def main():
parser = ArgumentParser(description=__doc__)
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('--eps', action='store', dest='eps',
default=1e-12, help=helps['eps'])
parser.add_argument('-o', '--filename-out',
action='store', dest='filename_out',
default=None, help=helps['filename-out'])
parser.add_argument('filename')
options = parser.parse_args()
filename = options.filename
mesh = Mesh.from_file(filename)
mesh_out = extract_edges(mesh, eps=float(options.eps))
mesh_out = merge_lines(mesh_out)
filename_out = options.filename_out
if filename_out is None:
filename_out = edit_filename(filename, prefix='edge_', new_ext='.vtk')
output('Outline mesh - vertices: %d, edges: %d, output filename: %s'
% (mesh_out[0].shape[0], mesh_out[2][0].shape[0], filename_out))
# hack to write '3_2' elements - edges
io = VTKMeshIO(None)
aux_mesh = Struct()
aux_mesh._get_io_data = lambda: mesh_out
aux_mesh.n_el = mesh_out[2][0].shape[0]
io.write(filename_out, aux_mesh)
def generate_gallery_html(output_filename, gallery_dir,
rst_dir, thumbnails_dir, dir_map, link_prefix=''):
"""
Generate the gallery html file with thumbnail images and links to
examples.
Parameters
----------
output_filename : str
The output html file name.
gallery_dir : str
The top level directory of gallery files.
rst_dir : str
The full path to rst files of examples within `gallery_dir`.
thumbnails_dir : str
The full path to thumbnail images within `gallery_dir`.
dir_map : dict
The directory mapping returned by `generate_rst_files()`
link_prefix : str, optional
The prefix to prepend to links to individual pages of examples.
"""
output('generating %s...' % output_filename)
lines = []
for dirname, filenames in ordered_iteritems(dir_map):
full_dirname = os.path.join(rst_dir, dirname)
for ex_filename, rst_filename in filenames:
full_rst_filename = os.path.join(full_dirname, rst_filename)
ebase = full_rst_filename.replace(rst_dir, '')[1:]
ebase = edit_filename(ebase, new_ext='.py')
link_base = full_rst_filename.replace(gallery_dir, '')[1:]
link = os.path.join(link_prefix,
os.path.splitext(link_base)[0] + '.html')
_get_fig_filenames(ebase, thumbnails_dir).next()
for thumbnail_filename in _get_fig_filenames(ebase,
thumbnails_dir):
if not os.path.isfile(thumbnail_filename):
# Skip examples with no image (= failed examples).
continue
thumbnail_name = thumbnail_filename.replace(gallery_dir,
'')[1:]
line = _link_template % (link, thumbnail_name,
os.path.splitext(ebase)[0])
lines.append(line)
fd = open(output_filename, 'w')
fd.write(_gallery_template % (link_prefix, '\n'.join(lines)))
fd.close()
output('...done')
def main():
parser = ArgumentParser(description=__doc__)
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('--eps',
action='store',
dest='eps',
default=1e-12,
help=helps['eps'])
parser.add_argument('-o',
'--filename-out',
action='store',
dest='filename_out',
default=None,
help=helps['filename-out'])
parser.add_argument('filename')
options = parser.parse_args()
filename = options.filename
mesh = Mesh.from_file(filename)
mesh_out = extract_edges(mesh, eps=float(options.eps))
mesh_out = merge_lines(mesh_out)
filename_out = options.filename_out
if filename_out is None:
filename_out = edit_filename(filename, prefix='edge_', new_ext='.vtk')
output('Outline mesh - vertices: %d, edges: %d, output filename: %s' %
(mesh_out[0].shape[0], mesh_out[2][0].shape[0], filename_out))
# hack to write '3_2' elements - edges
io = MeshioLibIO()
aux_mesh = Struct()
aux_mesh._get_io_data = lambda: mesh_out
aux_mesh.n_el = mesh_out[2][0].shape[0]
io.write(filename_out, aux_mesh)
def generate_images(images_dir, examples_dir):
"""
Generate images from results of running examples found in
`examples_dir` directory.
The generated images are stored to `images_dir`,
"""
from sfepy.applications import solve_pde
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.utils import mlab
prefix = output.prefix
output_dir = tempfile.mkdtemp()
trunk = os.path.join(output_dir, 'result')
options = Struct(output_filename_trunk=trunk,
output_format='vtk',
save_ebc=False,
save_ebc_nodes=False,
save_regions=False,
save_field_meshes=False,
save_regions_as_groups=False,
solve_not=False)
default_views = {'' : {}}
ensure_path(images_dir + os.path.sep)
view = Viewer('', offscreen=False)
for ex_filename in locate_files('*.py', examples_dir):
if _omit(ex_filename): continue
output.level = 0
output.prefix = prefix
ebase = ex_filename.replace(examples_dir, '')[1:]
output('trying "%s"...' % ebase)
try:
problem, state = solve_pde(ex_filename, options=options)
except KeyboardInterrupt:
raise
except:
problem = None
output('***** failed! *****')
if problem is not None:
if ebase in custom:
views = custom[ebase]
else:
views = default_views
tsolver = problem.get_time_solver()
if tsolver.ts is None:
suffix = None
else:
suffix = tsolver.ts.suffix % (tsolver.ts.n_step - 1)
filename = problem.get_output_name(suffix=suffix)
for suffix, kwargs in views.iteritems():
fig_filename = _get_fig_filename(ebase, images_dir, suffix)
fname = edit_filename(filename, suffix=suffix)
output('displaying results from "%s"' % fname)
disp_name = fig_filename.replace(sfepy.data_dir, '')
output('to "%s"...' % disp_name.lstrip(os.path.sep))
view.filename = fname
view(scene=view.scene, show=False, is_scalar_bar=True, **kwargs)
view.save_image(fig_filename)
mlab.clf()
output('...done')
remove_files(output_dir)
output('...done')
def generate_gallery_html(examples_dir, output_filename, gallery_dir,
rst_dir, thumbnails_dir, dir_map, link_prefix):
"""
Generate the gallery html file with thumbnail images and links to
examples.
