('l1448_13co.fits')
self.vol_data = np.nan_to_num(fitsdata[0].data)
"""
The transpose here and after is for solving the coordinate mismatch between volume visual input data and its
rendering result. The rendered volume shown on 2D screen, or 'what we see', is through displaying transform
(self.tr here) of 'transposed input data', thus we use 'transpose' to enable our selection focusing on 'what
we see' on the screen rather than the real input data of volume.
"""
new_pos = np.transpose(self.vol_data)
# TODO: replace the min&max threshold with real settings in Glue UI
self.pos_data = np.argwhere(new_pos >= np.min(self.vol_data)) # get voxel positions
grays = get_translucent_cmap(1, 1, 1)
self.volume_pool = [(self.vol_data, (1, 6), grays)]
self.volume = MultiVolume(self.volume_pool)
self.trans = [-self.vol_data.shape[2]/2., -self.vol_data.shape[1]/2., -self.vol_data.shape[0]/2.]
self.volume.transform = scene.STTransform(translate=self.trans)
self.view.add(self.volume)
self.tr = self.volume.node_transform(self.view) # ChainTransform
# create a volume for showing the selected part
self.volume1 = scene.visuals.Volume(self.vol_data, clim=(4, 6), parent=self.view.scene)
self.volume1.transform = scene.STTransform(translate=self.trans)
self.volume1.visible = False
# Add a text instruction
self.text = scene.visuals.Text('', color='white', pos=(self.canvas.size[0]/4.0, 20), parent=self.canvas.scene)
# Add a 3D axis to keep us oriented
axis = scene.visuals.XYZAxis(parent=self.view.scene)
# Set up for lasso drawing
self.line_pos = []
self.line = scene.visuals.Line(color='yellow', method='gl', parent=self.canvas.scene)
# Selection
self.selection_flag = False
self.selection_pool = {'1': 'lasso', '2': 'rectangle', '3': 'ellipse', '4': 'pick', '5': 'floodfill'}
self.selection_id = '1' # default as 1
self.selection_origin = (0, 0)
subset2[:,:33,-33:][keep] = data[:,:33,-33:][keep]
subset3 = np.zeros_like(data)
keep = data[:,-33:,-33:] > 0.5
subset3[:,-33:,-33:][keep] = data[:,-33:,-33:][keep]
subset4 = np.zeros_like(data)
keep = data[:,-33:,:33] > 0.5
subset4[:,-33:,:33][keep] = data[:,-33:,:33][keep]
# Create Vispy visualization
canvas = scene.SceneCanvas(keys='interactive', size=(800, 600), show=True)
view = canvas.central_widget.add_view()
grays = get_translucent_cmap(1, 1, 1)
reds = get_translucent_cmap(1, 0, 0)
greens = get_translucent_cmap(0, 1, 0)
blues = get_translucent_cmap(0, 0, 1)
oranges = get_translucent_cmap(1, 0.5, 0)
# Create the volume visuals, only one is visible
print(data.max())
volumes = [
(data, (0, 6), grays),
(subset1, (0, 4), reds),
(subset2, (0, 4), greens),
(subset3, (0, 4), blues),
(subset4, (0, 4), oranges)
]
def __init__(self, keys='interactive'):
super(DemoScene, self).__init__()
# Layout and canvas creation
box = QtGui.QVBoxLayout(self)
self.resize(800, 600)
self.setLayout(box)
self.canvas = scene.SceneCanvas(keys=keys)
box.addWidget(self.canvas.native)
# Connect events
self.canvas.events.mouse_press.connect(self.on_mouse_press)
self.canvas.events.mouse_release.connect(self.on_mouse_release)
self.canvas.events.mouse_move.connect(self.on_mouse_move)
self.canvas.events.key_press.connect(self.on_key_press)
# Setup some defaults
self.mesh = None
self.selected = []
self.white = (1.0, 1.0, 1.0, 1.0)
self.black = (0.0, 0.0, 0.0, 0.0)
# Camera
self.view = self.canvas.central_widget.add_view()
self.view.camera = scene.cameras.TurntableCamera(elevation=25,
azimuth=20,
distance=2.0,
center=(0, 0, 0))
# Data
fitsdata = pyfits.open('l1448_13co.fits')
vol1 = np.nan_to_num(fitsdata[0].data)
self.vol_data = vol1
"""
The transpose here and after is for solving the coordinate mismatch between volume visual input data and its
rendering result. The rendered volume shown on 2D screen, or 'what we see', is through displaying transform
(self.tr here) of 'transposed input data', thus we use 'transpose' to enable our selection focusing on 'what
we see' on the screen rather than the real input data of volume.
