def get_bifurcation_triple_point(p1x, p1d, p2x, p2d, p3x, p3d):
'''
Get coordinates and derivatives of triple point between p1, p2 and p3 with derivatives.
:param p1x..p3d: Point coordinates and derivatives, numbered anticlockwise around triple point.
All derivatives point away from triple point.
Returned d1 points from triple point to p2, d2 points from triple point to p3.
:return: x, d1, d2
'''
trx1 = interpolateCubicHermite(p1x, mult(p1d, -2.0), p2x, mult(p2d, 2.0), 0.5)
trx2 = interpolateCubicHermite(p2x, mult(p2d, -2.0), p3x, mult(p3d, 2.0), 0.5)
trx3 = interpolateCubicHermite(p3x, mult(p3d, -2.0), p1x, mult(p1d, 2.0), 0.5)
trx = [ (trx1[c] + trx2[c] + trx3[c])/3.0 for c in range(3) ]
td1 = interpolateLagrangeHermiteDerivative(trx, p1x, p1d, 0.0)
td2 = interpolateLagrangeHermiteDerivative(trx, p2x, p2d, 0.0)
td3 = interpolateLagrangeHermiteDerivative(trx, p3x, p3d, 0.0)
n12 = cross(td1, td2)
n23 = cross(td2, td3)
n31 = cross(td3, td1)
norm = normalize([ (n12[c] + n23[c] + n31[c]) for c in range(3) ])
sd1 = smoothCubicHermiteDerivativesLine([ trx, p1x ], [ normalize(cross(norm, cross(td1, norm))), p1d ], fixStartDirection=True, fixEndDerivative=True)[0]
sd2 = smoothCubicHermiteDerivativesLine([ trx, p2x ], [ normalize(cross(norm, cross(td2, norm))), p2d ], fixStartDirection=True, fixEndDerivative=True)[0]
sd3 = smoothCubicHermiteDerivativesLine([ trx, p3x ], [ normalize(cross(norm, cross(td3, norm))), p3d ], fixStartDirection=True, fixEndDerivative=True)[0]
trd1 = mult(sub(sd2, add(sd3, sd1)), 0.5)
trd2 = mult(sub(sd3, add(sd1, sd2)), 0.5)
return trx, trd1, trd2
def get_curve_circle_points(x1, xd1, x2, xd2, r1, rd1, r2, rd2, xi, dmag, side, elementsCountAround):
'''
:param dmag: Magnitude of derivative on curve.
:param side: Vector in side direction of first node around.
Need not be unit or exactly normal to curve at xi.
:return: x[], d1[] around, d2[] along
'''
cx = interpolateCubicHermite(x1, xd1, x2, xd2, xi)
cxd = interpolateCubicHermiteDerivative(x1, xd1, x2, xd2, xi)
mag_cxd = magnitude(cxd)
cxd2 = interpolateCubicHermiteSecondDerivative(x1, xd1, x2, xd2, xi)
mag_cxd2 = magnitude(cxd2)
r = interpolateCubicHermite([ r1 ], [ rd1 ], [ r2 ], [ rd2 ], xi)[0]
rd = interpolateCubicHermiteDerivative([ r1 ], [ rd1 ], [ r2 ], [ rd2 ], xi)[0]
axis1 = normalize(cxd)
axis3 = normalize(cross(axis1, side))
axis2 = cross(axis3, axis1)
x, d1 = createCirclePoints(cx, mult(axis2, r), mult(axis3, r), elementsCountAround)
curvatureVector = mult(cxd2, 1.0/(mag_cxd*mag_cxd))
d2 = []
radialGrowth = rd/(mag_cxd*r)
for e in range(elementsCountAround):
radialVector = sub(x[e], cx)
dmagFinal = dmag*(1.0 - dot(radialVector, curvatureVector))
# add curvature and radius change components:
d2.append(add(mult(cxd, dmagFinal/mag_cxd), mult(radialVector, dmagFinal*radialGrowth)))
return x, d1, d2
def mouseMoveEvent(self, event):
if self._model.isStateAlign() and self._alignKeyPressed and (
self._lastMousePos is not None):