Parameters
----------
output_filename : str
The output html file name.
gallery_dir : str
The top level directory of gallery files.
rst_dir : str
The full path to rst files of examples within `gallery_dir`.
thumbnails_dir : str
The full path to thumbnail images within `gallery_dir`.
dir_map : dict
The directory mapping returned by `generate_rst_files()`
link_prefix : str, optional
The prefix to prepend to links to individual pages of examples.
"""
output('generating %s...' % output_filename)
with open(_gallery_template_file, 'r') as fd:
gallery_template = fd.read()
div_lines=[]
sidebar = []
for dirname, filenames in ordered_iteritems(dir_map):
full_dirname = os.path.join(rst_dir, dirname)
dirnamenew = dirname.replace("_"," ")
sidebarline = _side_links % (dirname, dirnamenew.title())
lines = []
for ex_filename, rst_filename in filenames:
full_rst_filename = os.path.join(full_dirname, rst_filename)
ebase = full_rst_filename.replace(rst_dir, '')[1:]
ebase = edit_filename(ebase, new_ext='.py')
link_base = full_rst_filename.replace(gallery_dir, '')[1:]
link = os.path.join(link_prefix,
os.path.splitext(link_base)[0] + '.html')
_get_fig_filenames(ebase, thumbnails_dir).next()
for thumbnail_filename in _get_fig_filenames(ebase,
thumbnails_dir):
if not os.path.isfile(thumbnail_filename):
# Skip examples with no image (= failed examples).
continue
thumbnail_name = thumbnail_filename.replace(gallery_dir,
'')[1:]
path_to_file = os.path.join(examples_dir,ebase)
docstring = get_default(import_file(path_to_file).__doc__,
'missing description!')
docstring = docstring.replace('e.g.', 'eg:')
docstring = docstring.split('.')
line = _link_template % (link,os.path.splitext(ebase)[0],
thumbnail_name,link,docstring[0]+'.')
lines.append(line)
if(len(lines)!=0):
div_lines.append(_div_line % (dirname, dirnamenew.title(),
dirname, '\n'.join(lines)))
sidebar.append(sidebarline)
fd = open(output_filename, 'w')
fd.write(gallery_template % ((link_prefix,) * 7
+ ('\n'.join(sidebar), '\n'.join(div_lines))))
fd.close()
output('...done')
def generate_images(images_dir, examples_dir):
"""
Generate images from results of running examples found in
`examples_dir` directory.
The generated images are stored to `images_dir`,
"""
from sfepy.applications import solve_pde
from sfepy.postprocess import Viewer
from sfepy.postprocess.utils import mlab
prefix = output.prefix
output_dir = tempfile.mkdtemp()
trunk = os.path.join(output_dir, 'result')
options = Struct(output_filename_trunk=trunk,
output_format='vtk',
save_ebc=False,
save_ebc_nodes=False,
save_regions=False,
save_field_meshes=False,
save_regions_as_groups=False,
solve_not=False)
default_views = {'' : {}}
ensure_path(images_dir + os.path.sep)
view = Viewer('', offscreen=False)
for ex_filename in locate_files('*.py', examples_dir):
if _omit(ex_filename): continue
output.level = 0
output.prefix = prefix
ebase = ex_filename.replace(examples_dir, '')[1:]
output('trying "%s"...' % ebase)
try:
problem, state = solve_pde(ex_filename, options=options)
except KeyboardInterrupt:
raise
except:
problem = None
output('***** failed! *****')
if problem is not None:
if ebase in custom:
views = custom[ebase]
else:
views = default_views
tsolver = problem.get_time_solver()
if tsolver.ts is None:
suffix = None
else:
suffix = tsolver.ts.suffix % (tsolver.ts.n_step - 1)
filename = problem.get_output_name(suffix=suffix)
for suffix, kwargs in views.iteritems():
fig_filename = _get_fig_filename(ebase, images_dir, suffix)
fname = edit_filename(filename, suffix=suffix)
output('displaying results from "%s"' % fname)
disp_name = fig_filename.replace(sfepy.data_dir, '')
output('to "%s"...' % disp_name.lstrip(os.path.sep))
view.filename = fname
view(scene=view.scene, show=False, is_scalar_bar=True,
fig_filename=fig_filename, **kwargs)
mlab.clf()
output('...done')
remove_files(output_dir)
output('...done')
def main():
parser = OptionParser(usage = usage, version = "%prog " + sfepy.__version__)
parser.add_option( "-m", "--mesh",
action = "store_true", dest = "save_mesh",
default = True,
help = "save surface mesh [default: %default]" )
parser.add_option( "-n", "--no-surface",
action = "store_true", dest = "no_surface",
default = False,
help = "do not output surface [default: %default]" )
(options, args) = parser.parse_args()
if (len( args ) == 2):
filename_in = args[0];
filename_out = args[1];
else:
parser.print_help(),
return
if (filename_in == '-'):
file_in = sys.stdin
else:
file_in = open( filename_in, "r" );
mesh = Mesh.from_file( filename_in )
if (filename_in != '-'):
file_in.close()
