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 add_label(text,
pos,
angle=0,
fontName=None,
fontSize=9,
color='k',
bgcolor=None,
axes=None):
'''
Adds a label inside the axes. Returns the Label object.
Parameters:
text - String. The text of the label
pos - Tuple with two numbers. The (x,y) position of the label with origin
at the upper left corner.
angle - Float or int. The rotation of the label in degrees.
fontname- String. Either 'mono', 'sans' or 'serif'.
fontSize- Int. Size of the text. Default 9.
color - A 3-tuple or a character in 'rgbycmkw', etc that defines text color.
Default 'k' (black).
bgcolor - Background color. See color. Default None.
axes - Axes wherein the label is placed. If None then the current axes is
chosen.
'''
if axes is None:
axes = vv.gca()
label = vv.Label(axes, text, fontName, fontSize, color)
label.position = pos
label.bgcolor = bgcolor
label.textAngle = angle
return label
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()
f.position = 968.00, 30.00, 944.00, 1002.00
a = vv.gca()
show_ctvolume(vol, model, showVol=showVol, clim=clim0, isoTh=isoTh)
model.Draw(mc='b', mw = 10, lc='g')
vv.xlabel('x (mm)');vv.ylabel('y (mm)');vv.zlabel('z (mm)')
vv.title('Analysis for model LSPEAS %s - %s' % (ptcode[7:], ctcode))
a.axis.axisColor= 1,1,1
a.bgcolor= 0,0,0
a.daspect= 1, 1, -1 # z-axis flipped
a.axis.visible = showAxis
# Initialize labels GUI
from visvis import Pointset
from stentseg.stentdirect import stentgraph
t1 = vv.Label(a, 'Edge ctvalue: ', fontSize=11, color='c')
t1.position = 0.1, 5, 0.5, 20 # x (frac w), y, w (frac), h
t1.bgcolor = None
t1.visible = False
t2 = vv.Label(a, 'Edge cost: ', fontSize=11, color='c')
t2.position = 0.1, 25, 0.5, 20
t2.bgcolor = None
t2.visible = False
t3 = vv.Label(a, 'Edge length: ', fontSize=11, color='c')
t3.position = 0.1, 45, 0.5, 20
t3.bgcolor = None
t3.visible = False
#Add clickable nodes
node_points = _utils_GUI.interactive_node_points(model)
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()
fig = vv.figure(); vv.clf()
fig.position = 9.00, 30.00, 944.00, 1002.00
a = vv.gca()
label = DrawModelAxes(vol, model, a, getLabel=True, clim=clim, showVol=showVol, mw=10)
vv.title('Model for LSPEAS %s - %s' % (ptcode[7:], ctcode))
viewAP = {'zoom': 0.006,'fov': 0.0,
'daspect': (1.0, 1.0, -1.0),
'azimuth': 0.0,
'roll': 0.0}
# Set view
# a.SetView(viewAP)
# Initialize labels
t0 = vv.Label(a, '\b{Node nr|location}: ', fontSize=11, color='w')
t0.position = 0.1, 25, 0.5, 20 # x (frac w), y, w (frac), h
t0.bgcolor = None
t0.visible = True
t1 = vv.Label(a, '\b{Nodepair}: ', fontSize=11, color='w')
t1.position = 0.1, 45, 0.5, 20 # x (frac w), y, w (frac), h
t1.bgcolor = None
t1.visible = False
t2 = vv.Label(a, 'Node-to-node Min: ', fontSize=11, color='w')
t2.position = 0.1, 65, 0.5, 20
t2.bgcolor = None
t2.visible = False
t3 = vv.Label(a, 'Node-to-node Max: ', fontSize=11, color='w')
t3.position = 0.1, 85, 0.5, 20
t3.bgcolor = None
t3.visible = False
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()
import visvis as vv
# Create figure and figure
fig = vv.figure()
a = vv.cla()
a.cameraType = '2d'
a.daspectAuto = True
a.SetLimits((0, 8), (-1, 10))
# Create text inside the axes
vv.Text(a, 'These are texts living in the scene:', 1, 3)
vv.Text(a, 'Text can be made \b{bold} easil\by!', 1, 2)
vv.Text(a, 'Text can be made \i{italic} easil\iy!', 1, 1)
# Create text labels
label0 = vv.Label(a, 'These are texts in widget coordinates:')
label0.position = 10, 20
label1 = vv.Label(a, 'Sub_{script} and super^{script} are easy as pi^2.')
