def draw(self):
"""Draw data."""
if len(self.fitResults) == 0:
return
# Make sure our figure is the active one
vv.figure(self.fig.nr)
if not hasattr(self, 'subplot1'):
self.subplot1 = vv.subplot(211)
#self.subplot1.position = (30, 2, -32, -32)
self.subplot2 = vv.subplot(212)
#self.subplot1.position = (30, 2, -32, -32)
a, ed = numpy.histogram(self.fitResults['tIndex'], self.Size[0] / 6)
print((float(numpy.diff(ed[:2]))))
self.subplot1.MakeCurrent()
vv.cla()
vv.plot(ed[:-1], a / float(numpy.diff(ed[:2])), lc='b', lw=2)
#self.subplot1.set_xticks([0, ed.max()])
#self.subplot1.set_yticks([0, numpy.floor(a.max()/float(numpy.diff(ed[:2])))])
self.subplot2.MakeCurrent()
vv.cla()
#cs =
csa = numpy.cumsum(a)
vv.plot(ed[:-1], csa / float(csa[-1]), lc='g', lw=2)
#self.subplot2.set_xticks([0, ed.max()])
#self.subplot2.set_yticks([0, a.sum()])
self.fig.DrawNow()
self.subplot1.position = (20, 2, -22, -32)
self.subplot2.position = (20, 2, -22, -32)
def DisplayOptimization (self) :
"""
Display the progress of optimization
"""
wx.Yield()
# abort, if requested
if self.need_abort : return
def GetValueColourIter (d) :
return izip_longest( d.itervalues(), ['r', 'g', 'b', 'k'], fillvalue='y' )
visvis.cla(); visvis.clf()
visvis.subplot(211)
# Plot optimization statistics
for values, colour in GetValueColourIter(self.optimization_log) :
try : visvis.plot ( values, lc=colour )
except Exception : pass
visvis.xlabel ('iteration')
visvis.ylabel ('Objective function')
visvis.legend( self.optimization_log.keys() )
# Display reference signal
visvis.subplot(212)
# Plot reference signal
for values, colour in GetValueColourIter(self.log_reference_signal) :
try : visvis.plot ( values, lc=colour )
except Exception : pass
visvis.xlabel ('iteration')
visvis.ylabel ("Signal from reference pulse")
visvis.legend( ["channel %d" % x for x in self.log_reference_signal.keys()] )
def draw( self ):
"""Draw data."""
if len(self.fitResults) == 0:
return
# Make sure our figure is the active one
vv.figure(self.fig.nr)
if not hasattr( self, 'subplot1' ):
self.subplot1 = vv.subplot(211)
#self.subplot1.position = (30, 2, -32, -32)
self.subplot2 = vv.subplot(212)
#self.subplot1.position = (30, 2, -32, -32)
a, ed = numpy.histogram(self.fitResults['tIndex'], self.Size[0]/6)
print((float(numpy.diff(ed[:2]))))
self.subplot1.MakeCurrent()
vv.cla()
vv.plot(ed[:-1], a/float(numpy.diff(ed[:2])), lc='b', lw=2)
#self.subplot1.set_xticks([0, ed.max()])
#self.subplot1.set_yticks([0, numpy.floor(a.max()/float(numpy.diff(ed[:2])))])
self.subplot2.MakeCurrent()
vv.cla()
#cs =
csa = numpy.cumsum(a)
vv.plot(ed[:-1], csa/float(csa[-1]), lc='g', lw=2)
#self.subplot2.set_xticks([0, ed.max()])
#self.subplot2.set_yticks([0, a.sum()])
self.fig.DrawNow()
self.subplot1.position = (20, 2, -22, -32)
self.subplot2.position = (20, 2, -22, -32)
def figparts():
""" Visualize ring parts
"""
fig = vv.figure(4);
fig.position = 8.00, 30.00, 944.00, 1002.00
vv.clf()
a0 = vv.subplot(121)
show_ctvolume(vol, model, showVol=showVol, clim=clim0, isoTh=isoTh)
modelR1, modelR2 = modelsR1R2[0][0], modelsR1R2[0][1]
modelR1.Draw(mc='g', mw = 10, lc='g') # R1 = green
modelR2.Draw(mc='c', mw = 10, lc='c') # R2 = cyan
vv.xlabel('x (mm)');vv.ylabel('y (mm)');vv.zlabel('z (mm)')
vv.title('Analysis for model LSPEAS %s - %s' % (ptcode[7:], ctcode))
a0.axis.axisColor= 1,1,1
a0.bgcolor= 0,0,0
a0.daspect= 1, 1, -1 # z-axis flipped
a0.axis.visible = showAxis
a1 = vv.subplot(122)
show_ctvolume(vol, model, showVol=showVol, clim=clim0, isoTh=isoTh)
models[0][0].Draw(mc='y', mw = 10, lc='y') # struts = yellow
models[0][1].Draw(mc='r', mw = 10, lc='r') # hooks = red
vv.xlabel('x (mm)');vv.ylabel('y (mm)');vv.zlabel('z (mm)')
vv.title('Analysis for model LSPEAS %s - %s' % (ptcode[7:], ctcode))
a1.axis.axisColor= 1,1,1
a1.bgcolor= 0,0,0
a1.daspect= 1, 1, -1 # z-axis flipped
a1.axis.visible = showAxis
a0.camera = a1.camera
def PlotReferencePhase(self, event):
"""
Plot reference phase
"""
visvis.cla()
visvis.clf()
# get actual amplitude and phased
phase = self.GetReferencePhase()[0]
ampl = np.ones(phase.size)
ampl, phase = self.DevPulseShaper.GetUnwrappedAmplPhase(ampl, phase)
# Wrap the phase in radians
phase %= (2 * np.pi)
# Get the phase in unites of 2*pi
phase /= (2 * np.pi)
visvis.subplot(211)
visvis.plot(phase)
visvis.ylabel('Reference phase')
visvis.xlabel('puls shaper pixel number')
visvis.title('Current reference phase (in unites of 2*pi)')
visvis.subplot(212)
visvis.plot(self.corrections, lc='r', ms='*', mc='r')
visvis.ylabel('Value of coefficients')
visvis.xlabel('coefficient number')
visvis.title('Value of corrections')
def PlotReferencePhase (self, event) :
"""
Plot reference phase
"""
visvis.cla(); visvis.clf();
# get actual amplitude and phased
phase = self.GetReferencePhase()[0]
ampl = np.ones(phase.size)
ampl, phase = self.DevPulseShaper.GetUnwrappedAmplPhase(ampl, phase)
# Wrap the phase in radians
phase %= (2*np.pi)
# Get the phase in unites of 2*pi
phase /= (2*np.pi)
visvis.subplot(211)
visvis.plot(phase)
visvis.ylabel ('Reference phase')
visvis.xlabel ('puls shaper pixel number')
visvis.title ('Current reference phase (in unites of 2*pi)')
visvis.subplot(212)
visvis.plot( self.corrections, lc='r',ms='*', mc='r' )
visvis.ylabel ('Value of coefficients')
visvis.xlabel ('coefficient number')
visvis.title ('Value of corrections')
def select3dpoints(vol, nr_of_stents, fig=None, clim=None):
""" Manually select 3d points in a volume. In the given figure (or a new
figure if None), three axes are created that display the transversal,
sagittal and coronal slices of the volume. The user can then use the mouse
to scroll to the correct slice and select the current position as an
endpoint of a stent.
Input: Number of stents to select start- and endpoints for.
