def __init__(self, main_win):
super(VisVisWidget, self).__init__()
# self.app = vv.use()
self._vv_widget = vv.gcf()
self._vv_widget._widget.show()
self.main_win = main_win
self.create_gui()
def clf():
""" clf()
Clear current figure.
"""
f = vv.gcf()
f.Clear()
return f
def clf():
""" clf()
Clear current figure.
"""
f = vv.gcf()
f.Clear()
return f
def show_ctvolume(vol,
graph=None,
axis=None,
showVol='MIP',
clim=(0, 2500),
isoTh=250,
removeStent=True,
climEditor=False,
stripSize=6,
stripSizeZ=None):
""" Different ways to visualize the CT volume as reference
For '2D' clim (-550,500) often good range
"""
import visvis as vv
colormap = {
'r': [(0.0, 0.0), (0.17727272, 1.0)],
'g': [(0.0, 0.0), (0.27272728, 1.0)],
'b': [(0.0, 0.0), (0.34545454, 1.0)],
'a': [(0.0, 1.0), (1.0, 1.0)]
}
if axis is None:
axis = vv.gca()
axis.MakeCurrent()
if showVol == 'MIP':
t = vv.volshow(vol, clim=clim, renderStyle='mip')
elif showVol == 'ISO':
if removeStent == True:
vol = remove_stent_from_volume(
vol, graph, stripSize=stripSize,
stripSizeZ=stripSizeZ) # rings are removed for vis.
t = vv.volshow(vol, clim=clim, renderStyle='iso')
t.isoThreshold = isoTh
t.colormap = colormap
elif showVol == '2D':
t = vv.volshow2(vol)
t.clim = clim
# bind ClimEditor to figure
if climEditor:
if showVol == 'ISO':
c = _utils_GUI.IsoThEditor(axis)
else:
c = vv.ClimEditor(axis)
c.position = (10, 50)
# bind for show hide
fig = vv.gcf()
fig.eventKeyDown.Bind(
lambda event: _utils_GUI.ShowHideSlider(event, c))
print('****')
print('Use "s" to show/hide slider')
print('****')
return t
def volshow(*args, **kwargs):
""" volshow(vol, clim=None, cm=CM_GRAY, axesAdjust=True, axes=None)
Display a 3D image (a volume).
This is a convenience function that calls either volshow3() or
volshow2(). If the current system supports it (OpenGL version >= 2.0),
displays a 3D rendering (volshow3). Otherwise shows three slices
that can be moved interactively (volshow2).
Parameters
----------
vol : numpy array
The 3D image to visualize. Can be grayscale, RGB, or RGBA.
If the volume is an anisotropic array (vv.Aaray), the appropriate
scale and translate transformations are applied.
clim : 2-element tuple
The color limits to scale the intensities of the image. If not given,
the im.min() and im.max() are used (neglecting nan and inf).
cm : Colormap
Set the colormap to apply in case the volume is grayscale.
axesAdjust : bool
If axesAdjust==True, this function will call axes.SetLimits(), and set
the camera type to 3D. If daspectAuto has not been set yet, it is
set to False.
axes : Axes instance
Display the image in this axes, or the current axes if not given.
Any other keyword arguments are passed to either volshow2() or volshow3().
"""
# Make sure that a figure exists
vv.gcf()
# Test and run
if vv.settings.volshowPreference==3 and vv.misc.getOpenGlCapable(2.0):
return vv.volshow3(*args, **kwargs)
else:
return vv.volshow2(*args, **kwargs)
def volshow(*args, **kwargs):
""" volshow(vol, clim=None, cm=CM_GRAY, axesAdjust=True, axes=None)
Display a 3D image (a volume).
This is a convenience function that calls either volshow3() or
volshow2(). If the current system supports it (OpenGL version >= 2.0),
displays a 3D rendering (volshow3). Otherwise shows three slices
that can be moved interactively (volshow2).
Parameters
----------
vol : numpy array
The 3D image to visualize. Can be grayscale, RGB, or RGBA.
If the volume is an anisotropic array (vv.Aaray), the appropriate
scale and translate transformations are applied.
clim : 2-element tuple
The color limits to scale the intensities of the image. If not given,
the im.min() and im.max() are used (neglecting nan and inf).
cm : Colormap
Set the colormap to apply in case the volume is grayscale.
axesAdjust : bool
If axesAdjust==True, this function will call axes.SetLimits(), and set
the camera type to 3D. If daspectAuto has not been set yet, it is
set to False.
axes : Axes instance
Display the image in this axes, or the current axes if not given.
Any other keyword arguments are passed to either volshow2() or volshow3().
"""
# Make sure that a figure exists
vv.gcf()
# Test and run
if vv.settings.volshowPreference == 3 and vv.misc.getOpenGlCapable(2.0):
return vv.volshow3(*args, **kwargs)
else:
return vv.volshow2(*args, **kwargs)
def draw(figure=None, fast=False):
""" draw(figure=None, fast=False)
Makes the given figure (or the current figure if None) draw itself.
If fast is True, some wobjects can draw itself faster at reduced
quality.
"""
# Get figure
if figure is None:
figure = vv.gcf()
# Draw!
figure.Draw(fast)
def draw(figure=None, fast=False):
""" draw(figure=None, fast=False)
Makes the given figure (or the current figure if None) draw itself.
If fast is True, some wobjects can draw itself faster at reduced
quality.
"""
# Get figure
if figure is None:
figure = vv.gcf()
# Draw!
figure.Draw(fast)
def __init__(self, vol, direction, axes=None, clim=None):
self.direction = direction
# Store vol and init
if self.direction == 0:
self.vol = vol
elif self.direction == 1:
self.vol = np.transpose(vol, (1, 0, 2))
self.vol.origin = (vol.origin[1], vol.origin[0], vol.origin[2])
self.vol.sampling = (vol.sampling[1], vol.sampling[0],
vol.sampling[2])
elif self.direction == 2:
self.vol = np.transpose(vol, (2, 0, 1))
self.vol.origin = (vol.origin[2], vol.origin[0], vol.origin[1])
self.vol.sampling = (vol.sampling[2], vol.sampling[0],
vol.sampling[1])
else:
S('No valid input for direction, only 1,2 or 3 is possible')
self.slice = 0
# Prepare figure and axex
if axes is None:
self.a = vv.gca()
else:
self.a = axes
self.f = vv.gcf()
# Create slice in 2D texture
if clim:
self.t = vv.imshow(self.vol[self.round_slice, :, :],
clim=clim,
axes=self.a)
else:
self.t = vv.imshow(self.vol[self.round_slice, :, :], axes=self.a)
# Bind
self.a.eventScroll.Bind(self.on_scroll)
self.eventPositionUpdate = vv.events.BaseEvent(self)
axes.eventMouseDown.Bind(self.on_click)
# Fig properties
self.a.bgcolor = [0, 0, 0]
self.a.axis.visible = False
self.a.showAxis = False
def draw(figure=None, fast=False):
""" draw(figure=None, fast=False)
Makes the given figure (or the current figure if None) draw itself.
If fast is True, some wobjects can draw itself faster at reduced
quality.
This function is now more or less deprecated; visvis is designed to
invoke a draw whenever necessary.
"""
# Get figure
if figure is None:
figure = vv.gcf()
# Draw!
figure.Draw(fast)
def gca():
""" gca()
Get the current axes in the current figure. If there is
no axes, an Axes instance is created. To make an axes current,
use Axes.MakeCurrent().
See also gcf(), Figure.MakeCurrent(), Figure.currentAxes
"""
f = vv.gcf()
a = f.currentAxes
if not a:
# create axes
a = vv.Axes(f)
#a.position = 2, 2, -4, -4
a.position = 10, 10, -20, -20
return a
def draw(figure=None, fast=False):
""" draw(figure=None, fast=False)
Makes the given figure (or the current figure if None) draw itself.
If fast is True, some wobjects can draw itself faster at reduced
quality.
This function is now more or less deprecated; visvis is designed to
invoke a draw whenever necessary.
"""
# Get figure
if figure is None:
figure = vv.gcf()
# Draw!
figure.Draw(fast)
def gca():
""" gca()
Get the current axes in the current figure. If there is
no axes, an Axes instance is created. To make an axes current,
use Axes.MakeCurrent().
