Commit 58e2489c authored by Lars Bittrich's avatar Lars Bittrich

Zeiss Importer with permutation variation on the marker positions to allow...

Zeiss Importer with permutation variation on the marker positions to allow changing marker sequence between Zeiss measurement and at Raman microscope -> minimize human error; but at the cost of limiting maximum angle rotations to -45,45 degrees in each euler angle
parent 5fd1cb0c
......@@ -26,6 +26,7 @@ from helperfunctions import cv2imread_fix, cv2imwrite_fix
from ramancom.ramancontrol import defaultPath
from dataset import DataSet
from scipy.optimize import least_squares
from itertools import permutations
import cv2
import numpy as np
......@@ -228,20 +229,34 @@ class ZeissImporter(QtWidgets.QDialog):
[s1*c3+c1*c2*s3, -s1*s3+c1*c2*c3, -c1*s2],
[s1*s3, s2*c3, c2]])
def err(angles_shift):
T = getRotMat(angles_shift[:3]).T.A
return (, T)-angles_shift[np.newaxis,3:]-points).ravel()
# find the transformation matrix with best fit for small angles in
# [-45°,45°] for all permutation of markers
permbest = None
pointsbest = None
for perm in permutations(range(points.shape[0])):
ppoints = points[perm,:]
def err(angles_shift):
T = getRotMat(angles_shift[:3]).T.A
return (, T) - angles_shift[np.newaxis,3:] \
- ppoints).ravel()
best = None
for i in range(100):
angle = np.pi*np.random.rand(3)-np.pi/2.
opt = least_squares(err, np.concatenate((angle, np.zeros(3))), method='lm')
if best is None or best.cost>opt.cost:
best = opt
optangles = best.x[:3]
shift = best.x[3:]
angle = np.zeros(3)
opt = least_squares(err, np.concatenate((angle, np.zeros(3))),
if permbest is None or \
print("Current best permutation:", perm, flush=True)
permbest = opt
pointsbest = ppoints
optangles = permbest.x[:3]
shift = permbest.x[3:]
T = getRotMat(optangles).T.A
e = (, T)-shift[np.newaxis,:]-points)
e = (, T)-shift[np.newaxis,:]-pointsbest)
print("Transformation angles:", optangles, flush=True)
print("Transformation shift:", shift, flush=True)
print("Transformation err:", e, flush=True)
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