label1.position = 10, 40
label2 = vv.Label(a, u'You can use many Unicode characters: \\u0183 = \u0183')
label2.position = 10, 60
label3 = vv.Label(
a, 'And can use many Latex like commands: \\alpha \\Alpha' +
'\\approx, \sigma, \pi, ')
label3.position = 10, 80
for label in [label0, label1, label2, label3]:
label.bgcolor = (0.5, 1, 0.5)
label.position.w = 400
# Enter main loop
# 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
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([], [], [],
def pick3d(axes, vol):
""" Enable picking intensities in a 3D volume.
Given an Axes object and a volume (an Aarray), will show the value,
index and position of the voxel with maximum intentity under the
cursor when doing a SHIFT+RIGHTCLICK. Returns the label object, so
that it can be re-positioned.
Assumptions:
* ThreeDCamera is in use and in orthographic mode (no perspective).
* The volume does not have any transformations w.r.t the axes,
except for the implicit transformations defined by its sampling
and origin.
"""
assert hasattr(vol, 'sampling'), 'Vol must be an Aarray.'
line = vv.plot(vv.Pointset(3),
ms='o',
mw=12,
lc='c',
mc='c',
alpha=0.4,
axesAdjust=False)
label = vv.Label(axes)
label.position = 0, 0, 1, 20
@axes.eventMouseDown.Bind
def onClick(event):
if event.button == 2 and vv.KEY_SHIFT in event.modifiers:
# Get clicked location in NDC
w, h = event.owner.position.size
x, y = 2 * event.x / w - 1, -2 * event.y / h + 1
# Apply inverse camera transform to get two points on the clicked line
M = np.linalg.inv(get_camera_matrix(event.owner))
p1 = vv.Point(np.dot((x, y, -100, 1), M)[:3])
p2 = vv.Point(np.dot((x, y, +100, 1), M)[:3])
# Calculate center point and vector
pm = 0.5 * (p1 + p2)
vec = (p2 - p1).normalize()
# Prepare for searching in two directions
pp = [pm - vec, pm + vec]
status = 0 if sample(vol, pm) is None else 1
status = [status, status]
hit = None
max_sample = -999999
step = min(vol.sampling)
# Look in two directions simulaneously, search for volume, collect samples
for i in range(10000): # Safe while-loop
for j in (0, 1):
if status[j] < 2:
s = sample(vol, pp[j])
inside = s is not None
if inside:
if s > max_sample:
max_sample, hit = s, pp[j]
if status[j] == 0:
status[j] = 1
status[
not j] = 2 # stop looking in other direction
else:
if status[j] == 1:
status[j] = 2
pp[j] += (j * 2 - 1) * step * vec
if status[0] == 2 and status[1] == 2:
break
else:
print('Warning: ray casting to collect samples did not stop'
) # clicking outside the volume
# Draw
pp2 = vv.Pointset(3)
text = 'No point inside volume selected.'