pos = [event.x(), event.y()]
delta = [
pos[0] - self._lastMousePos[0], pos[1] - self._lastMousePos[1]
]
result, eye = self._sceneviewer.getEyePosition()
result, lookat = self._sceneviewer.getLookatPosition()
result, up = self._sceneviewer.getUpVector()
lookatToEye = vectorops.sub(eye, lookat)
eyeDistance = vectorops.magnitude(lookatToEye)
front = vectorops.div(lookatToEye, eyeDistance)
right = vectorops.cross(up, front)
if self._active_button == QtCore.Qt.LeftButton:
mag = vectorops.magnitude(delta)
prop = vectorops.div(delta, mag)
axis = vectorops.add(vectorops.mult(up, prop[0]),
vectorops.mult(right, prop[1]))
angle = mag * 0.002
self._model.rotateModel(axis, angle)
elif self._active_button == QtCore.Qt.MiddleButton:
result, l, r, b, t, near, far = self._sceneviewer.getViewingVolume(
)
viewportWidth = self.width()
viewportHeight = self.height()
if viewportWidth > viewportHeight:
eyeScale = (t - b) / viewportHeight
else:
eyeScale = (r - l) / viewportWidth
offset = vectorops.add(
vectorops.mult(right, eyeScale * delta[0]),
vectorops.mult(up, -eyeScale * delta[1]))
self._model.offsetModel(offset)
elif self._active_button == QtCore.Qt.RightButton:
factor = 1.0 + delta[1] * 0.0005
if factor < 0.9:
factor = 0.9
self._model.scaleModel(factor)
self._lastMousePos = pos
else:
super(AlignmentSceneviewerWidget, self).mouseMoveEvent(event)
def mouse_move_event(self, event):
if self._lastMousePos is not None:
pixel_scale = self._scene_viewer.get_pixel_scale()
pos = [event.x() * pixel_scale, event.y() * pixel_scale]
delta = [pos[0] - self._lastMousePos[0], pos[1] - self._lastMousePos[1]]
mag = vectorops.magnitude(delta)
if mag <= 0.0:
return
result, eye = self._zinc_sceneviewer.getEyePosition()
result, lookat = self._zinc_sceneviewer.getLookatPosition()
result, up = self._zinc_sceneviewer.getUpVector()
lookatToEye = vectorops.sub(eye, lookat)
eyeDistance = vectorops.magnitude(lookatToEye)
front = vectorops.div(lookatToEye, eyeDistance)
right = vectorops.cross(up, front)
viewportWidth = self._scene_viewer.width()
viewportHeight = self._scene_viewer.height()
if self._active_button == QtCore.Qt.LeftButton:
prop = vectorops.div(delta, mag)
axis = vectorops.add(vectorops.mult(up, prop[0]), vectorops.mult(right, prop[1]))
angle = mag * 0.002
self._model.rotateModel(axis, angle)
elif self._active_button == QtCore.Qt.MiddleButton:
result, l, r, b, t, near, far = self._zinc_sceneviewer.getViewingVolume()
if viewportWidth > viewportHeight:
eyeScale = (t - b) / viewportHeight
else:
eyeScale = (r - l) / viewportWidth
offset = vectorops.add(vectorops.mult(right, eyeScale * delta[0]), vectorops.mult(up, -eyeScale * delta[1]))
self._model.offsetModel(offset)
elif self._active_button == QtCore.Qt.RightButton:
factor = 1.0 + delta[1] * 0.0005
if factor < 0.9:
factor = 0.9
self._model.scaleModel(factor)
self._lastMousePos = pos
def extractImageCorners(directory, filename):
"""
Extract the image corners from an image that is assumed to be
a DICOM image.