domain = Domain('domain', mesh)
domain.setup_groups()
if domain.has_faces():
domain.fix_element_orientation()
domain.setup_facets(create_edges=False)
lst, surf_faces = domain.surface_faces()
surf_mesh = Mesh.from_surface( surf_faces, mesh )
if options.save_mesh:
aux = edit_filename(filename_in, prefix='surf_', new_ext='.mesh')
surf_mesh.write(aux, io='auto')
if options.no_surface:
return
gr_s = surface_graph( surf_faces, mesh.n_nod )
## import sfepy.base.plotutils as plu
## plu.spy( gr_s )
## plu.pylab.show()
n_comp, comps = surface_components( gr_s, surf_faces )
# print 'components:', n_comp
ccs, comps = comps, nm.zeros( (0,1), nm.int32 )
for cc in ccs:
comps = nm.concatenate( (comps, cc[:,nm.newaxis]), 0 )
out = nm.concatenate( (lst, comps), 1 )
if (filename_out == '-'):
file_out = sys.stdout
else:
file_out = open( filename_out, "w" );
for row in out:
file_out.write( '%d %d %d %d\n' % (row[0], row[1], row[2], row[3]) )
if (filename_out != '-'):
file_out.close()
def main():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument("--version", action="version",
version="%(prog)s " + sfepy.__version__)
parser.add_argument("-m", "--mesh",
action="store_true", dest="save_mesh",
default=False,
help="save surface mesh")
parser.add_argument("-n", "--no-surface",
action="store_true", dest="no_surface",
default=False,
help="do not output surface [default: %(default)s]")
parser.add_argument('filename_in', help="'-' is for stdin")
parser.add_argument('filename_out', help="'-' is for stdout")
options = parser.parse_args()
filename_in = options.filename_in
filename_out = options.filename_out
if (filename_in == '-'):
file_in = sys.stdin
else:
file_in = open(filename_in, "r")
mesh = Mesh.from_file(filename_in)
if (filename_in != '-'):
file_in.close()
domain = FEDomain('domain', mesh)
if options.save_mesh:
region = domain.create_region('surf', 'vertices of surface', 'facet')
surf_mesh = Mesh.from_region(region, mesh,
localize=True, is_surface=True)
aux = edit_filename(filename_in, prefix='surf_', new_ext='.mesh')
surf_mesh.write(aux, io='auto')
if domain.has_faces():
domain.fix_element_orientation()
lst, surf_faces = get_surface_faces(domain)
if options.no_surface:
return
gr_s = surface_graph(surf_faces, mesh.n_nod)
n_comp, comps = surface_components(gr_s, surf_faces)
output('number of surface components:', n_comp)
ccs, comps = comps, nm.zeros((0,1), nm.int32)
for cc in ccs:
comps = nm.concatenate((comps, cc[:,nm.newaxis]), 0)
out = nm.concatenate((lst, comps), 1)
if (filename_out == '-'):
file_out = sys.stdout
else:
file_out = open(filename_out, "w")
for row in out:
file_out.write('%d %d %d\n' % (row[0], row[1], row[2]))
if (filename_out != '-'):
file_out.close()
def main():
parser = OptionParser(usage=usage, version='%prog')
parser.add_option('-n', '--dry-run',
action='store_true', dest='dry_run',
default=False, help=help['dry_run'])
options, args = parser.parse_args()
if len(args) == 2:
doc_dir, top_dir = [os.path.realpath(ii) for ii in args]
else:
parser.print_help(),
return
docs = set(ii for ii in locate_files('*.rst', root_dir=doc_dir))
sources = set(ii for ii in
locate_files('*.py',
root_dir=os.path.join(top_dir, 'sfepy'))
if os.path.basename(ii) not in omits)
sources.update(ii for ii in
locate_files('*.pyx',
root_dir=os.path.join(top_dir, 'sfepy'))
if os.path.basename(ii) not in omits_pyx)
scripts = set(ii for ii in
locate_files('*.py',
root_dir=os.path.join(top_dir, 'script'))
if os.path.basename(ii) not in omits)
top_scripts = set(os.path.realpath(ii)
for ii in fnmatch.filter(os.listdir(top_dir), '*.py')
if os.path.basename(ii) not in omits)
all_sources = set()
all_sources.update(sources, scripts, top_scripts)
cwd = os.path.realpath(os.path.curdir) + os.path.sep
output.prefix = 'smd:'
output('removing unneeded rst files in "%s"...' % doc_dir)
for doc in sorted(docs):
aux = edit_filename(doc, new_ext='.py')
src1 = os.path.normpath(aux.replace(doc_dir, top_dir))
aux = edit_filename(doc, new_ext='.pyx')
src2 = os.path.normpath(aux.replace(doc_dir, top_dir))
if (src1 not in all_sources) and (src2 not in all_sources):
output('remove: %s' % doc.replace(cwd, ''))
if not options.dry_run:
os.remove(doc)
output('...done')
output('creating missing rst files in "%s"...' % doc_dir)
for src in sorted(all_sources):
aux = edit_filename(src, new_ext='.rst')
doc = os.path.normpath(aux.replace(top_dir, doc_dir))
if doc not in docs:
output('create: %s' % doc.replace(cwd, ''))
if not options.dry_run:
mod_filename = src.replace(top_dir + os.path.sep, '')
mod_name = mod_filename.replace(os.path.sep, '.')