if hit:
pp2.append(hit)
ii = vol.point_to_index(hit)
text = 'At z=%1.1f, y=%1.1f, x=%1.1f -> X[%i, %i, %i] -> %1.2f' % (
hit.z, hit.y, hit.x, ii[0], ii[1], ii[2], max_sample)
line.SetPoints(pp2)
label.text = text
return True # prevent default mouse action
return label
t1 = vv.Text(a, 'Visvis text', 0.2, 9, 0, 'mono', 30)
t2 = vv.Text(a, '... with FreeType!', 1, 8, 0, 'serif', 12)
t3 = vv.Text(a, '... and Unicode: %s!' % hello, 1, 7)
t3 = vv.Text(
a, '\Gamma\rho\epsilon\epsilon\kappa letters and ' +
' \rightarrow math \otimes symbols', 1, 6)
t2 = vv.Text(
a, '\b{bold}, \i{italic}, and \b{\i{bolditalic}} \bfon\its' +
' and sup^{script} and sub_{script}', 1, 5, 0, 'serif')
t3 = vv.Text(a, 'Look, I\'m at an angle!', 1, 4)
t3.textAngle = -20
t3.fontSize = 12
# Create text labels
label1 = vv.Label(a, 'This is a Label')
label1.position = 10, 0.9
label1.bgcolor = (0.5, 1, 0.5)
## A quick brown fox jumps over the lazy dog
testText = 'A quick brown fox jumps over the lazy dog'
# Create figure and figure
fig = vv.figure()
a = vv.cla()
a.cameraType = '2d'
vv.title(testText)
# Create text labels
for i in range(20):
dm.clim = clim3
dm.colormap = vv.CM_JET #todo: use colormap Viridis or Magma as JET is not linear (https://bids.github.io/colormap/)
vv.colorbar()
else:
dm.faceColor = 'g'
# Run mesh
a.SetLimits()
# a.SetView(viewringcrop)
dm.MotionPlay(motionPlay[0], motionPlay[1]) # (10, 0.2) = each 10 ms do a step of 20% for a phase
dm.motionSplineType = 'B-spline'
dm.motionAmplitude = 0.5 # 1 or less. For a mesh we can (more) safely increase amplitude
#todo: dm.SetValues in loop for changing color?
# Add clickable nodes
t0 = vv.Label(a, 'Node nr|location: ', fontSize=11, color='w')
t0.position = 0.01, 5, 0.5, 20
t0.bgcolor = None
t0.visible = False
if meshWithColors:
t1 = vv.Label(a, 'Node amplitude XYZ: ', fontSize=11, color='w')
t1.position = 0.01, 25, 0.5, 20 # x (frac w), y, w (frac), h
t1.bgcolor = None
t1.visible = False
t2 = vv.Label(a, 'Node amplitude Z: ', fontSize=11, color='w')
t2.position = 0.01, 45, 0.5, 20
t2.bgcolor = None
t2.visible = False
t3 = vv.Label(a, 'Node amplitude Y: ', fontSize=11, color='w')
t3.position = 0.01, 65, 0.5, 20
t3.bgcolor = None
def __init__(self,ptcode,ctcode,allcenterlines,basedir):
"""
Script to show the stent plus centerline model and select points on
centerlines for motion analysis
"""
import os, time
import pirt
import visvis as vv
import numpy as np
import math
import itertools
import xlsxwriter
from datetime import datetime
from stentseg.utils.datahandling import select_dir, loadvol, loadmodel
from stentseg.utils.new_pointset import PointSet
from stentseg.stentdirect.stentgraph import create_mesh
from stentseg.motion.vis import create_mesh_with_abs_displacement
from stentseg.utils.visualization import show_ctvolume
from pirt.utils.deformvis import DeformableTexture3D, DeformableMesh
from stentseg.utils import PointSet
from stentseg.stentdirect import stentgraph
from visvis import Pointset # for meshes
from stentseg.stentdirect.stentgraph import create_mesh
from visvis.processing import lineToMesh, combineMeshes
from visvis import ssdf
from stentseg.utils.picker import pick3d
try:
from PyQt4 import QtCore, QtGui # PyQt5
except ImportError:
from PySide import QtCore, QtGui # PySide2
from stentseg.apps.ui_dialog import MyDialog
from stentseg.utils.centerline import dist_over_centerline # added for Mirthe
import copy
cropname = 'prox'
exceldir = os.path.join(basedir,ptcode)
# Load deformations and avg ct (forward for mesh)
# centerlines combined in 1 model
m = loadmodel(basedir, ptcode, ctcode, cropname, modelname = 'centerline_total_modelavgreg_deforms')
model = m.model
