def drawPoints(Points,
mlab,
scale=0.025,
color=(np.random.rand(1)[0], np.random.rand(1)[0],
np.random.rand(1)[0])):
"""
用MayaVi绘制点
:param Points: 欲绘制的顶点 n * 3
:param mlab:
:return: 返回mlab
"""
if isinstance(Points, list):
Points = np.array(Points, dtype=np.float32)
mlab.points3d(Points[:, 0],
Points[:, 1],
Points[:, 2],
scale_factor=scale,
color=color)
for i in range(0, len(Points)):
mlab.text3d(Points[i, 0],
Points[i, 1],
Points[i, 2],
str(i + 1),
scale=scale * 1.5,
color=(0, 0, 0))
return mlab
def drawArrows(file1, file2, figure, bbox, index, descendant):
"""
Draw an 'arrow' from the cell 'index' to 'descendant'
'descendant' is assumed to be a 1D np.array with size 0, 1 or 2.
"""
#load the center of mass position
if descendant.size > 0 and descendant[0] != 0:
com1 = file1["features"][str(index[0])]["com"][:]
com2 = file2["features"][str(descendant[0])]["com"][:]
#write the cell label as text
mlab.text3d(com1[2]-bbox[2]+1,com1[1]-bbox[1]+1,com1[0]-bbox[0]+1, str(index), color=(1,1,1), figure=figure)
#plot a point where the current cell is
mlab.points3d([com1[2]-bbox[2]+1],[com1[1]-bbox[1]+1],[com1[0]-bbox[0]+1],color=(0,0,1), figure=figure)
#plot a line to the descendant's center
mlab.plot3d([com1[2]-bbox[2]+1,com2[2]-bbox[2]+1],
[com1[1]-bbox[1]+1,com2[1]-bbox[1]+1],
[com1[0]-bbox[0]+1,com2[0]-bbox[0]+1],
tube_radius=0.2, color=(1,0,0), figure=figure)
#plot a second line, if there is a split
if descendant.size == 2:
com3 = file2["features"][str(descendant[1])]["com"][:]
mlab.plot3d([com1[2]-bbox[2]+1,com3[2]-bbox[2]+1],
[com1[1]-bbox[1]+1,com3[1]-bbox[1]+1],
[com1[0]-bbox[0]+1,com3[0]-bbox[0]+1],
tube_radius=0.2, color=(1,0,0), figure=figure)
def _render(self, **kwargs):
from mayavi import mlab
# disabling the rendering greatly speeds up this for loop
self.figure.scene.disable_render = True
positions = []
for label, mask in self.labels_to_masks.iteritems():
p = self.pointcloud.from_mask(mask)
for i, p in enumerate(p.points):
positions.append(p)
l = '%s_%d' % (label, i)
# TODO: This is due to a bug in mayavi that won't allow
# rendering text to an empty figure
mlab.points3d(p[0], p[1], p[2])
mlab.text3d(p[0], p[1], p[2], l, figure=self.figure)
positions = np.array(positions)
os = np.zeros_like(positions)
os[:, 2] = 1
mlab.quiver3d(positions[:, 0],
positions[:, 1],
positions[:, 2],
os[:, 0],
os[:, 1],
os[:, 2],
figure=self.figure)
self.figure.scene.disable_render = False
return self
def plot(self, size=(800, 800), fig=None, HPI_ns=False):
"""
Plot sensor helmet and head. ``fig`` is used if provided, otherwise
a new mayavi figure is created with ``size``.
HPI_ns : bool
Add number labels to the HPI points.
"""
if fig is None:
fig = mlab.figure(size=size)
self.mrk.plot_points(fig, scale=1.1e-2, opacity=.5, color=(1, 0, 0))
self.sensors.plot_points(fig, scale=1e-2, color=(0, 0, 1))
self.HPI.plot_points(fig, scale=1e-2, color=(1, .8, 0))
self.headshape.plot_solid(fig, opacity=1., color=(1, 1, 1))
if self.MRI is not None:
self.MRI.plot_solid(fig, opacity=1., color=(.6, .6, .5))
# label marker points
for i, pt in enumerate(self.mrk.pts[:3].T):
x, y, z = pt
self.txt = mlab.text3d(x, y, z, str(i), scale=.01)
if HPI_ns: # label HPI points
for i, pt in enumerate(self.HPI.pts[:3].T):
x, y, z = pt
mlab.text3d(x, y, z, str(i), scale=.01, color=(1, .8, 0))
return fig
def draw_gt_boxes3d(gt_boxes3d, fig, color=(1,1,1), line_width=1, draw_text=True, text_scale=(1,1,1), color_list=None):
''' Draw 3D bounding boxes
Args:
gt_boxes3d: numpy array (n,8,3) for XYZs of the box corners
fig: mayavi figure handler
color: RGB value tuple in range (0,1), box line color
line_width: box line width
draw_text: boolean, if true, write box indices beside boxes
text_scale: three number tuple
color_list: a list of RGB tuple, if not None, overwrite color.
Returns:
fig: updated fig
'''
num = len(gt_boxes3d)
for n in range(num):
b = gt_boxes3d[n]
if color_list is not None:
color = color_list[n]
if draw_text: mlab.text3d(b[4,0], b[4,1], b[4,2], '%d'%n, scale=text_scale, color=color, figure=fig)
for k in range(0,4):
#http://docs.enthought.com/mayavi/mayavi/auto/mlab_helper_functions.html
i,j=k,(k+1)%4
mlab.plot3d([b[i,0], b[j,0]], [b[i,1], b[j,1]], [b[i,2], b[j,2]], color=color, tube_radius=None, line_width=line_width, figure=fig)
i,j=k+4,(k+1)%4 + 4
mlab.plot3d([b[i,0], b[j,0]], [b[i,1], b[j,1]], [b[i,2], b[j,2]], color=color, tube_radius=None, line_width=line_width, figure=fig)
i,j=k,k+4
mlab.plot3d([b[i,0], b[j,0]], [b[i,1], b[j,1]], [b[i,2], b[j,2]], color=color, tube_radius=None, line_width=line_width, figure=fig)
#mlab.show(1)
#mlab.view(azimuth=180, elevation=70, focalpoint=[ 12.0909996 , -1.04700089, -2.03249991], distance=62.0, figure=fig)
return fig
def render(self, scale_factor=1.0, text_scale=1.0, **kwargs):
import mayavi.mlab as mlab
# disabling the rendering greatly speeds up this for loop
self.figure.scene.disable_render = True
positions = []
for label in self.lmark_group:
p = self.lmark_group[label]
for i, p in enumerate(p.points):
positions.append(p)
l = '%s_%d' % (label, i)
# TODO: This is due to a bug in mayavi that won't allow
# rendering text to an empty figure
mlab.points3d(p[0], p[1], p[2], scale_factor=scale_factor)
mlab.text3d(p[0], p[1], p[2], l, figure=self.figure,
scale=text_scale)
positions = np.array(positions)
os = np.zeros_like(positions)
os[:, 2] = 1
mlab.quiver3d(positions[:, 0], positions[:, 1], positions[:, 2],
os[:, 0], os[:, 1], os[:, 2], figure=self.figure)
self.figure.scene.disable_render = False
# Ensure everything fits inside the camera viewport
mlab.get_engine().current_scene.scene.reset_zoom()
return self
def plot_structure(structure,
frac_coords=False,
to_unit_cell=False,
style="points+labels",
unit_cell_color=(0, 0, 0),
color_scheme="VESTA",
figure=None,
show=False,
**kwargs): # pragma: no cover
"""
Plot structure with mayavi.
