def multiple_plot(files, image=True):
from openalea.core.path import path
from matplotlib import pyplot as plt
import rsml
def get_file(f):
exts = ['.png', '.jpg', '.tif']
fn = f.splitext()[0]
for ext in exts:
_f = path(fn + ext)
if _f.exists():
return _f
n = len(files)
f, axes = plt.subplots(1, n, sharex=True, sharey=True)
f.set_size_inches(7 * n, 5)
for i in range(n):
fn = files[i]
g = rsml.rsml2mtg(fn)
if image:
plot2d(g, img_file=get_file(fn), axis=axes[i], ms=1)
else:
plot2d(g, axis=axes[i], ms=1)
if not image:
ax = axes[0]
ax.set_ylim(ax.get_ylim()[::-1])
def rw(fn, display=False):
gs = rsml.rsml2mtg(fn)
if display:
dump = rsml.Dumper()
s = dump.dump(gs)
print s
rsml.plot3d(gs, img_dir='.')
return gs
def rw(fn, display=False): gs = rsml.rsml2mtg(fn) if display: dump = rsml.Dumper() s = dump.dump(gs) print s rsml.plot3d(gs, img_dir='.') return gs
def f2():
rsml.plot3d(gs, img_dir='.')
# OK
data = shared_data(rsml) / 'rsml' / 'rootnav'
files = [fn for fn in data.glob('*.rsml') if 'old' not in fn]
fn = files[0]
print "read ", fn
def get_file(f, ext='.png'):
return f.splitext()[0] + ext
gs = rsml.rsml2mtg(fn)
rsml.plot2d(gs, img_file=get_file(fn))
def f2():
rsml.plot3d(gs, img_dir='.')
# OK
data = shared_data(rsml)/'rsml'/'rootnav'
files = [fn for fn in data.glob('*.rsml') if 'old' not in fn]
fn= files[0]
print "read ", fn
def get_file(f, ext='.png'):
return f.splitext()[0]+ext
gs = rsml.rsml2mtg(fn)
rsml.plot2d(gs, img_file=get_file(fn))
def plot_from_file(rsml_file, ax, split_plant, label=""):
g = rsml.rsml2mtg(rsml_file)
# extract properties & measurments for all roots
root = measurements.root_order(g) # ids of lateral roots
root = [r for r,o in root.iteritems() if o==2]
length = measurements.root_length(g,root) # length of roots
ppos = measurements.parent_position(g,roots=root,distance2tip=True) # branching position on parent
plant = dict((r,g.complex(r)) for r in root) # plant id of all roots
if split_plant:
# plot root length w.r.t parent_position, for each plant
for i,pid in enumerate(sorted(set(plant.values()))):
rids = [r for r,p in plant.iteritems() if p==pid]
x = np.array([ppos[r] for r in rids])
y = np.array([length[r] for r in rids])
plot(x,y,"plant %d"%(i+1))
else:
x = np.array([ppos[r] for r in root])
y = np.array([length[r] for r in root])
plot(x,y, label)
def plot_from_file(rsml_file, ax, split_plant, label=""):
g = rsml.rsml2mtg(rsml_file)
# extract properties & measurments for all roots
root = measurements.root_order(g) # ids of lateral roots
root = [r for r, o in root.iteritems() if o == 2]
length = measurements.root_length(g, root) # length of roots
ppos = measurements.parent_position(
g, roots=root, distance2tip=True) # branching position on parent
plant = dict((r, g.complex(r)) for r in root) # plant id of all roots
if split_plant:
# plot root length w.r.t parent_position, for each plant
for i, pid in enumerate(sorted(set(plant.values()))):
rids = [r for r, p in plant.iteritems() if p == pid]
x = np.array([ppos[r] for r in rids])
y = np.array([length[r] for r in rids])
plot(x, y, "plant %d" % (i + 1))
else:
x = np.array([ppos[r] for r in root])
y = np.array([length[r] for r in root])
plot(x, y, label)