def prune_branch(self, i): # i >= 1
if i == 0:
return
temp_min, stemx, stemy, stem_index, branchx, branchy, branch_index = self.get_coord_min_distance(
i)
poly = self.roi_array[i].getFloatPolygon()
poly_npoints = poly.npoints
poly_index = branch_index
if poly_npoints / 2 >= poly_index:
# print 'if', i+1
newx = poly.xpoints[poly_index:]
newy = poly.ypoints[poly_index:]
new_poly = FloatPolygon(newx, newy)
else:
# print 'else', i+1
newx = reversed(poly.xpoints[:poly_index + 1])
newy = reversed(poly.ypoints[:poly_index + 1])
new_poly = FloatPolygon(newx, newy)
new_roi = PolygonRoi(new_poly, Roi.POLYLINE)
new_roi.fitSpline()
self.RoiManager.setRoi(new_roi, i)
def selectionInterpolateAndFitSpline(roi, interval=1.0, smooth=True):
"""implement IJ.run(imp, "Interpolate", "interval=1.0 smooth adjust");IJ.run(imp, "Fit Spline", "");"""
roi = PolygonRoi(roi.getInterpolatedPolygon(-1.0 * interval, smooth),
Roi.FREELINE)
if roi.subPixelResolution():
roi = selectionTrimFloatPolygon(roi, roi.getUncalibratedLength())
else:
roi = selectionTrimPolygon(roi, roi.getUncalibratedLength())
roi.fitSpline()
return roi
def get_distance_from_stem(self, i):
if i == 0:
return 0
min_len, stemx, stemy, stem_index, _1, _2, _3 = self.get_coord_min_distance(
i)
stem_x_array = self.roi_array[0].getFloatPolygon().xpoints[:stem_index]
stem_y_array = self.roi_array[0].getFloatPolygon().ypoints[:stem_index]
new_poly = FloatPolygon(stem_x_array, stem_y_array)
new_roi = PolygonRoi(new_poly, Roi.POLYLINE)
new_roi.fitSpline()
return get_roi_length(new_roi)