Args:
structure: |Structure| object
frac_coords:
to_unit_cell: True if sites should be wrapped into the first unit cell.
style: "points+labels" to show atoms sites with labels.
unit_cell_color:
color_scheme: color scheme for atom types. Allowed values in ("Jmol", "VESTA")
figure:
kwargs:
Returns: mayavi figure
"""
figure, mlab = get_fig_mlab(figure=figure)
#if not frac_coords:
plot_unit_cell(structure.lattice, color=unit_cell_color, figure=figure)
from pymatgen.analysis.molecule_structure_comparator import CovalentRadius
from pymatgen.vis.structure_vtk import EL_COLORS
for site in structure:
symbol = site.specie.symbol
color = tuple(i / 255 for i in EL_COLORS[color_scheme][symbol])
radius = CovalentRadius.radius[symbol]
if to_unit_cell and hasattr(site, "to_unit_cell"):
site = site.to_unit_cell
x, y, z = site.frac_coords if frac_coords else site.coords
if "points" in style:
mlab.points3d(x,
y,
z,
figure=figure,
scale_factor=radius,
resolution=20,
color=color,
scale_mode='none',
**kwargs)
if "labels" in style:
mlab.text3d(x,
y,
z,
symbol,
figure=figure,
color=(0, 0, 0),
scale=0.2)
if show: mlab.show()
return figure
def draw_boxes3d(gt_boxes3d,
color=(1, 1, 1),
line_width=1,
draw_text=True,
text_scale=(0.01, 0.01, 0.01),
color_list=None):
from mayavi import mlab
num = len(gt_boxes3d)
for n in range(num):
b = gt_boxes3d[n]
if color_list is not None:
color = color_list[n]
if draw_text:
mlab.text3d(b[7, 0],
b[7, 1],
b[7, 2],
'%d' % n,
scale=text_scale,
color=color)
# hard coded
# pairs = [(0, 1), (1, 2), (1, 3), (3, 0), (4, 5), (5, 6), (6, 7), (7, 4), (0, 4), (1, 5), (2, 6), (3, 7)]
pairs = [(0, 1), (0, 2), (3, 1), (3, 2), (4, 5), (4, 6), (7, 5),
(7, 6), (0, 4), (1, 5), (2, 6), (3, 7)]
for i, j in pairs:
mlab.plot3d([b[i, 0], b[j, 0]], [b[i, 1], b[j, 1]],
[b[i, 2], b[j, 2]],
color=color,
tube_radius=None,
line_width=line_width)
def _show_labels(self, show):
_toggle_mlab_render(self, False)
while self.text3d:
text = self.text3d.pop()
text.remove()
if show and len(self.src.data.points) > 0:
fig = self.scene.mayavi_scene
if self._view == 'arrow': # for axes
x, y, z = self.src.data.points[0]
self.text3d.append(
text3d(x,
y,
z,
self.name,
scale=self.label_scale,
color=self.color,
figure=fig))
else:
for i, (x, y, z) in enumerate(np.array(self.src.data.points)):
self.text3d.append(
text3d(x,
y,
z,
' %i' % i,
scale=self.label_scale,
color=self.color,
figure=fig))
_toggle_mlab_render(self, True)
def draw_gt_boxes2d(gt_boxes2d,
fig,
color=(1, 1, 1),
line_width=1,
draw_text=True,
text_scale=(1, 1, 1),
color_list=None):
num = len(gt_boxes2d)
for n in range(num):
b = gt_boxes2d[n]
if color_list is not None:
color = color_list[n]
if draw_text:
mlab.text3d(b[4, 0],
b[4, 1],
b[4, 2],
'%d' % n,
scale=text_scale,
color=color,
figure=fig)
for i in range(4):
mlab.plot3d([b[i, 0], b[(i + 1) % 4, 0]],
[b[i, 1], b[(i + 1) % 4, 1]],
[b[i, 2], b[(i + 1) % 4, 2]],
color=color,
tube_radius=None,
line_width=line_width,
figure=fig)
return fig
def draw_3D_bboxes(self, bboxes3d, fig, line_width=2, draw_text=True, text_scale=(1, 1, 1)):
num = len(bboxes3d)
for n in range(num):
b = bboxes3d[n]
if b[0] != "None":
if b[0] == "car":
color = tuple(self.colorVehPC)
elif b[0] == "person":
color = tuple(self.colorPedPC)
elif b[0] == "cyclist":
color = tuple(self.colorCycPC)
else:
color = (0, 0, 0)
if draw_text:
mlab.text3d(b[1][0,0], b[1][1,0], b[1][2,0], '%s'%b[0], scale=text_scale, color=color, figure=fig)
for k in range(0,4):
i,j=k,(k+1)%4
#mlab.plot3d([b[i,0], b[j,0]], [b[i,1], b[j,1]], [b[i,2], b[j,2]], color=color, tube_radius=None, line_width=line_width, figure=fig)
mlab.plot3d([b[1][0,i], b[1][0,j]], [b[1][1,i], b[1][1,j]], [b[1][2,i], b[1][2,j]], color=color, tube_radius=None, line_width=line_width, figure=fig)
i,j=k+4,(k+1)%4 + 4
#mlab.plot3d([b[i,0], b[j,0]], [b[i,1], b[j,1]], [b[i,2], b[j,2]], color=color, tube_radius=None, line_width=line_width, figure=fig)
mlab.plot3d([b[1][0,i], b[1][0,j]], [b[1][1,i], b[1][1,j]], [b[1][2,i], b[1][2,j]], color=color, tube_radius=None, line_width=line_width, figure=fig)
i,j=k,k+4
#mlab.plot3d([b[i,0], b[j,0]], [b[i,1], b[j,1]], [b[i,2], b[j,2]], color=color, tube_radius=None, line_width=line_width, figure=fig)
mlab.plot3d([b[1][0,i], b[1][0,j]], [b[1][1,i], b[1][1,j]], [b[1][2,i], b[1][2,j]], color=color, tube_radius=None, line_width=line_width, figure=fig)
return fig
def render(self, scale_factor=1.0, text_scale=1.0, **kwargs):
import mayavi.mlab as mlab
# disabling the rendering greatly speeds up this for loop
self.figure.scene.disable_render = True
positions = []
for label in self.lmark_group:
p = self.lmark_group[label]
for i, p in enumerate(p.points):
positions.append(p)
l = '%s_%d' % (label, i)
# TODO: This is due to a bug in mayavi that won't allow
# rendering text to an empty figure
mlab.points3d(p[0], p[1], p[2], scale_factor=scale_factor)
mlab.text3d(p[0],
p[1],
p[2],
l,
figure=self.figure,
scale=text_scale)
positions = np.array(positions)
os = np.zeros_like(positions)
os[:, 2] = 1
mlab.quiver3d(positions[:, 0],
positions[:, 1],
positions[:, 2],
os[:, 0],
os[:, 1],
os[:, 2],
figure=self.figure)
self.figure.scene.disable_render = False
# Ensure everything fits inside the camera viewport
mlab.get_engine().current_scene.scene.reset_zoom()
return self
def quiver4(datas, length = 6000, skip=5):
black = (0,0,0)
white = (1,1,1)
mlab.figure(bgcolor=white)
triangles = [
(0, 1, 2),
(0, 2, 4),
(0, 4, 3),
(0, 3, 1),
]
for cam_id, data in datas.items():
if cam_id == '107':
continue
x0, y0, z0, phi, psi = \
[data[i] for i in ('x', 'y', 'z', 'bounding_phi', 'bounding_psi')]
x = x0 + length * np.sin(phi)
y = y0 + length * np.cos(phi)
z = z0 + length * np.cos(psi)
mlab.triangular_mesh(
np.insert(x, 0, x0),
np.insert(y, 0, y0),
np.insert(z, 0, z0),
triangles,
color=(0.5, 0.5, 0.5),
opacity=0.4
)
mlab.text3d(x0, y0, z0, cam_id, color=black, scale=100.)
mlab.show()
def draw_label(trk, handle):
p = trk.center
mlab.text3d(p[0],
p[1],
p[2] + 2,
str(trk.id),
scale=0.5,
figure=handle)
def draw_boxes(self,
boxes,
color=(1, 1, 1),
line_width=1,
draw_text=True,
text_scale=(1, 1, 1),
color_list=None):
''' Draw 3D bounding boxes
Args:
boxes: numpy array (n,8,3) for XYZs of the box corners
fig: mayavi figure handler
color: RGB value tuple in range (0,1), box line color
line_width: box line width
draw_text: boolean, if true, write box indices beside boxes
text_scale: three number tuple
color_list: a list of RGB tuple, if not None, overwrite color.