mod_name = edit_filename(mod_name, new_ext='')
if mod_name.startswith('sfepy'): # Module.
title = mod_name + ' module'
else: # Script.
title = mod_filename + ' script'
mod_name = mod_name.split('.')[-1]
underlines = '=' * len(title)
contents = doc_template % (title, underlines, mod_name)
ensure_path(doc)
fd = open(doc, 'w')
fd.write(contents)
fd.close()
output('...done')
def main():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-n',
'--dry-run',
action='store_true',
dest='dry_run',
default=False,
help=help['dry_run'])
parser.add_argument('doc_dir')
parser.add_argument('top_dir')
options = parser.parse_args()
doc_dir, top_dir = [
os.path.realpath(ii) for ii in [options.doc_dir, options.top_dir]
]
docs = set(ii for ii in locate_files('*.rst', root_dir=doc_dir))
sources = set(
ii
for ii in locate_files('*.py', root_dir=os.path.join(top_dir, 'sfepy'))
if os.path.basename(ii) not in omits)
sources.update(ii for ii in locate_files(
'*.pyx', root_dir=os.path.join(top_dir, 'sfepy'))
if os.path.basename(ii) not in omits_pyx)
scripts = set(ii for ii in locate_files(
'*.py', root_dir=os.path.join(top_dir, 'script'))
if os.path.basename(ii) not in omits)
top_scripts = set(
os.path.realpath(ii)
for ii in fnmatch.filter(os.listdir(top_dir), '*.py')
if os.path.basename(ii) not in omits)
all_sources = set()
all_sources.update(sources, scripts, top_scripts)
cwd = os.path.realpath(os.path.curdir) + os.path.sep
output.prefix = 'smd:'
output('removing unneeded rst files in "%s"...' % doc_dir)
for doc in sorted(docs):
aux = edit_filename(doc, new_ext='.py')
src1 = os.path.normpath(aux.replace(doc_dir, top_dir))
aux = edit_filename(doc, new_ext='.pyx')
src2 = os.path.normpath(aux.replace(doc_dir, top_dir))
if (src1 not in all_sources) and (src2 not in all_sources):
output('remove: %s' % doc.replace(cwd, ''))
if not options.dry_run:
os.remove(doc)
output('...done')
output('creating missing rst files in "%s"...' % doc_dir)
for src in sorted(all_sources):
aux = edit_filename(src, new_ext='.rst')
doc = os.path.normpath(aux.replace(top_dir, doc_dir))
if doc not in docs:
output('create: %s' % doc.replace(cwd, ''))
if not options.dry_run:
mod_filename = src.replace(top_dir + os.path.sep, '')
mod_name = mod_filename.replace(os.path.sep, '.')
mod_name = edit_filename(mod_name, new_ext='')
if mod_name.startswith('sfepy'): # Module.
title = mod_name + ' module'
else: # Script.