"""
# Create figure
if fig is None:
fig = vv.figure()
figCleanup = True
else:
fig.Clear()
figCleanup = False
# Create four axes and a wibject to attach text labels to
fig.position = 0, 22, 750, 700
fig.title = '3D Point Selector'
a1 = vv.subplot(321)
a2 = vv.subplot(322)
a3 = vv.subplot(323)
a4 = vv.subplot(324)
a5 = vv.Wibject(fig)
# x-richting, y-richting, x-breedte?, y-breedte?
a5.position = 0.5, 0.7, 0.5, 0.5
# Set settings
for a in [a1, a2, a3, a4]:
a.showAxis = False
# Create PointSelect instance
pointselect3d = PointSelect3D(vol, a1, a3, a2, a4, a5, nr_of_stents, clim)
# Enter a mainloop
while not pointselect3d._finished:
pointselect3d.Run()
time.sleep(0.01)
# Clean up figure (close if we opened it)
fig.Clear()
fig.DrawNow()
if figCleanup:
fig.Destroy()
# Done (return points)
Startpoints = []
Endpoints = []
for i in range(nr_of_stents):
if isinstance(pointselect3d.endpoints[i * 2], tuple):
Startpoints.append(pointselect3d.endpoints[i * 2])
if isinstance(pointselect3d.endpoints[(i * 2) + 1], tuple):
Endpoints.append(pointselect3d.endpoints[(i * 2) + 1])
return Startpoints, Endpoints
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 DrawSpectrum(self, event):
"""
Draw spectrum interactively
"""
spectrum = self.Spectrometer.AcquiredData()
if spectrum == RETURN_FAIL: return
# Display the spectrum
if len(spectrum.shape) > 1:
try:
self.__interact_2d_spectrum__.SetData(spectrum)
except AttributeError:
visvis.cla()
visvis.clf()
# Spectrum is a 2D image
visvis.subplot(211)
self.__interact_2d_spectrum__ = visvis.imshow(spectrum,
cm=visvis.CM_JET)
visvis.subplot(212)
# Plot a vertical binning
spectrum = spectrum.sum(axis=0)
# Linear spectrum
try:
self.__interact_1d_spectrum__.SetYdata(spectrum)
except AttributeError:
if self.wavelengths is None:
self.__interact_1d_spectrum__ = visvis.plot(spectrum, lw=3)
visvis.xlabel("pixels")
else:
self.__interact_1d_spectrum__ = visvis.plot(self.wavelengths,
spectrum,
lw=3)
visvis.xlabel("wavelength (nm)")
visvis.ylabel("counts")
if self.is_autoscaled_spectrum:
# Smart auto-scale linear plot
try:
self.spectrum_plot_limits = GetSmartAutoScaleRange(
spectrum, self.spectrum_plot_limits)
except AttributeError:
self.spectrum_plot_limits = GetSmartAutoScaleRange(spectrum)
visvis.gca().SetLimits(rangeY=self.spectrum_plot_limits)
# Display the current temperature
try:
visvis.title("Temperature %d (C)" %
self.Spectrometer.GetTemperature())
except AttributeError:
pass
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 plot(image):
# ax = vv.gca()
# ms = vv.Mesh(ax)
logging.warning([image.shape, image.spacing])
vol = image[:, :, :, 0]
logging.warning([vol.min(), vol.max()])
vol = util.normalize(vol, 'ADCm')
logging.warning([vol.min(), vol.max()])
vol = vv.Aarray(vol, image.spacing)
cmap = None
# cmap = vv.CM_VIRIDIS
render_style = 'mip'
# render_style = 'iso'
# render_style = 'ray'
# render_style = 'edgeray'
# render_style = 'litray'
vv.figure()
vv.xlabel('x axis')
vv.ylabel('y axis')
vv.zlabel('z axis')
a1 = vv.subplot(111)
t1 = vv.volshow(vol, cm=cmap, renderStyle=render_style)
t1.isoThreshold = 0.7
vv.title(render_style)
# a1.camera = a2.camera = a3.camera
vv.ColormapEditor(a1)
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 plot(image):
# ax = vv.gca()
# ms = vv.Mesh(ax)
logging.warning([image.shape, image.spacing])
vol = image[:, :, :, 0]
logging.warning([vol.min(), vol.max()])
vol = util.normalize(vol, 'ADCm')
logging.warning([vol.min(), vol.max()])
vol = vv.Aarray(vol, image.spacing)
cmap = None
# cmap = vv.CM_VIRIDIS
render_style = 'mip'
# render_style = 'iso'
# render_style = 'ray'
# render_style = 'edgeray'
# render_style = 'litray'
vv.figure()
vv.xlabel('x axis')
vv.ylabel('y axis')
vv.zlabel('z axis')
a1 = vv.subplot(111)
t1 = vv.volshow(vol, cm=cmap, renderStyle=render_style)
t1.isoThreshold = 0.7
vv.title(render_style)
# a1.camera = a2.camera = a3.camera
vv.ColormapEditor(a1)
def _visualize(self, gridStep=10):
""" _visualize(self)
Visualize the registration process.
"""
if self.visualizer.fig is None:
return
import visvis as vv
firstpass = not self.visualizer.fig.children
if True:
# Show
# Apply deformation to image
im1 = self.get_deformed_image(0, 0)
im2 = self.get_deformed_image(1, 0)
# Get grid images
grid1 = create_grid_image(im1.shape, im1.sampling, gridStep)
grid2 = grid1.copy()
deform1, deform2 = self._deforms.get(0, None), self._deforms.get(
1, None)
if deform1 and deform2:
grid1 = deform1.apply_deformation(
grid1) # + 0.1*self._deforms[0][0])
grid2 = deform2.apply_deformation(
grid2) # + 0.1*self._deforms[1][0])
# Get images
ims = [None, im1, grid1, None, im2, grid2]
# Update textures
for i in range(len(ims)):
if ims[i] is not None:
self.visualizer.imshow((2, 3, i + 1), ims[i])
if firstpass:
# Init
# Show originals
self.visualizer.imshow(231, self._ims[0])
self.visualizer.imshow(234, self._ims[1])
# Show titles
title_map = [
'im 1', 'deformed 1', 'grid 1', 'im 2', 'deformed 2', 'grid 2'
]
for i in range(len(title_map)):
a = vv.subplot(2, 3, i + 1)
vv.title(title_map[i])
a.axis.visible = False
# Draw now
self.visualizer.fig.DrawNow()
def DrawSpectrum (self, event) :
"""
Draw spectrum interactively
"""
spectrum = self.Spectrometer.AcquiredData()
if spectrum == RETURN_FAIL : return
# Display the spectrum
if len(spectrum.shape) > 1:
try :
self.__interact_2d_spectrum__.SetData(spectrum)
except AttributeError :
visvis.cla(); visvis.clf();
# Spectrum is a 2D image
visvis.subplot(211)
self.__interact_2d_spectrum__ = visvis.imshow(spectrum, cm=visvis.CM_JET)
visvis.subplot(212)
# Plot a vertical binning
spectrum = spectrum.sum(axis=0)
# Linear spectrum
try :
self.__interact_1d_spectrum__.SetYdata(spectrum)
except AttributeError :
if self.wavelengths is None :
self.__interact_1d_spectrum__ = visvis.plot (spectrum, lw=3)
visvis.xlabel ("pixels")
else :
self.__interact_1d_spectrum__ = visvis.plot (self.wavelengths, spectrum, lw=3)
visvis.xlabel("wavelength (nm)")
visvis.ylabel("counts")
if self.is_autoscaled_spectrum :
# Smart auto-scale linear plot
try :
self.spectrum_plot_limits = GetSmartAutoScaleRange(spectrum, self.spectrum_plot_limits)
except AttributeError :
self.spectrum_plot_limits = GetSmartAutoScaleRange(spectrum)
visvis.gca().SetLimits ( rangeY=self.spectrum_plot_limits )
# Display the current temperature
try : visvis.title ("Temperature %d (C)" % self.Spectrometer.GetTemperature() )
except AttributeError : pass
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__(self, parent, action=None, **kwargs):
pythics.libcontrol.Control.__init__(self, parent,
action=None,
save=False,
**kwargs)
Figure = parent.main_window.vv_app.GetFigureClass()
self.figure = Figure(parent)
self.widget = self.figure._widget
#vv.figure(self.figure)
self.axes = vv.subplot(1,1,1)
self.items = dict()
def _Plot(self, event):
# update status text
self.status.SetLabel("CPU:%.1f\nMemory:%.1f" % (cpudata[-1], vmemdata[-1]))
# Make sure our figure is the active one
# If only one figure, this is not necessary.
#vv.figure(self.fig.nr)
# Clear it
vv.clf()
# Plot
a = vv.subplot(211)
vv.plot(cpudata, lw=2, lc="c", mc ='y', ms='d')
vv.legend("cpu percent ")
a.axis.showGrid = True
a.axis.xlabel = "CPU Usage Percent"
a.axis.ylabel = "sampling time line"
a = vv.subplot(212)
vv.plot(vmemdata, lw=2, mew=1, lc='m', mc ='y', ms='d' )
vv.legend("virtual memory")
a.axis.showGrid = True
def imshow(self, subplot, im, *args, **kwargs):
""" imshow(subplot, im, *args, **kwargs)
Show the given image in specified subplot. If possible,
updates the previous texture object.
