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
def generate_cell_shape_results(rois,
intensity_channel_imp,
cal,
file_name,
no_nuclei_centroids=None,
no_enclosed_nuclei=None):
"""from list of rois, generate results describing the cell enclosed in each roi"""
pixel_width = 1.0 if cal is None else cal.pixelWidth
if no_nuclei_centroids is None:
no_nuclei_centroids = [0 for _ in rois]
if no_enclosed_nuclei is None:
no_enclosed_nuclei = [0 for _ in rois]
cell_shapes = []
for idx, roi in enumerate(rois):
intensity_channel_imp.setRoi(roi)
stats = roi.getStatistics()
I_mean = stats.mean
I_sd = stats.stdDev
area = stats.area * (pixel_width**2)
perimeter = roi.getLength()
aspect_ratio = stats.major / stats.minor
cvh_poly = roi.getConvexHull()
if cvh_poly is not None:
convex_hull_roi = PolygonRoi([x for x in cvh_poly.xpoints],
[y for y in cvh_poly.ypoints],
PolygonRoi.POLYGON)
else:
continue
print("roi length = {}".format(roi.getLength()))
print("convex hull roi length = {}".format(
convex_hull_roi.getLength()))
cell_spikiness_index = roi.getLength() / (pixel_width *
convex_hull_roi.getLength())
cell_shapes.append(
CellShapeResults(
file_name=file_name,
cell_index=idx + 1,
cell_area_um2=area,
cell_perimeter_um=perimeter,
cell_aspect_ratio=aspect_ratio,
cell_spikiness_index=cell_spikiness_index,
cell_gfp_I_mean=I_mean,
cell_gfp_I_sd=I_sd,
nuclear_centroids_in_cell=no_nuclei_centroids[idx],
nuclei_enclosed_in_cell=no_enclosed_nuclei[idx],
roi=roi))
return cell_shapes