Returns:
fig: updated fig
'''
self._create_figure()
num = len(boxes)
for n in range(num):
b = boxes[n]
if color_list is not None:
color = color_list[n]
if draw_text:
mlab.text3d(b[4, 0],
b[4, 1],
b[4, 2],
'%d' % n,
scale=text_scale,
color=color,
figure=fig)
for k in range(0, 4):
#http://docs.enthought.com/mayavi/mayavi/auto/mlab_helper_functions.html
i, j = k, (k + 1) % 4
mlab.plot3d([b[i, 0], b[j, 0]], [b[i, 1], b[j, 1]],
[b[i, 2], b[j, 2]],
color=color,
tube_radius=None,
line_width=line_width,
figure=fig)
i, j = k + 4, (k + 1) % 4 + 4
mlab.plot3d([b[i, 0], b[j, 0]], [b[i, 1], b[j, 1]],
[b[i, 2], b[j, 2]],
color=color,
tube_radius=None,
line_width=line_width,
figure=fig)
i, j = k, k + 4
mlab.plot3d([b[i, 0], b[j, 0]], [b[i, 1], b[j, 1]],
[b[i, 2], b[j, 2]],
color=color,
tube_radius=None,
line_width=line_width,
figure=fig)
def _add_points(self):
if self.map_surface:
temp = self.points.map_to_surface(self.map_surface)
mapped_vertices, mapped_coords_ras_tkr = temp['vertices'], temp[
'ras_tkr_coord']
mapped_coords = mapped_coords_ras_tkr
### FreesurferCoords.map_to_annot requires map_surface to be set ( set to white by default). Here, we use map_surface if it has been set, otherwise use 'white' by default.
if self.map_to_annot:
if self.map_surface:
self.points.name, self.points.color = self.points.map_to_annot(
self.map_to_annot, map_surface=self.map_surface)
else:
self.points.name, self.points.color = self.points.map_to_annot(
self.map_to_annot, map_surface='white')
for i in range(self.points.npoints):
point = self.points[i]
if point.hemi == self.hemi or self.hemi == 'both':
if self.map_surface:
self.brain.add_foci(mapped_coords[i, :],
hemi=point.hemi,
color=point.color,
scale_factor=point.scale_factor,
alpha=point.opacity)
else:
self.brain.add_foci(point.ras_tkr_coord,
hemi=point.hemi,
color=point.color,
scale_factor=point.scale_factor,
alpha=point.opacity)
if self.show_roi and hasattr(point, 'roi'):
self.brain.add_label(point.roi,
hemi=point.hemi,
color=point.roi.color)
if self.show_name and hasattr(point, 'name'):
mlab.text3d(point.ras_tkr_coord[0],
point.ras_tkr_coord[1],
point.ras_tkr_coord[2],
point.name,
scale=self.name_scale,
color=self.name_color)
if self.show_directions and hasattr(point, 'direction'):
origin = point.ras_tkr_coord.flatten().tolist()
X, Y, Z = zip(origin, origin, origin)
p0 = point.direction[0:3]
p1 = point.direction[3:6]
p2 = point.direction[6:9]
U, W, V = zip(p0, p1, p2)
plot_directions(X, Y, Z, U, W, V)
def draw_frame(self, pose, scale=10, label=''):
R, t = pose
scale = self.scale * scale
clr = [RED, GREEN, BLUE]
vecs = R[:, 0], R[:, 1], R[:, 2]
for k in range(3):
mlab.quiver3d(t[0], t[1], t[2], vecs[k][0], vecs[k][1], vecs[k][2],
color=clr[k], mode='arrow', scale_factor=scale)
mlab.text3d(t[0], t[1], t[2], label, scale=scale/5)
def res_names(atoms_df):
"""
"""
for row in atoms_df.iterrows():
mlab.text3d(row[1][3],
row[1][4],
row[1][5],
text=row[1][0] + " " + str(row[1][2]),
color=(0, 0, 0))
def draw_frame(self, pose, scale=10, label=''):
R, t = pose
scale = self.scale * scale
clr = [RED, GREEN, BLUE]
vecs = R[:, 0], R[:, 1], R[:, 2]
for k in range(3):
mlab.quiver3d(t[0], t[1], t[2], vecs[k][0], vecs[k][1], vecs[k][2],
color=clr[k], mode='arrow', scale_factor=scale)
mlab.text3d(t[0], t[1], t[2], label, scale=scale/5)
def draw_gt_boxes3d(gt_boxes3d,
conf,
thres=0,
color=(1, 1, 1),
fig=None,
engine=None,
line_width=1,
draw_text=True,
text_scale=(0.5, 0.5, 0.5),
color_list=None):
# if engine:
# fig = mlab.figure(figure=fig, engine =engine)
num = len(gt_boxes3d)
for n in range(num):
b = gt_boxes3d[n]
if color_list is not None:
color = color_list[n]
if n >= thres:
color = (0, 1, 0)
else:
color = (1, 0, 0)
if draw_text and n >= thres and n - thres <= len(conf):
mlab.text3d(b[3, 0],
b[3, 1],
b[3, 2],
'%.1f' % float(conf[n - thres]),
scale=text_scale,
color=color,
figure=fig)
for k in range(0, 4):
#http://docs.enthought.com/mayavi/mayavi/auto/mlab_helper_functions.html
i, j = k, (k + 1) % 4
mlab.plot3d([b[i, 0], b[j, 0]], [b[i, 1], b[j, 1]],
[b[i, 2], b[j, 2]],
color=color,
tube_radius=None,
line_width=line_width,
figure=fig)
i, j = k + 4, (k + 1) % 4 + 4
mlab.plot3d([b[i, 0], b[j, 0]], [b[i, 1], b[j, 1]],
[b[i, 2], b[j, 2]],
color=color,
tube_radius=None,
line_width=line_width,
figure=fig)
i, j = k, k + 4
mlab.plot3d([b[i, 0], b[j, 0]], [b[i, 1], b[j, 1]],
[b[i, 2], b[j, 2]],
color=color,
tube_radius=None,
line_width=line_width,
figure=fig)
def __plotObj(self,obj,obj_shape,base_color,obj_name):
# objera center
mi.points3d(obj[0],obj[1],obj[2],color=base_color,scale_factor=0.2)
mi.text3d( obj[0],obj[1],obj[2],obj_name,scale=0.3,color=(0,0,0))
# Transform
T,T_inv = mgo.transformLookAt(obj[0:3],obj[3:6],obj[6:9])
obj_shape = np.dot(T,np.r_[
obj_shape.transpose(),
np.ones([1,np.shape(obj_shape)[0]])])
mi.plot3d(obj_shape[0,:],obj_shape[1,:],obj_shape[2,:],tube_radius=None,reset_zoom=False)
def _set_numbering(figure, centers, render_numbering=True, numbers_size=None,
numbers_colour='k'):
import mayavi.mlab as mlab
numbers_colour = _parse_colour(numbers_colour)
numbers_size = _parse_marker_size(numbers_size, centers)
if render_numbering:
for k, p in enumerate(centers):
mlab.text3d(p[0], p[1], p[2], str(k), figure=figure,
scale=numbers_size, orient_to_camera=True,
color=numbers_colour, line_width=2)
def draw_feature_node(self):
label_text = []
junc_len = len(self.skel_data.junction_index)
for i in xrange(len(self.skel_data.feature_node_index)):
label_text.append(str(i))
#mlab.figure(self.program_id[0])
pts = mlab.points3d(self.skel_data.feature_node[:junc_len,0], self.skel_data.feature_node[:junc_len,1], self.skel_data.feature_node[:junc_len,2], color=(.7,.0,0.0), scale_factor=.135, resolution=20)
