def test_count_pixels():
scene_path = path("data/test_povray/scene.bmp")
scene_box_path = path("data/test_povray/scene_box.bmp")
rgb_colors = [[0, 170, 0],
[170, 170, 0],
[255, 0, 0],
[255, 170, 0],
[255, 201, 5],
[0, 0, 255],
[255, 170, 0],
[0, 0, 255],
[255, 201, 5],
[170, 255, 255],
[170, 255, 255]]
import tempfile
povray_results_directory = path(tempfile.mkdtemp(suffix='_povray_results'))
result_path = povray_results_directory.joinpath('scene_res.csv')
normalized_scene_path = povray_results_directory.joinpath('normalized_scene.bmp')
normalize = True
post_processing.count_pixels(scene_path=scene_path, scene_box_path=scene_box_path, rgb_colors=rgb_colors, result_path=result_path, normalize=normalize, normalized_scene_path=normalized_scene_path)
expected_result_array = np.array([['scene.bmp', 0, 28526, 375, 2253, 25, 83, 2959, 122786]], dtype=object)
result_array = pandas.read_csv(result_path).values
np.testing.assert_equal(result_array, expected_result_array)
def changeExtension(self, extension=None):
"""
Change to a new extension.
:param extension: can be "mini", "3d", "tissue", "plant"
"""
self.removeDocksWidgets()
filename = 'oalab.py'
conf = path(get_openalea_home_dir()) / filename
if extension in ["mini", "3d", "tissue", "plant"]:
filename = ('oalab_' + extension + '.py')
conf = path(get_openalea_home_dir()) / filename
if not conf.exists():
with conf.open('w') as f:
# TODO : auto generate config file
# f.write(self._config.generate_config_file())
if extension == "mini":
f.write(config_file_mini)
elif extension == "3d":
f.write(config_file_3d)
elif extension == "tissue":
f.write(config_file_tissue)
elif extension == "plant":
f.write(config_file_plant)
else:
f.write(config_file_default)
self.session.load_config_file(filename=filename,
path=get_openalea_home_dir())
self.setWidgets(self.controller)
def changeExtension(self, extension=None):
"""
Change to a new extension.
:param extension: can be "mini", "3d", "tissue", "plant"
"""
self.removeDocksWidgets()
filename = 'oalab.py'
conf = path(get_openalea_home_dir()) / filename
if extension in ["mini", "3d", "tissue", "plant"]:
filename = ('oalab_' + extension + '.py')
conf = path(get_openalea_home_dir()) / filename
if not conf.exists():
with conf.open('w') as f:
# TODO : auto generate config file
# f.write(self._config.generate_config_file())
if extension == "mini":
f.write(config_file_mini)
elif extension == "3d":
f.write(config_file_3d)
elif extension == "tissue":
f.write(config_file_tissue)
elif extension == "plant":
f.write(config_file_plant)
else:
f.write(config_file_default)
self.session.load_config_file(filename=filename, path=get_openalea_home_dir())
self.setWidgets(self.controller)
def test_count_pixels():
scene_path = path("data/test_povray/scene.bmp")
scene_box_path = path("data/test_povray/scene_box.bmp")
rgb_colors = [[0, 170, 0],
[170, 170, 0],
[255, 0, 0],
[255, 170, 0],
[255, 201, 5],
[0, 0, 255],
[255, 170, 0],
[0, 0, 255],
[255, 201, 5],
[170, 255, 255],
[170, 255, 255]]
import tempfile
povray_results_directory = path(tempfile.mkdtemp(suffix='_povray_results'))
result_path = povray_results_directory.joinpath('scene_res.csv')
normalized_scene_path = povray_results_directory.joinpath('normalized_scene.bmp')
normalize = True
post_processing.count_pixels(scene_path=scene_path, scene_box_path=scene_box_path, rgb_colors=rgb_colors, result_path=result_path, normalize=normalize, normalized_scene_path=normalized_scene_path)
expected_result_array = np.array([['scene.bmp', 0, 28526, 375, 2253, 25, 83, 2959, 122786]], dtype=object)
result_array = pandas.read_csv(result_path).values
np.testing.assert_equal(result_array, expected_result_array)
def test_post_processing():
adel_output_path = path('data/test_stand/adel_output.csv')
import tempfile
global_postprocessing_file_path = path(
tempfile.mktemp(prefix='global_postprocessing', suffix='.csv'))
peraxis_postprocessing_file_path = path(
tempfile.mktemp(prefix='peraxis_postprocessing', suffix='.csv'))
# launch the postprocessing
(global_postprocessing_file_path,
peraxis_postprocessing_file_path,
intermediate_results_file_path)= \
post_processing(adel_output_path,
3,
0.013824884792626729,
global_postprocessing_file_path,
peraxis_postprocessing_file_path)
expected_results_dir_path = path('data/test_stand')
# check intermediate results
intermediate_results_array = \
pandas.read_csv(intermediate_results_file_path).values
