def updatePointRoi(self):
# Surround with try/except to prevent blocking
# ImageJ's stack slice updater thread in case of error.
try:
# Update PointRoi
self.imp.killRoi()
point = self.nuclei[self.imp.getFrame()] # map 1-based slices
# to 0-based nuclei Z coords
if len(point) == 0:
return
IJ.log("Cell found in frame " + str(self.imp.getFrame()))
# New empty PointRoi for the current slice
roi = PointRoi(point[0], point[1])
# Style: large, red dots
roi.setSize(4) # ranges 1-4
roi.setPointType(2) # 2 is a dot (filled circle)
roi.setFillColor(Color.red)
roi.setStrokeColor(Color.red)
self.imp.setRoi(roi)
except:
IJ.error(sys.exc_info())
def findEndPoints(imageID, maskID):
endPoints1 = []
endPoints2 = []
imp = IJ.getImage()
imp.setSlice(1);
roiManager = RoiManager.getInstance2()
rois = roiManager.getRoisAsArray()
roisToBeRemoved = []
index = 0
for roi in rois:
outerBounds = roi.getBounds()
impMT, innerBounds = duplicateMaskInRoi(imp, roi)
nr, endPoint1, endPoint2 = findEndPointsInSkeleton(impMT)
if (nr==2):
endPoint1.x = endPoint1.x + outerBounds.x + innerBounds.x - 1
endPoint1.y = endPoint1.y + outerBounds.y + innerBounds.y - 1
endPoint2.x = endPoint2.x + outerBounds.x + innerBounds.x - 1
endPoint2.y = endPoint2.y + outerBounds.y + innerBounds.y - 1
endPoints1.append(endPoint1)
endPoints2.append(endPoint2)
else:
roisToBeRemoved.append(index)
impMT.close()
index = index + 1
if (len(roisToBeRemoved)>0):
roiManager.setSelectedIndexes(roisToBeRemoved)
roiManager.runCommand("Delete")
roiManager.moveRoisToOverlay(WindowManager.getImage(maskID))
inputIMP = WindowManager.getImage(imageID)
inputIMP.setOverlay(PointRoi([seq.x for seq in endPoints1], [seq.y for seq in endPoints1]), Color.magenta, 1, Color.magenta)
otherPoints = PointRoi([seq.x for seq in endPoints2], [seq.y for seq in endPoints2])
otherPoints.setStrokeColor(Color.cyan)
otherPoints.setFillColor(Color.cyan)
inputIMP.getOverlay().add(otherPoints)
def updatePointRoi(self):
# Surround with try/except to prevent blocking
# ImageJ's stack slice updater thread in case of error.
try:
# Update PointRoi
self.imp.killRoi()
points = self.nuclei[
self.imp.getSlice() -
1] # map 1-based slices to 0-based nuclei Z coords
if 0 == len(points):
IJ.log("No points for slice " + str(self.imp.getSlice()))
return
roi = PointRoi()
# Style: large, red dots
roi.setSize(4) # ranges 1-4
roi.setPointType(2) # 2 is a dot (filled circle)
roi.setFillColor(Color.red)
roi.setStrokeColor(Color.red)
# Add points
for point in points: # points are floats
roi.addPoint(self.imp, int(point[0]), int(point[1]))
self.imp.setRoi(roi)
except:
IJ.error(sys.exc_info())