"""
# Check if we can show
if not self.fig:
return
else:
self._f.MakeCurrent()
# Import visvis
import visvis as vv
# Get axes
if isinstance(subplot, tuple):
a = vv.subplot(*subplot)
else:
a = vv.subplot(subplot)
# Get what's in there
t = None
if len(a.wobjects) == 2 and isinstance(a.wobjects[1], vv.BaseTexture):
t = a.wobjects[1]
# Reuse, or clear and replace
if t is not None:
t.SetData(im)
else:
a.Clear()
t = vv.imshow(im, *args, **kwargs)
# Done
return t
def _Plot(self, event):
# update status text
self.status.SetLabel("CPU:%.1f\nMemory:%.1f" %
(cpudata[-1], vmemdata[-1]))
# Make sure our figure is the active one
# If only one figure, this is not necessary.
#vv.figure(self.fig.nr)
# Clear it
vv.clf()
# Plot
a = vv.subplot(211)
vv.plot(cpudata, lw=2, lc="c", mc='y', ms='d')
vv.legend("cpu percent ")
a.axis.showGrid = True
a.axis.xlabel = "CPU Usage Percent"
a.axis.ylabel = "sampling time line"
a = vv.subplot(212)
vv.plot(vmemdata, lw=2, mew=1, lc='m', mc='y', ms='d')
vv.legend("virtual memory")
a.axis.showGrid = True
def plot_progress(plots, sampler_info):
settings = requests.get(sampler_info['settings']).json()
lower = settings['lower']
upper = settings['upper']
subplt = vv.subplot(*(plots['shape'] + (1 + plots['count'], )))
plots['count'] += 1
# Request the training data
training_data = requests.get(sampler_info['training_data_uri']).json()
xres = 30
yres = 30
xeva, yeva = np.meshgrid(np.linspace(lower[0], upper[0], xres),
np.linspace(lower[1], upper[1], yres))
Xquery = np.array([xeva.flatten(), yeva.flatten()]).T
#Request the predictions from the server
r = requests.get(sampler_info['pred_uri'], json=Xquery.tolist())
r.raise_for_status()
pred = r.json()
pred_mean = np.array(pred['predictive_mean'])
id_matrix = np.reshape(
np.arange(Xquery.shape[0])[:, np.newaxis], xeva.shape)
n, n_outputs = pred_mean.shape
# Plot the training data and the predictions
vol = np.zeros((n_outputs, xeva.shape[0], xeva.shape[1]))
for x in range(xres):
for y in range(yres):
vol[:, x, y] = pred_mean[id_matrix[x, y]]
plt = vv.volshow(vol, renderStyle='mip', clim=(-0.5, 1))
plt.colormap = vv.CM_JET
subplt.axis.xLabel = 'input 1'
subplt.axis.yLabel = 'input 2'
subplt.axis.zLabel = 'model output'
a = ((np.asarray(training_data['X']) - np.array([np.min(xeva),
np.min(yeva)])[np.newaxis, :]) / np.array([np.max(xeva) -
np.min(xeva), np.max(yeva)-np.min(yeva)])[np.newaxis, :]) \
* np.array(xeva.shape) # NOQA
n = a.shape[0]
a = np.hstack((a, (n_outputs + 0.01) * np.ones((n, 1))))
pp = vv.Pointset(a)
vv.plot(pp, ms='.', mc='w', mw='9', ls='')
def __init__(self):
# Setup visualization
self._fig = fig = vv.figure()
self._a1 = a1 = vv.subplot(111)
# Init pointset with control points
self._pp = Pointset(2)
# Init lines to show control points
self._line1 = vv.plot(self._pp, ls='', ms='.', mc='r', mw=11, axes=a1)
self._line1.hitTest = True
# Init grid properties
self._fieldSize = 100
self._sampling = 10
self._levels = 5
# Member to indicate the point being dragged (as an index)
self._active = None
# Bind to events
a1.eventDoubleClick.Bind(self.on_doubleclick)
self._line1.eventDoubleClick.Bind(self.on_doubleclick_line)
self._line1.eventMouseDown.Bind(self.on_down_line)
self._line1.eventMouseUp.Bind(self.on_up_line)
a1.eventMotion.Bind(self.on_motion)
fig.eventKeyDown.Bind(self.on_key_down)
print(
'Use left/right to control #levels and up/down to control grid sampling.'
)
# Init
self.apply()
a1.daspectAuto = False
a1.SetLimits()
a1.axis.showGrid = True
def show(self):
import visvis as vv
# If there are many tests, make a selection
if len(self._tests) > 1000:
tests = random.sample(self._tests, 1000)
else:
tests = self._tests
# Get ticks
nn = [test[0] for test in tests]
# Create figure
vv.figure(1)
vv.clf()
# Prepare kwargs
plotKwargsText = {'ms': '.', 'mc': 'b', 'mw': 5, 'ls': ''}
plotKwargsBin = {'ms': '.', 'mc': 'r', 'mw': 5, 'ls': ''}
# File size against number of elements
vv.subplot(221)
vv.plot(nn, [test[2][0] for test in tests], **plotKwargsText)
vv.plot(nn, [test[2][1] for test in tests], **plotKwargsBin)
vv.legend('text', 'binary')
vv.title('File size')
# Speed against number of elements
vv.subplot(223)
vv.plot(nn, [test[1][4] for test in tests], **plotKwargsText)
vv.plot(nn, [test[1][6] for test in tests], **plotKwargsBin)
vv.legend('text', 'binary')
vv.title('Save time')
# Speed (file) against number of elements
vv.subplot(224)
vv.plot(nn, [test[1][5] for test in tests], **plotKwargsText)
vv.plot(nn, [test[1][7] for test in tests], **plotKwargsBin)
vv.legend('text', 'binary')
vv.title('Load time')
def show(self):
import visvis as vv
# If there are many tests, make a selection
if len(self._tests) > 1000:
tests = random.sample(self._tests, 1000)
else:
tests = self._tests
# Get ticks
nn = [test[0] for test in tests]
# Create figure
vv.figure(1)
vv.clf()
# Prepare kwargs
plotKwargsText = {'ms':'.', 'mc':'b', 'mw':5, 'ls':''}
plotKwargsBin = {'ms':'.', 'mc':'r', 'mw':5, 'ls':''}
# File size against number of elements
vv.subplot(221)
vv.plot(nn, [test[2][0] for test in tests], **plotKwargsText)
vv.plot(nn, [test[2][1] for test in tests], **plotKwargsBin)
vv.legend('text', 'binary')
vv.title('File size')
# Speed against number of elements
vv.subplot(223)
vv.plot(nn, [test[1][4] for test in tests], **plotKwargsText)
vv.plot(nn, [test[1][6] for test in tests], **plotKwargsBin)
vv.legend('text', 'binary')
vv.title('Save time')
# Speed (file) against number of elements
vv.subplot(224)
vv.plot(nn, [test[1][5] for test in tests], **plotKwargsText)
