""" Visualisation of an MTG computed from RSML
Visualisation:
1. PlantGL and Matplotlib
2. Time-series
3. Annotations
"""
[docs]
def plot3d(g, color=None, img_dir='.'):
import openalea.plantgl.all as pgl
from copy import copy
default_color = (177, 123, 6)
colors = {}
colors[0] = pgl.Color3.RED
colors[1] = pgl.Color3.GREEN
colors[2] = pgl.Color3.BLUE
colors[3] = pgl.Color3.YELLOW
colors[4] = pgl.Color3.CYAN
colors[5] = pgl.Color3.WHITE
colors[6] = pgl.Color3.BLACK
if color is None:
def my_color(vid):
order = g.order(vid)
return colors.get(order, default_color)
color = my_color
elif not callable(color):
_color = copy(color)
color = lambda x: _color
section = pgl.Polyline2D([(0.5, 0), (0, 0.5), (-0.5, 0), (0, -0.5), (0.5, 0)])
geoms = g.property('geometry')
diams = g.property('diameter')
def sweep(vid):
_color = pgl.Material(color(vid))
if diams and (vid in diams):
diameters = diams[vid]
if isinstance(diameters, (list, tuple)):
_geom = pgl.Extrusion(
pgl.Polyline(list(map(pgl.Vector3, geoms[vid]))),
section,
pgl.Point2Array(list(zip(diams[vid], diams[vid])))
)
else:
_geom = pgl.Extrusion(
pgl.Polyline(list(map(pgl.Vector3, geoms[vid]))),
section,
pgl.Point2Array([(diameters, diameters) for i in range(len(geoms))])
)
else:
_geom = pgl.Extrusion(
pgl.Polyline(list(map(pgl.Vector3, geoms[vid]))),
section)
return pgl.Shape(_geom, _color)
scene = pgl.Scene([sweep(i) for i in geoms])
pgl.Viewer.display(scene)
return scene
[docs]
def plot2d(g, img_file=None, axis=None, root_id=None, color=None, order=None, clear=True, **args):
""" Plot MTG with grains on the initial image.
:Parameters:
- g : MTG with properties like 2D coordinates and grains.
:Optional Parameters:
- img_file : an array, or the filename, of an image to display in background
- axis : matplotlib axis to display several plot in the same figure
- root_id : if None, root_id is the first root of the MTG at scale=max_scale .
Draw all the descendants of root_id.
root_id can also be a list of vertices.
- order : draw only vertices of order 'order'
- color: function or dict to define the color of each vertex.
Format is matplotlib colors (e.g. 'b', 'g', 'y', 'r')
"""
import numpy as np
from collections.abc import Iterable
from matplotlib import pyplot as plt
if img_file is not None:
if isinstance(img_file, str):
image = plt.imread(img_file)
else:
image = img_file
if axis:
ax_img = axis.imshow(image)
axis.autoscale(enable=False)
else:
ax_img = plt.imshow(image)
plt.gca().autoscale(enable=False)
##{0:'r', 1:'g', 2:'b', 3:'y', 4:'c', 5: 'm', 6:'y', 7:'k'}
colors = 'rgbycmyk'
root_scale = g.max_scale()
polylines = g.property('geometry')
if root_id is None:
vertices = list(polylines.keys())
elif isinstance(root_id, Iterable):
vertices = [v for r in root_id
for vr in g.component_roots_at_scale(r, scale=root_scale)
for v in g.Descendants(vr)]
else:
vid = g.component_roots_at_scale(root_id, scale=root_scale)
vertices = g.Descendants(vid)
check_order = order is not None
if axis:
plot_fct = axis.plot
else:
plot_fct = plt.plot
for v in vertices:
_order = g.order(v)
if check_order and _order != order:
continue
_color = color(v) if color else colors[_order % len(colors)] # .get(_order,'r')
poly = np.array(polylines[v])
plot_fct(poly[:, 0], poly[:, 1], color=_color, marker='.')
if img_file is None:
if axis:
ax = axis
else:
ax = plt.gca()
ax.set_ylim(sorted(ax.get_ylim(), reverse=True))
ax.set_aspect('equal', adjustable='box')
[docs]
def multiple_plot(files, image=True):
'''
horizontally plot several rsml architecture over images if image is True
:param files: str list of files path
:param image: if True plot rsml architecture over the image, else plot rsml only.
:return: plot of all files in the same figure.
'''
from openalea.core.path import path
from matplotlib import pyplot as plt
import openalea.rsml as rsml
import os
def get_file(f):
exts = ['.png', '.jpg', '.tif']
# fn = f.splitext()[0] # pb with posixpath has no splitext neither string path
fn = os.path.splitext(f)[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])