mlab.points3d(self.skel_data.feature_node[junc_len:,0], self.skel_data.feature_node[junc_len:,1], self.skel_data.feature_node[junc_len:,2], color=(.0,.0,0.7), scale_factor=.1, resolution=20)
for i in xrange(len(label_text)):
mlab.text3d(self.skel_data.feature_node[i,0], self.skel_data.feature_node[i,1], self.skel_data.feature_node[i,2], label_text[i], scale=.15)
def draw_gt_box3d(gt_box3d,
fig,
obj,
line_width=1,
draw_text=True,
text_scale=(1, 1, 1)):
if obj.type in class_colors:
color = class_colors[obj.type]
else:
color = (1, 0, 1)
if draw_text:
label = '%s: %.1f' % (obj.type, obj.score)
mlab.text3d(gt_box3d[4, 0],
gt_box3d[4, 1],
gt_box3d[4, 2],
label,
scale=text_scale,
color=color,
figure=fig)
for k in range(0, 4):
# http://docs.enthought.com/mayavi/mayavi/auto/mlab_helper_functions.html
i, j = k, (k + 1) % 4
mlab.plot3d([gt_box3d[i, 0], gt_box3d[j, 0]],
[gt_box3d[i, 1], gt_box3d[j, 1]],
[gt_box3d[i, 2], gt_box3d[j, 2]],
color=color,
tube_radius=None,
line_width=line_width,
figure=fig)
i, j = k + 4, (k + 1) % 4 + 4
mlab.plot3d([gt_box3d[i, 0], gt_box3d[j, 0]],
[gt_box3d[i, 1], gt_box3d[j, 1]],
[gt_box3d[i, 2], gt_box3d[j, 2]],
color=color,
tube_radius=None,
line_width=line_width,
figure=fig)
i, j = k, k + 4
mlab.plot3d([gt_box3d[i, 0], gt_box3d[j, 0]],
[gt_box3d[i, 1], gt_box3d[j, 1]],
[gt_box3d[i, 2], gt_box3d[j, 2]],
color=color,
tube_radius=None,
line_width=line_width,
figure=fig)
# mlab.show(1)
# mlab.view(azimuth=180, elevation=70, focalpoint=[ 12.0909996 , -1.04700089, -2.03249991], distance=62.0, figure=fig)
return fig
def _PlotQuiver(self, Phi, Theta, Figure, Origin, Coord, Vector, Scalar, Label=''):
FlatCoord = [1.01*Coord[i].flatten() + Origin[i] for i in range(3)]
A = Scalar.flatten()
A /= np.max(abs(A))
Vector = A * Vector
mlab.quiver3d(*FlatCoord, *Vector, color=(0,0,0), scale_factor=0.25, scale_mode = 'vector', figure=Figure)
mlab.text3d(x = Origin[0], y = Origin[1], z = Origin[2]+3.5, text = Label, line_width = 0.1, figure = Figure, scale = 0.25, color = (0,0,0))
def visualize_text(point, text):
try:
from mayavi import mlab
except ImportError:
return
mlab.figure('pc', bgcolor=(0.05, 0.05, 0.05))
mlab.text3d(point[0],
point[1],
point[2] + 0.03,
'{}'.format(int(point[3])),
scale=0.02,
color=(0, 0.8, 0))
def _plot_axes(lattice, color=(1, 0, 0)):
lat = np.transpose([x / np.linalg.norm(x) for x in lattice.T])
mlab.quiver3d([0, 0, 0], [0, 0, 0], [0, 0, 0],
lat[0],
lat[1],
lat[2],
color=color,
line_width=3,
scale_factor=1)
for c, v in zip(('a', 'b', 'c'), (lat * 1.3).T):
mlab.text3d(v[0] + 0.15, v[1], v[2], c, color=color, scale=0.3)
def draw_gt_boxes3d(gt_boxes3d,
iIndex,
fig,
color=(1, 1, 1),
line_width=1,
draw_text=True,
text_scale=(1, 1, 1),
color_list=None):
num = len(gt_boxes3d)
for n in range(num):
b = gt_boxes3d[n]
if color_list is not None:
color = color_list[n]
if draw_text:
mlab.text3d(b[4, 0],
b[4, 1],
b[4, 2],
'%d' % iIndex,
scale=text_scale,
color=color,
figure=fig)
for k in range(0, 4):
# http://docs.enthought.com/mayavi/mayavi/auto/mlab_helper_functions.html
i, j = k, (k + 1) % 4
mlab.plot3d([b[i, 0], b[j, 0]], [b[i, 1], b[j, 1]],
[b[i, 2], b[j, 2]],
color=color,
tube_radius=None,
line_width=line_width,
figure=fig)
i, j = k + 4, (k + 1) % 4 + 4
mlab.plot3d([b[i, 0], b[j, 0]], [b[i, 1], b[j, 1]],
[b[i, 2], b[j, 2]],
color=color,
tube_radius=None,
line_width=line_width,
figure=fig)
i, j = k, k + 4
mlab.plot3d([b[i, 0], b[j, 0]], [b[i, 1], b[j, 1]],
[b[i, 2], b[j, 2]],
color=color,
tube_radius=None,
line_width=line_width,
figure=fig)
# mlab.show()
mlab.view(azimuth=180,
elevation=70,
focalpoint=[12.0909996, -1.04700089, -2.03249991],
distance=62.0,
figure=fig)
return fig
def WavenumberArrow(Figure, Origin, Scale=0.5):
Vec = [0, 0, 1]
ArrowAVec(Origin=Origin, Vec=Vec, Scale=Scale, Color=YELLOW)
mlab.text3d(x=Vec[0] + Origin[0],
y=Vec[1] + Origin[1],
z=Vec[2] + Origin[2],
text='k',
line_width=0.1,
figure=Figure,
scale=0.25,
color=BLACK)
def ElectricFieldArrow(Figure, Origin, Pol, Scale=0.5):
Vec = [sin(Pol), cos(Pol), 0]
ArrowAVec(Origin=Origin, Vec=Vec, Scale=Scale, Color=RED)
mlab.text3d(x=Vec[0] + Origin[0],
y=Vec[1] + Origin[1],
z=Vec[2] + Origin[2],
text='E',
line_width=0.1,
figure=Figure,
scale=0.25,
color=RED)
def MagneticFieldArrow(Figure, Origin, Vec, Scale=0.5):
Vec = [Vec[0], Vec[1], 0]
ArrowAVec(Origin=Origin, Vec=Vec, Scale=Scale, Color=BLUE)
mlab.text3d(x=Vec[0] + Origin[0],
y=Vec[1] + Origin[1],
z=Vec[2] + Origin[2],
text='B',
line_width=0.1,
figure=Figure,
scale=0.25,
color=BLACK)
def draw_gt_boxes3d(gt_boxes3d, fig, color=(1, 0, 0), line_width=2):
num = len(gt_boxes3d)
for n in range(num):
b = gt_boxes3d[n]
mlab.text3d(b[0, 0],
b[0, 1],
b[0, 2],
'%d' % n,
scale=(1, 1, 1),
color=color,
figure=fig)
for k in range(0, 4):
#http://docs.enthought.com/mayavi/mayavi/auto/mlab_helper_functions.html
i, j = k, (k + 1) % 4
mlab.plot3d([b[i, 0], b[j, 0]], [b[i, 1], b[j, 1]],
[b[i, 2], b[j, 2]],
color=color,
tube_radius=None,
line_width=line_width,
figure=fig)
mlab.text3d(b[i, 0],
b[i, 1],
b[i, 2],
'%d' % i,
scale=(1, 1, 1),
color=color,
figure=fig)
i, j = k + 4, (k + 1) % 4 + 4
mlab.plot3d([b[i, 0], b[j, 0]], [b[i, 1], b[j, 1]],
[b[i, 2], b[j, 2]],
color=color,
tube_radius=None,
line_width=line_width,
figure=fig)
i, j = k, k + 4
mlab.plot3d([b[i, 0], b[j, 0]], [b[i, 1], b[j, 1]],
[b[i, 2], b[j, 2]],
color=color,
tube_radius=None,
line_width=line_width,
figure=fig)
mlab.view(azimuth=180,
elevation=None,
distance=50,
focalpoint=[12.0909996, -1.04700089,
-2.03249991]) #2.0909996 , -1.04700089, -2.03249991
def test_text3d(self):
"""Test if Text3D shows"""
# the points3d is there to provide data for
# attaching the text3d module. Opacity is set to
# zero so that the image should only show
# the text3d and we look for the pixels
mlab.points3d(0., 0., 0., opacity=0.)
