def mousePressed(self, keyEvent):
global iROI, xlist, ylist, zlist
iROI += 1
canv = imp.getCanvas()
p = canv.getCursorLoc()
z = imp.getCurrentSlice()
nCh = imp.getNChannels()
if nCh > 1:
z = (z + 1) / nCh
roi = OvalRoi(p.x - radius, p.y - radius, radius * 2, radius * 2)
roi.setName('z' + str(z) + 'cell' + str(iROI))
roi.setPosition(z)
xlist.append(p.x)
ylist.append(p.y)
zlist.append(z)
imp.setRoi(roi)
manager.addRoi(roi)
manager.runCommand('Draw')
if tempvar == []:
continue
idx = tempvar.index(max(tempvar))
start = frame[0]
metaphase = frame[idx+3]
if (division - start > 15 and division - start < 100):
if start>0:
for spot in sortedTrack:
# Fetch spot features directly from spot.
x=spot.getFeature('POSITION_X')
y=spot.getFeature('POSITION_Y')
t=spot.getFeature('FRAME')
roi2 = OvalRoi(x/dx - (6*dx), y/dy - (6*dy), 12, 12)
roi2.setPosition(int(t))
rm.add(imp, roi2, nextRoi)
nextRoi = nextRoi+1
resultstable.setValue("IMAGE_NAME", trackrowNumber, filename)
resultstable.setValue("TRACK_ID", trackrowNumber, id)
resultstable.setValue("START", trackrowNumber, start)
resultstable.setValue("METAPHASE", trackrowNumber, metaphase)
resultstable.setValue("END", trackrowNumber, division)
trackrowNumber = trackrowNumber + 1
# plot = Plot(str(id), "slice", "mean", frame, var)
# plot.show()
# break
# imp.close()
resultstable.show("Results")
# Loop through all the peak that were found
for peak in peaks:
# Print the current coordinates
print "peaks", peak.getDoublePosition(0), peak.getDoublePosition(
1), peak.getDoublePosition(2)
# Add the current peak to the Roi manager
roi = PointRoi(
peak.getDoublePosition(0) / cal.pixelWidth,
peak.getDoublePosition(1) / cal.pixelHeight)
oval = OvalRoi(
int(
peak.getDoublePosition(0) / cal.pixelWidth -
0.5 * radius / cal.pixelWidth),
int(
peak.getDoublePosition(1) / cal.pixelHeight -
0.5 * radius / cal.pixelHeight), radius / cal.pixelWidth,
radius / cal.pixelHeight)
oval.setColor(Color.RED)
# Set the Z position of the peak otherwise the peaks are all set on the same slice
oval.setPosition(
int(round(peak.getDoublePosition(2) / cal.pixelDepth)) + 1)
roi.setPosition(
int(round(peak.getDoublePosition(2) / cal.pixelDepth)) + 1)
overlay.add(oval)
imp.setOverlay(overlay)
imp.updateAndDraw()
rm.addRoi(roi)
else:
print "The detector could not process the data."
continue
idx = tempvar.index(max(tempvar))
start = frame[0]
metaphase = frame[idx + 3]
if (division - start > 15 and division - start < 100):
if start > 0:
for spot in sortedTrack:
# Fetch spot features directly from spot.
x = spot.getFeature('POSITION_X')
y = spot.getFeature('POSITION_Y')
t = spot.getFeature('FRAME')
roi2 = OvalRoi(x / dx - (6 * dx), y / dy - (6 * dy),
12, 12)
roi2.setPosition(int(t))
rm.add(imp, roi2, nextRoi)
nextRoi = nextRoi + 1
resultstable.setValue("IMAGE_NAME", trackrowNumber,
filename)
resultstable.setValue("TRACK_ID", trackrowNumber, id)
resultstable.setValue("START", trackrowNumber, start)
resultstable.setValue("METAPHASE", trackrowNumber,
metaphase)
resultstable.setValue("END", trackrowNumber, division)
trackrowNumber = trackrowNumber + 1
# plot = Plot(str(id), "slice", "mean", frame, var)
# plot.show()
# break