def __init__(self, vol, a_transversal, a_coronal, a_sagittal, a_text):
# Create text objects
self._labelx = vv.Label(a_text)
self._labely = vv.Label(a_text)
self._labelz = vv.Label(a_text)
self._labelx.position = 10, 10
self._labely.position = 10, 30
self._labelz.position = 10, 50
# Create Finish button
self._finished = False
self._but = vv.PushButton(a_text)
self._but.position = 10, 80
self._but.text = 'Finish'
# Get short name for sampling
if isinstance(vol, Aarray):
self._sam = sam = vol.sampling
else:
self._sam = None
sam = (1, 1, 1)
# Calculate mips and deal with anisotropy
mipz = np.max(vol, 0)
mipz = Aarray(mipz, (sam[1], sam[2]))
mipy = np.max(vol, 1)
mipy = Aarray(mipy, (sam[0], sam[2]))
mipx = np.max(vol, 2)
mipx = Aarray(mipx, (sam[0], sam[1]))
# Display the mips
vv.imshow(mipz, axes=a_transversal)
vv.imshow(mipy, axes=a_coronal)
vv.imshow(mipx, axes=a_sagittal)
# Initialize range objects
self._range_transversal = RangeWobject2D(a_transversal, mipz)
self._range_coronal = RangeWobject2D(a_coronal, mipy)
self._range_sagittal = RangeWobject2D(a_sagittal, mipx)
# Get list of all range wobjects
self._rangeWobjects = [
self._range_transversal, self._range_coronal, self._range_sagittal
]
# Bind events
fig = a_text.GetFigure()
fig.eventClose.Bind(self._OnFinish)
self._but.eventPress.Bind(self._OnFinish)
for r in self._rangeWobjects:
r.eventRangeUpdated.Bind(self._OnRangeUpdated)
# Almost done
self._SetTexts()
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()
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()
# 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
slider_ves.position = 10, 40, -20, 25
button_go.position = 10, 70, -20, 25
button_go.bgcolor = slider_ref.bgcolor = slider_ves.bgcolor = 0.8, 0.8, 1.0
# Initialize line objects for showing the plane orthogonal to centerline
slider_ref.line_plane = vv.plot([], [], [],
axes=axes1,
ls='-',
lw=3,
lc='w',
alpha=0.9)
slider_ves.line_plane = vv.plot([], [], [],
axes=axes1,
ls='-',