See also gcf(), Figure.MakeCurrent(), Figure.currentAxes
"""
f = vv.gcf()
a = f.currentAxes
if not a:
# create axes
a = vv.Axes(f)
#a.position = 2, 2, -4, -4
a.position = 10, 10, -20, -20
return a
def set_mesh(self, mesh):
vv.clf()
self._vv_widget = vv.gcf()
self._vv_widget._widget.show()
self.main_win.setCentralWidget(self.widget())
if mesh:
v_mesh = mesh.to_visvis_mesh()
v_mesh.faceColor = 'y'
v_mesh.edgeShading = 'plain'
v_mesh.edgeColor = (0, 0, 1)
axes = vv.gca()
if axes.daspectAuto is None:
axes.daspectAuto = False
axes.SetLimits()
axes.legend = 'X', 'Y', 'Z'
axes.axis.showGrid = True
axes.axis.xLabel = 'X'
axes.axis.yLabel = 'Y'
axes.axis.zLabel = 'Z'
def __init__(self,
fig=None,
filename=None,
dirsave=None,
fileformat='avi',
frameRate=None):
""" fig or axes can be given. gif swf or avi possible
framerate to save depends on graphics card pc. default is 10fps, if faster than real world, use 5-7fps
"""
# import os
# import imageio
# import visvis as vv
# import datetime
# from stentseg.utils.datahandling import select_dir
# self.os = os
# self.imageio = imageio
# self.vv = vv
# self.datetime = datetime
self.r = None
self.frameRate = frameRate
if fig is None:
self.fig = vv.gcf()
else:
self.fig = fig
self.filename = filename
self.fileformat = fileformat
if dirsave is None:
self.dirsave = select_dir(r'C:\Users\Maaike\Desktop',
r'D:\Profiles\koenradesma\Desktop')
else:
self.dirsave = dirsave
print(
'"recordMovie" active, use r (rec), t (stop), y (continue), m (save), q (clear)'
)
# Bind eventhandler record
self.fig.eventKeyUp.Bind(self.record)
def subplot(*args):
""" subplot(ncols, nrows, nr)
Create or return axes in current figure. Note that subplot(322) is the
same as subplot(3,2,2).
Parameters
----------
ncols : int
The number of columns to devide the figure in.
nrows : int
The number of rows to devide the figure in.
nr : int
The subfigure number on the grid specified by ncols and nrows.
Should be at least one. subplot(221) is the top left. subplot(222)
is the top right.
Notes
-----
It is checked whether (the center of) an axes is present at the
specified grid location. If so, that axes is returned. Otherwise
a new axes is created at that location.
"""
# parse input
if len(args)==1:
tmp = args[0]
if tmp>999 or tmp<111:
raise ValueError("Invalid cols/rows/nr specified.")
rows = tmp // 100
tmp = tmp % 100
cols = tmp // 10
tmp = tmp % 10
nr = tmp
elif len(args)==3:
rows, cols, nr = args
else:
raise ValueError("Invalid number of cols/rows/nr specified.")
# check if ok
if nr<=0 or cols<=0 or rows<=0:
raise ValueError("Invalid cols/rows/nr: all bust be >0.")
if nr > cols*rows:
raise ValueError("Invalid nr: there are not so many positions.")
# init
f = vv.gcf()
nr = nr-1
# check if an axes is there
for a in f._children:
if isinstance(a, AxesContainer):
n = laysin( cols, rows, getcenter(f, a) )
if n == nr:
# make current and return
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
and exported to gif/swf/avi.
This is not an interactive example, but a script.
"""
import visvis as vv
# Create something to show, let's show a red teapot!
mesh = vv.solidTeapot()
mesh.faceColor = 'r'
# Prepare
Nangles = 36
a = vv.gca()
f = vv.gcf()
rec = vv.record(a)
# Rotate camera
for i in range(Nangles):
a.camera.azimuth = 360 * float(i) / Nangles
if a.camera.azimuth > 180:
a.camera.azimuth -= 360
a.Draw() # Tell the axes to redraw
f.DrawNow() # Draw the figure NOW, instead of waiting for GUI event loop
# Export
rec.Stop()
rec.Export('teapot.gif')
""" NOTES
D = {0:-3,1:-2,2:-1,3:None}
slicey = slice(iy, D[iy])
slicex = slice(ix, D[ix])
# Get contribution and add to temp image
imTmp += w * im2[slicey, slicex, :]
# Store contributions
D = [-1 for tmp in range(s)]; D.append(None)
slicey = slice(dy,D[dy],s)
slicex = slice(dx,D[dx],s)
im3[slicey, slicex, :] = imTmp
# Correct for overshoot
im3[im3>1]=1
im3[im3<0]=0
# Store image to file
if filename is not None:
vv.imwrite(filename, im3, format)
else:
return im3
if __name__ == '__main__':
# Make plot
vv.plot([1,2,3,1,4,2,3], ms='.')
# Take screenshot, twice enlarged, on a white background
vv.screenshot('screenshot.jpg', vv.gcf(), sf=2, bg='w')
def screenshot(filename, ob=None, sf=2, bg=None, format=None, tension=-0.25):
""" screenshot(filename, ob=None sf=2, bg=None, format=None)
Make a screenshot and store it to a file, using cubic interpolation
to increase the resolution (and quality) of the image.
Parameters
----------
filename : string
The name of the file to store the screenshot to. If filename is None,
the interpolated image is returned as a numpy array.
ob : Axes, AxesContainer, or Figure
The object to take the screenshot of. The AxesContainer can be
obtained using vv.gca().parent. It can be usefull to take a
screeshot of an axes including thickmarks and labels.
sf : integer
The scale factor. The image is increased in size with this factor,
using a high quality interpolation method. A factor of 2 or 3
is recommended; the image quality does not improve with higher
factors. If using a sf larger than 1, the image is best saved in
the jpg format.
bg : 3-element tuple or char
The color of the background. If bg is given, ob.bgcolor is set to
bg before the frame is captured.
format : string
The format for the screenshot to be saved in. If not given, the
format is deduced from the filename.
Notes
-----
Uses vv.getframe(ob) to obtain the image in the figure or axes.
That image is interpolated with the given scale factor (sf) using
bicubic interpolation. Then vv.imwrite(filename, ..) is used to
store the resulting image to a file.
Rationale
---------
We'd prefer storing screenshots of plots as vector (eps) images, but
the nature of OpenGl prevents this. By applying high quality
interpolation (using a cardinal spline), the resolution can be increased,
thereby significantly improving the visibility/smoothness for lines
and fonts. Use this to produce publication quality snapshots of your
plots.
"""
# The tension controls the
# responsivenes of the filter. The more negative, the more overshoot,
# but the more it is capable to make for example font glyphs smooth.
# If tension is 0, the interpolator is a Catmull-Rom spline.
# Scale must be integer
s = int(sf)
# Object given?
if ob is None:
ob = vv.gcf()
# Get figure
fig = ob
if not hasattr(ob, 'DrawNow'):
fig = ob.GetFigure()
# Get object to set background of
bgob = ob
# Set background
if bg and fig:
bgOld = bgob.bgcolor
bgob.bgcolor = bg
fig.DrawNow()
# Obtain image
im1 = vv.getframe(ob)
shape1 = im1.shape
# Return background
if bg and fig:
bgob.bgcolor = bgOld
fig.Draw()
# Pad original image, so we have no trouble at the edges
shape2 = shape1[0]+2, shape1[1]+2, 3
im2 = np.zeros(shape2, dtype=np.float32) # Also make float
im2[1:-1,1:-1,:] = im1
im2[0,:,:] = im2[1,:,:]
im2[-1,:,:] = im2[-2,:,:]
im2[:,0,:] = im2[:,1,:]
im2[:,-1,:] = im2[:,-2,:]
# Create empty new image. It is sized by the scaleFactor,
# but the last row is not.
shape3 = (shape1[0]-1)*s+1, (shape1[1]-1)*s+1, 3
im3 = np.zeros(shape3, dtype=np.float32)
# Fill in values!
for dy in range(s+1):
for dx in range(s+1):
# Get interpolation fraction and coefs
ty = float(dy)/s
tx = float(dx)/s
cy = getCardinalSplineCoefs(ty, tension)
cx = getCardinalSplineCoefs(tx, tension)
# Create tmp image to which we add the contributions
# Note that this image is 1 pixel smaller in each dimension.
# The last pixel is filled because dy and dx iterate INCLUDING s.
shapeTmp = shape1[0]-1, shape1[1]-1, 3
imTmp = np.zeros(shapeTmp, dtype=np.float32)
# Collect all 16 neighbours and weight them apropriately
for iy in range(4):
for ix in range(4):
# Get weight
w = cy[iy]*cx[ix]
if w==0:
continue
# Get slice. Note that we start at 0,1,2,3 rather than
# -1,0,1,2, because we padded the image.
D = {0:-3,1:-2,2:-1,3:None}
slicey = slice(iy, D[iy])
slicex = slice(ix, D[ix])
# Get contribution and add to temp image
imTmp += w * im2[slicey, slicex, :]
# Store contributions
D = [-1 for tmp in range(s)]; D.append(None)
slicey = slice(dy,D[dy],s)
slicex = slice(dx,D[dx],s)
im3[slicey, slicex, :] = imTmp
# Correct for overshoot
im3[im3>1]=1
im3[im3<0]=0
# Store image to file
if filename is not None:
vv.imwrite(filename, im3, format)
else:
return im3
# Create visvis application app = vv.use() app.Create() # Create main window frame and set a resolution. main_w = MainWindow() main_w.resize(700, 320) # Create the 3 D shape model as a mesh. verticesPerFace equals 3 since triangles define the # mesh's surface in this case shape_obj = vv.mesh(vertices=VERTICES, faces=faces, verticesPerFace=3) shape_obj.specular = 0.0 shape_obj.diffuse = 0.9 # Get figure figure = vv.gcf() # Get axes objects and set figure parameters axes = vv.gca() axes.bgcolor = (0, 0, 0) axes.axis.showGrid = False axes.axis.visible = False # Set camera settings # axes.camera = '3d' axes.camera.fov = 60 axes.camera.zoom = 0.1 # Turn off the main light axes.light0.Off()
def subplot(*args):
""" subplot(ncols, nrows, nr)
Create or return axes in current figure. Note that subplot(322) is the
same as subplot(3,2,2).