vv.plot(nn, [test[1][7] for test in tests], **plotKwargsBin)
vv.legend('text', 'binary')
vv.title('Load time')
ringparts(ringpart=ringpart)
# Visualize ring parts
if ringpart:
figparts()
# Area and cyclic change -- ellipse fit
if ringpart:
# fit plane and ellipse
R1 = modelsR1R2[0][0]
R2 = modelsR1R2[0][1]
fittedR1, fittedR2, fittedR1R2 = _fit3D(R1), _fit3D(R2), _fit3D(models[0][4]) # [4]=model_noHooks
print("------------")
f = vv.figure(); vv.clf()
f.position = 258.00, 30.00, 1654.00, 1002.00
a1 = vv.subplot(231)
vis3Dfit(fittedR1,vol,model,ptcode,ctcode,showAxis,showVol=showVol, clim=clim0, isoTh=isoTh)
a2 = vv.subplot(232)
vis3Dfit(fittedR2,vol,model,ptcode,ctcode,showAxis,showVol=showVol, clim=clim0, isoTh=isoTh)
a3 = vv.subplot(233)
vis3Dfit(fittedR1R2,vol,model,ptcode,ctcode,showAxis,showVol=showVol, clim=clim0, isoTh=isoTh)
a1.camera = a2.camera = a3.camera
a1b = vv.subplot(2,3,4)
vis2Dfit(fittedR1,ptcode, ctcode, showAxis)
a2b = vv.subplot(2,3,5)
vis2Dfit(fittedR2,ptcode, ctcode, showAxis)
a3b = vv.subplot(2,3,6)
vis2Dfit(fittedR1R2,ptcode, ctcode, showAxis)
# cyclic change
A_R1 = calculateAreaChange(R1, 'R1')
A_R2 = calculateAreaChange(R2, 'R2')
if not y0:
continue
# Reflect
for y in range(N):
y1 = y0 - y - bool(not distance)
y2 = y0 + y + distance
im2[y2, x, :] = im1[y1, x, :]
im2[y2, x, 3] *= startAlpha * (1.0 - float(y / N))
y2_max = max(y2_max, y2)
# Return im2, cropped appropriately
return im2[:y2_max, : shape[1], :]
if __name__ == "__main__":
filename = "/home/almar/projects/www/pyzo-www/wwwpyzo/_static/pyzo_box.png"
im1 = imageio.imread(filename)
im2 = reflect_image(im1)
import visvis as vv
vv.clf()
vv.subplot(121)
vv.imshow(im1)
vv.subplot(122)
vv.imshow(im2)
# reflect(filename)
) * ( ( (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()
vv2[i] = cc[2]
vv3[i] = cc[3]
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.clf()
## 1D
# Input and result
pp = [2, 4, 3]
t_max, polynom = fitting.fit_lq1(pp)
# Sample polynom
polypp = PointSet(2)
for i in np.linspace(-1,1,100):
polypp.append(i, polynom[0]*i**2 + polynom[1]*i + polynom[2])
# Visualize
vv.subplot(121)
vv.plot([-1,0,1],pp)
vv.plot([t_max, t_max], [0,1], lc='r')
vv.plot(polypp, lc='r')
## 2D
# Input and result
im = vv.imread('astronaut.png')[::,::,2].copy()
Y,X = np.where(im==im.max())
Y,X = Y[0], X[0]
im[Y-1,X] -= 20 # make more interesting :)
mat = im[Y-1:Y+2, X-1:X+2]
# Normalize
mass = normalize(mass)
# Truncate
if truncate:
mass[mass < 0] = 0.0
soft_limit(mass, 1) # todo: half limit
#mass = mass**0.5
return mass
# Show
vv.figure(10)
vv.clf()
for i in range(3):
a = vv.subplot(3, 3, i + 1)
vv.imshow(ims[i])
a.axis.visible = False
for i in range(3):
a = vv.subplot(3, 3, i + 4)
vv.imshow(getMass(ims[i]))
a.axis.visible = False
for i in range(3):
a = vv.subplot(3, 3, i + 7)
vv.hist(getMass(ims[i], False), 64)
a.SetLimits()
im = gl.glReadPixels(x, y, w, h, gl.GL_RGB, gl.GL_FLOAT)
# reshape, flip, and store
im.shape = h,w,3
im = np.flipud(im)
# done
return im
if __name__ == '__main__':
import time
f = vv.figure()
a1 = vv.subplot(211)
a2 = vv.subplot(212)
vv.plot([2,3,4,2,4,3], axes=a1)
for i in range(4):
# draw and wait a bit
f.DrawNow()
time.sleep(1)
# make snapshots
im1 = getframe(f)
im2 = getframe(a1)
# clear and show snapshots
a1.Clear()
a2.Clear()
vv.imshow(im1,axes=a1, clim=(0,1))
# create axes in container
a = Axes(f)
c = a.parent
# calculate relative coordinates
dx, dy = 1.0/cols, 1.0/rows
y = int( nr / cols )
x = int( nr % cols )
# apply positions
c.position = dx*x, dy*y, dx, dy
a.position = 10, 10, -20, -20
# done
return a
if __name__ == "__main__":
f = vv.figure()
# Get axes on 2x2 grid
a1 = vv.subplot(221)
a2 = vv.subplot(221)
a3 = vv.subplot(224)
# Get axes on 3x3 grid
a4 = vv.subplot(331) # (center is inside 221)
a5 = vv.subplot(333)
# Check
print(a1 is a2, a1 is a4)
#!/usr/bin/env python
import visvis as vv
from visvis.pypoints import Aarray
app = vv.use()
# Let's say we have lena, but only the even pixels in the y dimension.
# So each pixel should have twice the size in the y direction.
im = vv.imread('lena.png')
im = im[::2,:,:]
# Init a figure with two axes
vv.figure()
a1 = vv.subplot(121); vv.title('pixel units')
a2 = vv.subplot(122); vv.title('real-world units')
# Method 1: scale the whole scene
# Use this if you want the axis to depict pixel units.
t1 = vv.imshow(im, axes=a1)
a1.daspect = 1,-2 # daspect works x,y,z, the y-axis is flipped for images
# Method 2: use the Aarray class to scale the image
# You could use this is you know the physical dimensions of a pixel,
# to have the axis depict, for example, mm.
im2 = Aarray(im,(2,1,1)) # sampling is given in y,x,color order
t2 = vv.imshow(im2, axes=a2)
app.Run()
""" This example demonstrates rendering a color volume.
This example demonstrates two render styles. Note that
all render styles are capable of rendering color data.
"""
import numpy as np
import visvis as vv
app = vv.use()
# Use vv.aVolume to create random bars for each color plane
N = 64
vol = np.empty((N,N,N,3), dtype='float32')
for i in range(3):
vol[:,:,:,i] = vv.aVolume(10,N)
# Show
vv.figure()
a1 = vv.subplot(121);
t1 = vv.volshow(vol[:,:,:,:], renderStyle = 'mip')
vv.title('color MIP render')
a2 = vv.subplot(122);
t2 = vv.volshow(vol[:,:,:,:], renderStyle = 'iso')
t2.isoThreshold = 0.5
vv.title('color ISO-surface render')
# Share cameras
a1.camera = a2.camera
# Run app
app.Run()
s2 = loadvol(basedir, ptcode, ctcode, 'ring', staticref)
vol = s2.vol
s3 = loadvol(basedir, ptcode, ctcode, cropname, 'phases')