intermediate_results_array = np.delete(intermediate_results_array, 2,
1).astype(float)
expected_intermediate_results_array = \
pandas.read_csv(expected_results_dir_path/'intermediate.csv').values
expected_intermediate_results_array = np.delete(
expected_intermediate_results_array, 2, 1).astype(float)
np.testing.assert_allclose(intermediate_results_array,
expected_intermediate_results_array,
relative_tolerance, absolute_tolerance)
# check per axis post processing results
peraxis_postprocessing_results_array = pandas.read_csv(
peraxis_postprocessing_file_path).values
peraxis_postprocessing_results_array = np.delete(
peraxis_postprocessing_results_array, [0, 2], 1).astype(float)
expected_peraxis_postprocessing_results_array = pandas.read_csv(
expected_results_dir_path / 'peraxis_postprocessing.csv').values
expected_peraxis_postprocessing_results_array = np.delete(
expected_peraxis_postprocessing_results_array, [0, 2], 1).astype(float)
np.testing.assert_allclose(peraxis_postprocessing_results_array,
expected_peraxis_postprocessing_results_array,
relative_tolerance, absolute_tolerance)
# check global post processing results
global_postprocessing_results_array = pandas.read_csv(
global_postprocessing_file_path).values
global_postprocessing_results_array = np.delete(
global_postprocessing_results_array, 0, 1).astype(float)
expected_global_postprocessing_results_array = pandas.read_csv(
expected_results_dir_path / 'global_postprocessing.csv').values
expected_global_postprocessing_results_array = np.delete(
expected_global_postprocessing_results_array, 0, 1).astype(float)
np.testing.assert_allclose(global_postprocessing_results_array,
expected_global_postprocessing_results_array,
relative_tolerance, absolute_tolerance)
def test_get_data():
res = run(('openalea.data file', 'get_data'), inputs={'package': 'alinea.caribu.data', 'filename': 'filterT.can'}, pm=pm)
assert path(res[0]).basename() == 'filterT.can'
res = run(('openalea.data file', 'get_data'), inputs={'package': 'openalea.core', 'filename': 'test_image.npy'}, pm=pm)
assert path(res[0]).basename() == 'test_image.npy'
res = run(('openalea.data file', 'get_data'), inputs={'package': 'vplants.fractalysis', 'filename': 'mango_f21_L.bgeom'}, pm=pm)
assert path(res[0]).basename() == 'mango_f21_L.bgeom'
res = run(('openalea.data file', 'get_data'), inputs={'package': 'openalea.stat_tool', 'filename': 'meri1.his'}, pm=pm)
assert res[0] == None
def showOpenFileDialog(extension=None, where=None, parent=None):
if extension is None:
extension = ""
if where is not None:
my_path = path(str(where)).abspath().splitpath()[0]
else:
my_path = path(settings.get_project_dir())
logger.debug("Search to open file with extension " + extension + " from " + my_path)
fname = QtGui.QFileDialog.getOpenFileName(parent, 'Select File to open',
my_path, "All (*);;Scripts Files (%s)" % extension)
return fname
def test_shared_data_browser():
res = run(('openalea.misc.test','shared_data_browser'), {}, pm=pm)
assert res == []
res = run(('openalea.misc', 'SharedDataBrowser'), inputs={'package': 'openalea.stat_tool', 'filename': 'meri1.his'}, pm=pm)
assert path(res[0]).basename() == 'meri1.his'
res = run(('openalea.misc', 'SharedDataBrowser'), inputs={'package': 'vplants.sequence_analysis', 'filename': 'cafe_ortho1.seq'}, pm=pm)
assert path(res[0]).basename() == 'cafe_ortho1.seq'
res = run(('openalea.misc', 'SharedDataBrowser'), inputs={'package': 'alinea.caribu', 'filename': 'filterT.can'}, pm=pm)
assert path(res[0]).basename() == 'filterT.can'
res = run(('openalea.misc', 'SharedDataBrowser'),inputs={'package': 'numpy', 'filename': 'something.something'}, pm=pm)
assert res[0] == None
res = run(('openalea.misc', 'SharedDataBrowser'),inputs={'package': 'alinea.adel.data', 'filename': 'dimTSoissons.csv'}, pm=pm)
assert res[0] == None
def test_to_csv():
tmp_filepath = tempfile.mkstemp()[1]
res = run(('openalea.pandas.io', 'to_csv'),
inputs={
'dataframe': expected_df,
'path_or_buf': tmp_filepath,
'index': False
},
pm=pm)
df = pandas.read_csv(path(res[0]))
np.testing.assert_allclose(df.values, expected_df.values,
relative_tolerance, absolute_tolerance)
path(tmp_filepath).remove()
def showOpenFileDialog(extension=None, where=None, parent=None):
if extension is None:
extension = ""
if where is not None:
my_path = path(str(where)).abspath().splitpath()[0]
else:
my_path = path(settings.get_project_dir())
logger.debug("Search to open file with extension " + extension + " from " +
my_path)