title = mod_filename + ' script'
mod_name = mod_name.split('.')[-1]
underlines = '=' * len(title)
contents = doc_template % (title, underlines, mod_name)
ensure_path(doc)
fd = open(doc, 'w')
fd.write(contents)
fd.close()
output('...done')
def main():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument("--version",
action="version",
version="%(prog)s " + sfepy.__version__)
parser.add_argument("-m",
"--mesh",
action="store_true",
dest="save_mesh",
default=False,
help="save surface mesh")
parser.add_argument("-n",
"--no-surface",
action="store_true",
dest="no_surface",
default=False,
help="do not output surface [default: %(default)s]")
parser.add_argument('filename_in', help="'-' is for stdin")
parser.add_argument('filename_out', help="'-' is for stdout")
options = parser.parse_args()
filename_in = options.filename_in
filename_out = options.filename_out
if (filename_in == '-'):
file_in = sys.stdin
else:
file_in = open(filename_in, "r")
mesh = Mesh.from_file(filename_in)
if (filename_in != '-'):
file_in.close()
domain = FEDomain('domain', mesh)
if options.save_mesh:
region = domain.create_region('surf', 'vertices of surface', 'facet')
surf_mesh = Mesh.from_region(region,
mesh,
localize=True,
is_surface=True)
aux = edit_filename(filename_in, prefix='surf_', new_ext='.mesh')
surf_mesh.write(aux, io='auto')
if domain.has_faces():
domain.fix_element_orientation()
lst, surf_faces = get_surface_faces(domain)
if options.no_surface:
return
gr_s = surface_graph(surf_faces, mesh.n_nod)
n_comp, comps = surface_components(gr_s, surf_faces)
output('number of surface components:', n_comp)
ccs, comps = comps, nm.zeros((0, 1), nm.int32)
for cc in ccs:
comps = nm.concatenate((comps, cc[:, nm.newaxis]), 0)
out = nm.concatenate((lst, comps), 1)
if (filename_out == '-'):
file_out = sys.stdout
else:
file_out = open(filename_out, "w")
for row in out:
file_out.write('%d %d %d\n' % (row[0], row[1], row[2]))
if (filename_out != '-'):
file_out.close()
def main():
parser = OptionParser(usage=usage, version="%prog " + sfepy.__version__)
parser.add_option("-m", "--mesh",
action="store_true", dest="save_mesh",
default=False,
help="save surface mesh")
parser.add_option("-n", "--no-surface",
action="store_true", dest="no_surface",
default=False,
help="do not output surface [default: %default]")
(options, args) = parser.parse_args()
if (len(args) == 2):
filename_in = args[0];
filename_out = args[1];
else:
parser.print_help(),
return
if (filename_in == '-'):
file_in = sys.stdin
else:
file_in = open(filename_in, "r");
mesh = Mesh.from_file(filename_in)
if (filename_in != '-'):
file_in.close()
domain = FEDomain('domain', mesh)
if options.save_mesh:
region = domain.create_region('surf', 'vertices of surface', 'facet')
surf_mesh = Mesh.from_region(region, mesh,
localize=True, is_surface=True)
aux = edit_filename(filename_in, prefix='surf_', new_ext='.mesh')
surf_mesh.write(aux, io='auto')
if domain.has_faces():
domain.fix_element_orientation()
lst, surf_faces = get_surface_faces(domain)
if options.no_surface:
return
gr_s = surface_graph(surf_faces, mesh.n_nod)
n_comp, comps = surface_components(gr_s, surf_faces)
output('number of surface components:', n_comp)
ccs, comps = comps, nm.zeros((0,1), nm.int32)
for cc in ccs:
comps = nm.concatenate((comps, cc[:,nm.newaxis]), 0)
out = nm.concatenate((lst, comps), 1)
if (filename_out == '-'):
file_out = sys.stdout
else:
file_out = open(filename_out, "w");
for row in out:
file_out.write('%d %d %d\n' % (row[0], row[1], row[2]))
if (filename_out != '-'):
file_out.close()
def save_state(self, filename, state=None, out=None,
fill_value=None, post_process_hook=None,
linearization=None, file_per_var=False, **kwargs):
"""
Parameters
----------
file_per_var : bool or None
If True, data of each variable are stored in a separate
file. If None, it is set to the application option value.
linearization : Struct or None
The linearization configuration for higher order
approximations. If its kind is 'adaptive', `file_per_var` is
assumed True.
"""
linearization = get_default(linearization, self.linearization)
if linearization.kind != 'adaptive':
file_per_var = get_default(file_per_var, self.file_per_var)
else:
file_per_var = True
extend = not file_per_var
if (out is None) and (state is not None):
out = state.create_output_dict(fill_value=fill_value,
extend=extend,
linearization=linearization)
if post_process_hook is not None:
out = post_process_hook(out, self, state, extend=extend)
if linearization.kind == 'adaptive':
for key, val in out.iteritems():
mesh = val.get('mesh', self.domain.mesh)
aux = io.edit_filename(filename, suffix='_' + val.var_name)
mesh.write(aux, io='auto', out={key : val},
float_format=self.float_format, **kwargs)
if hasattr(val, 'levels'):
output('max. refinement per group:', val.levels)
elif file_per_var:
meshes = {}
if self.equations is None:
varnames = {}
for key, val in out.iteritems():
varnames[val.var_name] = 1
varnames = varnames.keys()
outvars = self.create_variables(varnames)
itervars = outvars.__iter__
else:
itervars = self.equations.variables.iter_state
for var in itervars():
rname = var.field.region.name
if meshes.has_key(rname):
mesh = meshes[rname]
else:
mesh = Mesh.from_region(var.field.region, self.domain.mesh,
localize=True,
is_surface=var.is_surface)
meshes[rname] = mesh
vout = {}
for key, val in out.iteritems():
try:
if val.var_name == var.name:
vout[key] = val
except AttributeError:
msg = 'missing var_name attribute in output!'
