# Now use IJ1 RoiManager to display the detected regions
rm = get_roi_manager(new=True)
for label in region_labels:
region = regions.getLabelRegion(label)
# Get the center of mass of the region
center = region.getCenterOfMass()
x = center.getDoublePosition(0)
y = center.getDoublePosition(1)
roi = PointRoi(x, y)
if center.numDimensions() >= 3:
z = center.getDoublePosition(2)
roi.setPosition(int(z))
rm.addRoi(roi)
# You can also iterate over the `data` pixel by LabelRegion
cursor = region.localizingCursor()
dataRA = data.randomAccess()
while cursor.hasNext():
cursor.fwd()
dataRA.setPosition(cursor)
x = cursor.getDoublePosition(0)
y = cursor.getDoublePosition(1)
# Pixel of `data`
# Now use IJ1 RoiManager to display the detected regions
rm = get_roi_manager(new=True)
for label in region_labels:
region = regions.getLabelRegion(label)
# Get the center of mass of the region
center = region.getCenterOfMass()
x = center.getDoublePosition(0)
y = center.getDoublePosition(1)
roi = PointRoi(x, y)
if center.numDimensions() >= 3:
z = center.getDoublePosition(2)
roi.setPosition(int(z))
rm.addRoi(roi)
# You can also iterate over the `data` pixel by LabelRegion
cursor = region.localizingCursor()
dataRA = data.randomAccess()
while cursor.hasNext():
cursor.fwd()
dataRA.setPosition(cursor)
x = cursor.getDoublePosition(0)
y = cursor.getDoublePosition(1)
# Pixel of `data`
# 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."