# centerlines separated in a model for each centerline
# m_sep = loadmodel(basedir, ptcode, ctcode, cropname, modelname = 'centerline_modelavgreg_deforms')
s = loadvol(basedir, ptcode, ctcode, cropname, what='avgreg')
vol_org = copy.deepcopy(s.vol)
s.vol.sampling = [vol_org.sampling[1], vol_org.sampling[1], vol_org.sampling[2]]
s.sampling = s.vol.sampling
vol = s.vol
# Start visualization and GUI
fig = vv.figure(30); vv.clf()
fig.position = 0.00, 30.00, 944.00, 1002.00
a = vv.gca()
a.axis.axisColor = 1,1,1
a.axis.visible = True
a.bgcolor = 0,0,0
a.daspect = 1, 1, -1
lim = 2500
t = vv.volshow(vol, clim=(0, lim), renderStyle='mip')
pick3d(vv.gca(), vol)
b = model.Draw(mc='b', mw = 0, lc='g', alpha = 0.5)
vv.xlabel('x (mm)');vv.ylabel('y (mm)');vv.zlabel('z (mm)')
vv.title('Model for LSPEAS %s - %s' % (ptcode[7:], ctcode))
# Add clickable nodes
t0 = time.time()
node_points = []
for i, node in enumerate(sorted(model.nodes())):
node_point = vv.solidSphere(translation = (node), scaling = (0.6,0.6,0.6))
node_point.faceColor = 'b'
node_point.alpha = 0.5
node_point.visible = True
node_point.node = node
node_point.nr = i
node_points.append(node_point)
t1 = time.time()
print('Clickable nodes created, which took %1.2f min.' % ((t1-t0)/60))
# list of correctly clicked nodes
selected_nodes_sum = set()
# Initialize labels
t0 = vv.Label(a, '\b{Node nr|location}: ', fontSize=11, color='w')
t0.position = 0.1, 25, 0.5, 20 # x (frac w), y, w (frac), h
t0.bgcolor = None
t0.visible = True
t1 = vv.Label(a, '\b{Nodepair}: ', fontSize=11, color='w')
t1.position = 0.1, 45, 0.5, 20
t1.bgcolor = None
t1.visible = True
# Initialize output variable to store pulsatility analysis
storeOutput = list()
def on_key(event):
if event.key == vv.KEY_ENTER:
# mogenlijkheden aantal nodes
# 1 voor relative beweging vanuit avg punt
# 2 voor onderlinge beweging tussen twee punten
# 3 voor hoek in punt 2 van punt 1 naar punt 3
if len(selected_nodes) == 1:
selectn1 = selected_nodes[0].node
n1index = selected_nodes[0].nr
n1Deforms = model.node[selectn1]['deforms']
output = point_pulsatility(selectn1, n1Deforms)
output['NodesIndex'] = [n1index]
# Store output with name
dialog_output = get_index_name()
output['Name'] = dialog_output
storeOutput.append(output)
# update labels
t1.text = '\b{Node}: %i' % (n1index)
t1.visible = True
print('selection of 1 node stored')
if len(selected_nodes) == 2:
# get nodes
selectn1 = selected_nodes[0].node
selectn2 = selected_nodes[1].node
# get index of nodes which are in fixed order
n1index = selected_nodes[0].nr
n2index = selected_nodes[1].nr
nindex = [n1index, n2index]
# get deforms of nodes
n1Deforms = model.node[selectn1]['deforms']
n2Deforms = model.node[selectn2]['deforms']
# get pulsatility
cl_merged = append_centerlines(allcenterlines)
output = point_to_point_pulsatility(cl_merged, selectn1,
n1Deforms, selectn2, n2Deforms, type='euclidian')
output['NodesIndex'] = nindex
# get distance_centerline
#dist_cl = dist_over_centerline(cl_merged, selectn1, selectn2, type='euclidian') # toegevoegd Mirthe
#dist_cl = dist_centerline_total(cl_merged, selectn1,
# n1Deforms, selectn2, n2Deforms, type='euclidian')
# Store output with name
dialog_output = get_index_name()
output['Name'] = dialog_output
storeOutput.append(output)
# update labels
t1.text = '\b{Node pair}: %i - %i' % (nindex[0], nindex[1])
t1.visible = True
print('selection of 2 nodes stored')
if len(selected_nodes) == 3:
# get nodes
selectn1 = selected_nodes[0].node
selectn2 = selected_nodes[1].node
selectn3 = selected_nodes[2].node
# get index of nodes which are in fixed order
n1index = selected_nodes[0].nr
n2index = selected_nodes[1].nr
n3index = selected_nodes[2].nr
nindex = [n1index, n2index, n3index]