vol0ori = s3.vol0
# todo: backward/forward based on how deforms were obtained??
# deforms was obtained as backward, from original phases to mean volume avgreg
deform = pirt.DeformationFieldBackward(deforms[0])
# vol2 = pirt.interp.deform_backward(vol, deforms[0]) # te low level, gebruikt awarp niet
vol2 = deform.inverse().as_backward().apply_deformation(
vol0ori) # gebruikt pirt deformation.py
vv.figure(1)
vv.clf()
a1 = vv.subplot(131)
t1 = vv.volshow(vol)
a1.daspect = (1, 1, -1)
vv.title('vol average of cardiac cycle')
# vv.figure(2); vv.clf()
a2 = vv.subplot(132)
t2 = vv.volshow(vol2)
a2.daspect = (1, 1, -1)
vv.title('vol 0 deformed to avg volume')
# vv.figure(3); vv.clf()
a3 = vv.subplot(133)
t3 = vv.volshow2((vol2 - vol), clim=(-500, 500))
a3.daspect = (1, 1, -1)
vv.title('difference')
a1.camera = a2.camera = a3.camera
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()
def __init__(self,ptcode,ctcode,basedir, seed_th=[600], show=True,
normalize=False, modelname='model'):
import os
import numpy as np
import visvis as vv
from visvis import ssdf
from stentseg.utils import PointSet, _utils_GUI
from stentseg.utils.datahandling import select_dir, loadvol, loadmodel
from stentseg.stentdirect.stentgraph import create_mesh
from stentseg.stentdirect import stentgraph, StentDirect, getDefaultParams
from stentseg.stentdirect import AnacondaDirect, EndurantDirect, NellixDirect
from stentseg.utils.visualization import show_ctvolume
from stentseg.utils.picker import pick3d, label2worldcoordinates, label2volindices
import scipy
from scipy import ndimage
import copy
# Select dataset to register
cropname = 'prox'
# phase = 10
#dataset = 'avgreg'
#what = str(phase) + dataset # avgreg
what = 'avgreg'
# Load volumes
s = loadvol(basedir, ptcode, ctcode, cropname, what)
# sampling was not properly stored after registration for all cases: reset sampling
vol_org = copy.deepcopy(s.vol)
s.vol.sampling = [vol_org.sampling[1], vol_org.sampling[1], vol_org.sampling[2]] # z,y,x
s.sampling = s.vol.sampling
vol = s.vol
## Initialize segmentation parameters
stentType = 'nellix' # 'zenith';'nellix' runs modified pruning algorithm in Step3
p = getDefaultParams(stentType)
p.seed_threshold = seed_th # step 1 [lower th] or [lower th, higher th]
# p.seedSampleRate = 7 # step 1, nellix
p.whatphase = what
## Perform segmentation
# Instantiate stentdirect segmenter object
if stentType == 'anacondaRing':
sd = AnacondaDirect(vol, p) # inherit _Step3_iter from AnacondaDirect class
#runtime warning using anacondadirect due to mesh creation, ignore
elif stentType == 'endurant':
sd = EndurantDirect(vol, p)
elif stentType == 'nellix':
sd = NellixDirect(vol, p)
else:
sd = StentDirect(vol, p)
## show histogram and normalize
# f = vv.figure(3)
# a = vv.gca()
# vv.hist(vol, drange=(300,vol.max()))
# normalize vol to certain limit
if normalize:
sd.Step0(3071)
vol = sd._vol
# b= vv.hist(vol, drange=(300,3071))
# b.color = (1,0,0)
## Perform step 1 for seeds
sd.Step1()
## Visualize
if show:
fig = vv.figure(2); vv.clf()
fig.position = 0.00, 22.00, 1920.00, 1018.00
clim = (0,2000)
# Show volume and model as graph
a1 = vv.subplot(121)
a1.daspect = 1,1,-1
# t = vv.volshow(vol, clim=clim)
t = show_ctvolume(vol, axis=a1, showVol='MIP', clim =clim, isoTh=250,
removeStent=False, climEditor=True)
label = pick3d(vv.gca(), vol)
sd._nodes1.Draw(mc='b', mw = 2) # draw seeded nodes
#sd._nodes2.Draw(mc='b', lc = 'g') # draw seeded and MCP connected nodes
vv.xlabel('x (mm)');vv.ylabel('y (mm)');vv.zlabel('z (mm)')
# Show volume and cleaned up graph
a2 = vv.subplot(122)
a2.daspect = 1,1,-1
sd._nodes1.Draw(mc='b', mw = 2) # draw seeded nodes
# t = vv.volshow(vol, clim=clim)
# label = pick3d(vv.gca(), vol)
# sd._nodes2.Draw(mc='b', lc='g')
# sd._nodes3.Draw(mc='b', lc='g')
vv.xlabel('x (mm)');vv.ylabel('y (mm)');vv.zlabel('z (mm)')
# # Show the mesh
#===============================================================================
# a3 = vv.subplot(133)
# a3.daspect = 1,1,-1
# t = vv.volshow(vol, clim=clim)
# pick3d(vv.gca(), vol)
# #sd._nodes3.Draw(mc='b', lc='g')
# m = vv.mesh(bm)
# m.faceColor = 'g'
# # _utils_GUI.vis_spared_edges(sd._nodes3)
# vv.xlabel('x (mm)');vv.ylabel('y (mm)');vv.zlabel('z (mm)')
#===============================================================================
# Use same camera
a1.camera = a2.camera #= a3.camera
switch = True
a1.axis.visible = switch
a2.axis.visible = switch
#a3.axis.visible = switch
## Store segmentation to disk
# Get graph model
model = sd._nodes1
# Build struct
s2 = vv.ssdf.new()
s2.sampling = s.sampling
s2.origin = s.origin
s2.stenttype = s.stenttype
s2.croprange = s.croprange
for key in dir(s):
if key.startswith('meta'):
suffix = key[4:]
s2['meta'+suffix] = s['meta'+suffix]
s2.what = what
s2.params = p
s2.stentType = stentType
# Store model (not also volume)
s2.model = model.pack()
# Save
filename = '%s_%s_%s_%s.ssdf' % (ptcode, ctcode, cropname, modelname+ what)
ssdf.save(os.path.join(basedir, ptcode, filename), s2)
print('saved to disk as {}.'.format(filename) )
## Make model dynamic (and store/overwrite to disk)
#===============================================================================
#
# import pirt
# from stentsegf.motion.dynamic import incorporate_motion_nodes, incorporate_motion_edges
#
# # Load deforms
# s = loadvol(basedir, ptcode, ctcode, cropname, '10deforms')
# deformkeys = []
# for key in dir(s):
# if key.startswith('deform'):
# deformkeys.append(key)
# deforms = [s[key] for key in deformkeys]
# deforms = [pirt.DeformationFieldBackward(*fields) for fields in deforms]
# paramsreg = s.params
#
# # Load model
# s = loadmodel(basedir, ptcode, ctcode, cropname, 'model'+what)
# model = s.model
#
# # Combine ...
# incorporate_motion_nodes(model, deforms, s.origin)
# incorporate_motion_edges(model, deforms, s.origin)
#
# # Save back
# filename = '%s_%s_%s_%s.ssdf' % (ptcode, ctcode, cropname, 'model'+what)
# s.model = model.pack()
# s.paramsreg = paramsreg
# ssdf.save(os.path.join(basedir, ptcode, filename), s)
# print('saved to disk as {}.'.format(filename) )
#===============================================================================
import visvis as vv
app = vv.use()
# Load volume
vol = vv.volread('stent')
# 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
# Create colormap editor in first axes
cme = vv.ColormapEditor(vv.gcf(), *tt[3:])
# Run app
def DoScannning (self, event) :
"""
Perform scanning of different phase mask
"""
# Create pseudonyms of necessary devices
self.DevSpectrometer = self.parent.Spectrometer.dev
self.DevPulseShaper = self.parent.PulseShaper.dev
self.DevSampleSwitcher = self.parent.SampleSwitcher.dev
# Save global settings and get the name of log file
self.log_filename = SaveSettings(SettingsNotebook=self.parent,
title="Select file to save phase mask scanning", filename="scanning_phase_mask.hdf5")
if self.log_filename is None : return
####################### Initiate devices #############################
# Initiate spectrometer
settings = self.parent.Spectrometer.GetSettings()
if self.DevSpectrometer.SetSettings(settings) == RETURN_FAIL : return
# Initiate pulse shaper
settings = self.parent.PulseShaper.GetSettings()
if self.DevPulseShaper.Initialize(settings) == RETURN_FAIL : return
# Get number of optimization variables
self.num_pixels = self.DevPulseShaper.GetParamNumber()
if self.num_pixels == RETURN_FAIL :
raise RuntimeError ("Optimization cannot be started since calibration file was not loaded")
# Initiate sample switcher
settings = self.parent.SampleSwitcher.GetSettings()
if self.DevSampleSwitcher.Initialize(settings) == RETURN_FAIL : return
# Saving the name of channels
odd_settings = self.GetSettings()
self.channels = sorted(eval( "(%s,)" % odd_settings["channels"] ))
if self.DevSampleSwitcher.GetChannelNum()-1 < max(self.channels) :
raise ValueError ("Error: Some channels specified are not accessible by sample switcher.")
