def bleb_area(membrane_edge, midpoint_anchor):
"""calculate the area of the drawn bleb, accounting for membrane crossing line joining anchors"""
poly = membrane_edge.getFloatPolygon()
xs = [x for x in poly.xpoints]
ys = [y for y in poly.ypoints]
rotangle = membrane_edge.getAngle(int(round(xs[0])), int(round(
ys[0])), int(round(xs[-1])), int(round(ys[-1]))) / 180 * math.pi
rotY = [(x * math.sin(rotangle) + y * math.cos(rotangle))
for x, y in zip(xs, ys)]
rotYmpa = midpoint_anchor[0] * math.sin(
rotangle) + midpoint_anchor[1] * math.cos(rotangle)
meanRotY = sum(rotY) / len(rotY)
seg1 = rotY[:int(round(len(rotY) / 2))]
seg1.reverse()
seg2 = rotY[int(round(len(rotY) / 2)):]
if rotYmpa > rotY[0]:
idx1 = len(seg1) - seg1.index(min(seg1))
idx2 = int(round(len(rotY) / 2)) + seg2.index(min(seg2))
else:
idx1 = len(seg1) - seg1.index(max(seg1))
idx2 = int(round(len(rotY) / 2)) + seg2.index(max(seg2))
area_poly_xs = xs[idx1:idx2 + 1]
area_poly_ys = ys[idx1:idx2 + 1]
len_roi = PolygonRoi(area_poly_xs, area_poly_ys, Roi.POLYLINE)
length = len_roi.getLength()
area_roi = PolygonRoi(area_poly_xs, area_poly_ys, Roi.POLYGON)
area = area_roi.getStatistics().area
#print(area);
return length, area, area_roi
membrane_indices_available = [
membrane['position number'] for membrane in membranes
]
for membrane_index in membrane_indices_available:
print("Analysing frame " + str(frame_idx) + ", membrane_index = " +
str(membrane_index))
membrane_xy_list = membranes[membrane_indices_available.index(
membrane_index)]['roi']
roi = PolygonRoi([x for x, y in membrane_xy_list],
[y for x, y in membrane_xy_list], Roi.FREELINE)
imp.setRoi(roi)
roi.setStrokeWidth(line_width)
if line_width > 1:
IJ.run(imp, "Line to Area", "")
roi = imp.getRoi()
stats = roi.getStatistics()
output.append((t, membrane_index, stats.mean, stats.max, stats.min,
stats.median, stats.stdDev))
imp.killRoi()
print(output)
# save output to csv
csv_path = os.path.join(os.path.dirname(edges_file_path),
"intensity_stats.csv")
f = open(csv_path, 'wb')
try:
writer = csv.writer(f)
writer.writerow([
"Time, s", "Membrane index", "Mean intensity", "Max intensity",
"Min intensity", "Median intensity", "Std intensity"
])
