def _doMorph(self):
"""Apply a gaussian blur and then a tophat."""
tophatKernel = im.makeCircularKernel(self._featureRadius)
morphed = []
for image in self._images:
scaled = im.forceRange(image, 0.0, 1.0) # scale pixel values to 0-1
blurred = cv2.GaussianBlur(scaled, (0, 0), self._blurSigma)
tophat = cv2.morphologyEx(blurred, cv2.MORPH_TOPHAT, tophatKernel)
# maximize contrast by forcing the range to be 0-1 again
morphed.append(im.forceRange(tophat, 0.0, 1.0))
self._morphed = morphed
def run(self):
images = self._import(im.LoadImages, "images")
ellipses = self._import(pt.FindParticlesViaMorph, "ellipses")
color = self._param(RENDER_ELLIPSES_COLOR)
drawn = []
drawn2 = []
for image, group in zip(images, pt.groupEllipsesByFrame(ellipses)):
self.context.debug("Group len={0}", len(group))
canvas = cv2.imread(".\\Misc\\Base.tif")
canvas2 = im.toColor(im.forceRange(image, 0, 255))
for row in group:
cv2.ellipse(
canvas2,
tuple(map(int, ellipses[row]["position"])),
tuple(map(int, ellipses[row]["axes"])),
ellipses[row]["angle"] * _TO_DEGREES,
0,
360,
color,
1,
cv2.CV_AA,
0,
)
cv2.ellipse(
canvas,
tuple(map(int, ellipses[row]["position"])),
tuple(map(int, ellipses[row]["axes"])),
ellipses[row]["angle"] * _TO_DEGREES,
0,
360,
color,
1,
cv2.CV_AA,
0,
)
drawn.append(canvas)
drawn2.append(canvas2)
self._save(drawn)
self._render(drawn2)
def run(self):
diffs = self._import(im.ComputeForegroundMasks, "diffs")
mapping = lambda image: im.forceRange(image*(image > 0), 0, 255)\
.astype(np.uint8)
self._render(diffs, mapping)
def run(self):
images = self._import(im.LoadImages, "images")
ellipses = self._import(pt.FindParticlesViaMorph, "ellipses")
tracks = self._import(pt.TrackParticles, "tracksrender")
ellipse_color = self._param(RENDER_ELLIPSES_COLOR)
N = 200 # np.max(tracks[:]["trackID"])
HSV_tuples = [(x * 1.0 / N, 0.99, 0.99) for x in range(N)]
tracks_color = map(lambda x: colorsys.hsv_to_rgb(*x), HSV_tuples)
# print tracks_color
arrow_color = self._param(RENDER_TRACKS_COLOR)
drawn = []
for image, group_ellipse, group_tracks in zip(
images, pt.groupEllipsesByFrame(ellipses), pt.groupEllipsesByFrame(tracks)
):
self.context.debug("Ellipse len={0}", len(group_ellipse))
self.context.debug("Track len={0}", len(group_tracks))
canvas = im.toColor(im.forceRange(image, 0, 255))
for row in group_ellipse:
cv2.ellipse(
canvas,
tuple(map(int, ellipses[row]["position"])),
tuple(map(int, ellipses[row]["axes"])),
ellipses[row]["angle"] * _TO_DEGREES,
0,
360,
ellipse_color,
1,
cv2.CV_AA,
0,
)
for row in group_tracks:
angle = tracks[row]["angle"]
radius = tracks[row]["axes"][0]
color = tracks_color[int(tracks[row]["trackID"] - 1) % 200]
color = map(lambda x: 255 * x, color)
# print int(tracks[row]["trackID"]%200),color
cv2.ellipse(
canvas,
tuple(map(int, tracks[row]["position"])),
tuple(map(int, [radius, radius])),
tracks[row]["angle"] * _TO_DEGREES,
0,
360,
color,
2,
cv2.CV_AA,
0,
)
cv2.line(
canvas,
tuple(map(int, tracks[row]["position"])),
tuple(map(int, tracks[row]["position"] + 10 * np.array([math.cos(angle), math.sin(angle)]))),
(arrow_color),
1,
cv2.CV_AA,
0,
)
drawn.append(canvas)
self._render(drawn)