# get deforms of nodes
n1Deforms = model.node[selectn1]['deforms']
n2Deforms = model.node[selectn2]['deforms']
n3Deforms = model.node[selectn3]['deforms']
# get angulation
output = line_line_angulation(selectn1,
n1Deforms, selectn2, n2Deforms, selectn3, n3Deforms)
output['NodesIndex'] = nindex
# Store output with name
dialog_output = get_index_name()
output['Name'] = dialog_output
storeOutput.append(output)
# update labels
t1.text = '\b{Nodes}: %i - %i - %i' % (nindex[0], nindex[1], nindex[2])
t1.visible = True
print('selection of 3 nodes stored')
if len(selected_nodes) > 3:
for node in selected_nodes:
node.faceColor = 'b'
selected_nodes.clear()
print('to many nodes selected, select 1,2 or 3 nodes')
if len(selected_nodes) < 1:
for node in selected_nodes:
node.faceColor = 'b'
selected_nodes.clear()
print('to few nodes selected, select 1,2 or 3 nodes')
# Visualize analyzed nodes and deselect
for node in selected_nodes:
selected_nodes_sum.add(node)
for node in selected_nodes_sum:
node.faceColor = 'g' # make green when analyzed
selected_nodes.clear()
if event.key == vv.KEY_ESCAPE:
# FINISH MODEL, STORE TO EXCEL
# Store to EXCEL
storeOutputToExcel(storeOutput, exceldir)
vv.close(fig)
print('output stored to excel')
selected_nodes = list()
def select_node(event):
""" select and deselect nodes by Double Click
"""
if event.owner not in selected_nodes:
event.owner.faceColor = 'r'
selected_nodes.append(event.owner)
elif event.owner in selected_nodes:
event.owner.faceColor = 'b'
selected_nodes.remove(event.owner)
def pick_node(event):
nodenr = event.owner.nr
node = event.owner.node
t0.text = '\b{Node nr|location}: %i | x=%1.3f y=%1.3f z=%1.3f' % (nodenr,node[0],node[1],node[2])
def unpick_node(event):
t0.text = '\b{Node nr|location}: '
def point_pulsatility(point1, point1Deforms):
n1Indices = point1 + point1Deforms
pos_combinations = list(itertools.combinations(range(len(point1Deforms)),2))
distances = []
for i in pos_combinations:
v = point1Deforms[i[0]] - point1Deforms[i[1]]
distances.append(((v[0]**2 + v[1]**2 + v[2]**2)**0.5 ))
distances = np.array(distances)
# get max distance between phases
point_phase_max = distances.max()
point_phase_max = [point_phase_max, [x*10 for x in (pos_combinations[list(distances).index(point_phase_max)])]]
# get min distance between phases
point_phase_min = distances.min()
point_phase_min = [point_phase_min, [x*10 for x in (pos_combinations[list(distances).index(point_phase_min)])]]
return {'point_phase_min':point_phase_min,'point_phase_max': point_phase_max, 'Node1': [point1, point1Deforms]}
def point_to_point_pulsatility(cl, point1, point1Deforms,
point2, point2Deforms,type='euclidian'):
import numpy as np
n1Indices = point1 + point1Deforms
n2Indices = point2 + point2Deforms
# define vector between nodes
v = n1Indices - n2Indices
distances = ( (v[:,0]**2 + v[:,1]**2 + v[:,2]**2)**0.5 ).reshape(-1,1)
# get min and max distance
point_to_pointMax = distances.max()
point_to_pointMin = distances.min()
# add phase in cardiac cycle where min and max where found (5th = 50%)
point_to_pointMax = [point_to_pointMax, (list(distances).index(point_to_pointMax) )*10]
point_to_pointMin = [point_to_pointMin, (list(distances).index(point_to_pointMin) )*10]
# get median of distances
point_to_pointMedian = np.percentile(distances, 50) # Q2
# median of the lower half, Q1 and upper half, Q3
point_to_pointQ1 = np.percentile(distances, 25)
point_to_pointQ3 = np.percentile(distances, 75)
# Pulsatility min max distance point to point
point_to_pointP = point_to_pointMax[0] - point_to_pointMin[0]
# add % change to pulsatility
point_to_pointP = [point_to_pointP, (point_to_pointP/point_to_pointMin[0])*100 ]