Parameters
----------
ncols : int
The number of columns to devide the figure in.
nrows : int
The number of rows to devide the figure in.
nr : int
The subfigure number on the grid specified by ncols and nrows.
Should be at least one. subplot(221) is the top left. subplot(222)
is the top right.
Notes
-----
It is checked whether (the center of) an axes is present at the
specified grid location. If so, that axes is returned. Otherwise
a new axes is created at that location.
"""
# parse input
if len(args) == 1:
tmp = args[0]
if tmp > 999 or tmp < 111:
raise ValueError("Invalid cols/rows/nr specified.")
rows = tmp // 100
tmp = tmp % 100
cols = tmp // 10
tmp = tmp % 10
nr = tmp
elif len(args) == 3:
rows, cols, nr = args
else:
raise ValueError("Invalid number of cols/rows/nr specified.")
# check if ok
if nr <= 0 or cols <= 0 or rows <= 0:
raise ValueError("Invalid cols/rows/nr: all bust be >0.")
if nr > cols * rows:
raise ValueError("Invalid nr: there are not so many positions.")
# init
f = vv.gcf()
nr = nr - 1
# check if an axes is there
for a in f._children:
if isinstance(a, AxesContainer):
n = laysin(cols, rows, getcenter(f, a))
if n == nr:
# make current and return
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
#vol[i,j,k] = (2.0/N)*(i-N/2)*(i-N/2) - (1/N)*(j-N/2)*(j-N/2) - (k-N/2) # Paraboloide hiperbolico #vol[i,j,k] = cos(i) + cos(j) + cos(k) # Triply periodic minimal surface (Schwarz) # show #impl_surf = vv.volshow(vol, renderStyle='iso') # try the differtent render styles, for examample # "t.renderStyle='iso'" or "t.renderStyle='ray'" # If the drawing hangs, your video drived decided to render in software mode. # This is unfortunately (as far as I know) not possible to detect. # It might help if your data is shaped a power of 2. #impl_surf.isoThreshold = 0.0 #impl_surf.colormap = vv.CM_WINTER # Create colormap editor wibject. #vv.ColormapEditor(axs) # # Graficación # axs = vv.gca() # "Get Current Axes" #axs.bgcolor = (0.0, 0.0, 0.0) axs.camera.fov = 60 fig = vv.gcf() # "Get Current Figure" fig._widget.showFullScreen() # Pantalla completa, para RaspberryPi app.Run() # Corre aplicación/ventana
def converge_to_centre(pp, c, nDirections=5, maxRadius=50, pauseTime=0):
""" converge_to_centre(pp, c)
Given a set of points and an initial center point c,
will find a better estimate of the center.
Returns (c, L), with L indices in pp that were uses to fit
the final circle.
"""
# Shorter names
N = nDirections
pi = np.pi
# Init point to return on error
ce = Point(0,0)
ce.r = 0
# Are there enough points?
if len(pp) < 3:
return ce, []
# Init a pointset of centers we've has so far
cc = Pointset(2)
# Init list with vis objects (to be able to delete them)
showObjects = []
if pauseTime:
fig = vv.gcf()
while c not in cc:
# Add previous center
cc.append(c)
# Calculate distances and angles
dists = c.distance(pp)
angs = c.angle2(pp)
# Get index of closest points
i, = np.where(dists==dists.min())
i = iClosest = int(i[0])
# Offset the angles with the angle relative to the closest point.
refAng = angs[i]
angs = subtract_angles(angs, refAng)
# Init L, the indices to the closest point in each direction
L = []
# Get closest point on N directions
for angle in [float(angnr)/N*2*pi for angnr in range(N)]:
# Get indices of points that are in this direction
dangs = subtract_angles(angs, angle)
I, = np.where(np.abs(dangs) < pi/N )
# Select closest
if len(I):
distSelection = dists[I]
minDist = distSelection.min()
J, = np.where(distSelection==minDist)
if len(J) and minDist < maxRadius:
L.append( int(I[J[0]]) )
# Check if ok
if len(L) < 3:
return ce, []
# Remove spurious points (points much furter away that the 3 closest)
distSelection = dists[L]
tmp = [d for d in distSelection]
d3 = sorted(tmp)[2] # Get distance of 3th closest point
I, = np.where(distSelection < d3*2)
L = [L[i] for i in I]
# Select points
ppSelect = Pointset(2)
for i in L:
ppSelect.append(pp[i])
# Refit circle
cnew = fit_cirlce(ppSelect,False)
if cnew.r==0:
return ce, []
# Show
if pauseTime>0:
# Delete
for ob in showObjects:
ob.Destroy()
# Plot center and new center
ob1 = vv.plot(c, ls='', ms='x', mc='r', mw=10, axesAdjust=0)
ob2 = vv.plot(cnew, ls='', ms='x', mc='r', mw=10, mew=0, axesAdjust=0)
# Plot selection points
ob3 = vv.plot(ppSelect, ls='', ms='.', mc='y', mw=10, axesAdjust=0)
# Plot lines dividing the directions
tmpSet1 = Pointset(2)
tmpSet2 = Pointset(2)
for angle in [float(angnr)/N*2*pi for angnr in range(N)]:
angle = -subtract_angles(angle, refAng)
dx, dy = np.cos(angle), np.sin(angle)
tmpSet1.append(c.x, c.y)
tmpSet1.append(c.x+dx*d3*2, c.y+dy*d3*2)
for angle in [float(angnr+0.5)/N*2*pi for angnr in range(N)]:
angle = -subtract_angles(angle, refAng)
dx, dy = np.cos(angle), np.sin(angle)
tmpSet2.append(c.x, c.y)
tmpSet2.append(c.x+dx*d3*2, c.y+dy*d3*2)
ob4 = vv.plot(tmpSet1, lc='y', ls='--', axesAdjust=0)
ob5 = vv.plot(tmpSet2, lc='y', lw=3, axesAdjust=0)
# Store objects and wait
showObjects = [ob1,ob2,ob3,ob4,ob5]
fig.DrawNow()
time.sleep(pauseTime)
# Use new
c = cnew
# Done
for ob in showObjects:
ob.Destroy()
return c, L
def showModelsStatic(ptcode,codes, vols, ss, mm, vs, showVol, clim, isoTh, clim2,
clim2D, drawMesh=True, meshDisplacement=True, drawModelLines=True,
showvol2D=False, showAxis=False, drawVessel=False, vesselType=1,
meshColor=None, **kwargs):
""" show one to four models in multipanel figure.