Corners are returned as:
[bl, br, tl, tr]
:param directory: the directory where the file given with filename exists.
:param filename: the filename of the file to interrogate.
:return: the corners of the image [bl, br, tl, tr]
"""
ds = dicom.read_file(os.path.join(directory, filename))
pixel_spacing = ds.PixelSpacing
# delta_i = float(0.1)
# delta_j = float(0.1)
delta_i = float(pixel_spacing[0])
delta_j = float(pixel_spacing[1])
orient = [float(iop) for iop in ds.ImageOrientationPatient]
pos = [float(ipp) for ipp in ds.ImagePositionPatient]
rows = ds.Rows
columns = ds.Columns
# vectorops version
orient_1 = orient[:3]
orient_2 = orient[3:]
pos_o = pos[:]
pos = vectorops.sub(
pos_o,
vectorops.mult(
vectorops.add(vectorops.mult(orient_1, 0.5),
vectorops.mult(orient_2, 0.5)), delta_i))
A = [[orient[0] * delta_i, orient[3] * delta_j, 0, pos[0]],
[orient[1] * delta_i, orient[4] * delta_j, 0, pos[1]],
[orient[2] * delta_i, orient[5] * delta_j, 0, pos[2]], [0, 0, 0, 1]]
b_tl = [0, 0, 0, 1]
b_tr = [rows, 0, 0, 1]
b_bl = [0, columns, 0, 1]
b_br = [rows, columns, 0, 1]
tl = vectorops.mxvectormult(A, b_tl)
tr = vectorops.mxvectormult(A, b_tr)
bl = vectorops.mxvectormult(A, b_bl)
br = vectorops.mxvectormult(A, b_br)
return [bl[:3], br[:3], tl[:3], tr[:3]]
def transform_coordinates(field: Field,
rotation_scale,
offset,
time=0.0) -> bool:
"""
Transform finite element field coordinates by matrix and offset, handling nodal derivatives and versions.
Limited to nodal parameters, rectangular cartesian coordinates
:param field: the coordinate field to transform
:param rotation_scale: square transformation matrix 2-D array with as many rows and columns as field components.
:param offset: coordinates offset.
:param time: time value.
:return: True on success, otherwise false.
"""
ncomp = field.getNumberOfComponents()
if (ncomp != 2) and (ncomp != 3):
print('transform_coordinates: field has invalid number of components')
return False
if (len(rotation_scale) != ncomp) or (len(offset) != ncomp):
print(
'transform_coordinates: invalid matrix number of columns or offset size'
)
return False
for matRow in rotation_scale:
if len(matRow) != ncomp:
print('transform_coordinates: invalid matrix number of columns')
return False
if field.getCoordinateSystemType(
) != Field.COORDINATE_SYSTEM_TYPE_RECTANGULAR_CARTESIAN:
print('transform_coordinates: field is not rectangular cartesian')
return False
fe_field = field.castFiniteElement()
if not fe_field.isValid():
print('transform_coordinates: field is not finite element field type')
return False
success = True
fm = field.getFieldmodule()
fm.beginChange()
cache = fm.createFieldcache()
cache.setTime(time)
nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
node_template = nodes.createNodetemplate()
node_iter = nodes.createNodeiterator()
node = node_iter.next()
while node.isValid():
node_template.defineFieldFromNode(fe_field, node)
cache.setNode(node)
for derivative in [
Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1,
Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2,
Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS3,
Node.VALUE_LABEL_D2_DS2DS3, Node.VALUE_LABEL_D3_DS1DS2DS3
]:
versions = node_template.getValueNumberOfVersions(
fe_field, -1, derivative)
for v in range(versions):
result, values = fe_field.getNodeParameters(
cache, -1, derivative, v + 1, ncomp)
if result != RESULT_OK:
success = False
else:
new_values = vectorops.matrix_vector_mult(
rotation_scale, values)
if derivative == Node.VALUE_LABEL_VALUE:
new_values = vectorops.add(new_values, offset)
result = fe_field.setNodeParameters(
cache, -1, derivative, v + 1, new_values)
if result != RESULT_OK:
success = False
node = node_iter.next()
fm.endChange()
if not success:
print('transform_coordinates: failed to get/set some values')
return success
def translateModel(self, relativeOffset):
self._alignSettings["offset"] = add(self._alignSettings["offset"],
relativeOffset)
self._applyAlignSettings()
def make_tube_bifurcation_points(paCentre, pax, pad2, c1Centre, c1x, c1d2, c2Centre, c2x, c2d2):
'''
Gets first ring of coordinates and derivatives between parent pa and
children c1, c2, and over the crotch between c1 and c2.