# find index of point on cll and calculate length change cll ???
if isinstance(cl, PointSet):
cl = np.asarray(cl).reshape((len(cl),3))
indpoint1 = np.where( np.all(cl == point1, axis=-1) )[0] # -1 counts from last to the first axis
indpoint2 = np.where( np.all(cl == point2, axis=-1) )[0] # renal point
n1Indices = point1 + point1Deforms
n2Indices = point2 + point2Deforms
clDeforms = []
clpart_deformed = []
vectors = []
clpart = []
d = []
dist_cl = []
clpartDeforms = []
clpart_deformed_test = []
for i in range(len(cl)):
clDeforms1 = model.node[cl[i,0], cl[i,1], cl[i,2]]['deforms']
clDeforms.append(clDeforms1)
clpart_deformed1 = cl[i] + clDeforms1
clpart_deformed.append(clpart_deformed1)
# clpart = cl[min(indpoint1[0], indpoint2[0]):max(indpoint1[0], indpoint2[0])+1]
clpart = clpart_deformed[min(indpoint1[0], indpoint2[0]):max(indpoint1[0], indpoint2[0])+1]
# for i in range(len(clpart)):
# clpartDeforms1 = model.node[clpart[i,0], clpart[i,1], clpart[i,2]]['deforms']
# clpartDeforms.append(clpartDeforms1)
# clpart_deformed1_test = cl[i] + clpartDeforms1
# clpart_deformed_test.append(clpart_deformed1_test)
# for k in range(len(n1Indices)):
# vectors_phases = np.vstack([clpart_deformed_test[i+1][k]-clpart_deformed_test[i][k] for i in range(len(clpart)-1)])
# vectors.append(vectors_phases)
for k in range(len(n1Indices)):
vectors_phases = np.vstack([clpart[i+1][k]-clpart[i][k] for i in range(len(clpart)-1)])
vectors.append(vectors_phases)
for i in range(len(vectors)):
if type == 'euclidian':
d1 = (vectors[i][:,0]**2 + vectors[i][:,1]**2 + vectors[i][:,2]**2)**0.5 # 3Dvector length in mm
d.append(d1)
elif type == 'z':
d = abs(vectors[i][:,2]) # x,y,z ; 1Dvector length in mm
for i in range(len(d)):
dist = d[i].sum()
dist_cl.append(dist)
#if indpoint2 > indpoint1: # stent point proximal to renal on centerline: positive
#dist_cl*=-1
cl_min_index1 = np.argmin(dist_cl)
cl_min_index = cl_min_index1*10
cl_min = min(dist_cl)
cl_max_index1 = np.argmax(dist_cl)
cl_max_index = cl_max_index1*10
cl_max = max(dist_cl)
print ([dist_cl])
print ([point1, point2])
return {'point_to_pointMin': point_to_pointMin,
'point_to_pointQ1': point_to_pointQ1,
'point_to_pointMedian': point_to_pointMedian,
'point_to_pointQ3': point_to_pointQ3,
'point_to_pointMax': point_to_pointMax,
'point_to_pointP': point_to_pointP,
'Node1': [point1, point1Deforms],
'Node2': [point2, point2Deforms], 'distances': distances,
'dist_cl': dist_cl, 'cl_min_index': cl_min_index,
'cl_max_index': cl_max_index, 'cl_min': cl_min, 'cl_max': cl_max}
def line_line_angulation(point1, point1Deforms, point2, point2Deforms, point3, point3Deforms):
n1Indices = point1 + point1Deforms
n2Indices = point2 + point2Deforms
n3Indices = point3 + point3Deforms
# get vectors
v1 = n1Indices - n2Indices
v2 = n3Indices - n2Indices
# get angles
angles = []
for i in range(len(v1)):
angles.append(math.degrees(math.acos((np.dot(v1[i],v2[i]))/
(np.linalg.norm(v1[i])*np.linalg.norm(v2[i])))))
angles = np.array(angles)
# get all angle differences of all phases
pos_combinations = list(itertools.combinations(range(len(v1)),2))
angle_diff = []
for i in pos_combinations:
v = point1Deforms[i[0]] - point1Deforms[i[1]]
angle_diff.append(abs(angles[i[0]] - angles[i[1]]))
angle_diff = np.array(angle_diff)
# get max angle differences
point_angle_diff_max = angle_diff.max()