self.addCleanup(self.mlab_close_all)
mlab.text3d(0., 0., 0., "X")
mlab.savefig(self.filename)
self.check()
def _plot_axes(lattice, color=(1, 0, 0)):
lat = np.transpose([x/np.linalg.norm(x) for x in lattice.T])
mlab.quiver3d([0, 0, 0],
[0, 0, 0],
[0, 0, 0],
lat[0],
lat[1],
lat[2],
color=color,
line_width=3,
scale_factor=1)
for c, v in zip(('a','b','c'), (lat * 1.3).T):
mlab.text3d(v[0]+0.15, v[1], v[2], c, color=color, scale=0.3)
def test_text3d(self):
"""Test if Text3D shows"""
# the points3d is there to provide data for
# attaching the text3d module. Opacity is set to
# zero so that the image should only show
# the text3d and we look for the pixels
mlab.points3d(0., 0., 0., opacity=0.)
self.addCleanup(self.mlab_close_all)
mlab.text3d(0., 0., 0., "X")
mlab.savefig(self.filename)
self.check()
def mayaplot(xyznamearray): x = xyznamearray[1] y = xyznamearray[2] z = xyznamearray[3] labels = xyznamearray[0] s = mlab.points3d(x[0], y[0], z[0], color=(0,1,1), mode='sphere', scale_factor=100) for i in range(0,26): mlab.points3d(x[i], y[i], z[i], color=(0,1,1), mode='sphere', scale_factor=5000, opacity=0.5) mlab.text3d(x[i], y[i], z[i], labels[i], scale=5000) axes = mlab.axes(s, extent = (-220000,220000, -220000,220000, -220000,220000), nb_labels=3)
def displayGeneratedEvent(tree, evID, forward=0):
global fname, branches
print
print "<displayGeneratedEvent> evID =", evID, ", forward =", forward
print " genpart fields :"
for name in tree.keys():
if 'genpart_' in name:
print " ", tree[name]
# x = tree[name].array()
# print len( x[evID] ), "-->", x[evID ]
#
g = tree["genpart_gen"].array()[evID]
r = tree["genpart_reachedEE"].array()[evID]
x = tree["genpart_posx"].array()[evID]
y = tree["genpart_posy"].array()[evID]
z = tree["genpart_posz"].array()[evID]
e = tree["genpart_energy"].array()[evID]
pid = tree["genpart_pid"].array()[evID]
print ' pid', pid
for i in range(len(g)):
if (r[i] > 1):
xg = np.array(x[i], dtype=np.float32)
yg = np.array(y[i], dtype=np.float32)
zg = np.array(z[i], dtype=np.float32)
if (forward > 0):
f = (zg >= 0.0)
elif (forward < 0):
f = (zg < 0.0)
else:
f = np.ones(zg.size, dtype=bool)
#
xg = xg[f]
yg = yg[f]
zg = zg[f]
if (xg.size != 0):
# mlab.text3d( xg[0], yg[0], zg[0], pidToName[pid[i]])
# mlab.text3d( xg[0], yg[0], zg[0], "xxx")
u = mlab.points3d(xg,
yg,
zg,
color=(1, 1, 1),
scale_factor=0.2)
str = '{:.1}'.format(e[i])
mlab.text3d(xg[-1], yg[-1], zg[-1], str)
str = pidToName[pid[i]]
mlab.text3d(xg[0], yg[0], zg[0], str)
def plot_text(self, label, X, text, size=1):
view = mlab.view()
roll = mlab.roll()
self.figure.scene.disable_render = True
scale = (size, size, size)
mlab_objs = self.plots.get(label)
if mlab_objs != None:
if len(mlab_objs) != len(text):
for obj in mlab_objs:
obj.remove()
self.plots.pop(label)
mlab_objs = self.plots.get(label)
if mlab_objs == None:
text_objs = []
for x, t in zip(X, text):
text_objs.append(mlab.text3d(x[0], x[1], x[2], str(t), scale=scale))
self.plots[label] = text_objs
elif len(mlab_objs) == len(text):
for i, obj in enumerate(mlab_objs):
obj.position = X[i,:]
obj.text = str(text[i])
obj.scale = scale
else:
print "HELP, I shouldn\'t be here!!!!!"
self.figure.scene.disable_render = False
mlab.view(*view)
mlab.roll(roll)
def nodes_gen(self): #assumes that all LH nodes start with L. This is not ideal. nodesource_lh = mlab.pipeline.scalar_scatter( self.ds.lab_pos[self.ds.lhnodes,0], self.ds.lab_pos[self.ds.lhnodes,1], self.ds.lab_pos[self.ds.lhnodes,2], figure=self.scene.mayavi_scene) self.nodes_lh=mlab.pipeline.glyph(nodesource_lh, scale_mode='none',scale_factor=3.0,mode='sphere', figure=self.scene.mayavi_scene) nodesource_rh=mlab.pipeline.scalar_scatter( self.ds.lab_pos[self.ds.rhnodes,0], self.ds.lab_pos[self.ds.rhnodes,1], self.ds.lab_pos[self.ds.rhnodes,2], figure=self.scene.mayavi_scene) self.nodes_rh=mlab.pipeline.glyph(nodesource_rh, scale_mode='none',scale_factor=3.0,mode='sphere', figure=self.scene.mayavi_scene) self.txt = mlab.text3d(0,0,83,'',scale=4.0,color=(.8,.6,.98,), figure=self.scene.mayavi_scene) self.txt.actor.actor.pickable=0 for nodes in (self.nodes_lh,self.nodes_rh): nodes.glyph.color_mode='color_by_scalar' self.ds.chg_lh_nodemask(); self.ds.chg_rh_nodemask() self.draw_nodes()
def drawLabels(figure, handle, vol, bbox):
"""
Draw all labels in the volume 'vol' at the center of mass position of the object
into the figure 'figure'. Therefore, the bounding box 'bbox' coordinates of 'vol'
must be specified.