# Check whether the background signal array is present
self.CheckBackground()
#####################################################################
# Get range of coefficient
coeff_range = np.linspace( odd_settings["coeff_min"], odd_settings["coeff_max"], odd_settings["coeff_num"] )
# List all polynomial coefficients
N = odd_settings["polynomial_order"]
poly_coeffs = np.zeros( (coeff_range.size*N, N+1) )
for n in range(1,N+1) :
poly_coeffs[(n-1)*coeff_range.size:n*coeff_range.size, n ] = coeff_range
# Chose max amplitude
max_ampl = odd_settings["max_ampl"]*np.ones(self.num_pixels)
# Arguments of the basis
X = np.linspace(-1., 1., self.num_pixels)
# Retrieve the basis type
polynomial_basis = self.polynomial_bases[ odd_settings["polynomial_basis"] ]
# Adjusting button's settings
button = event.GetEventObject()
button.SetLabel (button._stop_label)
button.SetBackgroundColour('red')
button.Bind( wx.EVT_BUTTON, button._stop_method)
self.need_abort = False
#####################################################################
# Start scanning
with h5py.File (self.log_filename, 'a') as log_file :
for channel in self.channels :
# Move to a selected channel
self.DevSampleSwitcher.MoveToChannel(channel)
# abort, if requested
wx.Yield()
if self.need_abort : break
# Looping over pulse shapes
for scan_num, coeff in enumerate(poly_coeffs) :
# Calculate new phase
phase = polynomial_basis(coeff)(X)
# Set the pulse shape
self.DevPulseShaper.SetAmplPhase(max_ampl, phase)
# Save phase in radians
ampl, phase = self.DevPulseShaper.GetUnwrappedAmplPhase(max_ampl, phase)
if scan_num == 0 :
# Initialize the array
phases_rad = np.zeros( (len(poly_coeffs), phase.size), dtype=phase.dtype )
amplitudes = np.zeros_like(phases_rad)
amplitudes[:] = ampl.min()
# Save phase
phases_rad[scan_num] = phase
amplitudes[scan_num] = ampl
# abort, if requested
wx.Yield()
if self.need_abort : break
# Get spectrum
spectrum = self.GetSampleSpectrum(channel)
# Vertical binning
spectrum = ( spectrum.sum(axis=0) if len(spectrum.shape) == 2 else spectrum )
if scan_num == 0 :
# Initialize the array
spectra = np.zeros( (len(poly_coeffs), spectrum.size), dtype=spectrum.dtype )
spectra[:] = spectrum.min()
# Save the spectrum
spectra[scan_num] = spectrum
# Display the currently acquired data
try :
spectra_2d_img.SetData(spectra)
phases_rad_2d_img.SetData( phases_rad%(2*np.pi) )
#amplitudes_2d_img.SetData( amplitudes )
except NameError :
visvis.cla(); visvis.clf()
visvis.subplot(121)
spectra_2d_img = visvis.imshow(spectra, cm=visvis.CM_JET)
visvis.ylabel ('scans'); visvis.xlabel ('wavelegth')
visvis.title("spectral scan")
visvis.subplot(122)
phases_rad_2d_img = visvis.imshow( phases_rad%(2*np.pi), cm=visvis.CM_JET)
visvis.title("phase shapes")
#visvis.subplot(133)
#amplitudes_2d_img = visvis.imshow(amplitudes, cm=visvis.CM_JET)
#visvis.title("amplitudes")
# Save the data for the given channel
try : del log_file[ str(channel) ]
except KeyError : pass
channel_grp = log_file.create_group( str(channel) )
channel_grp["spectra"] = spectra
channel_grp["phases_rad"] = phases_rad
channel_grp["amplitudes"] = amplitudes
channel_grp["poly_coeffs"] = poly_coeffs
# Readjust buttons settings
self.StopScannning(event)
def GetDeltaScan (self, event) :
"""
Measure spectra by varying parameter delta in reference phase mask
"""
# Create pseudonyms of necessary devices
self.DevSpectrometer = self.parent.Spectrometer.dev
self.DevPulseShaper = self.parent.PulseShaper.dev
####################### Initiate devices #############################
# Initiate spectrometer
settings = self.parent.Spectrometer.GetSettings()
if self.DevSpectrometer.SetSettings(settings) == RETURN_FAIL : return
# Initiate pulse shaper
settings = self.parent.PulseShaper.GetSettings()
if self.DevPulseShaper.Initialize(settings) == RETURN_FAIL : return
# Get number of optimization variables
self.num_pixels = self.DevPulseShaper.GetParamNumber()
if self.num_pixels == RETURN_FAIL :
raise RuntimeError ("Optimization cannot be started since calibration file was not loaded")
miips_settings = self.GetSettings()
#####################################################################
# Get range of coefficient
coeff_range = np.linspace( miips_settings["coeff_min"], miips_settings["coeff_max"], miips_settings["coeff_num"] )
# Get reference phase based on the corrections already obtained
reference_phase, X, polynomial_basis = self.GetReferencePhase(miips_settings)
# Get new polynomial
new_coeffs = np.zeros(miips_settings["polynomial_order"] + 1)
new_coeffs[-1] = 1
current_polynomial = polynomial_basis(new_coeffs)(X)
# Chose max amplitude
max_ampl = miips_settings["max_ampl"]*np.ones(self.num_pixels)
# Adjusting button's settings
button = event.GetEventObject()
button.SetLabel (button._stop_label)
button.SetBackgroundColour('red')
button.Bind( wx.EVT_BUTTON, button._stop_method)
self.need_abort = False
for scan_num, coeff in enumerate(coeff_range) :
# Get current phase mask
current_phase = coeff*current_polynomial
current_phase += reference_phase
# Check for consistency
current_phase %= 1
# Set the pulse shape
self.DevPulseShaper.SetAmplPhase(max_ampl, current_phase)
wx.Yield()
# abort, if requested
if self.need_abort : break
# Get spectrum
spectrum = self.DevSpectrometer.AcquiredData()
# Vertical binning
spectrum = ( spectrum.sum(axis=0) if len(spectrum.shape) == 2 else spectrum )
try : spectral_scans
except NameError :
# Allocate space for spectral scans
spectral_scans = np.zeros( (coeff_range.size, spectrum.size), dtype=spectrum.dtype )
# Save spectrum
spectral_scans[ scan_num ] = spectrum
# Display the currently acquired data
try : spectral_scan_2d_img.SetData(spectral_scans)
except NameError :
visvis.cla(); visvis.clf();
spectral_scan_2d_img = visvis.imshow(spectral_scans, cm=visvis.CM_JET)