point_angle_diff_max = [point_angle_diff_max, [x*10 for x in
(pos_combinations[list(angle_diff).index(point_angle_diff_max)])]]
# get min angle differences
point_angle_diff_min = angle_diff.min()
point_angle_diff_min = [point_angle_diff_min, [x*10 for x in
(pos_combinations[list(angle_diff).index(point_angle_diff_min)])]]
return {'point_angle_diff_min':point_angle_diff_min,
'point_angle_diff_max': point_angle_diff_max, 'angles': angles,
'Node1': [point1, point1Deforms], 'Node2': [point2, point2Deforms],
'Node3': [point3, point1Deforms]}
def append_centerlines(allcenterlines):
""" Merge seperated PointSet centerlines into one PointSet
"""
# cl_merged = allcenterlines[0]
cl_merged = PointSet(3)
for i in range(0,len(allcenterlines)):
for point in allcenterlines[i]:
cl_merged.append(point)
return cl_merged
def get_index_name():
# Gui for input name
app = QtGui.QApplication([])
m = MyDialog()
m.show()
m.exec_()
dialog_output = m.edit.text()
return dialog_output
def storeOutputToExcel(storeOutput, exceldir):
"""Create file and add a worksheet or overwrite existing
"""
# https://pypi.python.org/pypi/XlsxWriter
workbook = xlsxwriter.Workbook(os.path.join(exceldir,'storeOutput.xlsx'))
worksheet = workbook.add_worksheet('General')
# set column width
worksheet.set_column('A:A', 35)
worksheet.set_column('B:B', 30)
# add a bold format to highlight cells
bold = workbook.add_format({'bold': True})
# write title and general tab
worksheet.write('A1', 'Output ChEVAS dynamic CT, 10 Phases', bold)
analysisID = '%s_%s_%s' % (ptcode, ctcode, cropname)
worksheet.write('A2', 'Filename:', bold)
worksheet.write('B2', analysisID)
worksheet.write('A3', 'Date and Time:', bold)
date_time = datetime.now() #strftime("%d-%m-%Y %H:%M")
date_format_str = 'dd-mm-yyyy hh:mm'
date_format = workbook.add_format({'num_format': date_format_str,
'align': 'left'})
worksheet.write_datetime('B3', date_time, date_format)
# write 'storeOutput'
sort_index = []
for i in range(len(storeOutput)):
type = len(storeOutput[i]['NodesIndex'])
sort_index.append([i, type])
sort_index = np.array(sort_index)
sort_index = sort_index[sort_index[:,1].argsort()]
for i, n in sort_index:
worksheet = workbook.add_worksheet(storeOutput[i]['Name'])
worksheet.set_column('A:A', 35)
worksheet.set_column('B:B', 20)
worksheet.write('A1', 'Name:', bold)
worksheet.write('B1', storeOutput[i]['Name'])
if n == 1:
worksheet.write('A2', 'Type:', bold)
worksheet.write('B2', '1 Node')
worksheet.write('A3', 'Minimum translation (mm, Phases)',bold)
worksheet.write('B3', storeOutput[i]['point_phase_min'][0])
worksheet.write_row('C3', list(storeOutput[i]['point_phase_min'][1]))
worksheet.write('A4', 'Maximum translation (mm, Phases)',bold)
worksheet.write('B4', storeOutput[i]['point_phase_max'][0])
worksheet.write_row('C4', list(storeOutput[i]['point_phase_max'][1]))
worksheet.write('A5', 'Avg node position and deformations', bold)
worksheet.write('B5', str(list(storeOutput[i]['Node1'][0])))
worksheet.write_row('C5', [str(x)for x in list(storeOutput[i]['Node1'][1])])
worksheet.write('A6', 'Node Index Number', bold)
worksheet.write_row('B6', list(storeOutput[i]['NodesIndex']))
elif n == 2:
worksheet.write('A2', 'Type:', bold)
worksheet.write('B2', '2 Nodes')
worksheet.write('A3', 'Minimum distance (mm, Phases)',bold)
worksheet.write('B3', storeOutput[i]['point_to_pointMin'][0])