Input: arrays of codes, vols, ssdfs; params from show_models_static
Output: axes, colorbars
"""
# init fig
f = vv.figure(1); vv.clf()
# f.position = 0.00, 22.00, 1920.00, 1018.00
mw = 5
if drawMesh == True:
lc = 'w'
meshColor = meshColor
else:
lc = 'g'
# create subplots
if isinstance(codes, str): # if 1 ctcode, otherwise tuple of strings
a1 = vv.subplot(111)
axes = [a1]
elif codes == (codes[0],codes[1]):
a1 = vv.subplot(121)
a2 = vv.subplot(122)
axes = [a1,a2]
elif codes == (codes[0],codes[1], codes[2]):
a1 = vv.subplot(131)
a2 = vv.subplot(132)
a3 = vv.subplot(133)
axes = [a1,a2,a3]
elif codes == (codes[0],codes[1], codes[2], codes[3]):
a1 = vv.subplot(141)
a2 = vv.subplot(142)
a3 = vv.subplot(143)
a4 = vv.subplot(144)
axes = [a1,a2,a3,a4]
elif codes == (codes[0],codes[1], codes[2], codes[3], codes[4]):
a1 = vv.subplot(151)
a2 = vv.subplot(152)
a3 = vv.subplot(153)
a4 = vv.subplot(154)
a5 = vv.subplot(155)
axes = [a1,a2,a3,a4,a5]
else:
a1 = vv.subplot(111)
axes = [a1]
for i, ax in enumerate(axes):
ax.MakeCurrent()
vv.xlabel('x (mm)');vv.ylabel('y (mm)');vv.zlabel('z (mm)')
vv.title('Model for LSPEAS %s - %s' % (ptcode[7:], codes[i]))
t = show_ctvolume(vols[i], ss[i].model, axis=ax, showVol=showVol, clim=clim, isoTh=isoTh, **kwargs)
label = pick3d(ax, vols[i])
if drawModelLines == True:
ss[i].model.Draw(mc='b', mw = mw, lc=lc)
if showvol2D:
for i, ax in enumerate(axes):
t2 = vv.volshow2(vols[i], clim=clim2D, axes=ax)
cbars = [] # colorbars
if drawMesh:
for i, ax in enumerate(axes):
m = vv.mesh(mm[i], axes=ax)
if meshDisplacement:
m.clim = clim2
m.colormap = vv.CM_JET #todo: use colormap Viridis or Magma as JET is not linear (https://bids.github.io/colormap/)
cb = vv.colorbar(ax)
cbars.append(cb)
elif meshColor is not None:
if len(meshColor) == 1:
m.faceColor = meshColor[0] # (0,1,0,1)
else:
m.faceColor = meshColor[i]
else:
m.faceColor = 'g'
if drawVessel:
for i, ax in enumerate(axes):
v = showVesselMesh(vs[i], ax, type=vesselType)
for ax in axes:
ax.axis.axisColor = 1,1,1
ax.bgcolor = 25/255,25/255,112/255 # midnightblue
# http://cloford.com/resources/colours/500col.htm
ax.daspect = 1, 1, -1 # z-axis flipped
ax.axis.visible = showAxis
# set colorbar position
for cbar in cbars:
p1 = cbar.position
cbar.position = (p1[0], 20, p1[2], 0.98) # x,y,w,h
# bind rotate view and view presets [1,2,3,4,5]
f = vv.gcf()
f.eventKeyDown.Bind(lambda event: _utils_GUI.RotateView(event,axes,axishandling=False) )
f.eventKeyDown.Bind(lambda event: _utils_GUI.ViewPresets(event,axes) )
return axes, cbars
vv.xlabel('x'), vv.ylabel('y'), vv.zlabel('z')
vv.title('Overlay')
a2.daspect = 1, 1, -1
a3 = vv.subplot(223)
vv.volshow(volTr, clim=clim)
vv.xlabel('x'), vv.ylabel('y'), vv.zlabel('z')
vv.title(
'Im2:Original transformed (DataDressedInterpolated u_\magnitude {})'
.format(mat2['u_magnitude'][0][0]))
a3.daspect = 1, 1, -1
a4 = vv.subplot(224)
a4.daspect = 1, 1, -1
c = vv.ClimEditor(vv.gcf())
a1.camera = a2.camera = a3.camera = a4.camera
# Remove .mat for savename and loading below
if fileTr.endswith('.mat'):
fileTr = fileTr.replace('.mat', '')
## Do registration
if True:
t0 = time.time()
# set final scale based on pixelwidth (scale should be =<0.5*pixelwidth)
if max(sampling2) > 2:
final_scale = max(sampling2) / 2
def screenshot(filename, ob=None, sf=2, bg=None, format=None, tension=-0.25):
""" screenshot(filename, ob=None sf=2, bg=None, format=None)
Make a screenshot and store it to a file, using cubic interpolation
to increase the resolution (and quality) of the image.
Parameters
----------
filename : string
The name of the file to store the screenshot to. If filename is None,
the interpolated image is returned as a numpy array.
ob : Axes, AxesContainer, or Figure
The object to take the screenshot of. The AxesContainer can be
obtained using vv.gca().parent. It can be usefull to take a
screeshot of an axes including thickmarks and labels.
sf : integer
The scale factor. The image is increased in size with this factor,
using a high quality interpolation method. A factor of 2 or 3
is recommended; the image quality does not improve with higher
factors. If using a sf larger than 1, the image is best saved in
the jpg format.
bg : 3-element tuple or char
The color of the background. If bg is given, ob.bgcolor is set to
bg before the frame is captured.
format : string
The format for the screenshot to be saved in. If not given, the
format is deduced from the filename.
Notes
-----
Uses vv.getframe(ob) to obtain the image in the figure or axes.
That image is interpolated with the given scale factor (sf) using
bicubic interpolation. Then vv.imwrite(filename, ..) is used to
store the resulting image to a file.
Rationale
---------
We'd prefer storing screenshots of plots as vector (eps) images, but
the nature of OpenGl prevents this. By applying high quality
interpolation (using a cardinal spline), the resolution can be increased,
thereby significantly improving the visibility/smoothness for lines
and fonts. Use this to produce publication quality snapshots of your
plots.
"""
# The tension controls the
# responsivenes of the filter. The more negative, the more overshoot,
# but the more it is capable to make for example font glyphs smooth.
# If tension is 0, the interpolator is a Catmull-Rom spline.
# Scale must be integer
s = int(sf)
# Object given?
if ob is None:
ob = vv.gcf()
# Get figure
fig = ob
if not hasattr(ob, 'DrawNow'):
fig = ob.GetFigure()
# Get object to set background of
bgob = ob
# Set background
if bg and fig:
bgOld = bgob.bgcolor
bgob.bgcolor = bg
fig.DrawNow()
# Obtain image
im1 = vv.getframe(ob)
shape1 = im1.shape
# Return background
if bg and fig:
bgob.bgcolor = bgOld
fig.Draw()
# Pad original image, so we have no trouble at the edges
shape2 = shape1[0] + 2, shape1[1] + 2, 3
im2 = np.zeros(shape2, dtype=np.float32) # Also make float
im2[1:-1, 1:-1, :] = im1
im2[0, :, :] = im2[1, :, :]
im2[-1, :, :] = im2[-2, :, :]
im2[:, 0, :] = im2[:, 1, :]
im2[:, -1, :] = im2[:, -2, :]
# Create empty new image. It is sized by the scaleFactor,
# but the last row is not.
shape3 = (shape1[0] - 1) * s + 1, (shape1[1] - 1) * s + 1, 3
im3 = np.zeros(shape3, dtype=np.float32)
# Fill in values!
for dy in range(s + 1):
for dx in range(s + 1):
# Get interpolation fraction and coefs
ty = float(dy) / s
tx = float(dx) / s
cy = getCardinalSplineCoefs(ty, tension)
cx = getCardinalSplineCoefs(tx, tension)
# Create tmp image to which we add the contributions
# Note that this image is 1 pixel smaller in each dimension.
# The last pixel is filled because dy and dx iterate INCLUDING s.
shapeTmp = shape1[0] - 1, shape1[1] - 1, 3
imTmp = np.zeros(shapeTmp, dtype=np.float32)
# Collect all 16 neighbours and weight them apropriately
for iy in range(4):
for ix in range(4):
# Get weight
w = cy[iy] * cx[ix]
if w == 0:
continue
# Get slice. Note that we start at 0,1,2,3 rather than
# -1,0,1,2, because we padded the image.
D = {0: -3, 1: -2, 2: -1, 3: None}
slicey = slice(iy, D[iy])
slicex = slice(ix, D[ix])
# Get contribution and add to temp image
imTmp += w * im2[slicey, slicex, :]
# Store contributions
D = [-1 for tmp in range(s)]
D.append(None)
slicey = slice(dy, D[dy], s)
slicex = slice(dx, D[dx], s)
im3[slicey, slicex, :] = imTmp
# Correct for overshoot
im3[im3 > 1] = 1
im3[im3 < 0] = 0
# Store image to file
if filename is not None:
vv.imwrite(filename, im3, format)
else:
return im3
tex3d.visible = False
# VesselMeshes
vesselVisMesh1 = axes1.wobjects[4]
vesselVisMesh1.cullFaces = "front" # Show the back
# vesselVisMesh2 = vv.Mesh(axes1, *vesselMesh.get_vertices_and_faces())
vesselVisMesh2 = vv.Mesh(axes1, np.zeros((6, 3), np.float32),
np.zeros((3, 3), np.int32))
vesselVisMesh2.cullFaces = "back"
vesselVisMesh2.faceColor = "red"
# Show the centerline
vv.plot(centerline, ms='.', ls='', mw=8, mc='b', alpha=0.5)
# Initialize 2D view
axes2 = vv.Axes(vv.gcf())
axes2.position = 0.65, 0.05, 0.3, 0.4
axes2.daspectAuto = False
axes2.camera = '2d'
axes2.axis.showGrid = True
axes2.axis.axisColor = 'k'
# Initialize axes to put widgets and labels in
container = vv.Wibject(vv.gcf())
container.position = 0.65, 0.5, 0.3, 0.5
# Create labels to show measurements
labelpool = []
for i in range(16):
label = vv.Label(container)
label.fontSize = 11
#Use the gradient operator on the velocity array: gradient(m)[0]
#Makes the velocity be on the columns instead of rows.
