def main(jsonfile):
with open(jsonfile, 'r') as data_file1:
data1 = json.load(data_file1)
ts1_fname = data1["tilespec1"].replace("file://", "")
with open(ts1_fname, 'r') as ts_file1:
ts1 = json.load(ts_file1)
ts1_indexed = utils.index_tilespec(ts1)
# The mfovs list in the match file must be a subset of the mfovs list in the tilespec
mfov1_to_center2 = {}
for mfov_match in data1["matches"]:
mfov1_to_center2[mfov_match["mfov1"]] = np.array(
mfov_match["section2_center"])
centers2 = [
mfov1_to_center2[mfov1] for mfov1 in sorted(mfov1_to_center2.keys())
]
mfovs1_bb = [
BoundingBox.read_bbox_from_ts(ts1_indexed[mfov].values())
for mfov in sorted(mfov1_to_center2.keys())
]
centers1 = [
np.array([(bb.from_x + bb.to_x) / 2.0, (bb.from_y + bb.to_y) / 2.0])
for bb in mfovs1_bb
]
pointmatches = []
for i in range(0, len(centers1)):
pointmatches.append((centers1[i], centers2[i]))
if (len(pointmatches) == 0):
return
point1s = map(list, zip(*pointmatches))[0]
point1s = map(lambda x: np.matrix(x).T, point1s)
point2s = map(list, zip(*pointmatches))[1]
point2s = map(lambda x: np.matrix(x).T, point2s)
centroid1 = [
np.array(point1s)[:, 0].mean(),
np.array(point1s)[:, 1].mean()
]
centroid2 = [
np.array(point2s)[:, 0].mean(),
np.array(point2s)[:, 1].mean()
]
h = np.matrix(np.zeros((2, 2)))
for i in range(0, len(point1s)):
sumpart = (np.matrix(point1s[i]) - centroid1).dot(
(np.matrix(point2s[i]) - centroid2).T)
h = h + sumpart
U, S, Vt = np.linalg.svd(h)
R = Vt.T.dot(U.T)
plt.figure()
for i in range(0, len(pointmatches)):
point1, point2 = pointmatches[i]
point1 = np.matrix(point1 - centroid1).dot(R.T).tolist()[0]
point2 = point2 - centroid2
plt.plot([point1[0], point2[0]], [point1[1], point2[1]])
plt.scatter(point1[0], point1[1])
axis('equal')