:return rox, rod1, rod2, cox, cod1, cod2
'''
paCount = len(pax)
c1Count = len(c1x)
c2Count = len(c2x)
pac1Count, pac2Count, c1c2Count = get_tube_bifurcation_connection_elements_counts(paCount, c1Count, c2Count)
# convert to number of nodes, includes both 6-way points
pac1NodeCount = pac1Count + 1
pac2NodeCount = pac2Count + 1
c1c2NodeCount = c1c2Count + 1
paStartIndex = 0
c1StartIndex = 0
c2StartIndex = 0
pac1x = [ None ]*pac1NodeCount
pac1d1 = [ None ]*pac1NodeCount
pac1d2 = [ None ]*pac1NodeCount
for n in range(pac1NodeCount):
pan = (paStartIndex + n) % paCount
c1n = (c1StartIndex + n) % c1Count
x1, d1, x2, d2 = pax[pan], mult(pad2[pan], 2.0), c1x[c1n], mult(c1d2[c1n], 2.0)
pac1x [n] = interpolateCubicHermite(x1, d1, x2, d2, 0.5)
pac1d1[n] = [ 0.0, 0.0, 0.0 ]
pac1d2[n] = mult(interpolateCubicHermiteDerivative(x1, d1, x2, d2, 0.5), 0.5)
paStartIndex2 = paStartIndex + pac1Count
c1StartIndex2 = c1StartIndex + pac1Count
c2StartIndex2 = c2StartIndex + c1c2Count
pac2x = [ None ]*pac2NodeCount
pac2d1 = [ None ]*pac2NodeCount
pac2d2 = [ None ]*pac2NodeCount
for n in range(pac2NodeCount):
pan = (paStartIndex2 + n) % paCount
c2n = (c2StartIndex2 + n) % c2Count
x1, d1, x2, d2 = pax[pan], mult(pad2[pan], 2.0), c2x[c2n], mult(c2d2[c2n], 2.0)
pac2x [n] = interpolateCubicHermite(x1, d1, x2, d2, 0.5)
pac2d1[n] = [ 0.0, 0.0, 0.0 ]
pac2d2[n] = mult(interpolateCubicHermiteDerivative(x1, d1, x2, d2, 0.5), 0.5)
c1c2x = [ None ]*c1c2NodeCount
c1c2d1 = [ None ]*c1c2NodeCount
c1c2d2 = [ None ]*c1c2NodeCount
for n in range(c1c2NodeCount):
c1n = (c1StartIndex2 + n) % c1Count
c2n = (c2StartIndex2 - n) % c2Count # note: reversed
x1, d1, x2, d2 = c2x[c2n], mult(c2d2[c2n], -2.0), c1x[c1n], mult(c1d2[c1n], 2.0)
c1c2x [n] = interpolateCubicHermite(x1, d1, x2, d2, 0.5)
c1c2d1[n] = [ 0.0, 0.0, 0.0 ]
c1c2d2[n] = mult(interpolateCubicHermiteDerivative(x1, d1, x2, d2, 0.5), 0.5)
# get hex triple points
hex1, hex1d1, hex1d2 = get_bifurcation_triple_point(
pax[paStartIndex], mult(pad2[paStartIndex], -1.0),
c1x[c1StartIndex], c1d2[c1StartIndex],
c2x[c1StartIndex], c2d2[c2StartIndex])
hex2, hex2d1, hex2d2 = get_bifurcation_triple_point(
pax[paStartIndex2], mult(pad2[paStartIndex2], -1.0),
c2x[c2StartIndex2], c2d2[c2StartIndex2],
c1x[c1StartIndex2], c1d2[c1StartIndex2])
# smooth around loops through hex points to get d1
loop1x = [ hex2 ] + pac2x[1:-1] + [ hex1 ]
loop1d1 = [ [ -d for d in hex2d2 ] ] + pac2d1[1:-1] + [ hex1d1 ]
loop2x = [ hex1 ] + pac1x[1:-1] + [ hex2 ]
loop2d1 = [ [ -d for d in hex1d2 ] ] + pac1d1[1:-1] + [ hex2d1 ]
loop1d1 = smoothCubicHermiteDerivativesLine(loop1x, loop1d1, fixStartDirection=True, fixEndDirection=True, magnitudeScalingMode=DerivativeScalingMode.HARMONIC_MEAN)
