def surface(volume, threshold=0.5, verbose=1):
verts, faces = measure.marching_cubes(volume, threshold)
if verbose == 2:
import visvis as vv
vv.mesh(np.fliplr(verts), faces)
vv.use().Run()
def visualize(im, vol, sz=0.25, thr=0.99):
im, vol = im.numpy(), vol.numpy()
print("Image shape:", im.shape)
print("Volume shape:", vol.shape)
# overlap with 3d representation + BGR->RGB
im = im.transpose(1, 2, 0) # H,W,C
im = im[:, :, ::-1]
im = cv2.resize(im, (128, 128))
t = vv.imshow(im)
t.interpolate = True # interpolate pixels
# volshow will use volshow3 and rendering the isosurface if OpenGL version is >= 2.0
# Otherwise, it will show slices with bars that you can move (much less useful).
im = (im * 128 + 128).astype(np.uint8)
# im = np.ones_like(im)
volRGB = np.stack(((vol >= thr) * im[:, :, 0], (vol >= thr) * im[:, :, 1],
(vol >= thr) * im[:, :, 2]),
axis=3)
v = vv.volshow(volRGB, renderStyle='iso')
v.transformations[1].sz = sz # Z rescaling
l0 = vv.gca()
l0.light0.ambient = 0.9 # 0.2 is default for light 0
l0.light0.diffuse = 1.0 # 1.0 is default
a = vv.gca()
a.axis.visible = 0
a.camera.fov = 0 # orthographic
vv.use().Run()
def crop3d(vol, fig=None):
""" crop3d(vol, fig=None)
Manually crop a volume. In the given figure (or a new figure if None),
three axes are created that display the transversal, sagittal and
coronal MIPs (maximum intensity projection) of the volume. The user
can then use the mouse to select a 3D range to crop the data to.
"""
vv.use()
# Create figure?
if fig is None:
fig = vv.figure()
figCleanup = True
else:
fig.Clear()
figCleanup = False
# Create three axes and a wibject to attach text labels to
a1 = vv.subplot(221)
a2 = vv.subplot(222)
a3 = vv.subplot(223)
a4 = vv.Wibject(fig)
a4.position = 0.5, 0.5, 0.5, 0.5
# Set settings
for a in [a1, a2, a3]:
a.showAxis = False
# Create cropper3D instance
cropper3d = Cropper3D(vol, a1, a3, a2, a4)
# Enter a mainloop
while not cropper3d._finished:
vv.processEvents()
time.sleep(0.01)
# Clean up figure (close if we opened it)
fig.Clear()
fig.DrawNow()
if figCleanup:
fig.Destroy()
# Obtain ranges
rx = cropper3d._range_transversal._rangex
ry = cropper3d._range_transversal._rangey
rz = cropper3d._range_coronal._rangey
# Perform crop
# make sure we have int not float
rzmin, rzmax = int(rz.min), int(rz.max)
rymin, rymax = int(ry.min), int(ry.max)
rxmin, rxmax = int(rx.min), int(rx.max)
vol2 = vol[rzmin:rzmax, rymin:rymax, rxmin:rxmax]
# vol2 = vol[rz.min:rz.max, ry.min:ry.max, rx.min:rx.max]
# Done
return vol2
def main(select=3, **kwargs):
"""Script main function.
select: int
1: Medical data
2: Blocky data, different every time
3: Two donuts
4: Ellipsoid
"""
import visvis as vv # noqa: delay import visvis and GUI libraries
# Create test volume
if select == 1:
vol = vv.volread('stent')
isovalue = kwargs.pop('level', 800)
elif select == 2:
vol = vv.aVolume(20, 128)
isovalue = kwargs.pop('level', 0.2)
elif select == 3:
with timer('computing donuts'):
vol = donuts()
isovalue = kwargs.pop('level', 0.0)
# Uncommenting the line below will yield different results for
# classic MC
# vol *= -1
elif select == 4:
vol = ellipsoid(4, 3, 2, levelset=True)
isovalue = kwargs.pop('level', 0.0)
else:
raise ValueError('invalid selection')
# Get surface meshes
with timer('finding surface lewiner'):
vertices1, faces1 = marching_cubes_lewiner(vol, isovalue, **kwargs)[:2]
with timer('finding surface classic'):
vertices2, faces2 = marching_cubes_classic(vol, isovalue, **kwargs)
# Show
vv.figure(1)
vv.clf()
a1 = vv.subplot(121)
vv.title('Lewiner')
m1 = vv.mesh(np.fliplr(vertices1), faces1)
a2 = vv.subplot(122)
vv.title('Classic')
m2 = vv.mesh(np.fliplr(vertices2), faces2)
a1.camera = a2.camera
# visvis uses right-hand rule, gradient_direction param uses left-hand rule
m1.cullFaces = m2.cullFaces = 'front' # None, front or back
vv.use().Run()
def main(select=3, **kwargs):
"""Script main function.
select: int
1: Medical data
2: Blocky data, different every time
3: Two donuts
4: Ellipsoid
"""
import visvis as vv # noqa: delay import visvis and GUI libraries
# Create test volume
if select == 1:
vol = vv.volread('stent')
isovalue = kwargs.pop('level', 800)
elif select == 2:
vol = vv.aVolume(20, 128)
isovalue = kwargs.pop('level', 0.2)
elif select == 3:
with timer('computing donuts'):
vol = donuts()
isovalue = kwargs.pop('level', 0.0)
# Uncommenting the line below will yield different results for
# classic MC
# vol *= -1
elif select == 4:
vol = ellipsoid(4, 3, 2, levelset=True)
isovalue = kwargs.pop('level', 0.0)
else:
raise ValueError('invalid selection')
# Get surface meshes
with timer('finding surface lewiner'):
vertices1, faces1 = marching_cubes_lewiner(vol, isovalue, **kwargs)[:2]
with timer('finding surface classic'):
vertices2, faces2 = marching_cubes_classic(vol, isovalue, **kwargs)
# Show
vv.figure(1)
vv.clf()
a1 = vv.subplot(121)
vv.title('Lewiner')
m1 = vv.mesh(np.fliplr(vertices1), faces1)
a2 = vv.subplot(122)
vv.title('Classic')
m2 = vv.mesh(np.fliplr(vertices2), faces2)
a1.camera = a2.camera
# visvis uses right-hand rule, gradient_direction param uses left-hand rule
m1.cullFaces = m2.cullFaces = 'front' # None, front or back
vv.use().Run()
def init_form(self):
self._form = QWidget()
layout = QVBoxLayout()
layout.setMargin(0)
if conf.PYFORMS_USE_QT5:
layout.setContentsMargins(0, 0, 0, 0)
else:
layout.setMargin(0)
self._form.setLayout(layout)
self._app = vv.use('pyqt4')
self._app.Create()
self._first = True
Figure = self._app.GetFigureClass()
self._fig = Figure(self._form)
vv.figure(self._fig.nr)
policy = QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
widget = self._fig._widget
widget.setSizePolicy(policy)
widget.setMinimumSize(100, 100)
layout.addWidget(widget)
self._colorMap = vv.CM_AUTUMN
self._colors_limits = None
def show(items, normals=None):
"""Function that shows a mesh object.
