def getconfig(configfile=None):
if configfile is None:
configfile = shared_data(alinea.phenomenal) / 'config.cfg'
p = PhenomenalConfigParser()
p.read(configfile)
if p.has_option('General', 'configdir'):
confdir = p.get('General', 'configdir')
if confdir == 'SharedData':
confdir = str(shared_data(alinea.phenomenal))
for s in p._sections:
for it in p.items(s, raw=True):
if it[0] == 'mask' or it[0] == 'background':
p.set(s, it[0],
os.path.join(confdir, os.path.basename(it[1])))
if p.has_option('General', 'config_images_dir'):
confdir = p.get('General', 'config_images_dir')
if confdir == 'SharedData':
confdir = str(shared_data(alinea.phenomenal))
s = 'config_images'
for it in p.items(s, raw=True):
p.set(s, it[0], os.path.join(confdir, os.path.basename(it[1])))
return p
def __init__(self, banner_path=None, content=None):
QtGui.QWidget.__init__(self)
if banner_path is None:
banner_path = shared_data(openalea.oalab, 'icons/logo/banner.png')
self._lay = QtGui.QVBoxLayout(self)
p = QtGui.QSizePolicy
self._banner = QtGui.QLabel()
self._banner.setStyleSheet("QLabel { background-color : #ffffff;}")
banner = QtGui.QPixmap(banner_path)
size = banner.size()
self._banner.setPixmap(banner)
self._content = QWebView()
if hasattr(self._content, "setReadOnly"):
self._content.setReadOnly(True)
self._content.setHtml(content)
self._footer = QtGui.QLabel()
self._footer.setStyleSheet("QLabel { background-color : #459454;}")
self._lay.addWidget(self._banner)
self._lay.addWidget(self._content)
self._lay.addWidget(self._footer)
self._lay.setContentsMargins(0, 0, 0, 0)
self._lay.setSpacing(0)
def createTutorialMenu(self):
self.menuTutorials.clear()
iconfile = qt.QtGui.QIcon()
iconfile.addPixmap(qt.QtGui.QPixmap(":/images/icons/codefile.png"),qt.QtGui.QIcon.Normal,qt.QtGui.QIcon.Off)
iconfolder = qt.QtGui.QIcon()
iconfolder.addPixmap(qt.QtGui.QPixmap(":/images/icons/fileopen.png"),qt.QtGui.QIcon.Normal,qt.QtGui.QIcon.Off)
from openalea.deploy.shared_data import shared_data
import openalea.lpy
shared_data_path = shared_data(openalea.lpy.__path__, share_path='share/tutorial')
if not shared_data_path is None:
import os
cpath = os.path.abspath(shared_data_path)
cmenu = self.menuTutorials
toprocess = [(cpath,cmenu)]
while len(toprocess) > 0:
cpath,cmenu = toprocess.pop(0)
for fname in os.listdir(cpath):
absfname = os.path.join(cpath,fname)
if os.path.isdir(absfname):
childmenu = cmenu.addMenu(iconfolder,os.path.basename(str(fname)))
toprocess.append( (absfname,childmenu) )
qt.QtCore.QObject.connect(childmenu,qt.QtCore.SIGNAL("triggered(QAction *)"),self.recentMenuAction)
elif fname[-4:] == '.lpy':
action = qt.QtGui.QAction(os.path.basename(str(fname)),cmenu)
action.setData(to_qvariant(absfname))
action.setIcon(iconfile)
cmenu.addAction(action)
def updateColormap(self, colormap_index):
self.colormap_name = self.combobox.itemText(colormap_index)
colormap_path = shared_data(openalea.oalab, 'colormaps/' + self.colormap_name + '.lut')
colormap = colormap_from_file(colormap_path, name=self.colormap_name)
self.setValue(dict(name=self.colormap_name, color_points=colormap._color_points))
def _repr_html_(self):
import openalea.core
import base64
from openalea.deploy.shared_data import shared_data
from openalea.core.project.formatting.html import html_metainfo_summary, html_item_summary
from openalea.core.formatting.util import obj_icon_path
from IPython.display import Image
stylesheet_path = shared_data(openalea.core, 'stylesheet.css')
if stylesheet_path and stylesheet_path.isfile():
with open(stylesheet_path) as f:
stylesheet = f.read()
html = '<style>%s</style>' % stylesheet
else:
html = ''
icon = obj_icon_path(self, paths=[self.path])
if icon:
data = base64.b64encode(Image(filename=icon)._repr_png_()).decode('ascii')
image = '<image width="64px" style="vertical-align:middle;" src="data:image/png;base64,%s">' % data
else:
image = ''
args = dict(image=image, title=self.title)
html += '<div class="summary"><p class="title">%(image)s%(title)s</p>' % args
html += '\n<hr>'
html += html_metainfo_summary(self)
html += html_item_summary(self)
html += '</div>'
return html
def loadconfig(config='SideCamera2013_ZoomOut.cfg'):
""" load a configuration from shared data directory
"""
confdir = shared_data(alinea.phenomenal)
p = PhenomenalConfigParser()
p.read(confdir / config)
d = p.as_dict()
if p.has_section('config_images'):
for it in p.items('config_images', raw=True):
flag = cv2.IMREAD_UNCHANGED
if it[1].endswith('mask'):
flag = cv2.IMREAD_GRAYSCALE
d['config_images'][it[0]] = cv2.imread(confdir / it[1], flag)
if p.has_section('config_images_elcom'):
for it in p.items('config_images_elcom', raw=True):
