def generate_intensity_weighted_curvature(curvature_overlay,
curvature_profiles,
intensity_channel_imp,
colormap_string):
"""Generate intensity-weighted curvature image"""
w = intensity_channel_imp.getWidth()
h = intensity_channel_imp.getHeight()
curv_impRGB = curvature_overlay.clone()
IJ.run(curv_impRGB, colormap_string, "")
IJ.run(curv_impRGB, "RGB Color", "")
int_imp16 = intensity_channel_imp.clone()
base_impRGB = intensity_channel_imp.clone()
IJ.run(base_impRGB, "Grays", "")
IJ.run(base_impRGB, "RGB Color", "")
maxes = []
for fridx in range(0, int_imp16.getNFrames()):
int_imp16.setPositionWithoutUpdate(1, 1, fridx + 1)
maxes.append(int_imp16.getStatistics(Measurements.MIN_MAX).max)
mx = float(max(maxes))
for idx, profile in enumerate(curvature_profiles):
print("Frame = " + str(idx))
curv_impRGB.setPosition(idx + 1)
curvCP = curv_impRGB.getProcessor()
base_impRGB.setPosition(idx + 1)
baseCP = base_impRGB.getProcessor()
int_imp16.setPosition(idx + 1)
for chidx in range(0, 3):
c = ['r', 'g', 'b']
print("Image channel = " + c[chidx])
baseBP = ByteProcessor(base_impRGB.getWidth(),
base_impRGB.getHeight())
curvBP = ByteProcessor(base_impRGB.getWidth(),
base_impRGB.getHeight())
baseBP = baseCP.getChannel(chidx, baseBP)
curvBP = curvCP.getChannel(chidx, curvBP)
for ((x, y), c) in profile:
# ensure that no rounding issues cause pixels to fall outside image...
if x > (w - 1):
x = w - 1
if y > (h - 1):
y = h - 1
if x < 0:
x = 0
if y < 0:
y = 0
x = int(round(x))
y = int(round(y))
baseBP.putPixelValue(
x, y,
int(
curvBP.getPixel(x, y) *
float(int_imp16.getPixel(x, y)[0]) / mx))
#baseBP.putPixelValue(x, y, int(curvBP.getPixel(x,y)));
baseCP.setChannel(chidx, baseBP)
base_impRGB.setProcessor(baseCP)
base_impRGB.setTitle("Merged")
base_impRGB.show()
curv_impRGB.show()
pause_for_debug()
def hyst(ima, T1, T2):
la = ima.getWidth()
ha = ima.getHeight()
res = ByteProcessor(la, ha)
for x in xrange(la):
for y in xrange(ha):
pix = ima.getPixelValue(x, y)
if pix >= T1:
res.putPixel(x, y, 255)
elif pix >= T2:
res.putPixel(x, y, 128)
change = True
while (change):
change = False
for x in xrange(1, la - 1):
for y in xrange(1, ha - 1):
if (res.getPixelValue(x, y) == 255):
if (res.getPixelValue(x + 1, y) == 128):
change = True
res.putPixelValue(x + 1, y, 255)
if (res.getPixelValue(x - 1, y) == 128):
change = True
res.putPixelValue(x - 1, y, 255)
if (res.getPixelValue(x, y + 1) == 128):
change = True
res.putPixelValue(x, y + 1, 255)
if (res.getPixelValue(x, y - 1) == 128):
change = True
res.putPixelValue(x, y - 1, 255)
if (res.getPixelValue(x + 1, y + 1) == 128):
change = True
res.putPixelValue(x + 1, y + 1, 255)
if (res.getPixelValue(x - 1, y - 1) == 128):
change = True
res.putPixelValue(x - 1, y - 1, 255)
if (res.getPixelValue(x - 1, y + 1) == 128):
change = True
res.putPixelValue(x - 1, y + 1, 255)
if (res.getPixelValue(x + 1, y - 1) == 128):
change = True
res.putPixelValue(x + 1, y - 1, 255)
if (change):
for x in xrange(la - 2, 0, -1):
for y in xrange(ha - 2, 0, -1):
if (res.getPixelValue(x, y) == 255):
if (res.getPixelValue(x + 1, y) == 128):
change = True
res.putPixelValue(x + 1, y, 255)
if (res.getPixelValue(x - 1, y) == 128):
change = True
res.putPixelValue(x - 1, y, 255)
if (res.getPixelValue(x, y + 1) == 128):
change = True
res.putPixelValue(x, y + 1, 255)
if (res.getPixelValue(x, y - 1) == 128):
change = True
res.putPixelValue(x, y - 1, 255)
if (res.getPixelValue(x + 1, y + 1) == 128):
change = True
res.putPixelValue(x + 1, y + 1, 255)
if (res.getPixelValue(x - 1, y - 1) == 128):
change = True
res.putPixelValue(x - 1, y - 1, 255)
if (res.getPixelValue(x - 1, y + 1) == 128):
change = True
res.putPixelValue(x - 1, y + 1, 255)
if (res.getPixelValue(x + 1, y - 1) == 128):
change = True
res.putPixelValue(x + 1, y - 1, 255)
for x in xrange(la):
for y in xrange(ha):
if (res.getPixelValue(x, y) == 128):
res.putPixelValue(x, y, 0)
return res