"""
for item in items:
vv.clf()
# convert to visvis.Mesh class
new_normals = []
new_vertices = []
for k, v in item.vertices.iteritems():
new_normals.append(item.normal(k))
new_vertices.append(v)
mesh = item.to_visvis_mesh()
mesh.SetVertices(new_vertices)
mesh.SetNormals(new_normals)
mesh.faceColor = 'y'
mesh.edgeShading = 'plain'
mesh.edgeColor = (0, 0, 1)
axes = vv.gca()
if axes.daspectAuto is None:
axes.daspectAuto = False
axes.SetLimits()
if normals is not None:
for normal in normals:
sl = solidLine(normal, 0.15)
sl.faceColor = 'r'
# Show title and enter main loop
vv.title('Show')
app = vv.use()
app.Run()
def init_form(self):
self._form = QWidget()
layout = QVBoxLayout()
if _api.USED_API == _api.QT_API_PYQT5:
layout.setContentsMargins(0, 0, 0, 0)
elif _api.USED_API == _api.QT_API_PYQT4:
layout.setMargin(0)
self._form.setLayout(layout)
self._app = vv.use('pyqt5')
self._app.Create()
self._first = True
Figure = self._app.GetFigureClass()
self._fig = Figure(self._form)
vv.figure(self._fig.nr)
policy = QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
widget = self._fig._widget
widget.setSizePolicy(policy)
widget.setMinimumSize(100, 100)
layout.addWidget(widget)
self._colorMap = vv.CM_AUTUMN
self._colors_limits = None
super(ControlVisVisVolume, self).init_form()
def appInstance(useVisVis=True):
"""Create a suitable application instance"""
print("Creating application instance...")
global g_haveVisVis
app = None
if g_haveVisVis and useVisVis:
print("Using VisVis application instance...")
app = vv.use()
app.Create()
else:
print("Trying Qt application instance...")
app = QtGui.QApplication.instance()
if app is None:
print("Creating new Qt application instance...")
app = QtGui.QApplication(sys.argv)
else:
print("Reusing existing Qt application instance...")
if app != None:
app.Run = app.exec_
if app is None:
print("No application instance found. Exiting...")
sys.exit(-1)
return app
def __init__(self, audiofile=None, fs=22050, bandwidth=300,freqRange= 5000, dynamicRange=48, noiseFloor =-72, parent = None):
super(Spec, self).__init__()
backend = 'pyqt4'
app = vv.use(backend)
Figure = app.GetFigureClass()
self.fig= Figure(self)
self.fig.enableUserInteraction = True
self.fig._widget.setMinimumSize(700,350)
self.axes = vv.gca()
self.audiofilename = audiofile
self.freqRange = freqRange
self.fs = fs
self.NFFT = int(1.2982804/bandwidth*self.fs)
self.overlap = int(self.NFFT/2)
self.noiseFloor = noiseFloor
self.dynamicRange = dynamicRange
self.timeLength = 60
self.resize(700,250)
layout = QtGui.QVBoxLayout()
layout.addWidget(self.fig._widget)
self.setLayout(layout)
self.win = gaussian(self.NFFT,self.NFFT/6)
self.show()
def appInstance(useVisVis=True):
"""Create a suitable application instance"""
print("Creating application instance...")
global g_haveVisVis
app = None
if g_haveVisVis and useVisVis:
print("Using VisVis application instance...")
app = vv.use()
app.Create()
else:
print("Trying Qt application instance...")
app = QtGui.QApplication.instance()
if app is None:
print("Creating new Qt application instance...")
app = QtGui.QApplication(sys.argv)
else:
print("Reusing existing Qt application instance...")
if app!=None:
app.Run = app.exec_
if app is None:
print("No application instance found. Exiting...")
sys.exit(-1)
return app
def _visualise_world_visvis(X, Y, Z, format="surf"):
"""
Legacy function to produce a surface render using visvis
:param X:
:param Y:
:param Z:
:param format:
"""
import visvis as vv
# m2 = vv.surf(worldx[::detail], worldy[::detail], worldz[::detail])
app = vv.use()
# prepare axes
a = vv.gca()
a.cameraType = '3d'
a.daspectAuto = False
# print("view", a.camera.GetViewParams())
# a.SetView(loc=(-1000,0,0))
# a.camera.SetView(None, loc=(-1000,0,0))
if format == "surf":
l = vv.surf(X, Y, Z)
a.SetLimits(rangeX=(-0.2, 0.2),
rangeY=(-0.5, 0.5),
rangeZ=(-0.5, 0),
margin=0.02)
else:
# draw points
pp = vv.Pointset(
np.concatenate([X.flatten(), Y.flatten(),
Z.flatten()], axis=0).reshape((-1, 3)))
l = vv.plot(pp, ms='.', mc='r', mw='5', ls='', mew=0)
l.alpha = 0.2
app.Run()
def main():
p = Path('/mri/images/DWI-Mono/42-1a/42-1a_ADCm.zip')
image = Image.read(p, dtype='float32')
image = image[image.mbb()]
app = vv.use()
# vv.figure()
# vv.title(p.name)
plot(image)
app.Run()
def main():
p = Path('/mri/images/DWI-Mono/42-1a/42-1a_ADCm.zip')
image = Image.read(p, dtype='float32')
image = image[image.mbb()]
app = vv.use()
# vv.figure()
# vv.title(p.name)
plot(image)
app.Run()
def plot_3d(image, threshold=100):
# Position the scan upright,
# so the head of the patient would be at the top facing the camera
p = image.transpose(2, 1, 0)
p = p[::2, ::2, ::2]
# verts, faces = measure.marching_cubes(p, threshold)
# verts, faces,_,_ = measure.marching_cubes_lewiner(p, threshold)
verts, faces, normals, values = measure.marching_cubes(p, threshold)
'''
verts, faces, normals, values = marching_cubes_lewiner(myvolume, 0.0) # doctest: +SKIP
>>> vv.mesh(np.fliplr(verts), faces, normals, values) # doctest: +SKIP
>>> vv.use().Run() # doctest: +SKIP
'''
lung_mesh = vv.mesh(np.fliplr(verts),
faces,
normals,
values,
verticesPerFace=4,
colormap=None,
clim=None,
texture=None,
axesAdjust=True,
axes=None)
# lung_mesh.setcolor([0.45, 0.45, 0.75])
faceColor = 'g'
vv.use().Run()
fig = plt.figure(figsize=(10, 10))
ax = fig.add_subplot(111, projection='3d')
# Fancy indexing: `verts[faces]` to generate a collection of triangles
mesh = Poly3DCollection(verts[faces], alpha=0.1)
face_color = [0.5, 0.5, 1]
mesh.set_facecolor(face_color)
ax.add_collection3d(mesh)
ax.set_xlim(0, p.shape[0])
ax.set_ylim(0, p.shape[1])
ax.set_zlim(0, p.shape[2])
plt.show()
def initControl(self):
self._form = QtGui.QWidget();layout = QtGui.QVBoxLayout();layout.setMargin(0);self._form.setLayout( layout )
self._app = vv.use('pyqt4')
Figure = self._app.GetFigureClass()
self._fig = Figure(self._form)
policy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Expanding)
widget = self._fig._widget
widget.setSizePolicy(policy)
layout.addWidget(widget)
def crop3d(vol, fig=None):
""" crop3d(vol, fig=None)
Manually crop a volume. In the given figure (or a new figure if None),
three axes are created that display the transversal, sagittal and
coronal MIPs (maximum intensity projection) of the volume. The user
can then use the mouse to select a 3D range to crop the data to.