flag = cv2.IMREAD_UNCHANGED
if it[1].endswith('mask'):
flag = cv2.IMREAD_GRAYSCALE
d['config_images_elcom'][it[0]] = cv2.imread(confdir / it[1], flag)
for key in d:
for sub_key in d[key]:
if str(sub_key).startswith('mask'):
d[key][sub_key] = cv2.imread(confdir / str(d[key][sub_key]),
cv2.IMREAD_GRAYSCALE)
if str(sub_key).startswith('background'):
d[key][sub_key] = cv2.imread(confdir / str(d[key][sub_key]),
cv2.IMREAD_UNCHANGED)
return d
def get_filename(name):
from os.path import join, exists
from openalea.deploy.shared_data import shared_data
import openalea.vmango
share_dir = shared_data(openalea.vmango,
share_path=join("share", 'digitized_mango_mtg'))
return join(share_dir, name)
def test_all_lpy_controls():
from openalea.plantlab.lpycontrol import import_lpy_controls
from openalea.deploy.shared_data import shared_data
import openalea.lpy
lpydir = shared_data(openalea.lpy.__path__, share_path='share/tutorial')
for lpypath in lpydir.walkfiles('*.lpy'):
import_lpy_controls(lpypath)
def icon_path(filepath, default=None, paths=None, packages=None):
if filepath is None or isinstance(filepath, basestring) and filepath.startswith(':/'):
return None
if paths is None:
paths = []
if packages is None:
packages = []
# Search filename in all paths given by user
_paths = [Path(filepath)] + [Path(p) / filepath for p in paths]
# Search icons generated by oalab
_paths += [Path(p) / '._icon.png' for p in paths]
# If a path is found, try to find absolute path
# Try to get icon path from object
for path in _paths:
if path.isfile():
return path
# Search in shared icons provided by packages given by user
for package in packages:
for path in (filepath, 'icons/%s' % filepath):
path = shared_data(package, path)
if path and path.isfile():
return path
def import_mtgfile(filename):
"""
parameters:
-----------
filename : names of mtg
return:
-------
a function which import mtg corresponding to the mtg names
"""
def name(f):
"return base name without extension"
return f.basename().splitext()[0]
filenames = filename
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
mtgfile = dict((k, f) for k, f in mtg_path.items() if k in filenames)
if len(filenames) == 1:
g = MTG(mtgfile[filenames[0]])
return g
else:
metaMTG = MTG()
for i in mtgfile:
metaMTG = algo.union(metaMTG, MTG(mtgfile[i]))
return metaMTG
def _repr_html_(self):
import openalea.core
import base64
from openalea.deploy.shared_data import shared_data
from openalea.core.project.formatting.html import html_metainfo_summary, html_item_summary
from openalea.core.formatting.util import obj_icon_path
from IPython.display import Image
stylesheet_path = shared_data(openalea.core, 'stylesheet.css')
if stylesheet_path and stylesheet_path.isfile():
with open(stylesheet_path) as f:
stylesheet = f.read()
html = '<style>%s</style>' % stylesheet
else:
html = ''
icon = obj_icon_path(self, paths=[self.path])
if icon:
data = base64.b64encode(
Image(filename=icon)._repr_png_()).decode('ascii')
image = '<image width="64px" style="vertical-align:middle;" src="data:image/png;base64,%s">' % data
else:
image = ''
args = dict(image=image, title=self.title)
html += '<div class="summary"><p class="title">%(image)s%(title)s</p>' % args
html += '\n<hr>'
html += html_metainfo_summary(self)
html += html_item_summary(self)
html += '</div>'
return html
def test_load_discrete():
import cPickle
from openalea.deploy.shared_data import shared_data
import rsml
filename = shared_data(rsml) / 'discrete.bmtg'
with open(filename) as f:
g = cPickle.load(f)
return g
def updateColormap(self,colormap_index):
self.colormap_name = self.combobox.itemText(colormap_index)
from tissuelab.gui.vtkviewer.colormap_utils import Colormap, colormap_from_file
colormap_path = shared_data(tissuelab,'colormaps/'+self.colormap_name+'.lut')
colormap = colormap_from_file(colormap_path,name=self.colormap_name)
self.setValue(dict(name=self.colormap_name,color_points=colormap._color_points))
def test_obj_reading():
dirname = shared_data(openalea.cellcomplex)
filename = os.path.join(dirname, "icosahedron.obj")
topomesh = read_obj_property_topomesh(filename)
print topomesh.nb_wisps(0)
assert topomesh.nb_wisps(0) == 12
assert topomesh.nb_wisps(2) == 20
def test_length():
data = shared_data(openalea.groalea)
f = data / 'length' / 'L_XEG_r.xml'
parser = Parser()
g, scene = parser.parse(f)
mtg = topo.spanning_mtg(g)
return mtg, g, scene
def updateColormap(self, colormap_index):
self.colormap_name = self.combobox.itemText(colormap_index)
from openalea.oalab.colormap.colormap_utils import colormap_from_file