loop2d1 = smoothCubicHermiteDerivativesLine(loop2x, loop2d1, fixStartDirection=True, fixEndDirection=True, magnitudeScalingMode=DerivativeScalingMode.HARMONIC_MEAN)
# smooth over "crotch" between c1 and c2
crotchx = [ hex2 ] + c1c2x[1:-1] + [ hex1 ]
crotchd1 = [ add(hex2d1, hex2d2) ] + c1c2d1[1:-1] + [ [ (-hex1d1[c] - hex1d2[c]) for c in range(3) ] ]
crotchd1 = smoothCubicHermiteDerivativesLine(crotchx, crotchd1, fixStartDerivative=True, fixEndDerivative=True, magnitudeScalingMode=DerivativeScalingMode.HARMONIC_MEAN)
rox = [ hex1 ] + pac1x[1:-1] + [ hex2 ] + pac2x[1:-1]
rod1 = [ loop1d1[-1] ] + loop2d1[1:] + loop1d1[1:-1]
rod2 = [ [ -d for d in loop2d1[ 0] ] ] + pac1d2[1:-1] + [ [ -d for d in loop1d1[0] ] ] + pac2d2[1:-1]
cox = crotchx [1:-1]
cod1 = crotchd1[1:-1]
cod2 = c1c2d2[1:-1]
return rox, rod1, rod2, cox, cod1, cod2, paStartIndex, c1StartIndex, c2StartIndex
def mouseMoveEvent(self, event):
if self._editNode:
mousePos = [event.x(), event.y()]
nodeset = self._editNode.getNodeset()
fieldmodule = nodeset.getFieldmodule()
with ChangeManager(fieldmodule):
meshEditsNodeset = self._model.getOrCreateMeshEditsNodesetGroup(
nodeset)
meshEditsNodeset.addNode(self._editNode)
editCoordinateField = coordinateField = self._editGraphics.getCoordinateField(
)
localScene = self._editGraphics.getScene(
) # need set local scene to get correct transformation
if coordinateField.getCoordinateSystemType(
) != Field.COORDINATE_SYSTEM_TYPE_RECTANGULAR_CARTESIAN:
editCoordinateField = fieldmodule.createFieldCoordinateTransformation(
coordinateField)
editCoordinateField.setCoordinateSystemType(
Field.COORDINATE_SYSTEM_TYPE_RECTANGULAR_CARTESIAN)
fieldcache = fieldmodule.createFieldcache()
fieldcache.setNode(self._editNode)
componentsCount = coordinateField.getNumberOfComponents()
result, initialCoordinates = editCoordinateField.evaluateReal(
fieldcache, componentsCount)
if result == RESULT_OK:
for c in range(componentsCount, 3):
initialCoordinates.append(0.0)
pointattr = self._editGraphics.getGraphicspointattributes()
editVectorField = vectorField = pointattr.getOrientationScaleField(
)
pointBaseSize = pointattr.getBaseSize(3)[1][0]
pointScaleFactor = pointattr.getScaleFactors(3)[1][0]
if editVectorField.isValid() and (vectorField.getNumberOfComponents() == componentsCount) \
and (pointBaseSize == 0.0) and (pointScaleFactor != 0.0):
if vectorField.getCoordinateSystemType(
) != Field.COORDINATE_SYSTEM_TYPE_RECTANGULAR_CARTESIAN:
editVectorField = fieldmodule.createFieldCoordinateTransformation(
vectorField, coordinateField)
editVectorField.setCoordinateSystemType(
Field.