"""
app = vv.use()
# Create figure?
if fig is None:
fig = vv.figure()
figCleanup = True
else:
fig.Clear()
figCleanup = False
# Create three axes and a wibject to attach text labels to
a1 = vv.subplot(221)
a2 = vv.subplot(222)
a3 = vv.subplot(223)
a4 = vv.Wibject(fig)
a4.position = 0.5, 0.5, 0.5, 0.5
# Set settings
for a in [a1, a2, a3]:
a.showAxis = False
# Create cropper3D instance
cropper3d = Cropper3D(vol, a1, a3, a2, a4)
# Enter a mainloop
while not cropper3d._finished:
vv.processEvents()
time.sleep(0.01)
# Clean up figure (close if we opened it)
fig.Clear()
fig.DrawNow()
if figCleanup:
fig.Destroy()
# Obtain ranges
rx = cropper3d._range_transversal._rangex
ry = cropper3d._range_transversal._rangey
rz = cropper3d._range_coronal._rangey
# Perform crop
vol2 = vol[rz.min:rz.max, ry.min:ry.max, rx.min:rx.max]
# Done
return vol2
def visVol(volData):
""" This example demonstrates rendering a color volume.
We demonstrate two renderers capable of rendering color data:
the colormip and coloriso renderer.
"""
import visvis as vv
app = vv.use()
# Load volume
vol = volData
# set labels
vv.xlabel("x axis")
vv.ylabel("y axis")
vv.zlabel("z axis")
# # Create figure and make subplots with different renderers
# vv.figure(1); vv.clf()
# RS = ['mip', 'iso', 'edgeray', 'ray', 'litray']
# a0 = None
# tt = []
# for i in range(5):
# a = vv.subplot(3,2,i+2)
# t = vv.volshow(vol)
# vv.title('Renderstyle ' + RS[i])
# t.colormap = vv.CM_HOT
# t.renderStyle = RS[i]
# t.isoThreshold = 200 # Only used in iso render style
# tt.append(t)
# if a0 is None:
# a0 = a
# else:
# a.camera = a0.camera
t = vv.volshow(vol, renderStyle="edgeray")
t.colormap = vv.CM_HOT
# Get axes and set camera to orthographic mode (with a field of view of 70)
a = vv.gca()
a.camera.fov = 45
# Create colormap editor wibject.
vv.ColormapEditor(a)
# Create colormap editor in first axes
# cme = vv.ColormapEditor(vv.gcf(), t)
# Run app
# app.Create()
app.Run()
def initForm(self):
self._form = QtGui.QWidget()
layout = QtGui.QVBoxLayout()
layout.setMargin(0)
self._form.setLayout(layout)
self._app = vv.use('pyqt4')
self._app.Create()
Figure = self._app.GetFigureClass()
self._fig = Figure(self._form)
policy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
QtGui.QSizePolicy.Expanding)
widget = self._fig._widget
widget.setSizePolicy(policy)
layout.addWidget(widget)
def initForm(self):
self._form = QtGui.QWidget();layout = QtGui.QVBoxLayout();layout.setMargin(0);self._form.setLayout( layout )
self._app = vv.use('pyqt4')
self._first=True
Figure = self._app.GetFigureClass()
self._fig = Figure(self._form)
vv.figure(self._fig.nr)
policy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Expanding)
widget = self._fig._widget
widget.setSizePolicy(policy)
widget.setMinimumSize(100, 100)
layout.addWidget(widget)
self._colorMap = vv.CM_AUTUMN
def __init__(self, sampleinterval=0.1, timewindow=10.0, size=(600, 350)):
# Data stuff
self._interval = int(sampleinterval * 1000)
self._bufsize = int(timewindow / sampleinterval)
self.databuffer = collections.deque([0.0] * self._bufsize, self._bufsize)
self.x = np.linspace(-timewindow, 0.0, self._bufsize)
self.y = np.zeros(self._bufsize, dtype=np.float)
# Visvis stuff
self.app = vv.use("qt4")
vv.title("Dynamic Plotting with VisVis")
self.line = vv.plot(self.x, self.y, lc="b", lw=3, ms="+")
vv.xlabel("time")
vv.ylabel("amplitude")
self.ax = vv.gca()
self.timer = vv.Timer(self.app, 50, oneshot=False)
self.timer.Bind(self.updateplot)
self.timer.Start()
def show(self):
for projection_name in self.rsa_assessment.projection_list():
rsa_projection = self.rsa_assessment.projection(projection_name)
# projection = self.assessment.projection(i)
# projector = self.projectors[i]
self.plot_image_data(rsa_projection.image,
rsa_projection.t,
sampling=0.1)
for image_segment_name in rsa_projection.image_segment_list():
try:
rsa_image_segment = rsa_projection.image_segment(
image_segment_name)
except NotImplementedError:
continue
for line in rsa_projection.segment_point_lines(
rsa_image_segment):
ps = vv.Pointset(3)
ps.append(*list(line.a[:3]))
ps.append(*list(line.b[:3]))
vl = vv.solidLine(ps, radius=self.lineSize, N=self.lineN)
vl.faceColor = self.lineColor
for scene_segment_name in self.rsa_assessment.scene_segment_list():
try:
scene_segment = self.rsa_assessment.scene_segment(
scene_segment_name)
except NotImplementedError:
continue
scene_segment.match_crossing_lines()
for i in range(len(scene_segment.points)):
vs = vv.solidSphere(translation=tuple(
scene_segment.points[i][:3]),
scaling=([self.pointSize] * 3),
N=self.sphereN,
M=self.sphereM)
vs.faceColor = self.pointColor
# Enter main loop
app = vv.use()
app.Run()
def __init__(self, sampleinterval=0.1, timewindow=10., size=(600, 350)):
# Data stuff
self._interval = int(sampleinterval * 1000)
self._bufsize = int(timewindow / sampleinterval)
self.databuffer = collections.deque([0.0] * self._bufsize,
self._bufsize)
self.x = np.linspace(-timewindow, 0.0, self._bufsize)
self.y = np.zeros(self._bufsize, dtype=np.float)
# Visvis stuff
self.app = vv.use('qt4')
vv.title('Dynamic Plotting with VisVis')
self.line = vv.plot(self.x, self.y, lc='b', lw=3, ms='+')
vv.xlabel('time')
vv.ylabel('amplitude')
self.ax = vv.gca()
self.timer = vv.Timer(self.app, 50, oneshot=False)
self.timer.Bind(self.updateplot)
self.timer.Start()
def show_vox(self, vfunc):
"""
Displays a 3-D rendering of a voxelized property.
:param vfunc: function accepting this MasonView instance and
returning a 3-D np.array of some voxelized property
"""
app = vv.use()
vv.figure(1)
vv.xlabel('Eastings (units)')
vv.ylabel('Northings (units)')
vv.zlabel('Depth (units)')
a = vv.gca()
a.camera.fov = 70
a.daspect = 1, 1, -1
vox = vfunc(self)
t = vv.volshow(vox, cm=vv.CM_JET, renderStyle='ray')
vv.ColormapEditor(a)
app.Run()
def psf_volume(stack, xyz_ratio, filepath):
app = vv.use()
# Init a figure with two axes
a1 = vv.subplot(121)
vv.title('PSF Volume')
a2 = vv.subplot(122)
vv.title('PSF XYZ Cross Sections')
# show
t1 = vv.volshow(stack, axes=a1) # volume
t2 = vv.volshow2(stack, axes=a2) # cross-section interactive
# set labels for both axes
vv.xlabel('Pixel X', axes=a1)
vv.ylabel('Pixel Y', axes=a1)
vv.zlabel('Z-Slice', axes=a1)
vv.xlabel('Pixel X', axes=a2)
vv.ylabel('Pixel Y', axes=a2)
vv.zlabel('Z-Slice', axes=a2)
# set colormaps
t1.colormap = vv.CM_JET
t2.colormap = vv.CM_JET
# set correct aspect ration corresponding to voxel size
a1.daspect = 1, 1, xyz_ratio
a2.daspect = 1, 1, xyz_ratio
# show grid
a1.axis.showGrid = 1
a2.axis.showGrid = 1
# run visvis and show results
app.Run()
# save screenshot
if filepath != 'nosave':
print 'Saving PSF volume.'