raise ValueError(msg)
aux = io.edit_filename(filename, suffix='_' + var.name)
mesh.write(aux, io='auto', out=vout,
float_format=self.float_format, **kwargs)
else:
mesh = out.pop('__mesh__', self.domain.mesh)
mesh.write(filename, io='auto', out=out,
float_format=self.float_format, **kwargs)
def main():
parser = OptionParser(usage=usage, version="%prog " + sfepy.__version__)
parser.add_option("-m",
"--mesh",
action="store_true",
dest="save_mesh",
default=False,
help="save surface mesh")
parser.add_option("-n",
"--no-surface",
action="store_true",
dest="no_surface",
default=False,
help="do not output surface [default: %default]")
(options, args) = parser.parse_args()
if (len(args) == 2):
filename_in = args[0]
filename_out = args[1]
else:
parser.print_help(),
return
if (filename_in == '-'):
file_in = sys.stdin
else:
file_in = open(filename_in, "r")
mesh = Mesh.from_file(filename_in)
if (filename_in != '-'):
file_in.close()
domain = FEDomain('domain', mesh)
if options.save_mesh:
region = domain.create_region('surf', 'vertices of surface', 'facet')
surf_mesh = Mesh.from_region(region,
mesh,
localize=True,
is_surface=True)
aux = edit_filename(filename_in, prefix='surf_', new_ext='.mesh')
surf_mesh.write(aux, io='auto')
if domain.has_faces():
domain.fix_element_orientation()
lst, surf_faces = get_surface_faces(domain)
if options.no_surface:
return
gr_s = surface_graph(surf_faces, mesh.n_nod)
n_comp, comps = surface_components(gr_s, surf_faces)
output('number of surface components:', n_comp)
ccs, comps = comps, nm.zeros((0, 1), nm.int32)
for cc in ccs:
comps = nm.concatenate((comps, cc[:, nm.newaxis]), 0)
out = nm.concatenate((lst, comps), 1)
if (filename_out == '-'):
file_out = sys.stdout
else:
file_out = open(filename_out, "w")
for row in out:
file_out.write('%d %d %d\n' % (row[0], row[1], row[2]))
if (filename_out != '-'):
file_out.close()
def generate_gallery_html(examples_dir, output_filename, gallery_dir,
rst_dir, thumbnails_dir, dir_map, link_prefix):
"""
Generate the gallery html file with thumbnail images and links to
examples.
Parameters
----------
output_filename : str
The output html file name.
gallery_dir : str
The top level directory of gallery files.
rst_dir : str
The full path to rst files of examples within `gallery_dir`.
thumbnails_dir : str
The full path to thumbnail images within `gallery_dir`.
dir_map : dict
The directory mapping returned by `generate_rst_files()`
link_prefix : str, optional
The prefix to prepend to links to individual pages of examples.
"""
output('generating %s...' % output_filename)
with open(_gallery_template_file, 'r') as fd:
gallery_template = fd.read()
div_lines=[]
sidebar = []
for dirname, filenames in ordered_iteritems(dir_map):
full_dirname = os.path.join(rst_dir, dirname)
dirnamenew = dirname.replace("_"," ")
sidebarline = _side_links % (dirname, dirnamenew.title())
lines = []
for ex_filename, rst_filename in filenames:
full_rst_filename = os.path.join(full_dirname, rst_filename)
ebase = full_rst_filename.replace(rst_dir, '')[1:]
ebase = edit_filename(ebase, new_ext='.py')
link_base = full_rst_filename.replace(gallery_dir, '')[1:]
link = os.path.join(link_prefix,
os.path.splitext(link_base)[0] + '.html')
_get_fig_filenames(ebase, thumbnails_dir).next()
for thumbnail_filename in _get_fig_filenames(ebase,
thumbnails_dir):
if not os.path.isfile(thumbnail_filename):
# Skip examples with no image (= failed examples).
continue
thumbnail_name = thumbnail_filename.replace(gallery_dir,
'')[1:]
path_to_file = os.path.join(examples_dir,ebase)
docstring = get_default(import_file(path_to_file).__doc__,
'missing description!')
docstring = docstring.replace('e.g.', 'eg:')
docstring = docstring.split('.')
line = _link_template % (link,os.path.splitext(ebase)[0],
thumbnail_name,link,docstring[0]+'.')
lines.append(line)
if(len(lines)!=0):
div_lines.append(_div_line % (dirname, dirnamenew.title(),
dirname, '\n'.join(lines)))
sidebar.append(sidebarline)
fd = open(output_filename, 'w')
fd.write(gallery_template % ((link_prefix,) * 7
+ ('\n'.join(sidebar), '\n'.join(div_lines))))
fd.close()
output('...done')
def generate_probes(filename_input, filename_results, options,
conf=None, problem=None, probes=None, labels=None,
probe_hooks=None):
"""
Generate probe figures and data files.
"""
if conf is None:
required, other = get_standard_keywords()
conf = ProblemConf.from_file(filename_input, required, other)
opts = conf.options
if options.auto_dir:
output_dir = opts.get_('output_dir', '.')