COORDINATE_SYSTEM_TYPE_RECTANGULAR_CARTESIAN)
result, initialVector = editVectorField.evaluateReal(
fieldcache, componentsCount)
for c in range(componentsCount, 3):
initialVector.append(0.0)
initialTipCoordinates = [
(initialCoordinates[c] +
initialVector[c] * pointScaleFactor)
for c in range(3)
]
windowCoordinates = self.projectLocal(
initialTipCoordinates[0], initialTipCoordinates[1],
initialTipCoordinates[2], localScene)
finalTipCoordinates = self.unprojectLocal(
mousePos[0], -mousePos[1], windowCoordinates[2],
localScene)
finalVector = [
(finalTipCoordinates[c] - initialCoordinates[c]) /
pointScaleFactor for c in range(3)
]
result = editVectorField.assignReal(
fieldcache, finalVector)
else:
windowCoordinates = self.projectLocal(
initialCoordinates[0], initialCoordinates[1],
initialCoordinates[2], localScene)
xa = self.unprojectLocal(self._lastMousePos[0],
-self._lastMousePos[1],
windowCoordinates[2],
localScene)
xb = self.unprojectLocal(mousePos[0], -mousePos[1],
windowCoordinates[2],
localScene)
finalCoordinates = [
(initialCoordinates[c] + xb[c] - xa[c])
for c in range(3)
]
result = editCoordinateField.assignReal(
fieldcache, finalCoordinates)
del editVectorField
del editCoordinateField
del fieldcache
self._lastMousePos = mousePos
event.accept()
return
if self._alignMode != self.AlignMode.NONE:
mousePos = [event.x(), event.y()]
delta = [
mousePos[0] - self._lastMousePos[0],
mousePos[1] - self._lastMousePos[1]
]
result, eye = self._sceneviewer.getEyePosition()
result, lookat = self._sceneviewer.getLookatPosition()
result, up = self._sceneviewer.getUpVector()
lookatToEye = sub(eye, lookat)
eyeDistance = magnitude(lookatToEye)
front = div(lookatToEye, eyeDistance)
right = cross(up, front)
if self._alignMode == self.AlignMode.ROTATION:
mag = magnitude(delta)
prop = div(delta, mag)
axis = add(mult(up, prop[0]), mult(right, prop[1]))
angle = mag * 0.002
# print('delta', delta, 'axis', axis, 'angle', angle)
self._model.interactionRotate(axis, angle)
elif self._alignMode == self.AlignMode.SCALE:
factor = 1.0 + delta[1] * 0.0005
if factor < 0.9:
factor = 0.9
self._model.interactionScale(factor)
elif self._alignMode == self.AlignMode.TRANSLATION:
result, l, r, b, t, near, far = self._sceneviewer.getViewingVolume(
)
viewportWidth = self.width()
viewportHeight = self.height()
if viewportWidth > viewportHeight:
eyeScale = (t - b) / viewportHeight
else:
eyeScale = (r - l) / viewportWidth
offset = add(mult(right, eyeScale * delta[0]),
mult(up, -eyeScale * delta[1]))
self._model.interactionTranslate(offset)
self._lastMousePos = mousePos
event.accept()
return
else:
super(NodeEditorSceneviewerWidget, self).mouseMoveEvent(event)