def test_s2a(ds, group=2, start=0):
from rhizoscan.root.graph.to_tree import make_tree
from rhizoscan.root.graph.to_tree import set_downward_segment
from rhizoscan import geometry as geo
d1 = ds[group][start]
d2 = ds[group][start + 1]
d1.load()
d2.load()
g1 = d1.graph
g2 = d2.graph
t1 = make_tree(g1)
T = geo.dot(geo.inv(d1.image_transform), d2.image_transform)
# set graph into the same frame as tree
# -------------------------------------
g2 = g2.copy()
g2.node = g2.node.copy()
g2.node.position = geo.transform(T=T, coordinates=g2.node.position)
g2.segment = g2.segment.copy() # copy with transformed _node_list
g2.segment._node_list = g2.node # maybe not useful...
return (t1, g2, T) + seg_to_axe_distance(t1, g2)
g2 = set_downward_segment(g2) ## for debug visualisation
t2 = axe_projection(t1, g2, T)
def track_plate(sequence, step=1, stand=False):
"""
##Obsolete
warning: since implementation find_plate changed fitting direction => NOT WORKING
"""
import matplotlib.pyplot as plt
if isinstance(sequence, basestring):
import glob
sequence = glob.glob(sequence)
plt.ion()
plt.gray()
for f in sequence:
img = _pad(_Image(f, color='gray', format='f'),
200,
200,
fill_value='nearest')
H = find_plate(img,
border=0.06,
plate_width=1200,
fit='homography',
white_stand=stand)
im = _geo.transform(img, H, ((0, 1200 + 1, step), (0, 1200 + 1, step)))
plt.imshow(im, hold=0)
k = raw_input(" 'q' to quit':")
if k == 'q': break
def correction_projection(p,i, box_size):
from rhizoscan import geometry as geo
Y,X = np.mgrid[map(lambda x: slice(x+1),p.cluster[0].shape)]
x,y = box_size*geo.transform(T=p.transform[0],coordinates=(X,Y)) # to 125mm square box
du = (np.diff(x[:-1,:],axis=1)**2 + np.diff(y[:-1,:],axis=1)**2)**.5
dv = (np.diff(x[:,:-1],axis=0)**2 + np.diff(y[:,:-1],axis=0)**2)**.5
return du, dv
def E(T):
return _np.sum(
_geo.transform(dmap, T=_np.reshape(T, (3, 3)),
coordinates=ind))
def E(T):
return _np.sum(
_geo.transform(dmap, T=rigid(*T), coordinates=ind, cval=1))