visvis.ylabel ('coefficeints')
visvis.xlabel ('wavelegth')
#######################################################
# Get current wavelength
wavelength = self.DevSpectrometer.GetWavelengths()
# Adding the scan to log
self.scan_log.append( {
"spectral_scans" : spectral_scans,
"reference_phase" : reference_phase,
"current_polynomial": current_polynomial,
"coeff_range" : coeff_range,
"wavelength" : wavelength
} )
# Plotting fit
visvis.cla(); visvis.clf();
################ Find the value of coeff such that it maximizes the total intensity of SHG
# Method 1: use polynomial filter
# Ignored not scanned parameter
spectral_sum = spectral_scans.sum(axis=1)
indx = np.nonzero(spectral_sum > 0)
# Fit the total spectral intensity with chosen polynomials
spectral_sum_fit = polynomial_basis.fit(coeff_range[indx], spectral_sum[indx] , 10)
# Find extrema of the polynomial fit
opt_coeff = spectral_sum_fit.deriv().roots()
# Find maximum
fit_max_sum_val = opt_coeff[ np.argmax(spectral_sum_fit(opt_coeff)) ].real
print "\n\nOptimal value of the coefficient (using the polynomial fit) is ", fit_max_sum_val
# Method 2: Use Gaussian filter
# Smoothing spectral scans
filtered_spectral_scans = gaussian_filter(spectral_scans, (2, 0.5) )
gauss_max_sum_val = coeff_range[ np.argmax(filtered_spectral_scans.sum(axis=1)) ]
print "\nOptimal value of the coefficient (using the Gaussian filter) is ", gauss_max_sum_val
# If the difference between methods is great then use the Gaussian filter
if abs(gauss_max_sum_val - fit_max_sum_val)/np.abs([gauss_max_sum_val, fit_max_sum_val]).max() > 0.3 :
max_sum_val = gauss_max_sum_val
else :
max_sum_val = fit_max_sum_val
self.current_coeff_val.SetValue( max_sum_val )
filtered_spectral_scans[ np.searchsorted(coeff_range, max_sum_val) ][0:-1:2] = spectral_scans.min()
################ Plotting results ####################
#spectral_scan_2d_img.SetData(spectral_scans)
#spectral_scan_2d_img.SetClim( spectral_scans.min(), spectral_scans.max() )
visvis.subplot(121)
visvis.title("Raw spectral scans")
visvis.imshow(spectral_scans, cm=visvis.CM_JET)
visvis.ylabel ('coefficeints'); visvis.xlabel ('wavelegth')
visvis.subplot(122)
visvis.title("Finding maximum")
visvis.imshow(filtered_spectral_scans, cm=visvis.CM_JET)
visvis.ylabel ('coefficeints'); visvis.xlabel ('wavelegth')
# Readjust buttons settings
self.StopScannning(event)
astro = vv.imread('astronaut.png').astype(np.float32)
astro = astro[100:-100, 100:-100, :]
# Smooth a bit
im = astro.copy()
im[1:, :, :] = astro[:-1, :, :]
im[:-1, :, :] += astro[1:, :, :]
im[:, :-1, :] += astro[:, 1:, :]
im[:, 1:, :] += astro[:, :-1, :]
im /= 4
# Prepare figure
vv.figure()
# Without color, with colormap
a1 = vv.subplot(121)
m1 = vv.surf(im[:, :, 0])
m1.colormap = vv.CM_HOT
vv.title('With colormap')
# With color
a2 = vv.subplot(122)
m2 = vv.surf(im[:, :, 0], im)
vv.title('With original texture')
# Flip y-axis, otherwise the image is upside down
a1.daspect = 1, -1, 1
a2.daspect = 1, -1, 1
# Enter mainloop
app = vv.use()
#if (y-circLoc[0])**2 + (x-circLoc[1])**2 < radius**2: # circles
if abs(y - circLoc[0]) + abs(
x - circLoc[1]) < radius * 1.1: # diamonds
im[y, x] += 1.0
# Add
ims.append(im)
INDEXMAP = {0: 1, 1: 2, 2: 4, 3: 3} # map index to subplot location
# Show images
fig = vv.figure(1)
vv.clf()
fig.position = 200, 200, 500, 500
for i in range(4):
j = INDEXMAP[i] # map index to subplot location
a = vv.subplot(2, 2, j)
vv.imshow(ims[i])
a.axis.visible = False
# vv.screenshot('c:/almar/projects/fourBlocks_initial.jpg', vv.gcf(), sf=2, bg='w')
## Register groupwise
# Init figure for registration
fig = vv.figure(2)
vv.clf()
fig.position = 200, 100, 900, 500
# Apply registration
reg = pirt.GravityRegistration(*ims)
# reg = pirt.DiffeomorphicDemonsRegistration(*ims)
# reg = pirt.ElastixGroupwiseRegistration(*ims)
a = a.GetAxes()
f.currentAxes = a
return a
# create axes in container
a = Axes(f)
c = a.parent
# calculate relative coordinates
dx, dy = 1.0/cols, 1.0/rows
y = int( nr / cols )
x = int( nr % cols )
# apply positions
c.position = dx*x, dy*y, dx, dy
a.position = 10, 10, -20, -20
# done
return a
if __name__ == "__main__":
f = vv.figure()
a1=vv.subplot(221); a1.cameraType = '2d'
a2=vv.subplot(224)
a3=vv.subplot(221)
a3=vv.subplot(333)
f.Draw()
print a1 is a3
if not os.path.isfile(fname):
# try loading from the resource dir
path = visvis.misc.getResourceDir()
fname2 = os.path.join(path, fname)
if os.path.isfile(fname2):
fname = fname2
else:
raise IOError("Mesh file '%s' does not exist." % fname)
# Use file extension to read file
if fname.lower().endswith('.stl'):
readFunc = vv.io.stl.StlReader.read
elif fname.lower().endswith('.obj'):
readFunc = vv.io.wavefront.WavefrontReader.read
elif fname.lower().endswith('.ssdf') or fname.lower().endswith('.bsdf'):
readFunc = ssdfRead
else:
raise ValueError('meshRead cannot determine file type.')
# Read
return readFunc(fname, check)
if __name__ == '__main__':
bm = meshRead('bunny.ssdf')
vv.figure(1); vv.clf()
a = vv.subplot(121)
m = vv.mesh(bm)
# try loading from the resource dir
path = visvis.misc.getResourceDir()
fname2 = os.path.join(path, fname)
if os.path.isfile(fname2):
fname = fname2
else:
raise IOError("Mesh file '%s' does not exist." % fname)
# Use file extension to read file
if fname.lower().endswith('.stl'):
readFunc = vv.io.stl.StlReader.read
elif fname.lower().endswith('.obj'):
readFunc = vv.io.wavefront.WavefrontReader.read
elif fname.lower().endswith('.ssdf') or fname.lower().endswith('.bsdf'):
readFunc = ssdfRead
else:
raise ValueError('meshRead cannot determine file type.')
# Read
return readFunc(fname, check)
if __name__ == '__main__':
bm = meshRead('bunny.ssdf')
vv.figure(1)
vv.clf()
a = vv.subplot(121)
m = vv.mesh(bm)