"""
# find all labels
labels = np.unique(vol)
if(labels[0] == 0):
# remove background label
labels = labels[1:]
#write the cell label as text
for i in labels:
com = handle["features"][str(i)]["com"][:]
mlab.text3d(com[2]-bbox[2]+1,com[1]-bbox[1]+1,com[0]-bbox[0]+1, str(i), color=(1,1,1), figure=figure)
def plot_pose(T_frame_world, alpha=0.5, tube_radius=0.005, center_scale=0.025):
T_world_frame = T_frame_world.inverse()
R = T_world_frame.rotation
t = T_world_frame.translation
x_axis_tf = np.array([t, t + alpha * R[:,0]])
y_axis_tf = np.array([t, t + alpha * R[:,1]])
z_axis_tf = np.array([t, t + alpha * R[:,2]])
mv.points3d(t[0], t[1], t[2], color=(1,1,1), scale_factor=center_scale)
mv.plot3d(x_axis_tf[:,0], x_axis_tf[:,1], x_axis_tf[:,2], color=(1,0,0), tube_radius=tube_radius)
mv.plot3d(y_axis_tf[:,0], y_axis_tf[:,1], y_axis_tf[:,2], color=(0,1,0), tube_radius=tube_radius)
mv.plot3d(z_axis_tf[:,0], z_axis_tf[:,1], z_axis_tf[:,2], color=(0,0,1), tube_radius=tube_radius)
mv.text3d(t[0], t[1], t[2], ' %s' %T_frame_world.to_frame.upper(), scale=0.01)
def nodes_gen(self):
#assumes that all LH nodes start with L. This is not ideal.
nodesource_lh = mlab.pipeline.scalar_scatter(
self.ds.lab_pos[self.ds.lhnodes,0],
self.ds.lab_pos[self.ds.lhnodes,1],
self.ds.lab_pos[self.ds.lhnodes,2],
figure=self.scene.mayavi_scene)
self.nodes_lh=mlab.pipeline.glyph(nodesource_lh,
scale_mode='none',scale_factor=3.0,mode='sphere',
figure=self.scene.mayavi_scene)
nodesource_rh=mlab.pipeline.scalar_scatter(
self.ds.lab_pos[self.ds.rhnodes,0],
self.ds.lab_pos[self.ds.rhnodes,1],
self.ds.lab_pos[self.ds.rhnodes,2],
figure=self.scene.mayavi_scene)
self.nodes_rh=mlab.pipeline.glyph(nodesource_rh,
scale_mode='none',scale_factor=3.0,mode='sphere',
figure=self.scene.mayavi_scene)
self.txt = mlab.text3d(0,0,83,'',scale=4.0,color=(.8,.6,.98,),
figure=self.scene.mayavi_scene)
self.txt.actor.actor.pickable=0
for nodes in (self.nodes_lh,self.nodes_rh):
nodes.glyph.color_mode='color_by_scalar'
self.ds.chg_lh_nodemask(); self.ds.chg_rh_nodemask()
self.ds.chg_scalar_colorbar()
#scalar colorbar is tied to lh_surf, but we dont really care if surf switches
#between cracked and uncracked so it is more convenient to set up here
self.draw_nodes()
def test_text3d(self):
""" Test the text3d module.
"""
data = np.random.random((3, 3, 3))
src = mlab.pipeline.scalar_field(data)
t = mlab.text3d(0, 0, 0, 'foo', opacity=0.5, scale=2,
orient_to_camera=False, color=(0, 0, 0),
orientation=(90, 0, 0))
def plot_clusters():
points = np.genfromtxt('data.csv', delimiter=',')
means = np.genfromtxt('means.csv', delimiter=',')
points3d(
points[:,0],
points[:,1],
points[:,2],
color=(1,1,1),
mode='2dvertex')
points3d(means[:,0], means[:,1], means[:,2], color=(1,0,0), scale_factor=0.2)
for mean in means:
text3d(
mean[0],
mean[1],
mean[2],
text='({:01.1f}, {:01.1f}, {:01.1f})'.format(mean[0], mean[1], mean[2]),
scale=0.5,
color=(1,1,1))
def _show_labels(self, show):
_toggle_mlab_render(self, False)
while self.text3d:
text = self.text3d.pop()
text.remove()
if show and len(self.src.data.points) > 0:
fig = self.scene.mayavi_scene
if self._view == 'arrow': # for axes
x, y, z = self.src.data.points[0]
self.text3d.append(text3d(
x, y, z, self.name, scale=self.label_scale,
color=self.color, figure=fig))
else:
for i, (x, y, z) in enumerate(np.array(self.src.data.points)):
self.text3d.append(text3d(
x, y, z, ' %i' % i, scale=self.label_scale,
color=self.color, figure=fig))
_toggle_mlab_render(self, True)
def _plot_coordinate_transforms(*Targs, **kwargs):
tag = kwargs.get('tag', '')
origin = kwargs.get('origin', True)
scale = kwargs.get('scale', 0.1)
x, y, z, u, v, w, scalars = quiver_args_from_transforms(*Targs,
origin=origin)
pts = mlab.quiver3d(x, y, z, u, v, w,
scalars=scalars,
line_width=40.0 * scale,
scale_factor=scale)
pts.glyph.color_mode = 'color_by_scalar'
for i, (xi, yi, zi) in enumerate(zip(x, y, z)):
if not (i % 3):
txt = str(i / 3 - 1)
if i == 0:
txt = 'O'
txt = '%s%s' % (tag, txt)
mlab.text3d(xi, yi, zi, text=txt, scale=0.6 * scale)
mlab.gcf().scene.background = (1, 1, 1)
return pts
def plot_labels(labels, lattice=None, coords_are_cartesian=False, figure=None, **kwargs): # pragma: no cover
"""
Adds labels to a mayavi_ figure.
Args:
labels: dict containing the label as a key and the coordinates as value.
lattice: |Lattice| object used to convert from reciprocal to cartesian coordinates
coords_are_cartesian: Set to True if you are providing.
coordinates in cartesian coordinates. Defaults to False.
Requires lattice if False.
figure: mayavi figure, None to plot on the curretn figure
kwargs: kwargs passed to the mayavi function `text3d`. Color defaults to blue and size to 25.
Returns: mayavi figure
"""
figure, mlab = get_fig_mlab(figure=figure)
#if "color" not in kwargs:
# kwargs["color"] = "b"
#if "size" not in kwargs:
# kwargs["size"] = 25
#if "width" not in kwargs:
# kwargs["width"] = 0.8
if "scale" not in kwargs:
kwargs["scale"] = 0.1
for k, coords in labels.items():
label = k
if k.startswith("\\") or k.find("_") != -1:
label = "$" + k + "$"
off = 0.01
if coords_are_cartesian:
coords = np.array(coords)
else:
if lattice is None:
raise ValueError("coords_are_cartesian False requires the lattice")
coords = lattice.get_cartesian_coords(coords)
x, y, z = coords + off
mlab.text3d(x, y, z, label, figure=figure, **kwargs)
return figure
def _plot_axes(self, color=(1, 0, 0)):
shortest = min(np.linalg.norm(self._lattice, axis=1))
lat = np.array([x / np.linalg.norm(x) for x in self._lattice])
lat *= shortest
mlab.quiver3d([0, 0, 0],
[0, 0, 0],
[0, 0, 0],
lat[0],
lat[1],
lat[2],
color=color,
line_width=3,
scale_factor=1)
scale = shortest / 8
for c, v in zip(('a','b','c'), lat * (1 + scale / 2)):
x, y, z = v
x += scale / 2
y -= scale / 4
z -= scale / 4
mlab.text3d(x, y, z, c, color=color, scale=scale)
def draw_didi_boxes3d(fig, boxes3d, is_number=False, color=(1,1,1), line_width=1):
if boxes3d.shape==(8,3): boxes3d=boxes3d.reshape(1,8,3)
num = len(boxes3d)
for n in range(num):
b = boxes3d[n]
if is_number:
mlab.text3d(b[0,0], b[0,1], b[0,2], '%d'%n, scale=(1, 1, 1), color=color, figure=fig)
for k in range(0,4):
#http://docs.enthought.com/mayavi/mayavi/auto/mlab_helper_functions.html
i,j=k,(k+1)%4
mlab.plot3d([b[i,0], b[j,0]], [b[i,1], b[j,1]], [b[i,2], b[j,2]], color=color, tube_radius=None, line_width=line_width, figure=fig)
i,j=k+4,(k+1)%4 + 4
mlab.plot3d([b[i,0], b[j,0]], [b[i,1], b[j,1]], [b[i,2], b[j,2]], color=color, tube_radius=None, line_width=line_width, figure=fig)
i,j=k,k+4
mlab.plot3d([b[i,0], b[j,0]], [b[i,1], b[j,1]], [b[i,2], b[j,2]], color=color, tube_radius=None, line_width=line_width, figure=fig)
def plot_structure(structure, frac_coords=False, to_unit_cell=False, style="points+labels",
unit_cell_color=(0, 0, 0), color_scheme="VESTA", figure=None, show=False, **kwargs): # pragma: no cover
"""
Plot structure with mayavi.