savename = filepath[:-4] + '_PSF_3D.png'
# sf: scale factor
vv.screenshot(savename, sf=1, bg='w')
def init_form(self):
self._form = QWidget()
layout = QVBoxLayout()
if conf.PYFORMS_USE_QT5:
layout.setContentsMargins(0,0,0,0)
else:
layout.setMargin(0)
self._form.setLayout( layout )
self._app = vv.use('pyqt5')
self._app.Create()
Figure = self._app.GetFigureClass()
self._fig = Figure(self._form)
policy = QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
widget = self._fig._widget
widget.setSizePolicy(policy)
layout.addWidget(widget)
def init_form(self):
self._form = QWidget()
layout = QVBoxLayout()
if _api.USED_API == _api.QT_API_PYQT5:
layout.setContentsMargins(0, 0, 0, 0)
else:
layout.setMargin(0)
self._form.setLayout(layout)
self._app = vv.use('pyqt5')
self._app.Create()
Figure = self._app.GetFigureClass()
self._fig = Figure(self._form)
policy = QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
widget = self._fig._widget
widget.setSizePolicy(policy)
layout.addWidget(widget)
super(ControlVisVis, self).init_form()
def initForm(self):
self._form = QtGui.QWidget()
layout = QtGui.QVBoxLayout()
layout.setMargin(0)
self._form.setLayout(layout)
self._app = vv.use('pyqt4')
self._app.Create()
self._first = True
Figure = self._app.GetFigureClass()
self._fig = Figure(self._form)
vv.figure(self._fig.nr)
policy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
QtGui.QSizePolicy.Expanding)
widget = self._fig._widget
widget.setSizePolicy(policy)
widget.setMinimumSize(100, 100)
layout.addWidget(widget)
self._colorMap = vv.CM_AUTUMN
def show_layer_boundaries(self, sample):
"""
Displays a 3-D rendering of boundary surfaces.
:param sample: index of sample for which to plot boundaries
"""
app = vv.use()
vv.figure(1)
X = np.linspace(self.xbounds[0], self.xbounds[1], self.xres)
Y = np.linspace(self.ybounds[0], self.xbounds[1], self.yres)
Z = np.linspace(self.zbounds[0], self.xbounds[1], self.zres)
vv.xlabel('Eastings (m)')
vv.ylabel('Northings (m)')
vv.zlabel('Depth (m)')
a = vv.gca()
a.camera.fov = 70
a.daspect = 1, 1, -1
for i in range(len(self.layers)):
C = plt.cm.jet(i / float(len(self.layers)))
C = np.array([[[C[0], C[1], C[2]]]])
m = vv.surf(X, Y, self.fbounds[i][sample], C)
vv.ColormapEditor(a)
app.Run()
# Display a legend a1.legend = "Lena's face", "Lena's shoulder" # Create second axes (with a black background) a2 = vv.subplot(122) a2.bgcolor = 'k' a2.axis.axisColor = 'w' # Display a texture vol = vv.aVolume(2) # returns a test volume as a numpy array texture3d = vv.volshow(vol) # Display a mesh using one of the "solid" functions mesh = vv.solidTeapot((32,32,80), scaling=(50,50,50)) mesh.faceColor = 0.4, 1, 0.4 mesh.specular = 'r' # Set orthographic projection a2.camera.fov = 45 # Create labels for the axis a2.axis.xLabel = 'x-axis' a2.axis.yLabel = 'y-axis' a2.axis.zLabel = 'z-axis' # Enter main loop app = vv.use() # let visvis chose a backend for me app.Run()
def demo(*args, **kwargs):
import math
m = 80 # width of grid
n = m ** 2 # number of points
minVal = -2.0
maxVal = 2.0
delta = (maxVal - minVal) / (m - 1)
X, Y = numpy.mgrid[minVal:maxVal + delta:delta, minVal:maxVal + delta:delta]
X = X.flatten()
Y = Y.flatten()
Z = numpy.sin(X) * numpy.cos(Y)
# Create the data point-matrix
M = numpy.array([X, Y, Z]).T
# Translation values (a.u.):
Tx = 0.5
Ty = -0.3
Tz = 0.2
# Translation vector
T = numpyTransform.translation(Tx, Ty, Tz)
S = numpyTransform.scaling(1.0, N=4)
# Rotation values (rad.):
rx = 0.3
ry = -0.2
rz = 0.05
Rx = numpy.matrix([[1, 0, 0, 0],
[0, math.cos(rx), -math.sin(rx), 0],
[0, math.sin(rx), math.cos(rx), 0],
[0, 0, 0, 1]])
Ry = numpy.matrix([[math.cos(ry), 0, math.sin(ry), 0],
[0, 1, 0, 0],
[-math.sin(ry), 0, math.cos(ry), 0],
[0, 0, 0, 1]])
Rz = numpy.matrix([[math.cos(rz), -math.sin(rz), 0, 0],
[math.sin(rz), math.cos(rz), 0, 0],
[0, 0, 1, 0],
[0, 0, 0, 1]])
# Rotation matrix
R = Rx * Ry * Rz
transformMat = numpy.matrix(numpy.identity(4))
transformMat *= T
transformMat *= R
transformMat *= S
# Transform data-matrix plus noise into model-matrix
D = numpyTransform.transformPoints(transformMat, M)
# Add noise to model and data
M = M + 0.01 * numpy.random.randn(n, 3)
D = D + 0.01 * numpy.random.randn(n, 3)
# Run ICP (standard settings)
initialGuess = numpy.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0])
lowerBounds = numpy.array([-pi, -pi, -pi, -100.0, -100.0, -100.0])
upperBounds = numpy.array([pi, pi, pi, 100.0, 100.0, 100.0])
icp = ICP(M, D, maxIterations=15, dataDownsampleFactor=1, minimizeMethod='fmincon', **kwargs)
# icp = ICP(M, D, maxIterations=15, dataDownsampleFactor=1, minimizeMethod='point', **kwargs)
transform, err, t = icp.runICP(x0=initialGuess, lb=lowerBounds, ub=upperBounds)
# Transform data-matrix using ICP result
Dicp = numpyTransform.transformPoints(transform[-1], D)
# Plot model points blue and transformed points red
if False:
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
fig = plt.figure()
ax = fig.add_subplot(2, 2, 1, projection='3d')
ax.scatter(M[:, 0], M[:, 1], M[:, 2], c='r', marker='o')
ax.scatter(D[:, 0], D[:, 1], D[:, 2], c='b', marker='^')
ax.set_xlabel('X Label')
ax.set_ylabel('Y Label')
ax.set_zlabel('Z Label')
ax = fig.add_subplot(2, 2, 2, projection='3d')
ax.scatter(M[:, 0], M[:, 1], M[:, 2], c='r', marker='o')
ax.scatter(Dicp[:, 0], Dicp[:, 1], Dicp[:, 2], c='b', marker='^')
ax.set_xlabel('X Label')
ax.set_ylabel('Y Label')
ax.set_zlabel('Z Label')
ax = fig.add_subplot(2, 2, 3)
ax.plot(t, err, 'x--')
ax.set_xlabel('X Label')
ax.set_ylabel('Y Label')
plt.show()
else:
import visvis as vv
app = vv.use()
vv.figure()
vv.subplot(2, 2, 1)
vv.plot(M[:, 0], M[:, 1], M[:, 2], lc='b', ls='', ms='o')
vv.plot(D[:, 0], D[:, 1], D[:, 2], lc='r', ls='', ms='x')
vv.xlabel('[0,0,1] axis')
vv.ylabel('[0,1,0] axis')
vv.zlabel('[1,0,0] axis')
vv.title('Red: z=sin(x)*cos(y), blue: transformed point cloud')
# Plot the results
vv.subplot(2, 2, 2)
vv.plot(M[:, 0], M[:, 1], M[:, 2], lc='b', ls='', ms='o')
vv.plot(Dicp[:, 0], Dicp[:, 1], Dicp[:, 2], lc='r', ls='', ms='x')
vv.xlabel('[0,0,1] axis')
vv.ylabel('[0,1,0] axis')
vv.zlabel('[1,0,0] axis')