fname = QtGui.QFileDialog.getOpenFileName(
parent, 'Select File to open', my_path,
"All (*);;Scripts Files (%s)" % extension)
return fname
def __init__(self, camera = {'type':'perspective', 'distance':1., 'fov':45., 'xc':0., 'yc':0., 'azimuth':0, 'zenith':0.}, image_width = 320, image_height = 280, background = (0,0,0), light_position = (10,0,10), light_color=(1,1,1), working_dir = None):
""" Setup a Povray instance
:Parameters:
- camera: a dict of parameters for positioning the camera
- distance: distance from the position of the camera to the look_at point
- fov : angle corresponding to the width of the image
- xc, yc : coordinates of the center of the scene
- azimuth: angle in degree around the vertical axis. az=0. is equialent to have the width of the image align to X direction of the scene
- zenith: angle between the view direction and the vertical
- image_width: width of the final image in pixel
- image_height: height of the final image in pixel
- working_dir: A directory for storing povary files. If None, (default), a temporary directory will be created and removed onece the instance is deleted
"""
try:
if working_dir is not None:
self.wdir=path(path(working_dir).abspath())
if not self.wdir.exists():
self.wdir.mkdir()
self.cleanup_wdir = False
else:
# build a temporary directory
self.wdir = path(tempfile.mkdtemp())
self.cleanup_wdir = True
except:
raise PovRayError("PovRay can't create its working directory : check for read/write permission or security level")
if platform.system() is 'Windows':
self.cmdline = 'pvengine +FN +I%s +H%d +W%d -d /exit'
else:
self.cmdline = 'povray +FN +I%s +H%d +W%d'
self.image_width = image_width
self.image_height = image_height
self.camera = camera
self.light_position = light_position
self.light_color = light_color
self.background = background
self.soil = False
self.rendered_image_path = None
self.tesselator = pgl.Tesselator()
#to be removed once cv_camera has been properly integrated
self.user_camera = None
def __init__(self, camera = {'type':'perspective', 'distance':1., 'fov':45., 'xc':0., 'yc':0., 'azimuth':0, 'zenith':0.}, image_width = 320, image_height = 280, background = (0,0,0), light_position = (10,0,10), light_color=(1,1,1), working_dir = None):
""" Setup a Povray instance
:Parameters:
- camera: a dict of parameters for positioning the camera
- distance: distance from the position of the camera to the look_at point
- fov : angle corresponding to the width of the image
- xc, yc : coordinates of the center of the scene
- azimuth: angle in degree around the vertical axis. az=0. is equialent to have the width of the image align to X direction of the scene
- zenith: angle between the view direction and the vertical
- image_width: width of the final image in pixel
- image_height: height of the final image in pixel
- working_dir: A directory for storing povary files. If None, (default), a temporary directory will be created and removed onece the instance is deleted
"""
try:
if working_dir is not None:
self.wdir=path(path(working_dir).abspath())
if not self.wdir.exists():
self.wdir.mkdir()
self.cleanup_wdir = False
else:
# build a temporary directory
self.wdir = path(tempfile.mkdtemp())
self.cleanup_wdir = True
except:
raise PovRayError("PovRay can't create its working directory : check for read/write permission or security level")
if platform.system() is 'Windows':
self.cmdline = 'pvengine +FN +I%s +H%d +W%d -d /exit'
else:
self.cmdline = 'povray +FN +I%s +H%d +W%d'
self.image_width = image_width
self.image_height = image_height
self.camera = camera
self.light_position = light_position
self.light_color = light_color
self.background = background
self.soil = False
self.rendered_image_path = None
self.tesselator = pgl.Tesselator()
#to be removed once cv_camera has been properly integrated
self.user_camera = None
def simulation(lsystem_filename, nb_plants):
# write AleaPars.h
fn = path(lsystem_filename)
dir = fn.dirname()
param_fn = dir / "AleaPars.h"
s = '\n#define NB_PLANTS %d\n' % nb_plants
f = open(param_fn, "w")
f.write(s)
f.close()
view_file = 'view.v'
leaf_file = 'leaf.a'
color_file = 'color.map'
result_file = 'result.str'
cmd = "cpfg -g -h**o -str %s %s %s %s -m %s" % (
result_file, fn.basename(), view_file, leaf_file, color_file)
print cmd
curdir = os.getcwd()
print dir
os.chdir(dir)
os.system(cmd)
os.chdir(curdir)
result_file = dir / result_file
if not result_file.exists():
result_file = dir / '100plants' / 'bid050.str'