filename_results = os.path.join(output_dir, filename_results)
output('results in: %s' % filename_results)
io = MeshIO.any_from_filename(filename_results)
step = options.step if options.step >= 0 else io.read_last_step()
all_data = io.read_data(step)
output('loaded:', all_data.keys())
output('from step:', step)
if options.only_names is None:
data = all_data
else:
data = {}
for key, val in all_data.iteritems():
if key in options.only_names:
data[key] = val
if problem is None:
problem = ProblemDefinition.from_conf(conf,
init_equations=False,
init_solvers=False)
if probes is None:
gen_probes = conf.get_function(conf.options.gen_probes)
probes, labels = gen_probes(problem)
if probe_hooks is None:
probe_hooks = {None : conf.get_function(conf.options.probe_hook)}
if options.output_filename_trunk is None:
options.output_filename_trunk = problem.ofn_trunk
filename_template = options.output_filename_trunk \
+ ('_%%d.%s' % options.output_format)
if options.same_dir:
filename_template = os.path.join(os.path.dirname(filename_results),
filename_template)
output_dir = os.path.dirname(filename_results)
for ip, probe in enumerate(probes):
output(ip, probe.name)
probe.set_options(close_limit=options.close_limit)
for key, probe_hook in probe_hooks.iteritems():
out = probe_hook(data, probe, labels[ip], problem)
if out is None: continue
if isinstance(out, tuple):
fig, results = out
else:
fig = out
if key is not None:
filename = filename_template % (key, ip)
else:
filename = filename_template % ip
if fig is not None:
if isinstance(fig, dict):
for fig_name, fig_fig in fig.iteritems():
fig_filename = edit_filename(filename,
suffix='_' + fig_name)
fig_fig.savefig(fig_filename)
output('figure ->', os.path.normpath(fig_filename))
else:
fig.savefig(filename)
output('figure ->', os.path.normpath(filename))
if results is not None:
txt_filename = edit_filename(filename, new_ext='.txt')
write_results(txt_filename, probe, results)
output('data ->', os.path.normpath(txt_filename))
def generate_probes(filename_input,
filename_results,
options,
conf=None,
problem=None,
probes=None,
labels=None,
probe_hooks=None):
"""
Generate probe figures and data files.
"""
if conf is None:
required, other = get_standard_keywords()
conf = ProblemConf.from_file(filename_input, required, other)
opts = conf.options
if options.auto_dir:
output_dir = opts.get_('output_dir', '.')
filename_results = os.path.join(output_dir, filename_results)
output('results in: %s' % filename_results)
io = MeshIO.any_from_filename(filename_results)
step = options.step if options.step >= 0 else io.read_last_step()
all_data = io.read_data(step)
output('loaded:', list(all_data.keys()))
output('from step:', step)
if options.only_names is None:
data = all_data
else:
data = {}
for key, val in six.iteritems(all_data):
if key in options.only_names:
data[key] = val
if problem is None:
problem = Problem.from_conf(conf,
init_equations=False,
init_solvers=False)
if probes is None:
gen_probes = conf.get_function(conf.options.gen_probes)
probes, labels = gen_probes(problem)
if probe_hooks is None:
probe_hooks = {None: conf.get_function(conf.options.probe_hook)}
if options.output_filename_trunk is None:
options.output_filename_trunk = problem.ofn_trunk
filename_template = options.output_filename_trunk \
+ ('_%%d.%s' % options.output_format)
if options.same_dir:
filename_template = os.path.join(os.path.dirname(filename_results),
filename_template)
output_dir = os.path.dirname(filename_results)
for ip, probe in enumerate(probes):
output(ip, probe.name)
probe.set_options(close_limit=options.close_limit)
for key, probe_hook in six.iteritems(probe_hooks):
out = probe_hook(data, probe, labels[ip], problem)
if out is None: continue
if isinstance(out, tuple):
fig, results = out
else:
fig = out
if key is not None:
filename = filename_template % (key, ip)
else:
filename = filename_template % ip
if fig is not None:
if isinstance(fig, dict):
for fig_name, fig_fig in six.iteritems(fig):
fig_filename = edit_filename(filename,
suffix='_' + fig_name)
fig_fig.savefig(fig_filename)
output('figure ->', os.path.normpath(fig_filename))
else:
fig.savefig(filename)
output('figure ->', os.path.normpath(filename))
if results is not None:
txt_filename = edit_filename(filename, new_ext='.txt')
write_results(txt_filename, probe, results)
output('data ->', os.path.normpath(txt_filename))
def main():
parser = OptionParser(usage=usage, version="%prog " + sfepy.__version__)
parser.add_option("-m",
"--mesh",
action="store_true",
dest="save_mesh",
default=True,
help="save surface mesh [default: %default]")
parser.add_option("-n",
"--no-surface",
action="store_true",
dest="no_surface",
default=False,
help="do not output surface [default: %default]")
(options, args) = parser.parse_args()
if (len(args) == 2):
filename_in = args[0]
filename_out = args[1]
else:
parser.print_help(),
return
if (filename_in == '-'):
file_in = sys.stdin
else:
file_in = open(filename_in, "r")
mesh = Mesh.from_file(filename_in)
if (filename_in != '-'):
file_in.close()
domain = Domain('domain', mesh)
domain.setup_groups()
if domain.has_faces():
domain.fix_element_orientation()
domain.setup_facets(create_edges=False)
lst, surf_faces = domain.surface_faces()
surf_mesh = Mesh.from_surface(surf_faces, mesh)
if options.save_mesh:
aux = edit_filename(filename_in, prefix='surf_', new_ext='.mesh')
surf_mesh.write(aux, io='auto')
if options.no_surface:
return
gr_s = surface_graph(surf_faces, mesh.n_nod)
## import sfepy.base.plotutils as plu
## plu.spy( gr_s )
## plu.pylab.show()
n_comp, comps = surface_components(gr_s, surf_faces)
# print 'components:', n_comp
ccs, comps = comps, nm.zeros((0, 1), nm.int32)
for cc in ccs:
comps = nm.concatenate((comps, cc[:, nm.newaxis]), 0)
out = nm.concatenate((lst, comps), 1)
if (filename_out == '-'):
file_out = sys.stdout
else:
file_out = open(filename_out, "w")
for row in out:
file_out.write('%d %d %d %d\n' % (row[0], row[1], row[2], row[3]))
if (filename_out != '-'):
file_out.close()
def save_state(self, filename, state=None, out=None,
fill_value=None, post_process_hook=None,
linearization=None, file_per_var=False, **kwargs):
"""
Parameters
----------
file_per_var : bool or None
If True, data of each variable are stored in a separate
file. If None, it is set to the application option value.
linearization : Struct or None
The linearization configuration for higher order
approximations. If its kind is 'adaptive', `file_per_var` is
assumed True.