worksheet.write('C3', storeOutput[i]['point_to_pointMin'][1])
worksheet.write('A4', 'Q1 distance (mm)',bold)
worksheet.write('B4', storeOutput[i]['point_to_pointQ1'])
worksheet.write('A5', 'Median distance (mm)',bold)
worksheet.write('B5', storeOutput[i]['point_to_pointMedian'])
worksheet.write('A6', 'Q3 distance (mm)',bold)
worksheet.write('B6', storeOutput[i]['point_to_pointQ3'])
worksheet.write('A7', 'Maximum distance (mm, phases)',bold)
worksheet.write('B7', storeOutput[i]['point_to_pointMax'][0])
worksheet.write('C7', storeOutput[i]['point_to_pointMax'][1])
worksheet.write('A8', 'Maximum distance difference (mm)', bold)
worksheet.write('B8', storeOutput[i]['point_to_pointP'][0])
worksheet.write('A9', 'Distances for each phase', bold)
worksheet.write_row('B9', [str(x) for x in list(storeOutput[i]['distances'])])
worksheet.write('A10', 'Avg node1 position and deformations', bold)
worksheet.write('B10', str(list(storeOutput[i]['Node1'][0])))
worksheet.write_row('C10', [str(x) for x in list(storeOutput[i]['Node1'][1])])
worksheet.write('A11', 'Avg node2 position and deformations', bold)
worksheet.write('B11', str(list(storeOutput[i]['Node2'][0])))
worksheet.write_row('C11', [str(x) for x in list(storeOutput[i]['Node2'][1])])
worksheet.write('A12', 'Node Index Number', bold)
worksheet.write_row('B12', list(storeOutput[i]['NodesIndex']))
worksheet.write('A13', 'Length centerline', bold)
worksheet.write('B13', str(list(storeOutput[i]['dist_cl'])))
worksheet.write('A14', 'Minimum length centerline', bold)
worksheet.write('B14', storeOutput[i]['cl_min'])
worksheet.write('C14', storeOutput[i]['cl_min_index'])
worksheet.write('A15', 'Maximum length centerline', bold)
worksheet.write('B15', storeOutput[i]['cl_max'])
worksheet.write('C15', storeOutput[i]['cl_max_index'])
elif n == 3:
worksheet.write('A2', 'Type:', bold)
worksheet.write('B2', '3 Nodes')
worksheet.write('A3', 'Minimum angle difference (degrees, Phases)',bold)
worksheet.write('B3', storeOutput[i]['point_angle_diff_min'][0])
worksheet.write_row('C3', list(storeOutput[i]['point_angle_diff_min'][1]))
worksheet.write('A4', 'Maximum angle difference (degrees, Phases)',bold)
worksheet.write('B4', storeOutput[i]['point_angle_diff_max'][0])
worksheet.write_row('C4', list(storeOutput[i]['point_angle_diff_max'][1]))
worksheet.write('A5', 'Angles for each phase (degrees)',bold)
worksheet.write_row('B5', list(storeOutput[i]['angles']))
worksheet.write('A6', 'Avg node1 position and deformations', bold)
worksheet.write('B6', str(list(storeOutput[i]['Node1'][0])))
worksheet.write_row('C6', [str(x) for x in list(storeOutput[i]['Node1'][1])])
worksheet.write('A7', 'Avg node2 position and deformations', bold)
worksheet.write('B7', str(list(storeOutput[i]['Node2'][0])))
worksheet.write_row('C7', [str(x) for x in list(storeOutput[i]['Node2'][1])])
worksheet.write('A8', 'Avg node2 position and deformations', bold)
worksheet.write('B8', str(list(storeOutput[i]['Node3'][0])))
worksheet.write_row('C8', [str(x) for x in list(storeOutput[i]['Node3'][1])])
worksheet.write('A9', 'Node Index Number', bold)
worksheet.write_row('B9', list(storeOutput[i]['NodesIndex']))
workbook.close()
# Bind event handlers
fig.eventKeyDown.Bind(on_key)
for node_point in node_points:
node_point.eventDoubleClick.Bind(select_node)
node_point.eventEnter.Bind(pick_node)
node_point.eventLeave.Bind(unpick_node)