f = open(result_file)
s = f.read()
s = s.replace('\n', '')
f.close()
return s
def __init__(self, name=None, project='', dir='.', release='0.1'):
self.name = name # e.g. name = PlantGL
self.package = name.lower() # e.g. name = plantgl
self.dir = dir
self.pkg_dir = path(dir) / self.package
self.languages = ['python']
self.project = project.lower()
self.release = release
self.check_project()
self.metainfo = {
'PACKAGE':
self.package,
'PACKAGE_NAME':
self.name,
'PROJECT':
self.project,
'DEFAULT_PROJECT':
self.project if self.project else 'openalea',
'PROJECT_NAME':
self.project_name[self.project] if self.project else '',
'FULL_NAME':
self.project_name[self.project] + '.' +
self.name if self.project else self.name,
'RELEASE':
self.release,
}
def simulation(lsystem_filename, nb_plants):
# write AleaPars.h
fn = path(lsystem_filename)
dir = fn.dirname()
param_fn = dir / "AleaPars.h"
s = '\n#define NB_PLANTS %d\n'%nb_plants
f = open(param_fn, "w")
f.write(s)
f.close()
view_file = 'view.v'
leaf_file = 'leaf.a'
color_file = 'color.map'
result_file = 'result.str'
cmd = "cpfg -g -h**o -str %s %s %s %s -m %s" % (result_file, fn.basename(), view_file, leaf_file, color_file)
print cmd
curdir = os.getcwd()
print dir
os.chdir(dir)
os.system(cmd)
os.chdir(curdir)
result_file = dir / result_file
if not result_file.exists():
result_file = dir/'100plants'/'bid050.str'
f = open(result_file)
s = f.read()
s = s.replace('\n','')
f.close()
return s
def __call__(self, pov_file, povdir, wait):
path_ini = os.path.abspath(os.getcwd())
if win32api:
dir = pov_file[:-len(pov_file.split('\\')[-1]) -
1] #path du fichier .pov d'origine
name = pov_file.split('\\')[-1].split('.')[0]
#os.system('copy '+win32api.GetShortPathName(pov_file)+' '+win32api.GetShortPathName(povdir)) #copie du fichier pov dans le bin de povray pas necessaire : avec short paths peut executer diretcement
os.chdir(povdir)
os.system(
'pvengine.exe /RENDER ' + join(win32api.GetShortPathName(dir),
pov_file.split('\\')[-1])
) #short name pour le path, mais pas le nom de fichier pour conserver noms'd'image complets
ext = '.bmp'
else:
_pov_file = path(pov_file)
dir = _pov_file.dirname()
name = _pov_file.namebase
os.chdir(dir)
cmdline = 'povray +I%s' % (pov_file)
ext = '.png'
time.sleep(wait) #temps d'attente en secondes entre 2 simulations
os.chdir(path_ini)
return join(dir, name + ext)
def test_mtglpy_topvine():
fn = path('vinemtg_n.lpy')
if not fn.exists():
return
l = Lsystem(str(fn))
parameters = {}
parameters['carto_file'] = 'geom_n.dat'
parameters['picle_file'] = 'vine_n.dat'
parameters['TTfin'] = None
#l.context().updateNamespace(parameters)
c_iter = l.getLastIterationNb()
nbstep = l.derivationLength - c_iter
tree = l.iterate(l.axiom, c_iter, nbstep)
scene = l.sceneInterpretation(tree)
mtg = lpy2mtg(tree, l, scene)
print(len(mtg))
axial_tree = AxialTree()
axial_tree = mtg2lpy(mtg, l, axial_tree)
g = lpy2mtg(axial_tree, l, scene)
assert len(g) == len(mtg)
#axial_tree = mtg2axialtree(mtg, scale, parameters, axial_tree)
# Check
assert True
return mtg, tree, axial_tree
def save_as(self):
project = self.project()
if project:
p = path(self.showNewProjectDialog(default_name=None, text="Select name to save project")).abspath()
projectdir, name = p.splitpath()
if name:
project.save_as(projectdir, name)
def _update_available_project_menu(self):
"""
Discover all projects and generate an action for each one.
Then connect this action to _on_open_project_triggered
"""
self.menu_available_projects.clear()
self.action_available_project.clear()
all_projects = {} # dict parent dir -> list of Project objects
for project in projects():
all_projects.setdefault(project.projectdir, []).append(project)
home = path(get_default_home_dir())
for projectdir, _projects in all_projects.iteritems():
relpath = home.relpathto(projectdir)
label = unicode(relpath)
menu = QtGui.QMenu(label, self.menu_available_projects)
for project in sorted(_projects, key=lambda project: project.label):
icon = obj_icon(project, default=DEFAULT_PROJECT_ICON, paths=[project.path])
action = QtGui.QAction(icon, project.label, self.menu_available_projects)
action.triggered.connect(self._on_open_project_triggered)
menu.addAction(action)
self.action_available_project[action] = project
self.menu_available_projects.addMenu(menu)
return self.menu_available_projects
def find_vlab_dir(self, directory, recursive=True):
"""
Find in a directory vlab specification file.
