def pointOnPixel(self, location, zFilter=True):
dotSize = self.uiState.parent().dotSize
# TODO - share with below
closestDist, closestPoint = None, None
allPoints = self.uiState._tree.flattenPoints()
for point in allPoints:
if zFilter and round(point.location[2]) != round(location[2]):
continue
radius = dotSize
resizeRadius = False
if radius is None:
radius = point.radius
resizeRadius = (point.radius is not None)
if radius is None:
radius = DendritePainter.NODE_CIRCLE_DEFAULT_RADIUS
if resizeRadius:
radius, _ = self.imgView.fromSceneDist(radius, radius)
# TODO - verify this always needs to happen, but not below?
zLoc = self.zoomedLocation(location)
zPLoc = self.zoomedLocation(point.location)
dist = deltaSz(zLoc, zPLoc)
if dist > radius:
continue
if closestDist is None or dist < closestDist:
closestDist, closestPoint = dist, point
return closestPoint
def spatialAndTreeDist(self, p1: Point, p2: Point) -> Tuple[float, float]:
"""Given two points in the tree, return both the 3D spatial distance,
as well as how far to travel along the tree."""
path1, path2 = p1.pathFromRoot(), p2.pathFromRoot()
lastMatch = 0
while lastMatch < len(path1) and lastMatch < len(
path2) and path1[lastMatch].id == path2[lastMatch].id:
lastMatch += 1
lastMatch -= 1
path1X, path1Y, path1Z = self.worldCoordPoints(path1[lastMatch:])
path2X, path2Y, path2Z = self.worldCoordPoints(path2[lastMatch:])
treeDist = 0.0
for i in range(len(path1X) - 1):
pA = (path1X[i], path1Y[i], path1Z[i])
pB = (path1X[i + 1], path1Y[i + 1], path1Z[i + 1])
treeDist += util.deltaSz(pA, pB)
for i in range(len(path2X) - 1):
pA = (path2X[i], path2Y[i], path2Z[i])
pB = (path2X[i + 1], path2Y[i + 1], path2Z[i + 1])
treeDist += util.deltaSz(pA, pB)
return self.spatialDist(p1, p2), treeDist
def cumulativeWorldLengths(self) -> List[float]:
"""Calculate the length to all points along the branch.
:returns: List of cumulative lengths, how far along the branch to get to each point."""
pointsWithRoot = self.pointsWithParentIfExists()
x, y, z = self._parentTree.worldCoordPoints(pointsWithRoot)
cumulativeLength, lengths = 0.0, []
for i in range(len(x) - 1):
edgeDistance = util.deltaSz((x[i], y[i], z[i]),
(x[i + 1], y[i + 1], z[i + 1]))
cumulativeLength += edgeDistance
lengths.append(cumulativeLength)
return lengths
def closestPointToWorldLocation(
self, targetWorldLocation: Point3D) -> Optional[Point]:
"""Given a position in world space, find the point closest to it in world space.
:param targetWorldLocation: (x, y, z) location tuple.
:returns: Point object of point closest to the target location."""
closestDist, closestPoint = None, None
allPoints = self.flattenPoints()
allX, allY, allZ = self.worldCoordPoints(allPoints)
for point, loc in zip(allPoints, zip(allX, allY, allZ)):
dist = util.deltaSz(targetWorldLocation, loc)
if closestDist is None or dist < closestDist:
closestDist, closestPoint = dist, point
return closestPoint
def punctaOnPixel(self, location, zFilter=True):
# TODO - share with above
closestDist, closestPoint = None, None
if self.windowIndex < len(self.uiState._parent.puncta):
allPoints = self.uiState._parent.puncta[self.windowIndex]
for point in allPoints:
if zFilter and round(point.location[2]) != round(location[2]):
continue
dist = deltaSz(location, point.location)
if dist > point.radius:
continue
if closestDist is None or dist < closestDist:
closestDist, closestPoint = dist, point
return closestPoint
def closestPointTo(self,
targetLocation: Point3D,
zFilter: bool = False) -> Optional[Point]:
"""Given a position in the volume, find the point closest to it in image space.
:param targetLocation: (x, y, z) location tuple.
:param zFilter: If true, only items on the same zStack are considered.
:returns: Point object of point closest to the target location."""
closestDist, closestPoint = None, None
for point in self.flattenPoints():
if zFilter and round(point.location[2]) != round(
targetLocation[2]):
continue
dist = util.deltaSz(targetLocation, point.location)
if closestDist is None or dist < closestDist:
closestDist, closestPoint = dist, point
return closestPoint
def worldLengths(self, fromIdx: int = 0) -> Tuple[float, float]:
"""Returns world length of the branch, plus the length to the last branch point.