colormap_path = shared_data(openalea.oalab, 'colormaps/' + self.colormap_name + '.lut')
colormap = colormap_from_file(colormap_path, name=self.colormap_name)
self.setValue(dict(name=self.colormap_name, color_points=colormap._color_points))
def test_load_discrete():
import cPickle
from openalea.deploy.shared_data import shared_data
import rsml
filename = shared_data(rsml)/'discrete.bmtg'
with open(filename) as f:
g = cPickle.load(f)
return g
def test_length():
data = shared_data(openalea.groalea)
f = data / 'length' / 'L_XEG_r.xml'
parser = Parser()
g, scene = parser.parse(f)
mtg = topo.spanning_mtg(g)
return mtg, g, scene
def test_p():
data = shared_data(openalea.groalea)
f = data / 'P' / 'P_3Run_Interface_XEG.xml'
parser = Parser()
g, scene = parser.parse(f)
mtg = topo.spanning_mtg(g)
return mtg, g, scene
def list_colormaps():
colormap_names = []
colormaps_path = Path(shared_data(openalea.oalab, 'colormaps/grey.lut')).parent
for colormap_file in colormaps_path.walkfiles('*.lut'):
colormap_name = str(colormap_file.name[:-4])
colormap_names.append(colormap_name)
colormap_names.sort()
return colormap_names
def test_extraction_at_node_scale():
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
gariguette = read_mtg_file(mtg_path['Gariguette'])
gariguette_extraction_at_node_scale = extract_at_node_scale(gariguette)
assert len(gariguette_extraction_at_node_scale) == 784
gariguette_axillary_prod = prob_axillary_production(gariguette, order=0)
assert len(gariguette_axillary_prod) == 19
def test_p():
data = shared_data(openalea.groalea)
f = data/'P'/'P_3Run_Interface_XEG.xml'
parser = Parser()
g, scene = parser.parse(f)
mtg = topo.spanning_mtg(g)
return mtg, g, scene
def __init__(self, parent=None, style=None):
AbstractListener.__init__(self)
QtGui.QWidget.__init__(self, parent=parent)
self.world = None
self.name = ""
self._controls = []
self._manager = ControlContainer()
self.interpreter = get_interpreter()
self.interpreter.locals['draco_control'] = self
self._layout = QtGui.QVBoxLayout(self)
self._title_img = QtGui.QWidget()
title_layout = QtGui.QHBoxLayout(self._title_img)
p = QtGui.QSizePolicy
pixmap_dirname = shared_data(openalea.draco_stem)
icon_img = QtGui.QLabel()
pixmap_icon = QtGui.QPixmap(os.path.join(pixmap_dirname,"../../src/openalea/draco_stem/draco_oalab/widget/draco_icon.png"))
icon_img.setPixmap(pixmap_icon)
icon_img.setScaledContents(True)
icon_img.setFixedWidth(60)
icon_img.setFixedHeight(60)
# icon_img.setSizePolicy(p(p.Expanding, p.Maximum))
title_layout.addWidget(icon_img)
# title_layout.addSpacing(20)
title_img = QtGui.QLabel()
pixmap_title = QtGui.QPixmap(os.path.join(pixmap_dirname,"../../src/openalea/draco_stem/draco_oalab/widget/draco_title.png"))
title_img.setPixmap(pixmap_title)
title_img.setScaledContents(True)
# title_img.setSizePolicy(p(p.Expanding, p.Maximum))
title_img.setFixedWidth(140)
title_img.setFixedHeight(60)
title_layout.addWidget(title_img)
# title_layout.addSpacing(20)
title_label = QtGui.QLabel(u'Dual Reconstruction\nby Adjacency\nComplex Optimization')
title_label.setAlignment(QtCore.Qt.AlignCenter)
# title_label.setFixedWidth(150)
title_layout.addWidget(title_label)
self._title_img.setFixedHeight(75)
self._title_img.setSizePolicy(p(p.Expanding, p.Maximum))
self._layout.addWidget(self._title_img,0)
self._view = None
self._set_manager(self._manager)
self.draco = None
def __test_2D():
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
gariguette = read_mtg_file(mtg_path['Gariguette'])
gariguette.properties()['order'] = orders(gariguette)
scene = visu2d.plot2d(gariguette,
gariguette.vertices(scale=1)[53:54],
dist=[3] * 3,
display=False)
PlantGL(scene)
def tutorials():
from openalea.core.path import path
try:
from openalea import oalab
from openalea.deploy.shared_data import shared_data
except ImportError:
return []
else:
oalab_dir = shared_data(oalab)
return [path(oalab_dir)]
def __call__(self):
from openalea.core.path import path
try:
from openalea import oalab
from openalea.deploy.shared_data import shared_data
except ImportError:
return []
else:
oalab_dir = shared_data(oalab)
return [path(oalab_dir)]
def updateColormap(self, colormap_index):
self.colormap_name = self.combobox.itemText(colormap_index)
from tissuelab.gui.vtkviewer.colormap_utils import Colormap, colormap_from_file
colormap_path = shared_data(tissuelab,
'colormaps/' + self.colormap_name + '.lut')
colormap = colormap_from_file(colormap_path, name=self.colormap_name)
self.setValue(
dict(name=self.colormap_name, color_points=colormap._color_points))
def create_project_shortcut():
"""
Create a shortcut/symlink inside project directory to oalab.share directory.