Search recursivly is recursive is True
:return: a list of pkgreader instances
"""
spec_files = set()
if(not os.path.isdir(directory)):
logger.error("Not a directory", directory, repr(directory))
# self.log.add("Not a directory", directory, repr(directory))
return []
p = path(directory).abspath()
spec_name = '*specifications'
# search for wralea.py
if(recursive and SEARCH_OUTSIDE_ENTRY_POINTS):
spec_files.update(p.walkfiles(spec_name))
else:
spec_files.update(p.glob(spec_name))
for f in spec_files:
logger.info("Package Manager : found VLAB %s" % p)
# self.log.add("Package Manager : found VLAB %s" % p)
return list(map(self.get_pkgreader, spec_files))
def _update_available_project_menu(self):
"""
Discover all projects and generate an action for each one.
Then connect this action to _on_open_project_triggered
"""
self.menu_available_projects.clear()
self.action_available_project.clear()
all_projects = {} # dict parent dir -> list of Project objects
for project in projects():
all_projects.setdefault(project.projectdir, []).append(project)
home = path(get_default_home_dir())
for projectdir, _projects in all_projects.iteritems():
relpath = home.relpathto(projectdir)
label = unicode(relpath)
menu = QtGui.QMenu(label, self.menu_available_projects)
for project in sorted(_projects,
key=lambda project: project.label):
icon = obj_icon(project,
default=DEFAULT_PROJECT_ICON,
paths=[project.path])
action = QtGui.QAction(icon, project.label,
self.menu_available_projects)
action.triggered.connect(self._on_open_project_triggered)
menu.addAction(action)
self.action_available_project[action] = project
self.menu_available_projects.addMenu(menu)
return self.menu_available_projects
def test_full():
data = path(scanalea.__path__[0]) / '..' / '..'
datadir = data / 'share' / 'INRIA_maize' / 'finemesh'
files = datadir.glob('*.ply')
report = pd.read_csv(datadir / 'report.txt',
sep=' *',
header=None,
names=['Date', 'num'],
infer_datetime_format=True)
report = report.sort('Date')
# bad option to do the trick...
def fun(x):
return [f for f in files if ('_' + str(x) + '_') in f][0]
report['filename'] = report['num'].map(fun)
scenes = [read(fn) for fn in report['filename']]
shapes = [
normalised(scenes[xx][0], (xx / 5, xx % 5., 0),
(xx * 10, 80, (xx * 30) % 255)) for xx in range(len(scenes))
]
scene = Scene(shapes)
return scene
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
def test_mtglpy_topvine():
fn = path('vinemtg_n.lpy')
if not fn.exists():
return
l = Lsystem(str(fn))
parameters = {}
parameters['carto_file'] = 'geom_n.dat'
parameters['picle_file'] = 'vine_n.dat'
parameters['TTfin'] = None
#l.context().updateNamespace(parameters)
c_iter = l.getLastIterationNb()
nbstep = l.derivationLength - c_iter
tree = l.iterate(l.axiom,c_iter,nbstep)
scene = l.sceneInterpretation(tree)
mtg = lpy2mtg(tree, l, scene)
print len(mtg)
axial_tree = AxialTree()
axial_tree = mtg2lpy(mtg, l, axial_tree)
g = lpy2mtg(axial_tree, l, scene)
assert len(g) == len(mtg)
#axial_tree = mtg2axialtree(mtg, scale, parameters, axial_tree)
# Check
assert True
return mtg, tree, axial_tree
def showNewProjectDialog(self, default_name=None, text=None, parent=None):
my_path = path(settings.get_project_dir())
if default_name:
my_path = my_path / default_name
if not text:
text = 'Select name to create project'
fname = QtGui.QFileDialog.getSaveFileName(parent, text, my_path)
return fname
def load_controls(self, filename=None):
if not filename:
filename = QtGui.QFileDialog.getOpenFileName(self, 'Select python file')
if filename:
if path(filename).exists():
self.model()._manager.clear()
code = file(filename, 'r').read()
exec(code)
def find_all_wralea(self):
"""
Find on the system all wralea.py files
:return : a list of file paths
"""
files = set()
directories = self.get_wralea_path()
recursive = True
if not SEARCH_OUTSIDE_ENTRY_POINTS:
recursive = False
if recursive:
files = set(f.abspath() for p in directories for f in path(p).walkfiles('*wralea*.py'))
else:
files = set(f.abspath() for p in directories for f in path(p).glob('*wralea*.py'))
return files
def glob(directory, pattern):
"""Return a list of path that match the pattern
:param pattern: a pattern to glob
:return: a list of paths that match the pattern
"""
ret = path.path(directory).glob(pattern)
return ret,
def showNewProjectDialog(self, default_name=None, text=None, parent=None):
my_path = path(settings.get_project_dir())
if default_name:
my_path = my_path / default_name
if not text:
text = 'Select name to create project'
fname = QtGui.QFileDialog.getSaveFileName(parent, text, my_path)
return fname
def glob(directory,pattern):
"""Return a list of path that match the pattern
:param pattern: a pattern to glob
:return: a list of paths that match the pattern
"""