vv.title('ICP result')
# Plot RMS curve
vv.subplot(2, 2, 3)
vv.plot(t, err, ls='--', ms='x')
vv.xlabel('time [s]')
vv.ylabel('d_{RMS}')
vv.title('KD-Tree matching')
if 'optAlg' in kwargs:
opt2 = nlopt.opt(kwargs['optAlg'], 2)
vv.title(opt2.get_algorithm_name())
del opt2
else:
vv.title('KD-Tree matching')
app.Run()
) * ( ( (8*x)**2 + ((8*y-2)+4)*((8*y-2)+4) + (8*z)**2 + 16 - 1.85*1.85 )
* ( (8*x)**2 + ((8*y-2)+4)*((8*y-2)+4) + (8*z)**2 + 16 - 1.85*1.85 ) -
64 * ( ((8*y-2)+4)*((8*y-2)+4) + (8*z)**2
) ) + 1025
# Uncommenting the line below will yield different results for classic MC
#vol = -vol
elif SELECT == 4:
vol = ellipsoid(4, 3, 2, levelset=True)
isovalue = 0
# Get surface meshes
t0 = time.time()
vertices1, faces1, _ = marching_cubes_lewiner(vol, isovalue, gradient_direction=gradient_dir, use_classic=False)
print('finding surface lewiner took %1.0f ms' % (1000*(time.time()-t0)) )
t0 = time.time()
vertices2, faces2, _ = marching_cubes_classic(vol, isovalue, gradient_direction=gradient_dir)
print('finding surface classic took %1.0f ms' % (1000*(time.time()-t0)) )
# Show
vv.figure(1); vv.clf()
a1 = vv.subplot(121); m1 = vv.mesh(np.fliplr(vertices1), faces1)
a2 = vv.subplot(122); m2 = vv.mesh(np.fliplr(vertices2), faces2)
a1.camera = a2.camera
# visvis uses right-hand rule, gradient_direction param uses left-hand rule
m1.cullFaces = m2.cullFaces = 'front' # None, front or back
vv.use().Run()
#!/usr/bin/env python
"""
This example illustrates embedding a visvis figure in a wx application.
"""
import wx
import visvis as vv
# Create a visvis app instance, which wraps a wx application object.
# This needs to be done *before* instantiating the main window.
app = vv.use('wx')
class MainWindow(wx.Frame):
def __init__(self):
wx.Frame.__init__(self, None, -1, "Embedding in WX", size=(560, 420))
# Make a panel with a button
self.panel = wx.Panel(self)
but = wx.Button(self.panel, -1, 'Click me')
# Make figure using "self" as a parent
Figure = app.GetFigureClass()
self.fig = Figure(self)
# Make sizer and embed stuff
self.sizer = wx.BoxSizer(wx.HORIZONTAL)
self.sizer.Add(self.panel, 1, wx.EXPAND)
self.sizer.Add(self.fig._widget, 2, wx.EXPAND)
# Make callback
#!/usr/bin/env python
import visvis as vv
app = vv.use()
# Get green channel of lena image
im = vv.imread('lena.png')[:,:,1]
# Make 4 subplots with different colormaps
cmaps = [vv.CM_GRAY, vv.CM_JET, vv.CM_SUMMER, vv.CM_HOT]
for i in range(4):
a = vv.subplot(2,2,i+1)
t = vv.imshow(im, clim=(0,255))
a.axis.visible = 0
t.colormap = cmaps[i]
vv.colorbar()
app.Run()
def __init__(self, display2d=True, camera_zoom=None, camera_location=None):
self.app = vv.use('qt5')
self.figsize = (1280 + 20, 720 + 20)
self.display2d = display2d
self.camera_zoom = camera_zoom
self.camera_location = camera_location
#!/usr/bin/env python
"""
This example illustrates embedding a visvis figure in an FLTK application.
"""
import fltk
import visvis as vv
# Create a visvis app instance, which wraps an fltk application object.
# This needs to be done *before* instantiating the main window.
app = vv.use("fltk")
class MainWindow(fltk.Fl_Window):
def __init__(self):
fltk.Fl_Window.__init__(self, 560, 420, "Embedding in FLTK")
# Make a panel with a button
but = fltk.Fl_Button(10, 10, 70, 30, "Click me")
but.callback(self._Plot)
# Make figure to draw stuff in
Figure = app.GetFigureClass()
self.fig = Figure(100, 10, 560 - 110, 420 - 20, "")
# Make box for resizing
box = fltk.Fl_Box(fltk.FL_NO_BOX, 100, 50, 560 - 110, 420 - 60, "")
self.resizable(box)
box.hide()
# Finish
#!/usr/bin/env python
"""
This example illustrates embedding a visvis figure in an FLTK application.
"""
import fltk
import visvis as vv
# Create a visvis app instance, which wraps an fltk application object.
# This needs to be done *before* instantiating the main window.
app = vv.use('fltk')
class MainWindow(fltk.Fl_Window):
def __init__(self):
fltk.Fl_Window.__init__(self, 560, 420, "Embedding in FLTK")
# Make a panel with a button
but = fltk.Fl_Button(10,10,70,30, 'Click me')
but.callback(self._Plot)
# Make figure to draw stuff in
self.fig = vv.backends.backend_fltk.Figure(100,10,560-110,420-20, "")
# Make box for resizing
box = fltk.Fl_Box(fltk.FL_NO_BOX,100,50, 560-110,420-60,"")
self.resizable(box)
box.hide()
# Finish
self.end()
#
import sys
import wx
from events import post_event, EventThread, Event
vvPresent = False
if not hasattr(sys, "frozen"):
try:
import visvis as vv
from visvis.core.line import Line
app = vv.use("wx")
vvPresent = True
except ImportError:
pass
class PlotterPreview(object):
def __init__(self, notify, figure, settings):
self.notify = notify
self.figure = figure
self.settings = settings
self.axes = None
self.window = None
self.preview = None
self.__setup_plot()
import numpy as np
import matplotlib.pyplot as plt
import OpenGL.GL as gl #@UnresolvedImport
from numpy import sin, cos, pi
from math import atan2
import logging as cflog
globalWindows = [] # For supporting ElementView:s for eldraw ...
global globalVisVisApp
global visApp
visApp = vv.use('qt5') # use qt4
def error(msg):
"""Log error message"""
cflog.error(msg)
def info(msg):
"""Log information message"""
cflog.info(msg)
def figure_class():
"""Return visvis Figure class."""
global visApp
vv.settings.preferredBackend first.
Note: the backend can be changed even when figures are created with
another backend, but this is not recommended.
Example embedding in Qt4
------------------------
# Near the end of the script:
# Get app instance and create native app
app = vv.use('pyside')
app.Create()
# Create window
m = MainWindow()
m.resize(560, 420)
m.show()
# Run main loop
app.Run()
"""
return vv.backends.use(backendName)
if __name__ == '__main__':
app = vv.use() # No arg provided: select backend automatically
print('Selected backend is %s.' % app.GetBackendName())
app.Create() # Create the backend's application
app.Run() # Enter the backend's mainloop (not in interactive mode)
def view(mol, viewer='native'):
'''Render the molecule
The mayavi backend doesn't work under python 3. The native backend uses
visvis to render the molecule. This is very slow.