:returns: (totalLength, totalLength to last branch)
"""
pointsWithRoot = self.pointsWithParentIfExists()[fromIdx:]
parentRadius = 0
if pointsWithRoot[0].isRoot() == False:
parentRadius = pointsWithRoot[0].returnWorldRadius(
self._parentTree._fullState())
x, y, z = self._parentTree.worldCoordPoints(pointsWithRoot)
lastBranchPoint = _lastPointWithChildren(pointsWithRoot)
totalLength, totalLengthToLastBranch = 0.0, 0.0
for i in range(len(x) - 1):
edgeDistance = util.deltaSz((x[i], y[i], z[i]),
(x[i + 1], y[i + 1], z[i + 1]))
totalLength += edgeDistance
if i < lastBranchPoint:
totalLengthToLastBranch += edgeDistance
totalLength = totalLength - parentRadius
return totalLength, totalLengthToLastBranch
def _averageIntensity(point: Point, image: np.ndarray, channel: int) -> float:
x, y, z = point.location
zAt = int(round(z))
plane = image[channel][zAt]
r = point.radius
if r is None:
r = point.radiusFromAncestors()
# HACK - find a better way to do this?
intensitySum = 0.0
intensityCount = 0
for r in range(plane.shape[0]):
for c in range(plane.shape[1]):
d = util.deltaSz((c + 0.5, r + 0.5, 0), (x, y, 0))
if d <= r:
intensitySum += 1.0 * plane[r, c]
intensityCount += 1
if intensityCount == 0:
return np.nan
return intensitySum / intensityCount / 255.0
def _pointNear(locA, locB):
return util.deltaSz(locA, locB) < 1e-9
def spatialDist(self, p1: Point, p2: Point) -> float:
"""Given two points in the tree, return the 3D spatial distance"""
x, y, z = self.worldCoordPoints([p1, p2])
p1Location = (x[0], y[0], z[0])
p2Location = (x[1], y[1], z[1])
return util.deltaSz(p1Location, p2Location)
def movePointBoundary(self, index, location):
localState = self._localState(index)
current = localState.currentPuncta()
if current is not None:
self.history.pushState()
current.radius = deltaSz(location, current.location)
def parseMatlabTree(fullState, saveState, removeOrphanBranches=True):
tree = Tree()
branchList = saveState['tree'][0]
if branchList.shape == (1, ):
branchList = branchList[0]
for i in range(branchList.shape[1]):
# HACK: Matlab uses branch index as ID:
fullState._nextBranchID = i
if len(branchList[0, i]) > 0:
# Load in branch:
branchData = branchList[0, i][0]
branch = parseMatlabBranch(
fullState,
branchData[0].T, # XYZ position
branchData[2][0], # Annotations
)
# ... and remove first point as it is duplicated data from parent:
rootPoint = branch.points[0]
branch.removePointLocally(rootPoint)
branch.setParentPoint(rootPoint)
if i == 0: # First branch is special, as first node is tree root
tree.rootPoint = rootPoint
tree.rootPoint.parentBranch = None
else:
# No branch data? Not sure what caused this in matlab...
branch = Branch(fullState.nextBranchID())
tree.addBranch(branch)
# For each point, hook up its child branches to it:
for i in range(branchList.shape[1]):
if len(branchList[0, i]) > 0:
childListForPoints = branchList[0, i][0][1][0] # Child index list
for j, childListForPoint in enumerate(childListForPoints):
for childIdx in np.nditer(childListForPoint,
['refs_ok', 'zerosize_ok']):
if tree.branches[childIdx - 1].parentPoint is not None:
oldParent = tree.branches[childIdx - 1].parentPoint
newParent = tree.branches[i].points[j - 1]
moved = deltaSz(oldParent.location, newParent.location)
if moved > 0.01:
print(
"WARNING: Branch %d parent location has moved %f"
% (childIdx - 1, moved))
print(
"%s to %s" %
(str(tree.branches[childIdx -
1].parentPoint.location),
str(tree.branches[i].points[j - 1].location)))
# HACK - add branch to children of parent, but keep old parent on branch
tree.branches[i].points[j - 1].children.append(
tree.branches[childIdx - 1])
tree.branches[
childIdx -
1].reparentTo = tree.branches[i].points[j - 1]
continue
tree.branches[childIdx - 1].setParentPoint(
tree.branches[i].points[j - 1])
if removeOrphanBranches:
tree.branches = [b for b in tree.branches if b.parentPoint is not None]
tree.transform = parseTransform(saveState['info'][0])
return tree