Permit to access to oalab examples simpler.
"""
project_dir = get_project_dir()
project_link_name = path(project_dir) / "oalab_examples"
if not project_link_name.exists():
oalab_dir = shared_data(oalab)
symlink(oalab_dir, project_link_name)
def list_colormaps():
colormap_names = []
colormaps_path = Path(shared_data(openalea.oalab,
'colormaps/grey.lut')).parent
for colormap_file in colormaps_path.walkfiles('*.lut'):
colormap_name = str(colormap_file.name[:-4])
colormap_names.append(colormap_name)
colormap_names.sort()
return colormap_names
def load_colormaps():
from openalea.oalab.colormap.colormap_utils import Colormap, colormap_from_file
colormaps = {}
colormaps_path = Path(shared_data(openalea.oalab, 'colormaps/grey.lut')).parent
for colormap_file in colormaps_path.walkfiles('*.lut'):
colormap_name = str(colormap_file.name[:-4])
colormaps[colormap_name] = colormap_from_file(
colormap_file, name=colormap_name)
return colormaps
def test_p():
data = shared_data(openalea.groalea)
f1 = data / "P" / "P_3Run_Interface_XEG.xml"
parser = Parser()
g1, scene1 = parser.parse(f1)
c3s1 = color3s(g1)
for i in [20, 21, 10, 18]:
assert c3s1[i] != c3s1[4]
def create_project_shortcut():
"""
Create a shortcut/symlink inside project directory to oalab.share directory.
Permit to access to oalab examples simpler.
"""
project_dir = get_project_dir()
project_link_name = path(project_dir)/"oalab_examples"
if not project_link_name.exists():
oalab_dir = shared_data(oalab)
symlink(oalab_dir,project_link_name)
def test_p():
data = shared_data(openalea.groalea)
f1 = data / 'L' / 'L.xml'
parser = Parser()
g1, scene1 = parser.parse(f1)
c3s1 = color3s(g1)
for i in [20, 21, 10, 18]:
assert c3s1[i] != c3s1[4]
def test_LMul_Branch():
data = shared_data(openalea.groalea)
f1 = data / 'LMul_Branch' / 'LMul_Branch_3Run_Interface_XEG.xml'
parser = Parser()
g1, scene1 = parser.parse(f1)
sh1 = geometries(g1)
assert fabs(volume(sh1[14]) -
volume(sh1[21])) < 1e-5, 'Not the same volume %f' % fabs(
volume(sh1[25]) - volume(sh1[13]))
def test_LMul_Branch():
data = shared_data(openalea.groalea)
f1 = data / "LMul_Branch" / "LMul_Branch_3Run_Interface_XEG.xml"
parser = Parser()
g1, scene1 = parser.parse(f1)
sh1 = geometries(g1)
assert fabs(volume(sh1[14]) - volume(sh1[21])) < 1e-5, "Not the same volume %f" % fabs(
volume(sh1[25]) - volume(sh1[13])
)
def get_filename(fungus = 'brown_rust', year=2012, variety = 'Tremie12',
nplants = 15, inoc=300, suffix=None):
inoc = str(inoc)
inoc = inoc.replace('.', '_')
if suffix is None:
suffix=''
else:
suffix='_'+suffix
filename= variety+'_'+str(year)+'_'+str(nplants)+'pl_inoc'+inoc+suffix+'.csv'
fungus_path = fungus + '_simulations'
return str(shared_data(alinea.alep)/fungus_path/filename)
def load_colormaps():
from openalea.oalab.colormap.colormap_utils import Colormap, colormap_from_file
colormaps = {}
colormaps_path = Path(shared_data(openalea.oalab,
'colormaps/grey.lut')).parent
for colormap_file in colormaps_path.walkfiles('*.lut'):
colormap_name = str(colormap_file.name[:-4])
colormaps[colormap_name] = colormap_from_file(colormap_file,
name=colormap_name)
return colormaps
class PluginFloatWidgetSelector(ControlWidgetSelectorPlugin):
controls = ['IFloat']
label = 'Float editor'
required = ['IFloat.min', 'IFloat.max', 'IFloat.step']
edit_shape = ['responsive']
icon_path = shared_data(openalea.oalab,
'icons/IntWidgetSelector_hline.png')
def __call__(self):
from openalea.oalab.control.selector import FloatWidgetSelector
return FloatWidgetSelector
def get_weather(start_date="2010-10-15 12:00:00", end_date="2011-08-01 01:00:00"):
""" Get weather data for simulation. """
start = datetime.datetime.strptime(start_date, '%Y-%m-%d %H:%M:%S')
if start.year >= 2010:
filename = 'Boigneville_0109'+str(start.year)+'_3108'+str(start.year+1)+'_h.csv'
meteo_path = shared_data(alinea.echap, filename)
weather = Weather(meteo_path, reader = arvalis_reader)
weather.check(['temperature_air', 'PPFD', 'relative_humidity',
'wind_speed', 'rain', 'global_radiation', 'vapor_pressure'])
notation_dates_file = shared_data(alinea.alep, 'notation_dates/notation_dates_'+str(start.year+1)+'.csv')
weather.check(varnames=['notation_dates'], models={'notation_dates':add_notation_dates}, notation_dates_file = notation_dates_file)
else:
start_yr = str(start.year)[2:4]
end_yr = str(start.year+1)[2:4]
filename = 'meteo'+ start_yr + '-' + end_yr + '.txt'
meteo_path = shared_data(alinea.septo3d, filename)
weather = Weather(data_file=meteo_path)
weather.check(varnames=['wetness'], models={'wetness':wetness_rapilly})
weather.check(varnames=['degree_days'], models={'degree_days':linear_degree_days}, start_date=start_date, base_temp=0., max_temp=30.)