It's better to use the molecular viewer.
Args:
mol (molecule.Molecule): The molecule instance to render
viewer: The backend to use. Valid choices are 'native', 'maya'
and, 'avogadro' (default: native).
Rturns:
None
'''
# mayavi
if viewer == 'maya':
from mayavi import mlab
for atom in mol.atoms:
pts = mlab.points3d(atom.r[0], atom.r[1], atom.r[2],
scale_factor=0.75,
scale_mode='none',
resolution=20,
color=atom.color())
for i, j in mol.bonds():
mlab.plot3d([mol.atoms[i].r[0], mol.atoms[j].r[0]],
[mol.atoms[i].r[1], mol.atoms[j].r[1]],
[mol.atoms[i].r[2], mol.atoms[j].r[2]],
tube_radius=0.1,
tube_sides=20)
mlab.show()
# avogadro
if viewer == 'avogadro':
from subprocess import call
write_xyz(mol, 'avogadro.xyz')
call(['avogadro', 'avogadro.xyz'])
call(['rm', 'avogadro.xyz'])
# visvis
if viewer == 'native':
import visvis as vv
for atom in mol.atoms:
x, y, z = atom.r
at = vv.solidSphere((x, y, z), atom.radius()*0.25)
at.faceColor = atom.color()
for bond in mol.bonds():
pp = vv.Pointset(3)
pp.append(bond.atoms[0].r)
pp.append(bond.atoms[1].r)
vv.solidLine(pp, radius=0.15, N=16)
pp = vv.Pointset(3)
pp.append([3, 3, 3])
pp.append([4, 3, 3])
x = vv.solidLine(pp, radius=0.05)
x.faceColor = 'r'
conex = vv.solidCone([4, 3, 3], scaling=[0.1, 0.1, 0.1], direction=[1, 0, 0])
conex.faceColor = 'r'
pp = vv.Pointset(3)
pp.append([3, 3, 3])
pp.append([3, 4, 3])
y = vv.solidLine(pp, radius=0.05)
y.faceColor = 'g'
coney = vv.solidCone([3, 4, 3], scaling=[0.1, 0.1, 0.1], direction=[0, 1, 0])
coney.faceColor = 'g'
pp = vv.Pointset(3)
pp.append([3, 3, 3])
pp.append([3, 3, 4])
z = vv.solidLine(pp, radius=0.05)
z.faceColor = 'b'
conez = vv.solidCone([3, 3, 4], scaling=[0.1, 0.1, 0.1], direction=[0, 0, 1])
conez.faceColor = 'b'
# Set axes settings
axes = vv.gca()
axes.SetLimits(rangeX=(-5, 5), rangeY=(-5, 5), rangeZ=(-5, 5))
vv.axis('off')
app = vv.use()
app.Run()
def plot(self, engine='pyplot', iterations=None):
"""Plots the system using a specified render engine.
Needs compute_3d_vectrices() to be called before.
- engine: String for the render engine. Can be 'pyplot', 'plotly' or 'visvis'.
pyplot is the nicest because it supports antialiasing on translucent objects.
plotly is a way faster alternative that uses your web browser's render engine.
visvis is faster but a bit rough.
- iterations: Limits the plotting to this number of iterations.
If None, the whole system states will be plotted."""
engine = engine.lower()
if iterations is None:
iterations = self.iterations
elif iterations > self.iterations:
raise ValueError("Unable to plot %s out of %s iterations"
% (iterations, self.iterations))
if engine == 'visvis':
try:
import visvis as vv
except ImportError:
raise ImportError("visvis must be installed in order to use it."
"Try to 'pip install visvis' in a command line.")
app = vv.use()
fig = vv.clf()
ax = vv.cla()
elif engine == 'pyplot':
try:
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
except ImportError:
raise ImportError("pyplot must be installed in order to use it."
"Try to 'pip install matplotlib' in a command line.")
fig = plt.figure(figsize=(32, 18), dpi=100)
ax = fig.gca(projection='3d')
ax.set_axis_off()
elif engine == 'plotly':
try:
import plotly as pl
from plotly.graph_objs import Scatter3d, Layout, Scene, Figure
except ImportError:
raise ImportError("plotly must be installed in order to use it."
"Try to 'pip install plotly' in a command line.")
data = []
layout = Layout(
scene = Scene(
xaxis=dict(
visible = False,
autorange = True,
),
yaxis=dict(
visible = False,
autorange = True,
),
zaxis=dict(
visible = False,
autorange = True,
)
),
margin=dict(
r=0, l=0,
b=0, t=0
),
showlegend = False,
hovermode = False
)
else:
raise ValueError("%s is not a supported render engine." % engine)
rings = self.rings[:iterations]
for i, ring in enumerate(rings):
color = self.cmap(i, 0, len(self.rings) / 2, 1)
if engine == 'visvis':
vv.plot(*ring, lc=color, mw=0, alpha=.2)
elif engine == 'pyplot':
ax.plot(*ring, c=color+(.4,)) # Adding alpha as (r, g, b, a)
else:
data.append(Scatter3d(
x = ring[0],
y = ring[1],
z = ring[2],
mode = 'lines',
opacity = .3,
line = dict(
color = ("rgb(%s,%s,%s)" % tuple([int(x*255) for x in color])),
width = 3)
))
curves = [curve[:iterations] for curve in self.curves]
for curve in curves:
if engine == 'visvis':
vv.plot(*curve, lc='k', mw=0, lw=2)
elif engine == 'pyplot':
ax.plot(*curve, c=(0, 0, 0, .8))
else:
data.append(Scatter3d(
x = curve[0],
y = curve[1],
z = curve[2],
mode = 'lines',
line = dict(
color = ("rgb(0, 0, 0)"),
width = 4)
))
if engine == 'visvis':
ax = vv.gca()
app.Run()
elif engine == 'pyplot':
fig.tight_layout()
# plt.draw()
mng = plt.get_current_fig_manager()
mng.full_screen_toggle()
plt.show()
else:
fig = Figure(data=data, layout=layout)
# pl.plot(fig, filename='3d-scatter-with-axes-titles')
pl.offline.plot(fig)
return
pass
try:
import matplotlib
matplotlib.interactive(True)
matplotlib.use('WXAgg')
import rtlsdr # @UnusedImport
import wx # @UnusedImport
except ImportError as error:
print 'Import error: {}'.format(error)
input('\nError importing libraries\nPress [Return] to exit')
exit(1)
try:
import visvis as vv
vv.use('wx')
except ImportError:
pass
import argparse
import multiprocessing
import os.path
from cli import Cli
from constants import APP_NAME
from file import File
from main_window import FrameMain, RtlSdrScanner
from misc import set_version_timestamp
def __init_worker():
__author__ = "Mathew Cosgrove"
__copyright__ = ""
__license__ = ""
__version__ = "0.0.1"
__maintainer__ = "Mathew Cosgrove"
__email__ = "*****@*****.**"
__status__ = "Development"
from collections import deque
import numpy as np
from PyQt4 import QtGui
import visvis as vv
backend = 'pyqt4'
vv_app = vv.use(backend)
class VisBaseCanvas(QtGui.QWidget):
"""docstring for VisCanvas"""
def __init__(self, parent):
if parent is not None:
super(VisBaseCanvas, self).__init__()
# Setup figure to attach to the QtApp
Figure = vv_app.GetFigureClass()
self.fig = Figure(parent)
self.fig.bgcolor = 0.1953, 0.1953, 0.1953
self.layout = QtGui.QHBoxLayout(parent)
self.layout.addWidget(self.fig._widget)
already loaded. If not, visvis tries to load the
vv.settings.preferredBackend first.