if(self.vMags == None):
self.velocityMag()
a = np.gradient(self.vels,1/self.fs)[0]
self.aMags = np.linalg.norm(a,axis=1)
return self.aMags
def peakAccelMag(self):
if(self.vMags == None):
self.velocityMag()
peakA = max(self.aMags)
return peakA
@staticmethod
def resetSensorCount():
Sensor.numSensors = 0
if(__name__ == '__main__'):
figure = vv.gcf()
axes = vv.gca()
audiofile = "C:/Data/05_ENGL_F_words6.wav"
kinfile = "C:/Data/05_ENGL_F_words6_BPC.tsv"
data = np.genfromtxt(unicode(kinfile), skip_header = 1, delimiter = '\t')
newSensor = Sensor(data[:,14:21], axes, 'Upper Lip','UL', 400)
newSensor.updateDataAndText(1000)
newSensor.accelerationMag()
D = {0: -3, 1: -2, 2: -1, 3: None}
slicey = slice(iy, D[iy])
slicex = slice(ix, D[ix])
# Get contribution and add to temp image
imTmp += w * im2[slicey, slicex, :]
# Store contributions
D = [-1 for tmp in range(s)]
D.append(None)
slicey = slice(dy, D[dy], s)
slicex = slice(dx, D[dx], s)
im3[slicey, slicex, :] = imTmp
# Correct for overshoot
im3[im3 > 1] = 1
im3[im3 < 0] = 0
# Store image to file
if filename is not None:
vv.imwrite(filename, im3, format)
else:
return im3
if __name__ == '__main__':
# Make plot
vv.plot([1, 2, 3, 1, 4, 2, 3], ms='.')
# Take screenshot, twice enlarged, on a white background
vv.screenshot('screenshot.jpg', vv.gcf(), sf=2, bg='w')
# The full license can be found in 'license.txt'.
from visvis import BaseFigure
import visvis as vv
def gcf():
""" gcf()
Get the current figure. If there is no figure yet, figure() is
called to create one. To make a figure current,
use Figure.MakeCurrent().
See also gca()
"""
if not BaseFigure._figures:
# no figure yet
return vv.figure()
nr = BaseFigure._currentNr
if not nr in BaseFigure._figures:
# erroneous nr
nr = list(BaseFigure._figures.keys())[0]
BaseFigure._currentNr = nr
return BaseFigure._figures[nr]
if __name__ == '__main__':
fig = vv.gcf()
for deform in deforms_forward] # get backward mapping
# Start vis
f = vv.figure(nr)
vv.clf()
if nr == 1:
f.position = 8.00, 30.00, 667.00, 690.00
else:
f.position = 691.00, 30.00, 667.00, 690.00
a = vv.gca()
a.axis.axisColor = 1, 1, 1
a.axis.visible = False
a.bgcolor = 0, 0, 0
a.daspect = 1, 1, -1
vv.title('Model for LSPEAS %s - %s' % (ptcode[7:], ctcode))
vv.ColormapEditor(vv.gcf())
# Setup motion container
dt = DeformableTexture3D(a, vol)
dt.clim = 0, 3000
dt.isoThreshold = 300
dt.renderStyle = 'iso' # iso or mip work well
dt.SetDeforms(*[list(reversed(deform)) for deform in deforms_backward])
dt.colormap = {
'g': [(0.0, 0.0), (0.33636364, 1.0)],
'b': [(0.0, 0.0), (0.49545455, 1.0)],
'a': [(0.0, 1.0), (1.0, 1.0)],
'r': [(0.0, 0.0), (0.22272727, 1.0)]
}
# Set limits and play!
from visvis import BaseFigure
import visvis as vv
def gcf():
""" gcf()
Get the current figure. If there is no figure yet, figure() is
called to create one. To make a figure current,
use Figure.MakeCurrent().
See also gca()
"""
if not BaseFigure._figures:
# no figure yet
return vv.figure()
nr = BaseFigure._currentNr
if not nr in BaseFigure._figures:
# erroneous nr
nr = list(BaseFigure._figures.keys())[0]
BaseFigure._currentNr = nr
return BaseFigure._figures[nr]
if __name__ == '__main__':
fig = vv.gcf()
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
app.Create()
app.Run()
# Zoom
axes.SetLimits(margin=0.0)
axes.SetLimits(margin=0.0, rangeX=(-1, 1))
# Control lighting
#axes.bgcolor='k'
# axes.light0.ambient = 0.0 # 0.2 is default for light 0
# axes.light0.diffuse = 0.0 # 1.0 is default
axes.light0.Off()
light1 = axes.lights[1]
light1.On()
light1.ambient = 0.8
light1.diffuse = 1.0
light1.isDirectional = True
light1.position = (2, -4, 2, 0)
rec = vv.record(vv.gcf())
# Timer for controlling rotation speed
timer = vv.Timer(axes, 100, False)
timer.Bind(onTimer)
timer.Start(interval=1)
app = vv.use()
app.Run()
# Output movie to gif
rec.Stop()
rec.Export('movie.gif')
# Old code that used matplotlib, which is like 10 times slower, but left in
# since visvis is discontinued
def plot3d(self,
img,
bodies={
'pose3d': np.empty((0, 13, 3)),
'pose2d': np.empty((0, 13, 2))
},
hands={
'pose3d': np.empty((0, 21, 3)),
'pose2d': np.empty((0, 21, 2))
},
faces={
'pose3d': np.empty((0, 84, 3)),
'pose2d': np.empty((0, 84, 2))
},
body_with_wrists=[],
body_with_head=[],
interactive=False):
"""
:param img: a HxWx3 numpy array
:param bodies: dictionnaroes with 'pose3d' (resp 'pose2d') with the body 3D (resp 2D) pose
:param faces: same with face pose
:param hands: same with hand pose
:param body_with_wrists: list with for each body, a tuple (left_hand_id, right_hand_id) of the index of the hand detection attached to this body detection (-1 if none) for left and right hands
:parma body_with_head: list with for each body, the index of the face detection attached to this body detection (-1 if none)
:param interactive: whether to open the viewer in an interactive manner or not
"""
# body pose do not use the same coordinate systems
bodies['pose3d'][:, :, 0] *= -1
bodies['pose3d'][:, :, 1] *= -1
# Compute 3D scaled representation of each part, stored in "points3d"
hands, bodies, faces = [copy.copy(s) for s in (hands, bodies, faces)]
parts = (hands, bodies, faces)
for part in parts:
part['points3d'] = np.zeros_like(part['pose3d'])
for part_idx in range(len(part['pose3d'])):
points3d = scale_orthographic(part['pose3d'][part_idx],
part['pose2d'][part_idx])
part['points3d'][part_idx] = points3d
# Various display tricks to make the 3D visualization of full-body nice
# (1) for faces, add a Z offset to faces to align them with the body
for body_id, face_id in enumerate(body_with_head):
if face_id != -1:
z_offset = bodies['points3d'][body_id, 12, 2] - np.mean(
faces['points3d'][face_id, :, 2])
faces['points3d'][face_id, :, 2] += z_offset
# (2) for hands, add a 3D offset to put them at the wrist location
for body_id, (lwrist_id, rwrist_id) in enumerate(body_with_wrists):
if lwrist_id != -1:
hands['points3d'][lwrist_id, :, :] = bodies['points3d'][
body_id, 7, :] - hands['points3d'][lwrist_id, 0, :]
if rwrist_id != -1:
hands['points3d'][rwrist_id, :, :] = bodies['points3d'][
body_id, 6, :] - hands['points3d'][rwrist_id, 0, :]
img = np.asarray(img)
height, width = img.shape[:2]
fig = vv.figure(1)
fig.Clear()
fig._SetPosition(0, 0, self.figsize[0], self.figsize[1])
if not interactive:
fig._enableUserInteraction = False
axes = vv.gca()
# Hide axis
axes.axis.visible = False
scaling_factor = 1.0 / height
# Camera interaction is not intuitive along z axis
# We reference every object to a parent frame that is rotated to circumvent the issue
ref_frame = vv.Wobject(axes)
ref_frame.transformations.append(vv.Transform_Rotate(-90, 1, 0, 0))
ref_frame.transformations.append(
vv.Transform_Translate(-0.5 * width * scaling_factor, -0.5, 0))
# Draw image
if self.display2d:
# Display pose in 2D
img = visu.visualize_bodyhandface2d(img,
dict_poses2d={
'body': bodies['pose2d'],
'hand': hands['pose2d'],
'face': faces['pose2d']
},
lw=2,
max_padding=0,
bgr=False)
XX, YY = np.meshgrid([0, width * scaling_factor], [0, 1])
img_z_offset = 0.5
ZZ = img_z_offset * np.ones(XX.shape)
# Draw image
embedded_img = vv.surf(XX, YY, ZZ, img)
embedded_img.parent = ref_frame
embedded_img.ambientAndDiffuse = 1.0
# Draw a grid on the bottom floor to get a sense of depth
XX, ZZ = np.meshgrid(