"""
linearization = get_default(linearization, self.linearization)
if linearization.kind != 'adaptive':
file_per_var = get_default(file_per_var, self.file_per_var)
else:
file_per_var = True
extend = not file_per_var
if (out is None) and (state is not None):
out = state.create_output_dict(fill_value=fill_value,
extend=extend,
linearization=linearization)
if post_process_hook is not None:
out = post_process_hook(out, self, state, extend=extend)
if linearization.kind == 'adaptive':
for key, val in out.iteritems():
mesh = val.get('mesh', self.domain.mesh)
aux = io.edit_filename(filename, suffix='_' + val.var_name)
mesh.write(aux, io='auto', out={key : val},
float_format=self.float_format, **kwargs)
if hasattr(val, 'levels'):
output('max. refinement per group:', val.levels)
elif file_per_var:
meshes = {}
if self.equations is None:
varnames = {}
for key, val in out.iteritems():
varnames[val.var_name] = 1
varnames = varnames.keys()
outvars = self.create_variables(varnames)
itervars = outvars.__iter__
else:
itervars = self.equations.variables.iter_state
for var in itervars():
rname = var.field.region.name
if meshes.has_key( rname ):
mesh = meshes[rname]
else:
mesh = Mesh.from_region(var.field.region, self.domain.mesh,
localize=True,
is_surface=var.is_surface)
meshes[rname] = mesh
vout = {}
for key, val in out.iteritems():
try:
if val.var_name == var.name:
vout[key] = val
except AttributeError:
msg = 'missing var_name attribute in output!'
raise ValueError(msg)
aux = io.edit_filename(filename, suffix='_' + var.name)
mesh.write(aux, io='auto', out=vout,
float_format=self.float_format, **kwargs)
else:
self.domain.mesh.write(filename, io='auto', out=out,
float_format=self.float_format, **kwargs)
def generate_probes(filename_input,
filename_results,
options,
conf=None,
problem=None,
probes=None,
labels=None,
probe_hooks=None):
"""
Generate probe figures and data files.
"""
if conf is None:
required, other = get_standard_keywords()
conf = ProblemConf.from_file(filename_input, required, other)
opts = conf.options
if options.auto_dir:
output_dir = get_default_attr(opts, 'output_dir', '.')
filename_results = os.path.join(output_dir, filename_results)
output('results in: %s' % filename_results)
io = MeshIO.any_from_filename(filename_results)
all_data = io.read_data(options.step)
output('loaded:', all_data.keys())
if options.only_names is None:
data = all_data
else:
data = {}
for key, val in all_data.iteritems():
if key in options.only_names:
data[key] = val
if problem is None:
problem = ProblemDefinition.from_conf(conf,
init_equations=False,
init_solvers=False)
if probes is None:
gen_probes = conf.get_function(conf.options.gen_probes)
probes, labels = gen_probes(problem)
if probe_hooks is None:
probe_hooks = {None: conf.get_function(conf.options.probe_hook)}
if options.output_filename_trunk is None:
options.output_filename_trunk = problem.ofn_trunk
filename_template = options.output_filename_trunk \
+ ('_%%d.%s' % options.output_format)
if options.same_dir:
filename_template = os.path.join(os.path.dirname(filename_results),
filename_template)
output_dir = os.path.dirname(filename_results)
for ip, probe in enumerate(probes):
output(ip, probe.name)
probe.set_options(close_limit=options.close_limit)
for key, probe_hook in probe_hooks.iteritems():
out = probe_hook(data, probe, labels[ip], problem)
if out is None: continue
if isinstance(out, tuple):
fig, results = out
else:
fig = out
if key is not None:
filename = filename_template % (key, ip)
else:
filename = filename_template % ip
if fig is not None:
if isinstance(fig, dict):
for fig_name, fig_fig in fig.iteritems():
fig_filename = edit_filename(filename,
suffix='_' + fig_name)
fig_fig.savefig(fig_filename)
output('figure ->', os.path.normpath(fig_filename))
else:
fig.savefig(filename)
output('figure ->', os.path.normpath(filename))
if results is not None:
txt_filename = edit_filename(filename, new_ext='.txt')
fd = open(txt_filename, 'w')
fd.write('\n'.join(probe.report()) + '\n')
for key, res in results.iteritems():
pars, vals = res
fd.write('\n# %s\n' % key)
if vals.ndim == 1:
aux = nm.hstack((pars[:, None], vals[:, None]))
else:
aux = nm.hstack((pars[:, None], vals))
nm.savetxt(fd, aux)
fd.close()
output('data ->', os.path.normpath(txt_filename))