Note: the backend can be changed even when figures are created with
another backend, but this is not recommended.
Example embedding in Qt4
------------------------
# Near the end of the script:
# Get app instance and create native app
app = vv.use('pyside')
app.Create()
# Create window
m = MainWindow()
m.resize(560, 420)
m.show()
# Run main loop
app.Run()
"""
return vv.backends.use(backendName)
if __name__=='__main__':
app = vv.use() # No arg provided: select backend automatically
print('Selected backend is %s.' % app.GetBackendName())
app.Create() # Create the backend's application
app.Run() # Enter the backend's mainloop (not in interactive mode)
__author__ = "Mathew Cosgrove"
__copyright__ = ""
__license__ = ""
__version__ = "0.0.1"
__maintainer__ = "Mathew Cosgrove"
__email__ = "*****@*****.**"
__status__ = "Development"
from collections import deque
import numpy as np
from PyQt4 import QtGui
import visvis as vv
backend = 'pyqt4'
vv_app = vv.use(backend)
class VisBaseCanvas(QtGui.QWidget):
"""docstring for VisCanvas"""
def __init__(self, parent):
if parent is not None:
super(VisBaseCanvas, self).__init__()
# Setup figure to attach to the QtApp
Figure = vv_app.GetFigureClass()
self.fig = Figure(parent)
self.fig.bgcolor = 0.1953, 0.1953, 0.1953
#!/usr/bin/env python
"""
This example illustrates embedding a visvis figure in a Qt application.
"""
from PyQt4 import QtGui, QtCore
import visvis as vv
# Create a visvis app instance, which wraps a qt4 application object.
# This needs to be done *before* instantiating the main window.
app = vv.use('qt4')
class MainWindow(QtGui.QWidget):
def __init__(self, *args):
QtGui.QWidget.__init__(self, *args)
# Make a panel with a button
self.panel = QtGui.QWidget(self)
but = QtGui.QPushButton(self.panel)
but.setText('Push me')
# Make figure using "self" as a parent
self.fig = vv.backends.backend_qt4.Figure(self)
# Make sizer and embed stuff
self.sizer = QtGui.QHBoxLayout(self)
self.sizer.addWidget(self.panel, 1)
self.sizer.addWidget(self.fig._widget, 2)
# Make callback
but.pressed.connect(self._Plot)
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
import sys
import wx
from events import post_event, EventThread, Event
vvPresent = False
if not hasattr(sys, 'frozen'):
try:
import visvis as vv
from visvis.core.line import Line
app = vv.use('wx')
vvPresent = True
except ImportError:
pass
class PlotterPreview(object):
def __init__(self, notify, figure, settings):
self.notify = notify
self.figure = figure
self.settings = settings
self.axes = None
self.window = None
self.preview = None
self.__setup_plot()
from PyQt4 import QtGui, QtCore
import numpy as np
import visvis as vv
app = vv.use("pyqt4")
class PlotHandler(object):
def __init__(self, parent):
Figure = app.GetFigureClass()
self.figure = Figure(parent)
# init plot
self.axes = vv.subplot(111)
# self.axes.axisType = "polar"
self.activePlot = None
def get_widget(self):
return self.figure._widget
def updatePlot(self, X, Y, Z):
self.activePlot = (X,Y,Z)
x, y = np.meshgrid(X,Y)
vv.clf()
surface = vv.surf(x,y,Z)
surface.colormap = vv.CM_HOT
def updateSpecimens(self, data):
pass
boxsizer.Add (wx.StaticText(self.panel), flag=wx.EXPAND, border=5)
# Save settings
boxsizer.Add( self.CreateSaveSettingsButton(), flag=wx.EXPAND, border=5)
# Load settings
boxsizer.Add( self.CreateLoadSettingsButton(), flag=wx.EXPAND, border=5)
sizer.Add(boxsizer, pos=(1, 0), span=(1, 1), flag=wx.EXPAND|wx.TOP|wx.LEFT|wx.RIGHT|wx.GROW, border=10)
########################### End of constructing panel ######################################
self.panel.SetSizer (sizer)
############################# Setting visvis #######################################
Figure = app.GetFigureClass()
self.fig = Figure(self)
boxsizer = wx.BoxSizer (wx.HORIZONTAL)
boxsizer.Add(self.panel, 0.5, wx.EXPAND)
boxsizer.Add(self.fig._widget, 2, wx.EXPAND)
#########################################################################################
self.SetSizer (boxsizer)
self.SetAutoLayout(True)
self.Layout()
#########################################################################
if __name__ == '__main__' :
app = visvis.use('wx')
app.Create()
ODDExperiment (None)
app.Run()
t_end = 3600
epsilon = 1E-10
diff = epsilon * 2
zeros = np.zeros(Ci.shape)
while(t <= t_end and diff >= epsilon):
#solve for the gradients in each direction
l_xyz = ndimage.convolve(Ci, l, mode = "constant",
cval = c_out)
# l_y = ndimage.convolve(Ci, ly, mode = "constant",
# cval = c_out)
# l_z = ndimage.convolve(Ci, lz, mode = "constant",
# cval = c_out)
#first diffusion
C = Ci + (l_xyz)*D*dt
#MUST BE normalized by unit VOLUME
temp_sink = (-sink*dt) / grid_vol
temp_source = source*dt / grid_vol
C += temp_sink + temp_source
#get the summed difference
diff = np.sum(np.abs(Ci - C))
#make sure its positive
C = C * (C > 0.0)
#update the old
Ci = C
#update the time step
t += dt
vv.use('qt4')
vv.volshow3(C)
app = vv.use()
app.Run()
boxsizer.Add(self.CreateLoadSettingsButton(), flag=wx.EXPAND, border=5)
sizer.Add(boxsizer,
pos=(1, 0),
span=(1, 1),
flag=wx.EXPAND | wx.TOP | wx.LEFT | wx.RIGHT | wx.GROW,
border=10)
########################### End of constructing panel ######################################
self.panel.SetSizer(sizer)
############################# Setting visvis #######################################
Figure = app.GetFigureClass()
self.fig = Figure(self)
boxsizer = wx.BoxSizer(wx.HORIZONTAL)
boxsizer.Add(self.panel, 0.5, wx.EXPAND)
boxsizer.Add(self.fig._widget, 2, wx.EXPAND)
#########################################################################################
self.SetSizer(boxsizer)
self.SetAutoLayout(True)
self.Layout()
#########################################################################
if __name__ == '__main__':
app = visvis.use('wx')
app.Create()
ODDExperiment(None)
app.Run()
def refresh(self):
vv.figure(self._fig.nr)
self._app = vv.use()
self.paint(vv)
def show_and_wait():
"""Show visvis windows and enter application loop."""
global globalVisVisApp
globalVisVisApp = vv.use()
globalVisVisApp.Create()
globalVisVisApp.Run()
def __init__(self, kinfile, audiofile, config, parent = None):
"""
Data Controller class receives a kinematic file, and an audiofile, and
sets them up to be played synchronously using the visvis Figure().
The LCDTimer is passed the time and updated regularly to display the current
time values that are playing in the audio and in the kinematic data.
The data controls are setup on top with the LCD timer, with the figure below.
The dataController supports switching views, stopping, pausing, rewinding,
fast forwarding, playing, etc. It's purdy neat.