Args:
structure: |Structure| object
frac_coords:
to_unit_cell: True if sites should be wrapped into the first unit cell.
style: "points+labels" to show atoms sites with labels.
unit_cell_color:
color_scheme: color scheme for atom types. Allowed values in ("Jmol", "VESTA")
figure:
kwargs:
Returns: mayavi figure
"""
figure, mlab = get_fig_mlab(figure=figure)
#if not frac_coords:
plot_unit_cell(structure.lattice, color=unit_cell_color, figure=figure)
from pymatgen.analysis.molecule_structure_comparator import CovalentRadius
from pymatgen.vis.structure_vtk import EL_COLORS
for site in structure:
symbol = site.specie.symbol
color = tuple(i / 255 for i in EL_COLORS[color_scheme][symbol])
radius = CovalentRadius.radius[symbol]
if to_unit_cell and hasattr(site, "to_unit_cell"): site = site.to_unit_cell
x, y, z = site.frac_coords if frac_coords else site.coords
if "points" in style:
mlab.points3d(x, y, z, figure=figure, scale_factor=radius,
resolution=20, color=color, scale_mode='none', **kwargs)
if "labels" in style:
mlab.text3d(x, y, z, symbol, figure=figure, color=(0, 0, 0), scale=0.2)
if show: mlab.show()
return figure
def _render(self, **kwargs):
from mayavi import mlab
# disabling the rendering greatly speeds up this for loop
self.figure.scene.disable_render = True
positions = []
for label, mask in self.labels_to_masks.iteritems():
p = self.pointcloud.from_mask(mask)
for i, p in enumerate(p.points):
positions.append(p)
l = '%s_%d' % (label, i)
# TODO: This is due to a bug in mayavi that won't allow
# rendering text to an empty figure
mlab.points3d(p[0], p[1], p[2])
mlab.text3d(p[0], p[1], p[2], l, figure=self.figure)
positions = np.array(positions)
os = np.zeros_like(positions)
os[:, 2] = 1
mlab.quiver3d(positions[:, 0], positions[:, 1], positions[:, 2],
os[:, 0], os[:, 1], os[:, 2], figure=self.figure)
self.figure.scene.disable_render = False
return self
def plotText(self, X, text, color=None, size=None):
if self.autoRemove: self.removeText()
if isinstance(X, list): X = scipy.asarray(X)
if len(X.shape)==1: X = scipy.array([X])
if isinstance(text, str): text = [text]
if color==None: color=(1,0,0)
if size==None: size=1.
for i, x in enumerate(X):
self.text.append(mlab.text3d(x[0], x[1], x[2], text[i], color=color, scale=size))
def plot_graphs(locs,stations,nbsta,CLUSTER,nbmin,threshold):
from mayavi import mlab
# Event coordinates
stack_x,stack_y,stack_z=[],[],[]
for loc in locs:
stack_x.append(loc['x_mean'])
stack_y.append(loc['y_mean'])
stack_z.append(-loc['z_mean'])
# Extract coordinates
xsta,ysta,zsta=[],[],[]
for sta in sorted(stations):
xsta.append(stations[sta]['x'])
ysta.append(stations[sta]['y'])
zsta.append(stations[sta]['elev'])
# 3D PLOT USING MAYAVI
logging.info("Plotting...")
s1=mlab.figure(1,bgcolor=(1,1,1),fgcolor=(0,0,0),size=(1000,900))
s1=mlab.points3d(xsta,ysta,zsta,color=(1,0,0),scale_factor=0.05,mode='cube')
s1=mlab.axes(extent=[362,370,7647,7653,-0.5,2.5],color=(0,0,0))
s1=mlab.outline(extent=[362,370,7647,7653,-0.5,2.5],color=(0,0,0))
s1=mlab.points3d(stack_x,stack_y,stack_z,scale_factor=0.1,color=(0.8,0.8,0.8))
s1=mlab.title("threshold=%s, nbmin=%s"%(threshold,nbmin),height=0.1,size=0.35,color=(0,0,0))
for i_ev in range(len(nbsta)):
for i_c in range(1,len(CLUSTER)+1):
if i_ev+1 in CLUSTER[i_c]:
s1=mlab.points3d(stack_x[i_ev],stack_y[i_ev],stack_z[i_ev],scale_factor=0.1,color=tuple(CZ_Clust_2_color(100*(len(CLUSTER)-i_c)/len(CLUSTER))))
s1=mlab.text3d(stack_x[i_ev],stack_y[i_ev],stack_z[i_ev],str(i_c),color=(0,0,0),scale=0.1)
logging.info("Done!")
logging.info("Plotting...")
s2=mlab.figure(2,bgcolor=(1,1,1),fgcolor=(0,0,0),size=(1000,900))
mlab.points3d(xsta,ysta,zsta,color=(1,0,0),scale_factor=0.05,mode='cube')
mlab.axes(extent=[362,370,7647,7653,-0.5,2.5],color=(0,0,0))
mlab.outline(extent=[362,370,7647,7653,-0.5,2.5],color=(0,0,0))
mlab.points3d(stack_x,stack_y,stack_z,scale_factor=0.1,color=(0.8,0.8,0.8))
mlab.title("threshold=%s, nbmin=%s"%(threshold,nbmin),height=0.1,size=0.35,color=(0,0,0))
for ind_I in range(len(nbsta)):
for ind_J in range(ind_I+1,len(nbsta)):
W_IJ=nbsta[ind_I,ind_J]
if W_IJ >= nbmin:
mlab.points3d(stack_x[ind_J],stack_y[ind_J],stack_z[ind_J],scale_factor=0.1,color=(0,0,0))
mlab.points3d(stack_x[ind_I],stack_y[ind_I],stack_z[ind_I],scale_factor=0.1,color=(0,0,0))
d=(stack_x[ind_J]-stack_x[ind_I],stack_y[ind_J]-stack_y[ind_I],stack_z[ind_J]-stack_z[ind_I])
norm=np.sqrt(d[0]**2+d[1]**2+d[2]**2)
s2=mlab.quiver3d(stack_x[ind_I],stack_y[ind_I],stack_z[ind_I],d[0],d[1],d[2],color=tuple(CZ_W_2_color(W_IJ)),mode='2ddash',scale_factor=norm,scale_mode='scalar')
#mlab.colorbar(s2)
logging.info("Done!")