weather.check(varnames=['septo_degree_days'], models={'septo_degree_days':linear_degree_days}, start_date=start_date, base_temp=0., max_temp=30.)
return weather
def __init__(self):
QtGui.QWidget.__init__(self)
self.colormap_bar = QColormapBar()
self.colormap_bar.setMinimumHeight(20)
self.colormap_bar.setMinimumWidth(120)
self.colormap_name = "grey"
# self.label = QtGui.QLabel(self)
# self.label.setText("Colormap")
self.combobox = QtGui.QComboBox(self)
# self.setMinimumHeight(50)
colormap_names = []
# colormaps_path = Path(shared_data(tissuelab, 'colormaps/grey.lut')).parent
colormaps_path = shared_data(openalea.oalab) / 'colormaps'
for colormap_file in colormaps_path.walkfiles('*.lut'):
colormap_name = str(colormap_file.name[:-4])
colormap_names.append(colormap_name)
colormap_names.sort()
# map between string and combobox index
self.map_index = {}
for s in colormap_names:
self.combobox.addItem(s)
self.map_index[s] = self.combobox.count() - 1
self.combobox.setCurrentIndex(self.map_index[self.colormap_name])
# Fill background to avoid to see text or widget behind
self.setAutoFillBackground(True)
AbstractQtControlWidget.__init__(self)
self.combobox.currentIndexChanged.connect(self.updateColormap)
self.colormap_bar.valueChanged.connect(self.valueChanged)
layout = QtGui.QHBoxLayout(self)
layout.setContentsMargins(0, 0, 0, 0)
# line = QtGui.QHBoxLayout(self)
# line.setContentsMargins(0, 0, 0, 0)
# line.addWidget(self.label)
# line.addWidget(self.combobox)
# layout.addLayout(line)
layout.addWidget(self.combobox)
layout.addWidget(self.colormap_bar)
self.value_changed_signal = self.valueChanged
def __init__(self):
QtGui.QWidget.__init__(self)
self.colormap_bar = QColormapBar()
self.colormap_bar.setMinimumHeight(20)
self.colormap_bar.setMinimumWidth(120)
self.colormap_name = "grey"
# self.label = QtGui.QLabel(self)
# self.label.setText("Colormap")
self.combobox = QtGui.QComboBox(self)
# self.setMinimumHeight(50)
colormap_names = []
# colormaps_path = Path(shared_data(tissuelab, 'colormaps/grey.lut')).parent
colormaps_path = shared_data(tissuelab) / 'colormaps'
for colormap_file in colormaps_path.walkfiles('*.lut'):
colormap_name = str(colormap_file.name[:-4])
colormap_names.append(colormap_name)
colormap_names.sort()
# map between string and combobox index
self.map_index = {}
for s in colormap_names:
self.combobox.addItem(s)
self.map_index[s] = self.combobox.count() - 1
self.combobox.setCurrentIndex(self.map_index[self.colormap_name])
# Fill background to avoid to see text or widget behind
self.setAutoFillBackground(True)
AbstractQtControlWidget.__init__(self)
self.combobox.currentIndexChanged.connect(self.updateColormap)
self.colormap_bar.valueChanged.connect(self.valueChanged)
layout = QtGui.QHBoxLayout(self)
layout.setContentsMargins(0, 0, 0, 0)
# line = QtGui.QHBoxLayout(self)
# line.setContentsMargins(0, 0, 0, 0)
# line.addWidget(self.label)
# line.addWidget(self.combobox)
# layout.addLayout(line)
layout.addWidget(self.combobox)
layout.addWidget(self.colormap_bar)
self.value_changed_signal = self.valueChanged
def test_3D():
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
gariguette = read_mtg_file(mtg_path['Gariguette'])
gariguette.properties()['order'] = orders(gariguette)
scene = visu3d.plot3d(gariguette,
by=["Sample_date"],
hide_leaves=False,
display=False)
assert scene.isValid() == True
p = PlantGL(scene, group_by_color=True)
assert len(p.object_ids) == 103
def test_length():
data = shared_data(openalea.groalea)
f1 = data / 'length' / 'L_XEG_r.xml'
f2 = data / 'length' / 'L_XEG_w.xml'