"""
super(DataController, self).__init__(parent)
backend = 'pyqt4'
app = vv.use(backend)
self.fileLoaded = False
#Set up the buttons for the player
self.playPauseButton = self.createButton(':/play.svg',50,44)
self.stopButton = self.createButton(':/stop.svg',40,34)
self.ffButton = self.createButton(":/fastForward.svg",30,24)
self.stepForwardButton = self.createButton(":/skipForward.svg",40,34)
self.stepBackwardButton = self.createButton(":/skipBackward.svg",40,34)
self.rewindButton = self.createButton(":/rewind.svg",30,24)
self.config= config
self.fs = self.config[0]
self.numSensors = self.config[1]
self.sensorDataFormat = [(14+9*i,21+9*i, self.config[2][i], self.config[3][i]) for i in range(self.numSensors)]
print self.sensorDataFormat
Figure = app.GetFigureClass()
self.setMinimumSize(750,700)
self.resize(750,700)
self.fig= Figure(self)
self.fig.enableUserInteraction = False
self.fig._widget.setMinimumSize(400,280)
self.spectrogram = specWidget.SpecWidget()
self.spectrogram.setMinimumSize(400, 150)
self.lcdTimer = lcd.LcdTimer()
self.lcdTimer.setMaximumHeight(60)
self.lcdTimer.setMinimumWidth(100)
self.dataViewers = [sdv.SensorDataWidget() for i in xrange(self.numSensors)];
playerLayout = QtGui.QHBoxLayout()
playerLayout.addStretch()
playerLayout.addWidget(self.rewindButton)
playerLayout.addWidget(self.stepBackwardButton)
playerLayout.addWidget(self.playPauseButton)
playerLayout.addWidget(self.stopButton)
playerLayout.addWidget(self.stepForwardButton)
playerLayout.addWidget(self.ffButton)
playerLayout.addWidget(self.lcdTimer)
playerGroup = QtGui.QGroupBox("Data Controls")
playerGroup.setLayout(playerLayout)
playerGroup.setMaximumHeight(100)
centerLayout= QtGui.QVBoxLayout()
centerLayout.addWidget(playerGroup)
centerLayout.addWidget(self.fig._widget)
centerLayout.addWidget(self.spectrogram)
finalLayout = QtGui.QHBoxLayout()
finalLayout.addLayout(centerLayout)
dataLayout = QtGui.QVBoxLayout()
for DV in self.dataViewers:
dataLayout.addWidget(DV)
finalLayout.addLayout(dataLayout)
self.setLayout(finalLayout)
self.connect(self.playPauseButton,QtCore.SIGNAL("clicked()"),self.playPause)
self.connect(self.stopButton,QtCore.SIGNAL("clicked()"),self.stop)
self.connect(self.ffButton,QtCore.SIGNAL("pressed()"),self.fastForward)
self.connect(self.rewindButton, QtCore.SIGNAL("pressed()"),self.rewind)
self.connect(self.stepForwardButton,QtCore.SIGNAL("pressed()"),self.stepForward)
self.connect(self.stepBackwardButton,QtCore.SIGNAL("pressed()"),self.stepBackward)
self.connect(self.spectrogram,QtCore.SIGNAL("pauseGUI()"),self.stepBackward)
self.connect(self.spectrogram,QtCore.SIGNAL("newInterval(PyQt_PyObject)"), self.setNewInterval)
self.playing,self.paused,self.stopped = range(3)
self.status = self.stopped
self.timer = vv.Timer(self)
self.timer.Bind(self.onTimer)
self.timer.nolag = True
self.disableButtons()
if((kinfile is not None) and (audiofile is not None)):
self.onFileLoaded(kinfile,audiofile)
This example illustrates embedding a visvis figure in a Qt application.
This example works for the pyqt4 and pyside backends.
"""
try:
from PySide import QtGui, QtCore
backend = 'pyside'
except ImportError:
from PyQt4 import QtGui, QtCore
backend = 'pyqt4'
import visvis as vv
# Create a visvis app instance, which wraps a qt4 application object.
# This needs to be done *before* instantiating the main window.
app = vv.use(backend)
class MainWindow(QtGui.QWidget):
def __init__(self, *args):
QtGui.QWidget.__init__(self, *args)
# Make a panel with a button
self.panel = QtGui.QWidget(self)
but = QtGui.QPushButton(self.panel)
but.setText('Push me')
# Make figure using "self" as a parent
Figure = app.GetFigureClass()
self.fig = Figure(self)
# Make sizer and embed stuff
vvt[i] = sum(cc)
# Interpolate (0 means Cardinal with tension 0)
samples = np.arange(0,len(data)-1,0.05, dtype=np.float32)
values1 = pirt.warp(np.array(data, dtype=np.float32), samples, 3, 'linear')
values2 = pirt.warp(np.array(data, dtype=np.float32), samples, 3, 'basis')
values3 = pirt.warp(np.array(data, dtype=np.float32), samples, 3, 0)
# Visualize
fig = vv.figure(1); vv.clf()
fig.position = 57.00, 45.00, 948.00, 969.00
vv.subplot(211)
vv.title('The basis functions for the %s spline' % type)
vv.plot(tt, vv0, lc='r')
vv.plot(tt, vv1, lc='g')
vv.plot(tt, vv2, lc='b')
vv.plot(tt, vv3, lc='m')
vv.plot(tt, vvt, lc='k', ls='--')
vv.subplot(212)
vv.plot(range(len(data)), data, ms='.', ls='')
vv.plot(samples, values1, lc='r')
vv.plot(samples, values2, lc='g')
vv.plot(samples, values3, lc='b', lw=3)
a = vv.gca()
a.legend = 'data', 'Linear', 'Basis', 'Cardinal'
vv.use().Run()
#!/usr/bin/env python
"""
This example illustrates embedding a visvis figure in a GTK application.
"""
import gtk
import visvis as vv
app = vv.use('gtk')
class MainWindow(gtk.Window):
def __init__(self, size=(560, 420)):
gtk.Window.__init__(self)
# Create boxes and button
hbox = gtk.HBox()
self.add(hbox)
vbox = gtk.VBox()
hbox.pack_start(vbox, False, False, 0)
button = gtk.Button('Click me')
vbox.pack_start(button, False, False, 0)
# Cteate visvis figure
Figure = app.GetFigureClass()
self.figure = Figure()
hbox.pack_start(self.figure._widget, True, True, 0)
# Connect signals
button.connect('clicked', self._Plot)
self.connect('delete_event', gtk.main_quit)
def main():
reqlog = logging.getLogger('requests')
reqlog.setLevel(logging.ERROR)
log = logging.getLogger(__name__)
server = subprocess.Popen([sys.executable, '../dora/server/server.py'])
time.sleep(5)
# Set up a sampling problem:
target_samples = 100
n_train = 20
lower = [1., 1.]
upper = [3., 3.]
acq_name = 'prod_max'
initialiseArgs = {
'lower': lower,
'upper': upper,
'acq_name': acq_name,
'n_train': n_train
}
# Initialise the sampler
sampler_info = requests.post('http://localhost:5000/samplers',
json=initialiseArgs).json()
log.info("Model Info: " + str(sampler_info))
# Set up plotting:
plots = {'fig': vv.figure(), 'count': 0, 'shape': (2, 3)}
plot_triggers = [22, 30, 40, 50, 65, target_samples - 1]
# Run the active sampling:
for i in range(target_samples):
log.info('Iteration: %d' % i)
# post a request to the sampler for a query location
req = requests.post(sampler_info['obs_uri'])
query_loc = req.json()
# Evaluate the sampler's query on the forward model
characteristic = np.array(query_loc['query'])
uid = query_loc['uid']
uid, measurement = simulate_measurement_vector(characteristic, uid)
# log.info('Generated measurement ' + measurement.__repr__())
# Update the sampler with the new observation
put_response = requests.put(query_loc['uri'],
json=measurement.tolist())
if i in plot_triggers:
log.info("Plotting")
plot_progress(plots, sampler_info)
print('Finished.')
vv.use().Run()
server.terminate()