np.linspace(0, width * scaling_factor, 10),
img_z_offset - np.linspace(0, width * scaling_factor, 10))
YY = np.ones_like(XX)
grid3d = vv.surf(XX, YY, ZZ)
grid3d.parent = ref_frame
grid3d.edgeColor = (0.1, 0.1, 0.1, 1.0)
grid3d.edgeShading = 'plain'
grid3d.faceShading = None
# Draw pose
for part in parts:
for part_idx in range(len(part['points3d'])):
points3d = part['points3d'][part_idx] * scaling_factor
# Draw bones
J = len(points3d)
is_body = (J == 13)
ignore_neck = False if not is_body else body_with_head[
part_idx] != -1
bones, bonecolors, pltcolors = visu._get_bones_and_colors(
J, ignore_neck=ignore_neck)
for (kpt_id1, kpt_id2), color in zip(bones, bonecolors):
color = color[2], color[1], color[0] # BGR vs RGB
p1 = visu._get_xyz(points3d, kpt_id1)
p2 = visu._get_xyz(points3d, kpt_id2)
pointset = vv.Pointset(3)
pointset.append(p1)
pointset.append(p2)
# Draw bones as solid capsules
bone_radius = 0.005
line = vv.solidLine(pointset, radius=bone_radius)
line.faceColor = color
line.ambientAndDiffuse = 1.0
line.parent = ref_frame
# Draw keypoints, except for faces
if J != 84:
keypoints_to_plot = points3d
if ignore_neck:
# for a nicer display, ignore head keypoint
keypoints_to_plot = keypoints_to_plot[:12, :]
# Use solid spheres
for i in range(len(keypoints_to_plot)):
kpt_wobject = vv.solidSphere(
translation=keypoints_to_plot[i, :].tolist(),
scaling=1.5 * bone_radius)
kpt_wobject.faceColor = (255, 0, 0)
kpt_wobject.ambientAndDiffuse = 1.0
kpt_wobject.parent = ref_frame
# Use just an ambient lighting
axes.light0.ambient = 0.8
axes.light0.diffuse = 0.2
axes.light0.specular = 0.0
cam = vv.cameras.ThreeDCamera()
axes.camera = cam
#z axis
cam.azimuth = -45
cam.elevation = 20
cam.roll = 0
# Orthographic camera
cam.fov = 0
if self.camera_zoom is None:
cam.zoom *= 1.3 # Zoom a bit more
else:
cam.zoom = self.camera_zoom
if self.camera_location is not None:
cam.loc = self.camera_location
cam.SetView()
if interactive:
self.app.Run()
else:
fig._widget.update()
self.app.ProcessEvents()
img3d = vv.getframe(vv.gcf())
img3d = np.clip(img3d * 255, 0, 255).astype(np.uint8)
# Crop gray borders
img3d = img3d[10:-10, 10:-10, :]
return img3d, img
def record(ob):
""" record(object)
Take a snapshot of the given figure or axes after each draw.
A Recorder instance is returned, with which the recording can
be stopped, continued, and exported to GIF, SWF or AVI.
"""
# establish wheter we can record that
if not isinstance(ob, (vv.BaseFigure, vv.Axes)):
raise ValueError("The given object is not a figure nor an axes.")
# create recorder
return Recorder(ob)
if __name__ == '__main__':
import time
l = vv.plot([1,2,3,1,4])
rec = vv.record(vv.gcf())
for i in range(20):
l.SetYdata([1+i/10.0, 2,3,1,4])
vv.processEvents() # Process gui events
time.sleep(0.1)
# Export to swf, gif or avi
fname = 'recordExample' # note: set location to an existing directory
for ext in ['.swf', '.gif', '.avi']:
try:
rec.Export(fname+ext)
except Exception:
print('could not do %s' % ext)
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
app.Create()
app.Run()
def cluster_points(pp, c, pauseTime=0, showConvergeToo=True):
""" cluster_points(pp, c, pauseTime=0)
Given a set of points, and the centreline position, this function
returns a set of points, which is a subset of pp. The returned pointset
is empty on error.
This algorithm uses the chopstick clustering implementation.
The first step is the "stick" method. We take the closest point from the
centre and attach one end of a stick to it. The stick has the length of
the radius of the fitted circle. We rotate the stick counterclockwise
untill it hits a point, or untill we rotate too far without finding a
point, thus failing. When it fails, we try again with a slighly larger
stick. This is to close gaps of up to almost 100 degrees. When we reach
a point were we've already been, we stop. Afterwards, the set of points
is sorted by angle.
In the second step we try to add points: we pick
two subsequent points and check what other points are closer than "stick"
to both these points, where "stick" is the distance between the points. We
will break this stick in two and take the best point in the cluster, thus
the name: chopstick. BUT ONLY if it is good enough! We draw two lines
from the points under consideration to the centre. The angle that these
two lines make is a reference for the allowed angle that the two lines
may make that run from the two points to the new point. To be precise:
ang > (180 - refang) - offset
offset is a parameter to control the strictness.
The third part of this step consists of removing points. We will only
remove points that are closer to the centre than both neighbours. We
check each point, comparing it with its two neighbours on each side,
applying the same criterion as above. This will remove outliers that lie
withing the stent, such as points found due to the contrast fluid...
The latter two parts are repeated untill the set of points does not change.
Each time the centre is recalculated by fitting a circle.
"""
# Get better center
if showConvergeToo:
c, I = converge_to_centre(pp, c, pauseTime=pauseTime)
else:
c, I = converge_to_centre(pp, c)
if not I:
return Pointset(2)
# Init list with vis objects (to be able to delete them)
showObjects = []
if pauseTime:
fig = vv.gcf()
# Short names
pi = np.pi
# Minimum and maximum angle that the stick is allowed to make with the line
# to the circle-centre. Pretty intuitive...
# it is a relative measure, we will multiply it with a ratio:
# radius/distance_current_point_to_radius. This allows ellipses to be
# segmented, while remaining strict for circles.
difAng1_p = 0.0*pi
difAng2_p = 0.7*pi
## Step 1, stick method to find an initial set of points
# Select start point (3th point returned by converge_to_centre)
icurr = I[2]
# Init list L, at the beginning only contains icurr
L = [icurr]
# Largest amount of iterations that makes sense. Probably the loop
# exits sooner.
maxIter = len(pp)
# Enter loop
for iter in range(maxIter):
# We can think of it as fixing the stick at one end at the current
# point and then rotating it in a direction such that a point is
# found in the clockwise direction of the current point. We thus
# need the angle between the next and current point to be not much
# more than the angle between the current point and the circle
# cenrre + 90 deg. But it must be larger than the angle between the
# current point and the circle centre.
# Calculate distances
dists = pp.distance(pp[icurr])
# Do the next bit using increasing stick length, untill success
for stick in [c.r*1.0, c.r*1.5, c.r*2.0]:
# Find subset of points that be "reached by the stick"
Is, = np.where(dists<stick)
# Calculate angle with circle centre
refAng = c.angle2(pp[icurr])
# Culcuate angles with points that are in reach of the stick
angs = pp[Is].angle2(pp[icurr])
# Select the points that are in the proper direction
# There are TWO PARAMETERS HERE (one important) the second TH can
# not be 0.5, because we allow an ellipse.
# Use distance measure to make sure not to select the point itself.
difAngs = subtract_angles(angs, refAng)
difAng2 = difAng2_p # pp[icurr].distance(c) / c.r
# Set current too really weid value
icurr2, = np.where(Is==icurr)
if len(icurr2):