ret = path.path(directory).glob(pattern)
return ret,
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 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 __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 _raw_data(self, mimedata, mimetype_in, mimetype_out):
"""
'text/uri-list' -> list of paths
'openalealab/data' -> name
"""
if mimetype_in == 'text/uri-list':
return [path(url.toLocalFile()) for url in mimedata.urls()]
elif mimetype_in == 'openalealab/data':
return mimedata.data('openalealab/data')
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_get_data():
res = run(
("openalea.data file", "get_data"), inputs={"package": "alinea.caribu.data", "filename": "filterT.can"}, pm=pm
)
assert path(res[0]).basename() == "filterT.can"
res = run(
("openalea.data file", "get_data"), inputs={"package": "openalea.core", "filename": "test_image.npy"}, pm=pm
)
assert path(res[0]).basename() == "test_image.npy"
res = run(
("openalea.data file", "get_data"),
inputs={"package": "vplants.fractalysis", "filename": "mango_f21_L.bgeom"},
pm=pm,
)
assert path(res[0]).basename() == "mango_f21_L.bgeom"
res = run(
("openalea.data file", "get_data"), inputs={"package": "openalea.stat_tool", "filename": "meri1.his"}, pm=pm
)
assert res[0] == None
def qt4(directory = path('qt4'), name='qt4'):
zip_name = path('..')/name + '.zip'
patterns = ['*2.5.dylib', '*.py', '*.api', '*.so', '*.txt', '*safe', '*INFO', '*.4.dylib']
curdir = path(os.curdir).abspath()
os.chdir(directory)
zf=zipfile.ZipFile(zip_name,compression=zipfile.ZIP_DEFLATED,mode='w')
d = path('.')
for pattern in patterns:
for fn in d.walkfiles(pattern):
print 'add ', fn
zf.write(fn)
zf.close()
os.chdir(curdir)
def decode(self, raw_data, mimetype_in, mimetype_out, **kwds):
"""
raw_data: list of urls
"""
if mimetype_in == 'text/uri-list':
for url in raw_data:
local_file = path(url)
return local_file, dict(path=local_file, name=local_file.namebase)
else:
return None, {}
def save_as(self):
project = self.project()
if project:
p = path(
self.showNewProjectDialog(
default_name=None,
text="Select name to save project")).abspath()
projectdir, name = p.splitpath()
if name:
project.save_as(projectdir, name)
def __call__(self, inputs):
"""
:param input: list of input values
:returns: the path string
"""
fname = str(inputs[0])
d = path.path(fname)
d.basename()
self.set_caption(str('.../'+d.basename()))
return (fname, )
def test_python_dict():
obj1 = {'test1': True, 'test2': 42, 'test3': 'ok'}
filename = path("temp.py")
saver = GenericSaver()
saver.save(obj1, filename)
loader = PythonLoader()
obj2 = loader.load(filename)
assert obj1 == obj2
if filename.exists():
os.remove(filename)
def test_python_dict():
obj1 = {'test1': True, 'test2': 42, 'test3': 'ok'}
filename = path("temp.py")
saver = CPickleSaver()
saver.save(obj1, filename)
loader = CPickleLoader()
obj2 = loader.load(filename)
assert obj1 == obj2
if filename.exists():
os.remove(filename)
def test_python_int():
obj1 = 42
filename = path("temp.py")
saver = CPickleSaver()
saver.save(obj1, filename)
loader = CPickleLoader()
obj2 = loader.load(filename)
assert obj1 == obj2
if filename.exists():
os.remove(filename)
def test_python_str():
obj1 = "this is a beautifull test text"
filename = path("temp.py")
saver = CPickleSaver()
saver.save(obj1, filename)
loader = CPickleLoader()
obj2 = loader.load(filename)
assert obj1 == obj2
if filename.exists():
os.remove(filename)
def __call__(self, inputs):
"""
:param input: list of input values
:returns: the path string
"""
fname = str(inputs[0])
d = path.path(fname)
d.basename()
self.set_caption(str('.../' + d.basename()))
return (fname, )
def test_python_int():
obj1 = 42
filename = path("temp.py")
saver = GenericSaver()
saver.save(obj1, filename)
loader = PythonLoader()
obj2 = loader.load(filename)
assert obj1 == obj2
if filename.exists():
os.remove(filename)
def test_python_str():
obj1 = "this is a beautifull test text"
filename = path("temp.py")
saver = GenericSaver()
saver.save(obj1, filename)
loader = GenericLoader()
obj2 = loader.load(filename)
assert obj1 == obj2
if filename.exists():
os.remove(filename)
def template_scons(self):
''' Build default SConstruct and SConscript files. '''
files = self.sconsfiles()
tpl_files = []
for f in files:
if not f.exists() or f.size == 0:
if 'wrapper' in f:
tpl_file = path(__file__).dirname()/'template_SConscript_wrapper.txt'
else:
tpl_file = path(__file__).dirname()/'template_'+f.namebase+'.txt'
tpl_files.append((f, tpl_file))
for f, tpl in tpl_files:
txt = Template(open(tpl).read())
txt = txt.substitute(**self.metainfo)
print "Creating a template version for %s ..." % ( f, )
py_file = open(f, "w")
py_file.write(txt)
py_file.close()
def add_wf_item(self, item, *args, **kwargs):
try:
prov_path = os.path.join(self.localpath,
str(item["workflow"]) + '.json')
with open(prov_path, 'a+') as fp:
json.dump(item, fp, indent=4)
except:
prov_path = path(settings.get_openalea_home_dir()
) / 'provenance' / 'wf_provenance.json'
print('Fail to open prov files. - Now write prov in : ', prov_path)
with open(prov_path, 'a+') as fp:
json.dump(item, fp, indent=4)
def test_post_processing():
adel_output_path = path('data/test_stand/adel_output.csv')
import tempfile
global_postprocessing_file_path = path(tempfile.mktemp(prefix='global_postprocessing', suffix='.csv'))
peraxis_postprocessing_file_path = path(tempfile.mktemp(prefix='peraxis_postprocessing', suffix='.csv'))
# launch the postprocessing
(global_postprocessing_file_path,
peraxis_postprocessing_file_path,
intermediate_results_file_path)= \
post_processing(adel_output_path,
3,
0.013824884792626729,
global_postprocessing_file_path,
peraxis_postprocessing_file_path)
expected_results_dir_path = path('data/test_stand')
# check intermediate results
intermediate_results_array = \
pandas.read_csv(intermediate_results_file_path).values
intermediate_results_array = np.delete(intermediate_results_array, 2, 1).astype(float)
expected_intermediate_results_array = \
pandas.read_csv(expected_results_dir_path/'intermediate.csv').values
expected_intermediate_results_array = np.delete(expected_intermediate_results_array, 2, 1).astype(float)
np.testing.assert_allclose(intermediate_results_array, expected_intermediate_results_array, relative_tolerance, absolute_tolerance)
# check per axis post processing results
peraxis_postprocessing_results_array = pandas.read_csv(peraxis_postprocessing_file_path).values
peraxis_postprocessing_results_array = np.delete(peraxis_postprocessing_results_array, [0, 2], 1).astype(float)
expected_peraxis_postprocessing_results_array = pandas.read_csv(expected_results_dir_path/'peraxis_postprocessing.csv').values
expected_peraxis_postprocessing_results_array = np.delete(expected_peraxis_postprocessing_results_array, [0, 2], 1).astype(float)
np.testing.assert_allclose(peraxis_postprocessing_results_array, expected_peraxis_postprocessing_results_array, relative_tolerance, absolute_tolerance)
# check global post processing results
global_postprocessing_results_array = pandas.read_csv(global_postprocessing_file_path).values
global_postprocessing_results_array = np.delete(global_postprocessing_results_array, 0, 1).astype(float)
expected_global_postprocessing_results_array = pandas.read_csv(expected_results_dir_path/'global_postprocessing.csv').values
expected_global_postprocessing_results_array = np.delete(expected_global_postprocessing_results_array, 0, 1).astype(float)
np.testing.assert_allclose(global_postprocessing_results_array, expected_global_postprocessing_results_array, relative_tolerance, absolute_tolerance)
def povray(scene,
pov_file = './scene.pov',
camera_distance=1., fov=45., width=320, height=280,
domain = ((-.5,-.5),(.5,.5)),
azimuth=0., zenith= 0., camera_type = 'perspective',
soil=False,
povray_cmd='povray'):
"""
!!!! Deprecated function, use alinea.povray.Povray class instead !!!!
Compute povray files based both on a scene and its stand box.
:Parameters:
- scene: a plantgl scene
- camera distance: distance from the position of the camera to the look_at point
- angle : angle corresponding to the width of the image
- width: width of the final image in pixel
- height: height of the final image in pixel
- domain: scene pattern used by caribu
- azimuth: angle in degree around the vertical axis. az=0. is equialent to have the width of the image align to X direction of the scene
- zenith: angle between the view direction and the vertical
- camera type: perspective, orthographic or fisheye
- soil: add a soil to the scene
- povray cmd : the path of the povray exe
"""
f = path(pov_file)
namebase = f.namebase
ext = f.ext
dirname = f.dirname()
xc=0.5*(domain[0][0]+domain[1][0])
yc=0.5*(domain[0][1]+domain[1][1])
camera = {'type':camera_type, 'distance':camera_distance, 'fov':fov, 'xc':xc, 'yc':yc, 'azimuth':azimuth, 'zenith':zenith}
pov = PovRay(camera=camera, image_width=width, image_height=height, working_dir=str(dirname))
pov.render(scene, namebase + ext)
image_name = pov.rendered_image_path
d3D = domain3D(domain, scene)
scene_box = pgl.Scene()
scene_box.add(stand_box(d3D))
f_box = namebase + '_box' + ext
pov.render(scene_box, f_box)
image_name_box = pov.rendered_image_path
return image_name, image_name_box
def povray(scene,
pov_file = './scene.pov',
camera_distance=1., fov=45., width=320, height=280,
domain = ((-.5,-.5),(.5,.5)),
azimuth=0., zenith= 0., camera_type = 'perspective',
soil=False,
povray_cmd='povray'):
"""
!!!! Deprecated function, use alinea.povray.Povray class instead !!!!