mlab.show()
def _show_labels(self, show):
self.scene.disable_render = True
while self.text3d:
text = self.text3d.pop()
text.remove()
if show:
fig = self.scene.mayavi_scene
for i, pt in enumerate(np.array(self.src.data.points)):
x, y, z = pt
t = text3d(x, y, z, " %i" % i, scale=0.01, color=self.rgbcolor, figure=fig)
self.text3d.append(t)
self.scene.disable_render = False
def _show_labels(self, show):
_toggle_mlab_render(self, False)
while self.text3d:
text = self.text3d.pop()
text.remove()
if show:
fig = self.scene.mayavi_scene
for i, pt in enumerate(np.array(self.src.data.points)):
x, y, z = pt
t = text3d(x, y, z, ' %i' % i, scale=.01, color=self.color,
figure=fig)
self.text3d.append(t)
_toggle_mlab_render(self, True)
def plotCosy(fig,R,t,scale,name='',col=None):
pts = np.zeros((3,6))
for i in range(0,3):
pts[:,i*2] = np.zeros(3)
pts[:,i*2+1] = R[:,i]
pts *= scale
pts+= t[:,np.newaxis]
if col is None:
mlab.plot3d(pts[0,0:2],pts[1,0:2],pts[2,0:2],figure=fig,color=(1.0,0.0,0.0),tube_radius=0.05*scale)
mlab.plot3d(pts[0,2:4],pts[1,2:4],pts[2,2:4],figure=fig,color=(0.0,1.0,0.0),tube_radius=0.05*scale)
mlab.plot3d(pts[0,4:6],pts[1,4:6],pts[2,4:6],figure=fig,color=(0.0,0.0,1.0),tube_radius=0.05*scale)
else:
mlab.plot3d(pts[0,0:2],pts[1,0:2],pts[2,0:2],figure=fig,color=col)
mlab.plot3d(pts[0,2:4],pts[1,2:4],pts[2,2:4],figure=fig,color=col)
mlab.plot3d(pts[0,4:6],pts[1,4:6],pts[2,4:6],figure=fig,color=col)
if name!='':
mlab.text3d(pts[0,1],pts[1,1],pts[2,1],name,
scale=.1*scale,color=(0,0,0),line_width=1.0,figure=fig)
mlab.text3d(pts[0,3],pts[1,3],pts[2,3],name,
scale=.1*scale,color=(0,0,0),line_width=1.0,figure=fig)
mlab.text3d(pts[0,5],pts[1,5],pts[2,5],name,
scale=.1*scale,color=(0,0,0),line_width=1.0,figure=fig)
def Scatter3d_Mayavi(xs, ys, zs, weights=None, weight_label=None, xlabel='x',
ylabel='y', zlabel='z', axes=True, **points3d_kw):
from mayavi import mlab
# XXX error when max() returns zero
def normalize(vs):
a = vs.min()
b = vs.max()
if a != b:
vs = vs / float(b - a)
return vs
xs = normalize(xs)
ys = normalize(ys)
zs = normalize(zs)
if 'scale_mode' not in points3d_kw:
points3d_kw['scale_mode'] = 'none'
if 'scale_factor' not in points3d_kw:
points3d_kw['scale_factor'] = .03
if weights is None:
mlab.points3d(xs, ys, zs, **points3d_kw)
else:
mlab.points3d(xs, ys, zs, weights, **points3d_kw)
if weight_label:
mlab.scalarbar(title=weight_label)
if axes:
extent = 1.2
scale = 0.05
tube_radius = 0.01
color = (1,1,1) # white
mlab.plot3d([0,extent], [0,0], [0,0], tube_radius=tube_radius, color=color)
mlab.plot3d([0,0], [0,extent], [0,0], tube_radius=tube_radius, color=color)
mlab.plot3d([0,0], [0,0], [0,extent], tube_radius=tube_radius, color=color)
if xlabel:
mlab.text3d(extent, 0, 0, xlabel, scale=scale, color=color)
if ylabel:
mlab.text3d(0, extent, 0, ylabel, scale=scale, color=color)
if zlabel:
mlab.text3d(0, 0, extent, zlabel, scale=scale, color=color)
def plot_pos_index(p):
pos = cent[p]
mlab.text3d(pos[0], pos[1], pos[2], str(p), scale=0.8)
def make_sphere(self):
"""
Plots Bloch sphere and data sets.
"""
# setup plot
# Figure instance for Bloch sphere plot
from mayavi import mlab
import matplotlib.colors as colors
if self.user_fig:
self.fig = self.user_fig
else:
self.fig = mlab.figure(
1, size=self.size,
bgcolor=colors.colorConverter.to_rgb(self.bgcolor),
fgcolor=colors.colorConverter.to_rgb(self.fgcolor))
sphere = mlab.points3d(
0, 0, 0, figure=self.fig, scale_mode='none', scale_factor=2,
color=colors.colorConverter.to_rgb(self.sphere_color),
resolution=100, opacity=self.sphere_alpha, name='bloch_sphere')
# Thse commands make the sphere look better
sphere.actor.property.specular = 0.45
sphere.actor.property.specular_power = 5
sphere.actor.property.backface_culling = True
# make frame for sphere surface
if self.frame:
theta = np.linspace(0, 2 * np.pi, 100)
for angle in np.linspace(-np.pi, np.pi, self.frame_num):
xlat = np.cos(theta) * np.cos(angle)
ylat = np.sin(theta) * np.cos(angle)
zlat = np.ones_like(theta) * np.sin(angle)
xlon = np.sin(angle) * np.sin(theta)
ylon = np.cos(angle) * np.sin(theta)
zlon = np.cos(theta)
mlab.plot3d(xlat, ylat, zlat,
color=colors.colorConverter.to_rgb(
self.frame_color),
opacity=self.frame_alpha,
tube_radius=self.frame_radius)
mlab.plot3d(xlon, ylon, zlon,
color=colors.colorConverter.to_rgb(
self.frame_color),
opacity=self.frame_alpha,
tube_radius=self.frame_radius)
# add axes
axis = np.linspace(-1.0, 1.0, 10)
other = np.zeros_like(axis)
mlab.plot3d(
axis, other, other,
color=colors.colorConverter.to_rgb(self.axes_color),
tube_radius=self.axes_radius, opacity=self.axes_alpha)
mlab.plot3d(
other, axis, other,
color=colors.colorConverter.to_rgb(self.axes_color),
tube_radius=self.axes_radius, opacity=self.axes_alpha)
mlab.plot3d(
other, other, axis,
color=colors.colorConverter.to_rgb(self.axes_color),
tube_radius=self.axes_radius, opacity=self.axes_alpha)
# add data to sphere
self.plot_points()
self.plot_vectors()
# #add labels
mlab.text3d(0, 0, self.zlpos[0], self.zlabel[0],
color=colors.colorConverter.to_rgb(self.font_color),
scale=self.font_scale)
mlab.text3d(0, 0, self.zlpos[1], self.zlabel[1],
color=colors.colorConverter.to_rgb(self.font_color),
scale=self.font_scale)
mlab.text3d(self.xlpos[0], 0, 0, self.xlabel[0],
color=colors.colorConverter.to_rgb(self.font_color),
scale=self.font_scale)
mlab.text3d(self.xlpos[1], 0, 0, self.xlabel[1],
color=colors.colorConverter.to_rgb(self.font_color),
scale=self.font_scale)
mlab.text3d(0, self.ylpos[0], 0, self.ylabel[0],
color=colors.colorConverter.to_rgb(self.font_color),
scale=self.font_scale)
mlab.text3d(0, self.ylpos[1], 0, self.ylabel[1],
color=colors.colorConverter.to_rgb(self.font_color),
scale=self.font_scale)