"""
new_pos = np.transpose(vol1)
# TODO: replace the min&max threshold with real settings in Glue UI
min_threshold = np.min(self.vol_data)
max_threshold = np.max(self.vol_data)
self.pos_data = np.argwhere(
new_pos >= min_threshold) # get voxel positions
grays = get_translucent_cmap(1, 1, 1)
self.volume_pool = [(vol1, (1, 6), grays)]
self.volume = MultiVolume(self.volume_pool)
self.trans = [
-vol1.shape[2] / 2., -vol1.shape[1] / 2., -vol1.shape[0] / 2.
]
self.volume.transform = scene.STTransform(translate=self.trans)
self.view.add(self.volume)
self.tr = self.volume.node_transform(self.view) # ChainTransform
# Add a text instruction
self.text = scene.visuals.Text('',
color='white',
pos=(self.canvas.size[0] / 4.0, 20),
parent=self.canvas.scene)
# Add a 3D axis to keep us oriented
axis = scene.visuals.XYZAxis(parent=self.view.scene)
# Set up for lasso drawing
self.line_pos = []
self.line = scene.visuals.Line(color='yellow',
method='gl',
parent=self.canvas.scene)
# Selection
self.selection_flag = False
self.selection_pool = {
'1': 'lasso',
'2': 'rectangle',
'3': 'ellipse',
'4': 'pick'
}
self.selection_id = '1' # default as 1
self.selection_origin = (0, 0)
# Read volume
vol1 = np.load(io.load_data_file('volume/stent.npz'))['arr_0']
vol2 = np.load(io.load_data_file('brain/mri.npz'))['data']
vol2 = np.flipud(np.rollaxis(vol2, 1))
# Prepare canvas
canvas = scene.SceneCanvas(keys='interactive', size=(800, 600), show=True)
canvas.measure_fps()
# Set up a viewbox to display the image with interactive pan/zoom
view = canvas.central_widget.add_view()
# Set whether we are emulating a 3D texture
emulate_texture = False
reds = get_translucent_cmap(1, 0, 0)
blues = get_translucent_cmap(0, 0, 1)
# Create the volume visuals, only one is visible
volumes = [(vol1, None, blues), (vol1[::-1,::-1,::-1], None, reds)]
volume1 = MultiVolume(volumes, parent=view.scene, threshold=0.225,
emulate_texture=emulate_texture)
volume1.transform = scene.STTransform(translate=(64, 64, 0))
# Create three cameras (Fly, Turntable and Arcball)
fov = 60.
cam2 = scene.cameras.TurntableCamera(parent=view.scene, fov=fov,
name='Turntable')
view.camera = cam2 # Select turntable at first
canvas.update()
# Read volume
vol1 = np.load(io.load_data_file('volume/stent.npz'))['arr_0']
vol2 = np.load(io.load_data_file('brain/mri.npz'))['data']
vol2 = np.flipud(np.rollaxis(vol2, 1))
# Prepare canvas
canvas = scene.SceneCanvas(keys='interactive', size=(800, 600), show=True)
canvas.measure_fps()
# Set up a viewbox to display the image with interactive pan/zoom
view = canvas.central_widget.add_view()
# Set whether we are emulating a 3D texture
emulate_texture = False
reds = get_translucent_cmap(1, 0, 0)
blues = get_translucent_cmap(0, 0, 1)
# Create the volume visuals, only one is visible
volumes = [(vol1, None, blues), (vol1[::-1, ::-1, ::-1], None, reds)]
volume1 = MultiVolume(volumes,
parent=view.scene,
threshold=0.225,
emulate_texture=emulate_texture)
volume1.transform = scene.STTransform(translate=(64, 64, 0))
# Create three cameras (Fly, Turntable and Arcball)
fov = 60.
cam2 = scene.cameras.TurntableCamera(parent=view.scene,
fov=fov,
name='Turntable')