Compute povray files based both on a scene and its stand box.
:Parameters:
- scene: a plantgl scene
- camera distance: distance from the position of the camera to the look_at point
- angle : angle corresponding to the width of the image
- width: width of the final image in pixel
- height: height of the final image in pixel
- domain: scene pattern used by caribu
- azimuth: angle in degree around the vertical axis. az=0. is equialent to have the width of the image align to X direction of the scene
- zenith: angle between the view direction and the vertical
- camera type: perspective, orthographic or fisheye
- soil: add a soil to the scene
- povray cmd : the path of the povray exe
"""
f = path(pov_file)
namebase = f.namebase
ext = f.ext
dirname = f.dirname()
xc=0.5*(domain[0][0]+domain[1][0])
yc=0.5*(domain[0][1]+domain[1][1])
camera = {'type':camera_type, 'distance':camera_distance, 'fov':fov, 'xc':xc, 'yc':yc, 'azimuth':azimuth, 'zenith':zenith}
pov = PovRay(camera=camera, image_width=width, image_height=height, working_dir=str(dirname))
pov.render(scene, namebase + ext)
image_name = pov.rendered_image_path
d3D = domain3D(domain, scene)
scene_box = pgl.Scene()
scene_box.add(stand_box(d3D))
f_box = namebase + '_box' + ext
pov.render(scene_box, f_box)
image_name_box = pov.rendered_image_path
return image_name, image_name_box
def vlab_object(directory, pkgmanager):
"""
Create an openalea package from a vlab object.
First, read the specification file and parse it.
Create the list of data, the list of editors,
and the list of programs.
Build the graph of dependencies.
Compute the layout of the graph.
Create a package with data and a composite node.
"""
directory = path(directory)
obj = VlabObject2(directory, pkgmanager)
return obj
def __init__(self):
import traceback
traceback.print_stack(file=sys.__stdout__)
self._project = None
self._is_proj = False
self._debug = False
self.gui = True
self.tmpdir = path(get_openalea_tmp_dir())
self._config = MainConfig()
self.extension = None
self.applet = {}
self.manager = {}
self.package_manager = package_manager
self.control_manager = ControlManager()
self.project_manager = ProjectManager()
self.plugin_manager = PluginManager()
self.plugin_instance_manager = PluginInstanceManager()
self.manager['control'] = self.control_manager
self.manager['package'] = self.package_manager
self.manager['project'] = self.project_manager
self.manager['plugin'] = self.plugin_manager
self.manager['plugin_instance'] = self.plugin_instance_manager
self.world = World()
self.interpreter = interpreter()
# Hack if interpreter is an object from class TerminalInteractiveShell
if not hasattr(self.interpreter, "shell"):
self.interpreter.shell = self.interpreter
if hasattr(self.interpreter.shell, "events"):
self.interpreter.shell.events.register("post_execute", self.add_to_history)
else:
print("You need ipython >= 2.0 to use history.")
# self.project_manager.set_shell(self.interpreter.shell)
self.interpreter.locals['session'] = self
self.old_syspath = sys.path
self.load_default()
self.__class__.instantiated = True
def read_image_path(urls, mimetype_in, mimetype_out):
if isinstance(urls, basestring):
urls = [urls]
for url in urls:
url = path(url)
if url.exists():
try:
data = imread(url)
except Exception, e:
e = MimeConversionError(url, mimetype_in, mimetype_out, e)
raise e
else:
return data, {}
def template_doc(self):
files = self.docfiles()
tpl_files = []
for f in files:
if not f.exists() or f.size == 0:
tpl_file = path(__file__).dirname()/'template_'+f.namebase+'.txt'
tpl_files.append((f, tpl_file))
for f, tpl in tpl_files:
txt = Template(open(tpl).read())
txt = txt.substitute(self.metainfo)
print "Creating a template version for %s ..." % ( f, )
py_file = open(f, "w")
py_file.write(txt)
py_file.close()
def qt4_dev (directory=path('qt4-dev'), name='qt4_dev'):
zip_name = path('..')/name + '.zip'
curdir = path(os.curdir).abspath()
os.chdir(directory)
zf=zipfile.ZipFile(zip_name,compression=zipfile.ZIP_DEFLATED,mode='w')
dirs = {}
dirs['EGG-INFO'] = ['*']
dirs['include'] = ['*']
dirs['bin'] = ['*']
dirs['sip'] = ['*']
dirs['lib'] = ['*.4.dylib', '*2.5.dylib']
for dir, patterns in dirs.iteritems():
d = path(dir)
for pattern in patterns:
for fn in d.walkfiles(pattern):
print 'add ', fn
zf.write(fn)
zf.close()
os.chdir(curdir)
