def __init__(self, dm, fig, ax, motionPlay=(10,0.5), **kwargs):
""" dm is deformable mesh
"""
self.container = vv.Wibject(ax)
self.slider = vv.Slider(self.container, fullRange=(0,90), value=0 )
# value decimals defined in vv.Slider under def _getformat(self)
self.slider.showTicks = True
self.slider.edgeColor = 0,0,0
self.slider._frontColor = 0,0,1#0.5, 0.7, 0.9
self.container.bgcolor = 1,0,0
self.container.position = 0.35, 0.98, 500, 20 # x y w h
self.slider.position = 0, 0, 1, 15
self.fig = fig
self.maxRange = self.slider.fullRange.max
self.dm = dm
self.motionPlay = motionPlay
self._finished = False
# Bind
fig.eventClose.Bind(self._OnClose)
fig.eventKeyDown.Bind(self._OnKey)
fig.eventPosition.Bind(self._OnPosition)
self._updateSlider()
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 __init__(self,
dirsave,
ptcode,
ctcode,
cropname,
s,
what='phases',
axes=None,
**kwargs):
""" s is struct from loadvol
"""
self.fig = vv.figure(1)
vv.clf()
self.fig.position = 0.00, 29.00, 1680.00, 973.00
self.defaultzoom = 0.025 # check current zoom with foo.ax.GetView()
self.what = what
self.ptcode = ptcode
self.dirsave = dirsave
self.ctcode = ctcode
self.cropname = cropname
if self.what == 'phases':
self.phase = 0
else:
self.phase = self.what # avgreg
# self.vol = s.vol0
self.s = s # s with vol(s)
self.s_landmarks = vv.ssdf.new()
self.graph = stentgraph.StentGraph()
self.points = [] # selected points
self.nodepoints = []
self.pointindex = 0 # for selected points
try:
self.vol = s.vol0 # when phases
except AttributeError:
self.vol = s.vol # when avgreg
self.ax = vv.subplot(121)
self.axref = vv.subplot(122)
self.label = DrawModelAxes(self.vol,
ax=self.ax) # label of clicked point
self.axref.bgcolor = 0, 0, 0
self.axref.visible = False
# create axis for buttons
a_select = vv.Wibject(self.ax) # on self.ax or fig?
a_select.position = 0.55, 0.7, 0.6, 0.5 # x, y, w, h
# Create text objects
self._labelcurrentIndexT = vv.Label(a_select) # for text title
self._labelcurrentIndexT.position = 125, 180
self._labelcurrentIndexT.text = ' Total selected ='
self._labelcurrentIndex = vv.Label(a_select)
self._labelcurrentIndex.position = 225, 180
# Create Select button
self._select = False
self._butselect = vv.PushButton(a_select)
self._butselect.position = 10, 150
self._butselect.text = 'Select'
# Create Back button
self._back = False
self._butback = vv.PushButton(a_select)
self._butback.position = 125, 150
self._butback.text = 'Undo'
# Create Next/Save button
self._finished = False
self._butclose = vv.PushButton(a_select)
self._butclose.position = 10, 230
self._butclose.text = 'Next/Save'
# # Create Save landmarks button
# self._save = False
# self._butsave = vv.PushButton(a_select)
# self._butsave.position = 125,230
# self._butsave.text = 'Save|Finished'
# Create Reset-View button
self._resetview = False
self._butresetview = vv.PushButton(a_select)
self._butresetview.position = 10, 180
self._butresetview.text = 'Default Zoom' # back to default zoom
# bind event handlers
self.fig.eventClose.Bind(self._onFinish)
self._butclose.eventPress.Bind(self._onFinish)
self._butselect.eventPress.Bind(self._onSelect)
self._butback.eventPress.Bind(self._onBack)
self._butresetview.eventPress.Bind(self._onView)
# self._butsave.eventPress.Bind(self._onSave)
self._updateTextIndex()
self._updateTitle()
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
label.position = 10, 100 + 25 * i, -20, 25
labelpool.append(label)
# Initialize sliders and buttons
slider_ref = vv.Slider(container, fullRange=(1, len(centerline) - 2), value=10)
slider_ves = vv.Slider(container, fullRange=(1, len(centerline) - 2), value=10)
button_go = vv.PushButton(container, "Take all measurements (incl. volume)")
slider_ref.position = 10, 5, -20, 25