# Degrees of freedom per node.
dofsPerNode= 1
# Create mesh
coords, edof, dofs, bdofs, elementmarkers = cfm.createGmshMesh(geometry=g,
elType = elType,
elSizeFactor = 0.3,
dofsPerNode = dofsPerNode)
# ---- Visualise mesh -------------------------------------------------------
# Create two axes that are viewed from the same camera:
vv.figure()
a1 = vv.subplot(121)
a2 = vv.subplot(122)
cam = vv.cameras.ThreeDCamera()
a1.camera = a2.camera = cam
# Draw geometry and mesh
cfv.drawGeometry(g, axes=a1)
cfv.drawMesh(coords=coords, edof=edof, dofsPerNode=dofsPerNode, elType=elType, filled=False, axes=a2)
# Enter main loop
app = vv.use()
app.Create()
app.Run()
isovalue = 0.0
#
vol = np.empty((n,n,n), 'float32')
for iz in range(vol.shape[0]):
for iy in range(vol.shape[1]):
for ix in range(vol.shape[2]):
z, y, x = float(iz)*a+b, float(iy)*a+b, float(ix)*a+b
vol[iz,iy,ix] = ( (
(8*x)**2 + (8*y-2)**2 + (8*z)**2 + 16 - 1.85*1.85 ) * ( (8*x)**2 +
(8*y-2)**2 + (8*z)**2 + 16 - 1.85*1.85 ) - 64 * ( (8*x)**2 + (8*y-2)**2 )
) * ( ( (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
# Get surface meshes
bm1 = isosurface(vol, isovalue, 1, useClassic=True)
t0 = time.time()
bm2 = isosurface(vol, isovalue, 1)
print('finding surface took %1.0f ms' % (1000*(time.time()-t0)) )
# Show
vv.figure(1); vv.clf()
vv.subplot(121); vv.imshow(im); vv.plot(pp, ls='+', lc='r', lw=2)
a1=vv.subplot(222); m1=vv.mesh(bm1) #t=vv.volshow(vol)
a2=vv.subplot(224); m2=vv.mesh(bm2)
a1.camera = a2.camera
def __init__(self, im, grid_sampling=40):
# Store image
self._im = im
# Setup visualization
self._fig = fig = vv.figure()
self._a1 = a1 = vv.subplot(231);
self._a2 = a2 = vv.subplot(232);
self._a3 = a3 = vv.subplot(233);
self._a4 = a4 = vv.subplot(234);
self._a5 = a5 = vv.subplot(235);
self._a6 = a6 = vv.subplot(236);
# Text objects
self._text1 = vv.Label(fig)
self._text1.position = 5, 2
self._text2 = vv.Label(fig)
self._text2.position = 5, 20
# Move axes
a1.parent.position = 0.0, 0.1, 0.33, 0.45
a2.parent.position = 0.33, 0.1, 0.33, 0.45
a3.parent.position = 0.66, 0.1, 0.33, 0.45
a4.parent.position = 0.0, 0.55, 0.33, 0.45
a5.parent.position = 0.33, 0.55, 0.33, 0.45
a6.parent.position = 0.66, 0.55, 0.33, 0.45
# Correct axes, share camera
cam = vv.cameras.TwoDCamera()
for a in [a1, a2, a3, a4, a5, a6]:
a.axis.visible = False
a.camera = cam
# Show images
im0 = im*0
self._t1 = vv.imshow(im, axes=a1)
self._t2 = vv.imshow(im, axes=a2)
self._t3 = vv.imshow(im, axes=a3)
self._t4 = vv.imshow(im0, axes=a4)
self._t5 = vv.imshow(im0, axes=a5)
self._t6 = vv.imshow(im0, axes=a6)
# Init pointsets
self._pp1 = Pointset(2)
self._pp2 = Pointset(2)
self._active = None
self._lines = []
# Init lines to show all deformations
tmp = vv.Pointset(2)
self._line1 = vv.plot(tmp, ls='', ms='.', mc='c', axes=a2)
self._line2 = vv.plot(tmp, ls='+', lc='c', lw='2', axes=a2)
# Init grid properties
self._sampling = grid_sampling
self._levels = 5
self._multiscale = True
self._injective = 0.5
self._frozenedge = 1
self._forward = True
# Init grid
self.DeformationField = DeformationFieldForward
self._field1 = self.DeformationField(FieldDescription(self._im))
self._field2 = self.DeformationField(FieldDescription(self._im))
# Bind to events
a2.eventMouseDown.Bind(self.on_down)
a2.eventMouseUp.Bind(self.on_up)
a2.eventMotion.Bind(self.on_motion)
fig.eventKeyDown.Bind(self.on_key_down)
#a1.eventDoubleClick.Bind(self.OnDone)
# Apply
self.apply()
if resolution is None: resolution = 128 supportedImageFormats = ['.jpg', '.png'] supportedMeshFormats = ['.stl', '.ply', '.off', '.obj'] ext = os.path.splitext(fileName)[-1] if ext.lower() in supportedImageFormats: im = vv.imread(fileName) imgArray = imToGS(im) if absT is None: absT = 5 * max(imgArray.shape) / 100 relT = 0.5 T = (np.max(imgArray) + np.min(imgArray))/2 imgArrayT = (imgArray < T).astype(np.uint8) vv.figure() ax1 = vv.subplot(121) ax2 = vv.subplot(122) t1 = vv.imshow(im, axes=ax1) t2 = vv.imshow(imgArray, axes=ax2) app = vv.use() app.Run() P = mcTSystem() P.fromBinaryArray(imgArrayT) P.doThinning(absT, relT) result = P.cellArray[::2,::2].astype(np.uint8)*255 + 255 - 255*imgArrayT Image.fromarray(result).show() elif ext.lower() in supportedMeshFormats: P = mcTSystem() bm = vv.meshRead(fileName) m = vv.mesh(bm)
# use floats to prevent strides etc. uint8 caused crash on qt backend.
im = gl.glReadPixels(x, y, w, h, gl.GL_RGB, gl.GL_FLOAT)
# reshape, flip, and store
im.shape = h, w, 3
im = np.flipud(im)
# done
return im
if __name__ == '__main__':
# Prepare
f = vv.figure()
a1 = vv.subplot(211)
a2 = vv.subplot(212)
# Draw some data
vv.plot([2, 3, 4, 2, 4, 3], axes=a1)
f.DrawNow()
# Take snapshots
im1 = vv.getframe(f)
im2 = vv.getframe(a1)
# clear and show snapshots
a1.Clear()
a2.Clear()
vv.imshow(im1, axes=a1, clim=(0, 1))
vv.imshow(im2, axes=a2, clim=(0, 1))
l = vv.Line(axes, pp)
l.lw = kwargs['lineWidth']
l.lc = kwargs['lineColor']
l.ls = kwargs['lineStyle']
l.mw = kwargs['markerWidth']
l.mc = kwargs['markerColor']
l.ms = kwargs['markerStyle']
l.mew = kwargs['markerEdgeWidth']
l.mec = kwargs['markerEdgeColor']
l.alpha = alpha
## done...
if axesAdjust:
if axes.daspectAuto is None:
axes.daspectAuto = True
axes.cameraType = str(camDim)+'d'
axes.SetLimits()
axes.Draw()
return l
if __name__ == '__main__':
vv.figure()
vv.subplot(311)
vv.plot([1,3,1,4,1,5,1,6,1,7,6,5,4,3,2,1]) # Passing 1D data
vv.subplot(312)
vv.plot([3,4,6,7],[7,5,4,6]) # Passing 2D data
vv.subplot(313)
vv.plot([3,4,6,7],[7,5,4,6], [1,2,3,2]) # Passing 3D data
def subplot(*args):
"""Create a visvis subplot."""
return vv.subplot(*args)
rData.buffer = self.__ai.integrate2d(data.buffer, self.outshape[0], self.outshape[1], unit="r_mm", method="lut_ocl")[0]
return rData
extMgr = ctrl.externalOperation()
myOp = extMgr.addOp(Core.USER_LINK_TASK, "myTask", 0)
myTask = MyLink(10)
myOp.setLinkTask(myTask)
a = ctrl.acquisition()
a.setAcqNbFrames(0)
a.setAcqExpoTime(acqt)
ctrl.prepareAcq()
ctrl.startAcq()
while ctrl.getStatus().ImageCounters.LastImageReady < 1:
print(ctrl.getStatus())
time.sleep(0.5)
print(ctrl.getStatus())
raw_img = ctrl.ReadBaseImage().buffer
fai_img = ctrl.ReadImage().buffer
vv.figure()
rawplot = vv.subplot(121)
faiplot = vv.subplot(122)
rawtex = vv.imshow(raw_img, axes=rawplot)
faitex = vv.imshow(fai_img, axes=faiplot)
while 1:
rawtex.SetData(ctrl.ReadBaseImage().buffer)
faitex.SetData(ctrl.ReadImage().buffer)
time.sleep(acqt)
vv.processEvents()
#!/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()
import visvis as vv
app = vv.use()
# Load volume
vol = vv.volread("stent")
# 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
# Create colormap editor in first axes
cme = vv.ColormapEditor(vv.gcf(), *tt[3:])
# Run app