parser = Parser()
g1, scene1 = parser.parse(f1)
parser = Parser()
g2, scene2 = parser.parse(f2)
assert len(g1) == len(g2)
assert fabs(volume(scene1) -
volume(scene2)) < 1e-5, 'Not the same volume %f' % fabs(
volume(scene1) - volume(scene2))
def test_length():
data = shared_data(openalea.groalea)
f1 = data / "length" / "L_XEG_r.xml"
f2 = data / "length" / "L_XEG_w.xml"
parser = Parser()
g1, scene1 = parser.parse(f1)
parser = Parser()
g2, scene2 = parser.parse(f2)
assert len(g1) == len(g2)
assert fabs(volume(scene1) - volume(scene2)) < 1e-5, "Not the same volume %f" % fabs(
volume(scene1) - volume(scene2)
)
def sample_weather(periods=24):
""" provides a sample weather instance for testing other modules
"""
from openalea.deploy.shared_data import shared_data
import alinea.septo3d
meteo_path = shared_data(alinea.septo3d, 'meteo00-01.txt')
t_deb = "2000-10-01 01:00:00"
seq = pandas.date_range(start="2000-10-02", periods=periods, freq='H')
weather = Weather(data_file=meteo_path)
weather.check(
['temperature_air', 'PPFD', 'relative_humidity', 'wind_speed', 'rain',
'global_radiation', 'vapor_pressure'])
return seq, weather
def test_extract_at_module_scale():
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
gariguette = read_mtg_file(mtg_path['Gariguette'])
gariguette_extraction_at_module_scale = extract_at_module_scale(gariguette)
assert len(gariguette_extraction_at_module_scale) == 241
gariguette_frequency = occurence_module_order_along_time(data= gariguette_extraction_at_module_scale,frequency_type= "cdf")
assert len(gariguette_frequency) == 6
mean= gariguette_extraction_at_module_scale.groupby(["Genotype", "order"]).mean()
sd= gariguette_extraction_at_module_scale.groupby(["Genotype", "order"]).std()
assert len(mean) == 6
assert len(sd) == 6
class PluginFloatWidgetSelector(ControlWidgetSelectorPlugin):
controls = ['IFloat']
name = 'FloatWidgetSelector'
alias = 'Float editor'
required = ['IFloat.min', 'IFloat.max', 'IFloat.step']
edit_shape = ['responsive']
icon_path = shared_data(openalea.oalab,
'icons/IntWidgetSelector_hline.png')
@classmethod
def load(cls):
from openalea.oalab.plugins.controls.selectors import FloatWidgetSelector
return FloatWidgetSelector
def get_weather(start_date="2010-10-15 12:00:00",
end_date="2011-08-01 01:00:00"):
""" Get weather data for simulation. """
start = datetime.datetime.strptime(start_date, '%Y-%m-%d %H:%M:%S')
if start.year >= 2010:
filename = 'Boigneville_0109' + str(
start.year) + '_3108' + str(start.year + 1) + '_h.csv'
meteo_path = shared_data(alinea.echap, filename)
weather = Weather(meteo_path, reader=arvalis_reader)
weather.check([
'temperature_air', 'PPFD', 'relative_humidity', 'wind_speed',
'rain', 'global_radiation', 'vapor_pressure'
])
notation_dates_file = shared_data(
alinea.alep,
'notation_dates/notation_dates_' + str(start.year + 1) + '.csv')
weather.check(varnames=['notation_dates'],
models={'notation_dates': add_notation_dates},
notation_dates_file=notation_dates_file)
else:
start_yr = str(start.year)[2:4]
end_yr = str(start.year + 1)[2:4]
filename = 'meteo' + start_yr + '-' + end_yr + '.txt'
meteo_path = shared_data(alinea.septo3d, filename)
weather = Weather(data_file=meteo_path)
weather.check(varnames=['wetness'], models={'wetness': wetness_rapilly})
weather.check(varnames=['degree_days'],
models={'degree_days': linear_degree_days},
start_date=start_date,
base_temp=0.,
max_temp=30.)
weather.check(varnames=['septo_degree_days'],
models={'septo_degree_days': linear_degree_days},
start_date=start_date,
base_temp=0.,
max_temp=30.)