difAngs[icurr2] = 99999.0
# Select. If a selection, we're good!
II, = np.where( (difAngs > difAng1_p) + (difAngs < difAng2))
if len(II):
break
else:
# No success
_objectClearer(showObjects)
return Pointset(2)
# Select the point with the smallest angle
tmp = difAngs[II]
inext, = np.where(tmp == tmp.min())
# inext is index in subset. Make it apply to global set
inext = Is[ II[ inext[0] ] ]
inext = int(inext)
# Show
if pauseTime>0:
# Delete
_objectClearer(showObjects)
# Show center
ob1 = vv.plot(c, ls='', ms='x', mc='r', mw=10, axesAdjust=0)
# Show all points
ob2 = vv.plot(pp, ls='', ms='.', mc='g', mw=6, axesAdjust=0)
# Show selected points L
ob3 = vv.plot(pp[L], ls='', ms='.', mc='y', mw=10, axesAdjust=0)
# Show next
ob4 = vv.plot(pp[inext], ls='', ms='.', mc='r', mw=12, axesAdjust=0)
# Show stick
vec = ( pp[inext]-pp[icurr] ).normalize()
tmp = Pointset(2)
tmp.append(pp[icurr]); tmp.append(pp[icurr]+vec*stick)
ob5 = vv.plot(tmp, lw=2, lc='b')
# Store objects and wait
showObjects = [ob1,ob2,ob3,ob4,ob5]
fig.DrawNow()
time.sleep(pauseTime)
# Check whether we completed a full round already
if inext in L:
break
else:
L.append(inext)
# Prepare for next round
icurr = inext
# Sort the list by the angles
tmp = zip( pp[L].angle2(c), L )
tmp.sort(key=lambda x:x[0])
L = [i[1] for i in tmp]
# Clear visualization
_objectClearer(showObjects)
## Step 2 and 3, chopstick algorithm to find more points and discard outliers
# Init
L = [int(i) for i in L] # Make Python ints
Lp = []
round = 0
# Iterate ...
while Lp != L and round < 20:
round += 1
#print 'round', round
# Clear list (but store previous)
Lp = [i for i in L]
L = []
# We need at least three points
if len(Lp)<3:
_objectClearer(showObjects)
print('oops: len(LP)<3' )
return []
# Recalculate circle
c = fit_cirlce(pp[Lp], False)
if c.r == 0.0:
print('oops: c.r==0' )
_objectClearer(showObjects)
return []
# Step2: ADD POINTS
for iter in range(len(Lp)):
# Current point
icurr = Lp[iter]
if iter < len(Lp)-1:
inext = Lp[iter+1]
else:
inext = Lp[0]
# Prepare, get p1 and p2
p1 = pp[icurr]
p2 = pp[inext]
# Apply masks to points in pp
M1, M2 = chopstick_criteria(c, p1, p2, pp)
# Combine measures. I is now the subset (of p) of OK points
I, = np.where(M1*M2)
if not len(I):
L.append(icurr)
continue
elif len(I)==1:
ibetw = int(I)
else:
# Multiple candidates: find best match
pptemp = pp[I]
dists = p1.distance(pptemp) + p2.distance(pptemp)
II, = np.where( dists==dists.min() )
ibetw = int( I[II[0]] )
# Add point
L.append(icurr)
if not ibetw in L:
L.append(ibetw)
# Check
assert ibetw not in [icurr, inext]
# Draw
if pauseTime>0:
# Delete
_objectClearer(showObjects)
# Show center
ob1 = vv.plot(c, ls='', ms='x', mc='r', mw=10, axesAdjust=0)
# Show all points
ob2 = vv.plot(pp, ls='', ms='.', mc='g', mw=6, axesAdjust=0)
# Show selected points L
ob3 = vv.plot(pp[L], ls='', ms='.', mc='y', mw=10, axesAdjust=0)
# Show between and vectors
ob4 = vv.plot(pp[ibetw], ls='', ms='.', mc='r', mw=12, axesAdjust=0)
ob5 = vv.plot(pp[[icurr, ibetw, inext]], ls='-', lc='g', axesAdjust=0)
ob6 = vv.plot(pp[[icurr, inext]], ls=':', lc='g', axesAdjust=0)
# Store objects and wait
showObjects = [ob1,ob2,ob3,ob4,ob5,ob6]
fig.DrawNow()
time.sleep(pauseTime)
# Lpp stores the set of points we have untill now, we will refill the
# set L, maybe with less points
Lpp = [int(i) for i in L]
L = []
# Step3: REMOVE POINTS
for iter in range(len(Lpp)):
# Current point and neighbours
ibetw = Lpp[iter]
if iter<len(Lpp)-1:
inext = Lpp[iter+1]
else:
inext = Lpp[0]
if iter>0:
icurr = Lpp[iter-1]
else:
icurr = Lpp[-1]
# Test
# print icurr, ibetw, inext
assert ibetw not in [icurr, inext]
# Prepare, get p1 and p2 and p3
p1 = pp[icurr]
p2 = pp[inext]
p3 = pp[ibetw]
# Apply masks to points in pp
M1, M2 = chopstick_criteria(c, p1, p2, p3)
M = M1*M2
# Do we keep the point?
if M.sum():
L.append(ibetw)
# Draw
if pauseTime>0 and not M.sum():
# Delete
_objectClearer(showObjects)
# Show center
ob1 = vv.plot(c, ls='', ms='x', mc='r', mw=10, axesAdjust=0)
# Show all points
ob2 = vv.plot(pp, ls='', ms='.', mc='g', mw=6, axesAdjust=0)
# Show selected points L
ob3 = vv.plot(pp[L], ls='', ms='.', mc='y', mw=10, axesAdjust=0)
# Show between and vectors
ob4 = vv.plot(pp[ibetw], ls='', ms='.', mc='r', mw=12, axesAdjust=0)
ob5 = vv.plot(pp[[icurr, ibetw, inext]], ls='-', lc='r', axesAdjust=0)
ob6 = vv.plot(pp[[icurr, inext]], ls='-', lc='g', axesAdjust=0)
# Store objects and wait
showObjects = [ob1,ob2,ob3,ob4,ob5,ob6]
fig.DrawNow()
time.sleep(pauseTime)
# Done
if round == 20:
print('Warning: chopstick seemed not to converge.')
_objectClearer(showObjects)
#print 'cluster end', len(L)
return pp[L]
def showVolPhases(basedir, vols=None, ptcode=None, ctcode=None, cropname=None,
showVol='iso', mipIsocolor=False, isoTh=310,
slider=False, clim=(0,3000), clim2D=(-550, 500), fname=None):
""" Show vol phases in motion container
showVol= mip or iso or 2D; Provide either vols or location
"""
if vols is None:
# Load volumes
s = loadvol(basedir, ptcode, ctcode, cropname, 'phases', fname=fname)
vols = []
for key in dir(s):
if key.startswith('vol'):
vols.append(s[key])
# Start vis
f = vv.figure(1); vv.clf()
f.position = 9.00, 38.00, 992.00, 944.00
a = vv.gca()
a.daspect = 1, 1, -1
a.axis.axisColor = 1,1,1
a.axis.visible = False
a.bgcolor = 0,0,0
if showVol=='mip':
if not ptcode is None and not ctcode is None:
vv.title('Maximum intensity projection cine-loop of the original ECG-gated CT volumes of patient %s at %s ' % (ptcode[8:], ctcode))
else:
vv.title('Maximum intensity projection cine-loop of the original ECG-gated CT volumes ')
else:
if not ptcode is None and not ctcode is None:
vv.title('ECG-gated CT scan cine-loop of the original ECG-gated CT volumes of patient %s at %s ' % (ptcode[8:], ctcode))
else:
vv.title('ECG-gated CT scan cine-loop of the original ECG-gated CT volumes ')
# Setup data container
container = vv.MotionDataContainer(a)
for vol in vols:
if showVol == '2D':
t = vv.volshow2(vol, clim=clim2D) # -750, 1000
t.parent = container
else:
t = vv.volshow(vol, clim=clim, renderStyle = showVol)
t.parent = container
if showVol == 'iso':
t.isoThreshold = isoTh # iso or mip work well
t.colormap = {'r': [(0.0, 0.0), (0.17727272, 1.0)],
'g': [(0.0, 0.0), (0.27272728, 1.0)],
'b': [(0.0, 0.0), (0.34545454, 1.0)],
'a': [(0.0, 1.0), (1.0, 1.0)]}
if mipIsocolor:
t.colormap = {'r': [(0.0, 0.0), (0.17727272, 1.0)],
'g': [(0.0, 0.0), (0.27272728, 1.0)],
'b': [(0.0, 0.0), (0.34545454, 1.0)],
'a': [(0.0, 1.0), (1.0, 1.0)]}
# bind ClimEditor to figure
if slider:
if showVol=='mip':
c = vv.ClimEditor(vv.gcf())
c.position = (10, 50)
f.eventKeyDown.Bind(lambda event: _utils_GUI.ShowHideSlider(event, c) )
if showVol=='iso':
c = IsoThEditor(vv.gcf())
c.position = (10, 50)
f.eventKeyDown.Bind(lambda event: _utils_GUI.ShowHideSlider(event, c) )
f.eventKeyDown.Bind(lambda event: _utils_GUI.ViewPresets(event, [a]) )
print('------------------------')
print('Use keys 1, 2, 3, 4 and 5 for preset anatomic views')
print('Use v for a default zoomed view')
print('Use x to show and hide axis')
print('------------------------')
return t
removeStent=removeStent,
showmodelavgreg=showmodelavgreg,
showvol=showvol,
phases=phases,
colors=colors,
meshWithColors=meshWithColors)