return weather
def on_widget_changed(self):
widget = None
if self.cb_widget.currentIndex() == -1:
return
widget_name = self.widget_plugins[self.cb_widget.currentIndex()].name
iname = self._interfaces[self.cb_interface.currentIndex()]
icon_path = None
for plugin in qt_widget_plugins(iname):
if widget_name == plugin.name:
widget = plugin.load()
if hasattr(plugin, 'icon_path'):
icon_path = plugin.icon_path
if icon_path and not icon_path.exists():
icon_path = None
else:
icon_path = None
if icon_path is None:
icon_path = shared_data(openalea.oalab,
'icons/preview_%s.png' % iname)
if icon_path and not icon_path.exists():
icon_path = None
break
if icon_path:
pixmap = QtGui.QPixmap(icon_path)
if pixmap.width() >= 400 or pixmap.height() >= 400:
pixmap = pixmap.scaled(400, 400, QtCore.Qt.KeepAspectRatio)
self.widget_preview.setPixmap(pixmap)
self.l_widget.setToolTip(
'<b>%s</b><br /><img src="%s" width="200" />' %
(widget_alias(plugin), icon_path))
else:
self.widget_preview.setText("No preview")
if self._constraints:
widget_constraints = self._constraints()
self._layout_constraints.removeWidget(widget_constraints)
widget_constraints.close()
self._constraints = None
# self.l_constraints.hide()
if widget and hasattr(widget, 'edit_constraints'):
widget_constraints = widget.edit_constraints()
widget_constraints.setAttribute(QtCore.Qt.WA_DeleteOnClose)
self._layout_constraints.addWidget(widget_constraints)
# self.l_constraints.show()
self._constraints = weakref.ref(widget_constraints)
def get_filename(fungus='brown_rust',
year=2012,
variety='Tremie12',
nplants=15,
inoc=300,
suffix=None):
inoc = str(inoc)
inoc = inoc.replace('.', '_')
if suffix is None:
suffix = ''
else:
suffix = '_' + suffix
filename = variety + '_' + str(year) + '_' + str(
nplants) + 'pl_inoc' + inoc + suffix + '.csv'
fungus_path = fungus + '_simulations'
return str(shared_data(alinea.alep) / fungus_path / filename)
def on_widget_changed(self):
widget = None
if self.cb_widget.currentIndex() == -1:
return
widget_name = self.widget_plugins[self.cb_widget.currentIndex()].name
iname = self._interfaces[self.cb_interface.currentIndex()]
icon_path = None
for plugin in qt_widget_plugins(iname):
if widget_name == plugin.name:
widget = plugin.load()
if hasattr(plugin, "icon_path"):
icon_path = plugin.icon_path
if icon_path and not icon_path.exists():
icon_path = None
else:
icon_path = None
if icon_path is None:
icon_path = shared_data(openalea.oalab, "icons/preview_%s.png" % iname)
if icon_path and not icon_path.exists():
icon_path = None
break
if icon_path:
pixmap = QtGui.QPixmap(icon_path)
if pixmap.width() >= 400 or pixmap.height() >= 400:
pixmap = pixmap.scaled(400, 400, QtCore.Qt.KeepAspectRatio)
self.widget_preview.setPixmap(pixmap)
self.l_widget.setToolTip('<b>%s</b><br /><img src="%s" width="200" />' % (widget_alias(plugin), icon_path))
else:
self.widget_preview.setText("No preview")
if self._constraints:
widget_constraints = self._constraints()
self._layout_constraints.removeWidget(widget_constraints)
widget_constraints.close()
self._constraints = None
# self.l_constraints.hide()
if widget and hasattr(widget, "edit_constraints"):
widget_constraints = widget.edit_constraints()
widget_constraints.setAttribute(QtCore.Qt.WA_DeleteOnClose)
self._layout_constraints.addWidget(widget_constraints)
# self.l_constraints.show()
self._constraints = weakref.ref(widget_constraints)
def import_mtgfile(filename):
"""Import a MTG file from genotype name, in sharedata repo
:param filename: genotype = name of the file
:type filename: string
:return: a MTG loaded from the file
:rtype: MTG
"""
filenames = filename
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
mtgfile = dict((k, f) for k, f in mtg_path.items() if k in filenames)
if len(filenames) == 1:
g = MTG(mtgfile[filenames[0]])
return g
else:
metaMTG = MTG()
for i in mtgfile:
metaMTG = algo.union(metaMTG, MTG(mtgfile[i]))
return metaMTG
def test_df2waffle():
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
mtg = read_mtg_file(mtg_path['Capriss'])
df = extract_at_node_scale(mtg)
node_scale = df2waffle(df,
index='rank',
date='2015/03/02',
variable='branching_type')
assert node_scale.shape == (20, 9)
df = extract_at_module_scale(mtg)
module_scale = df2waffle(df,
index='order',
date='2015/03/02',
variable='crown_status',
aggfunc='median')
assert module_scale.shape == (3, 9)
def read_config(config_file):
p = PhenomenalConfigParser()
p.read(config_file)
d = p.as_dict()
if d['General']['configdir'] == 'SharedData':
shared_directory = shared_data(alinea.phenomenal)
else:
shared_directory = d['General']['configdir']
for key in d:
for sub_key in d[key]:
if str(sub_key).startswith('mask'):
d[key][sub_key] = cv2.imread(
shared_directory / str(d[key][sub_key]),
cv2.IMREAD_GRAYSCALE)
if str(sub_key).startswith('background'):
d[key][sub_key] = cv2.imread(
shared_directory / str(d[key][sub_key]),
cv2.IMREAD_UNCHANGED)
return d
from openalea.deploy.shared_data import shared_data import openalea.mtg from openalea.mtg import * data = shared_data(openalea.mtg) ################################################################################ # 1. Object is directly compatible with viewer. Nothing to do ################################################################################ # Create object (big tree) g2 = MTG(data / 'agraf.mtg') dressing_data2 = dresser.DressingData(DiameterUnit=15) pf2 = PlantFrame(g2, TopDiameter='TopDia', DressingData=dressing_data2) pgl_scene = pf2.plot(gc=True, display=False) # Add it to world world['obj1'] = pgl_scene ################################################################################ # 2. Object is not directly compatible but provides # a method (_repr_geom_) to convert himself to a compatible type # (Currently PlantGL geometry, shape or scene) ################################################################################ # object type (generally defined in a separated module) from openalea.plantgl.all import Box class MyBox(object):
def get_shared_data(filename):
return shared_data(openalea.oalab, filename)
def run_simulation(start_year, variability=True, **kwds):
# Set the seed of the simulation
rd.seed(0)
np.random.seed(0)
# Read weather and adapt it to septoria (add wetness)
weather_file = 'meteo'+ str(start_year)[-2:] + '-' + str(start_year+1)[-2:] + '.txt'
meteo_path = shared_data(alinea.septo3d, weather_file)
weather = Weather(data_file=meteo_path)
weather.check(varnames=['wetness'], models={'wetness':wetness_rapilly})
seq = pandas.date_range(start = str(start_year)+"-10-01 01:00:00",
end = str(start_year+1)+"-07-01 01:00:00",
freq='H')
# Initialize a wheat canopy
g, wheat, domain_area, domain = initialize_stand(age=0., length=0.1,
width=0.2, sowing_density=150,
plant_density=150, inter_row=0.12,
seed=3)
# Initialize the models for septoria
if 'alinea.alep.septoria_age_physio' in sys.modules:
del(sys.modules['alinea.alep.septoria_age_physio'])
if variability==True:
septoria = variable_septoria(**kwds)
else:
septoria = plugin_septoria(model="septoria_age_physio")
DU = septoria.dispersal_unit()
inoculator = RandomInoculation()
growth_controler = NoPriorityGrowthControl()
infection_controler = BiotrophDUPositionModel()
sen_model = WheatSeptoriaPositionedSenescence(g, label='LeafElement')
emitter = SeptoriaRainEmission(domain_area=domain_area)
transporter = Septo3DSplash(reference_surface=domain_area)
washor = RapillyWashing()
# Define the schedule of calls for each model
every_h = time_filter(seq, delay=1)
every_24h = time_filter(seq, delay=24)
every_rain = rain_filter(seq, weather)
weather_timing = IterWithDelays(*time_control(seq, every_h, weather.data))
wheat_timing = IterWithDelays(*time_control(seq, every_24h, weather.data))
septo_timing = IterWithDelays(*time_control(seq, every_h, weather.data))
rain_timing = IterWithDelays(*time_control(seq, every_rain, weather.data))
# Call leaf inspectors for target blades (top 3)
inspectors = {}
first_blade = 80
ind = 4.
for blade in range(first_blade,104,8):
ind -= 1
inspectors[ind] = LeafInspector(g, blade_id=blade)
# Simulation loop
for i,controls in enumerate(zip(weather_timing, wheat_timing,
septo_timing, rain_timing)):
weather_eval, wheat_eval, septo_eval, rain_eval = controls
# Update date
date = weather_eval.value.index[0]
# Get weather for date and add it as properties on leaves
if weather_eval:
set_properties(g,label = 'LeafElement',
temp = weather_eval.value.temperature_air[0],
wetness = weather_eval.value.wetness[0],
relative_humidity = weather_eval.value.relative_humidity[0],
wind_speed = weather_eval.value.wind_speed[0])
if rain_eval:
set_properties(g,label = 'LeafElement',
rain_intensity = rain_eval.value.rain.mean(),
rain_duration = len(rain_eval.value.rain) if rain_eval.value.rain.sum() > 0 else 0.)
# Grow wheat canopy
if wheat_eval:
print(date)
g,_ = grow_canopy(g, wheat, wheat_eval.value)
# Note : The position of senescence goes back to its initial value after
# a while for undetermined reason
# --> temporary hack for keeping senescence position low when it is over
positions = g.property('position_senescence')
are_green = g.property('is_green')
leaves = get_leaves(g, label = 'LeafElement')
positions.update({leaf:(0 if positions[leaf]==1 and not are_green[leaf] else positions[leaf])
for leaf in leaves})
# Develop disease
if septo_eval:
sen_model.find_senescent_lesions(g, label = 'LeafElement')
update_healthy_area(g, label = 'LeafElement')
if rain_eval and i <= 500:
# Refill pool of initial inoculum to simulate differed availability
if rd.random()<0.4:
dispersal_units = [DU(nb_spores=rd.randint(1,100), status='emitted') for i in range(rd.randint(0,3))]
initiate(g, dispersal_units, inoculator)
infect(g, septo_eval.dt, infection_controler, label='LeafElement')
update(g, septo_eval.dt, growth_controler, sen_model, label='LeafElement')
les = g.property('lesions')
lesions = sum([l for l in les.values()], [])
print([l.fungus.degree_days_to_chlorosis for l in lesions])
# if len(lesions)>10:
# import pdb
# pdb.set_trace()
if rain_eval:
g, nb = disperse(g, emitter, transporter, "septoria", label='LeafElement')
wash(g, washor, rain_eval.value.rain.mean(), label='LeafElement')
# Save outputs
for inspector in inspectors.itervalues():
inspector.update_variables(g)
inspector.update_du_variables(g)
if wheat_eval:
plot_severity_by_leaf(g)
return inspectors