vv.title('Model for LSPEAS %s - %s' % (ptcode[7:], ctcode3))
axes.append(ax)
#bind view control
f.eventKeyDown.Bind(
lambda event: _utils_GUI.RotateView(event, axes, axishandling=False))
f.eventKeyDown.Bind(lambda event: _utils_GUI.ViewPresets(event, axes))
## Set view
# a1.SetView(view1)
# a2.SetView(view2)
# a3.SetView(view3)
## Use same camera
#a1.camera = a2.camera = a3.camera
if False:
a = vv.gca()
a.camera = ax.camera
## Save figure
if False:
vv.screenshot(r'D:\Profiles\koenradesma\Desktop\ZA3_phase90.jpg',
vv.gcf(),
sf=2) #phantom validation manuscript
def __init__(self,
vol,
a_transversal,
a_coronal,
a_sagittal,
a_MIP,
a_text,
nr_of_stents,
clim=None):
self.nr_of_stents = nr_of_stents
self.f = vv.gcf()
self.vol = vol
# Create empty list of endpoints
self.endpoints = []
self.endpoints = ['xx,yy,zz'] * nr_of_stents * 2
self.endpointsindex = 0
# Create text objects
self._labelcurrent = vv.Label(a_text)
self._labelx = vv.Label(a_text)
self._labelxslice = vv.Label(a_text)
self._labely = vv.Label(a_text)
self._labelyslice = vv.Label(a_text)
self._labelz = vv.Label(a_text)
self._labelzslice = vv.Label(a_text)
self._labelcurrent.position = -250, 10
self._labelx.position = -250, 35
self._labelxslice.position = -200, 35
self._labely.position = -250, 55
self._labelyslice.position = -200, 55
self._labelz.position = -250, 75
self._labelzslice.position = -200, 75
self._labelendpointstext = []
self._labelendpointstext.append(vv.Label(a_text))
self._labelendpointstext[0].position = 100, -5
self._labelendpointstext.append(vv.Label(a_text))
self._labelendpointstext[1].position = 230, -5
for i in range(2, self.nr_of_stents + 2):
self._labelendpointstext.append(vv.Label(a_text))
self._labelendpointstext[i].position = 40, 15 + (20 * (i - 2))
self._labelendpoints = []
for i in range(0, self.nr_of_stents * 2, 2):
self._labelendpoints.append(vv.Label(a_text))
self._labelendpoints[i].position = 100, 15 + (20 * (i / 2)), 50, 20
self._labelendpoints.append(vv.Label(a_text))
self._labelendpoints[i + 1].position = 230, 15 + (20 *
(i / 2)), 50, 20
# Create Select button
self._select = False
self._butselect = vv.PushButton(a_text)
self._butselect.position = -110, 150
self._butselect.text = 'Select'
# Create Back button
self._back = False
self._butback = vv.PushButton(a_text)
self._butback.position = 10, 150
self._butback.text = 'Back'
# Create Close button
self._finished = False
self._butclose = vv.PushButton(a_text)
self._butclose.position = -50, 180
self._butclose.text = 'Finish'
# Get short name for sampling
if isinstance(vol, Aarray):
self._sam = sam = vol.sampling
else:
self._sam = None
sam = (1, 1, 1)
# Display the slices and 3D MIP
self.b1 = VolViewer(vol, 0, axes=a_transversal, clim=clim)
self.b2 = VolViewer(vol, 1, axes=a_coronal, clim=clim)
self.b3 = VolViewer(vol, 2, axes=a_sagittal, clim=clim)
renderstyle = 'mip'
a_MIP.daspect = 1, 1, -1
self.b4 = vv.volshow(vol,
clim=(0, 2500),
renderStyle=renderstyle,
axes=a_MIP)
c = vv.ClimEditor(a_MIP)
c.position = (10, 50)
# set axis settings
for a in [a_transversal, a_coronal, a_sagittal, a_MIP]:
a.bgcolor = [0, 0, 0]
a.axis.visible = False
a.showAxis = True
# get current slice number
Zslice = self.b1.GetCurrentSlice()
Yslice = self.b2.GetCurrentSlice()
Xslice = self.b3.GetCurrentSlice()
size = vol.shape
# create lines for position of x,y and z slices
origin = vol.origin
Zrange = (origin[0], (size[0] * sam[0]) + origin[0])
Xrange = (origin[1], (size[1] * sam[1]) + origin[1])
Yrange = (origin[2], (size[2] * sam[2]) + origin[2])
self.l11 = vv.Line(a_transversal, [(Yslice, Xrange[0]),
(Yslice, Xrange[1])])
self.l12 = vv.Line(a_transversal, [(Yrange[0], Xslice),
(Yrange[1], Xslice)])
self.l21 = vv.Line(a_coronal, [(Zslice, Zrange[0]),
(Zslice, Zrange[1])])
self.l22 = vv.Line(a_coronal, [(Yrange[0], Xslice),
(Yrange[1], Xslice)])
self.l31 = vv.Line(a_sagittal, [(Zslice, Zrange[0]),
(Zslice, Zrange[1])])
self.l32 = vv.Line(a_sagittal, [(Xrange[0], Yslice),
(Xrange[1], Yslice)])
# change color of the lines
for i in [self.l11, self.l12, self.l21, self.l22, self.l31, self.l32]:
i.lc = 'g'
# create a point in the MIP figure for the current position
self.mippoint = vv.Line(a_MIP, [(Zslice, Xslice, Yslice)])
self.mippoint.ms = 'o'
self.mippoint.mw = 5
self.mippoint.mc = 'g'
self.mippoint.alpha = 0.9
# Get list of all range wobjects
self._volviewers = [self.b1, self.b2, self.b3]
# Bind events
fig = a_text.GetFigure()
fig.eventClose.Bind(self._OnFinish)
self._butclose.eventPress.Bind(self._OnFinish)
self._butselect.eventPress.Bind(self._OnSelect)
self._butback.eventPress.Bind(self._OnBack)
for r in self._volviewers:
r.eventPositionUpdate.Bind(self._OnMouseClickAxis)
for s in range(len(self._labelendpoints)):
self._labelendpoints[s].eventMouseDown.Bind(
self._OnMouseClickEndpoint)
# Almost done
self._SetTexts()
self.updatePosition()
and exported to gif/swf/avi.
This is not an interactive example, but a script.
"""
import visvis as vv
# Create something to show, let's show a red teapot!
mesh = vv.solidTeapot()
mesh.faceColor = 'r'
# Prepare
Nangles = 36
a = vv.gca()
f = vv.gcf()
rec = vv.record(a)
# Rotate camera
for i in range(Nangles):
a.camera.azimuth = 360 * float(i) / Nangles
if a.camera.azimuth>180:
a.camera.azimuth -= 360
a.Draw() # Tell the axes to redraw
f.DrawNow() # Draw the figure NOW, instead of waiting for GUI event loop
# Export
rec.Stop()
rec.Export('teapot.gif')
vv.xlabel('x axis')
vv.ylabel('y axis')
vv.zlabel('z axis')
# show
print np.sum(data)
t = vv.volshow(data,renderStyle='iso',axesAdjust=True)
#t.isoThreshold = 0.5
# try the differtent render styles, for examample
# "t.renderStyle='iso'" or "t.renderStyle='ray'"
# If the drawing hangs, your video drived decided to render in software mode.
# This is unfortunately (as far as I know) not possible to detect.
# It might help if your data is shaped a power of 2.
# Get axes and set camera to orthographic mode (with a field of view of 70)
a = vv.gcf()
f = vv.gca()#fqwang
#a.camera.fov = 45
# Create colormap editor wibject.
vv.ColormapEditor(a)
rec = vv.record(f)
# Rotate camera
#fqwang
Nangles = 36
for i in range(Nangles):
f.camera.azimuth = 360 * float(i) / Nangles
if f.camera.azimuth>180:
# Рисуем картинки
plot_bg_image(image, z=j.start_level_value)
ax = vv.gca()
ax.bgcolor = (
0.7, 0.7, 0.7
) # We draw path in white by default, so we need a dark background.
ax.light0.position = (200, 200, 200, 0)
# draw_arcs(ax, j.start_level_value * 1.01, color=(0.5, 0.5, 0.5))
for path in long_normal_paths:
if len(path) <= 3:
# Для кубического сплайна нужно 4 точки.
continue
draw_smoothed_path(ax, path, radius=2, color=(1, 1, 1))
# draw_critical_points(ax, 2, level=(j.start_level_value * 1.01), color=(1, 1, 1))
# draw_critical_points(ax, 1, level=(j.start_level_value * 1.01), color=(1, 1, 1))
# draw_critical_points(ax, 0, level=(j.start_level_value * 1.01), color=(1, 1, 1))
# draw_top_points(ax, long_normal_paths, color=(1, 1, 1))
# ax.camera.azimuth = 0.
# ax.camera.elevation = 90.
ax.camera.azimuth = 45.
ax.camera.elevation = 30.
ax.camera.daspect = (1, 1, 4) # Увеличиваем масштаб по Z
vv.gcf().relativeFontSize = 2.0
# import time
# print("Wait for rendering...")
# time.sleep(30)
# vv.screenshot(args.output, ob=ax)