def parse(self, opts, args):
if opts.tag:
self.tag = opts.tag
if opts.magnetic_moment:
self.magmoms = np.array(
[float(m) for m in opts.magnetic_moment.split(',')])
self.gui = opts.gui
self.write_summary = opts.write_summary
self.write_to_file = opts.write_to_file
self.use_lock_files = opts.use_lock_files
self.interactive_python_session = opts.interactive_python_session
self.contains = opts.contains
self.modify = opts.modify
if self.modify is not None:
try:
assert not isinstance(eval(self.modify), str), \
'--modify option received a string argument. Check quoting.'
except SyntaxError:
pass
self.after = opts.after
self.clean = opts.clean
if opts.slice:
self.slice = string2index(opts.slice)
def parse(self, opts, args):
if opts.tag:
self.tag = opts.tag
if opts.magnetic_moment:
self.magmoms = np.array(
[float(m) for m in opts.magnetic_moment.split(',')])
self.gui = opts.gui
self.write_summary = opts.write_summary
self.write_to_file = opts.write_to_file
self.use_lock_files = opts.use_lock_files
self.interactive_python_session = opts.interactive_python_session
self.contains = opts.contains
self.modify = opts.modify
if self.modify is not None:
try:
assert not isinstance(eval(self.modify), str), \
'--modify option received a string argument. Check quoting.'
except SyntaxError:
pass
self.after = opts.after
self.clean = opts.clean
if opts.slice:
self.slice = string2index(opts.slice)
def write(self,
filename,
rotations='',
show_unit_cell=False,
bbox=None,
**kwargs):
indices = range(self.nimages)
p = filename.rfind('@')
if p != -1:
try:
slice = string2index(filename[p + 1:])
except ValueError:
pass
else:
indices = indices[slice]
filename = filename[:p]
if isinstance(indices, int):
indices = [indices]
images = [self.get_atoms(i) for i in indices]
if len(filename) > 4 and filename[-4:] in ['.eps', '.png', '.pov']:
write(filename,
images,
rotation=rotations,
show_unit_cell=show_unit_cell,
bbox=bbox,
**kwargs)
else:
write(filename, images, **kwargs)
def run(opt, args):
images = Images()
if opt.aneb:
opt.image_number = '-1'
if len(args) > 0:
from ase.io import string2index
try:
images.read(args, string2index(opt.image_number))
except IOError as e:
if len(e.args) == 1:
parser.error(e.args[0])
else:
parser.error(e.args[1] + ': ' + e.filename)
else:
images.initialize([Atoms()])
if opt.interpolate:
images.interpolate(opt.interpolate)
if opt.aneb:
images.aneb()
if opt.repeat != '1':
r = opt.repeat.split(',')
if len(r) == 1:
r = 3 * r
images.repeat_images([int(c) for c in r])
if opt.radii_scale:
images.set_radii(opt.radii_scale)
if opt.output is not None:
images.write(opt.output,
rotations=opt.rotations,
show_unit_cell=opt.show_unit_cell)
opt.terminal = True
if opt.terminal:
if opt.graph is not None:
data = images.graph(opt.graph)
for line in data.T:
for x in line:
print(x, end=' ')
print()
else:
from ase.gui.gui import GUI
import ase.gui.gtkexcepthook
ase
gui = GUI(images, opt.rotations, opt.show_unit_cell, opt.bonds)
gui.run(opt.graph)
def read(self, filenames, default_index=':', filetype=None):
from ase.utils import basestring
if isinstance(default_index, basestring):
default_index = string2index(default_index)
images = []
names = []
for filename in filenames:
from ase.io.formats import parse_filename
if '.json@' in filename or '.db@' in filename:
# Ugh! How would one deal with this?
# The parse_filename and string2index somehow conspire
# to cause an error. See parse_filename
# in ase.io.formats for this particular
# special case. -askhl
#
# TODO Someone figure out how to see what header
# a JSON file should have.
imgs = read(filename, default_index, filetype)
if hasattr(imgs, 'iterimages'):
imgs = list(imgs.iterimages())
names += [filename] * len(imgs)
images += imgs
continue # Argh!
if '@' in filename:
actual_filename, index = parse_filename(filename, None)
else:
actual_filename, index = parse_filename(
filename, default_index)
imgs = read(filename, default_index, filetype)
if hasattr(imgs, 'iterimages'):
imgs = list(imgs.iterimages())
images.extend(imgs)
# Name each file as filename@index:
if isinstance(index, slice):
start = index.start or 0
step = index.step or 1
else:
start = index # index is just an integer
assert len(imgs) == 1
step = 1
for i, img in enumerate(imgs):
names.append('{}@{}'.format(actual_filename, start + i * step))
self.initialize(images, names)
def run(opt, args):
images = Images()
if opt.aneb:
opt.image_number = '-1'
if len(args) > 0:
from ase.io import string2index
try:
images.read(args, string2index(opt.image_number))
except IOError, e:
if len(e.args) == 1:
parser.error(e.args[0])
else:
parser.error(e.args[1] + ': ' + e.filename)
def run(opt, args):
images = Images()
if opt.aneb:
opt.image_number = '-1'
if len(args) > 0:
from ase.io import string2index
try:
images.read(args, string2index(opt.image_number))
except IOError, e:
if len(e.args) == 1:
parser.error(e.args[0])
else:
parser.error(e.args[1] + ': ' + e.filename)
def read(self, filenames, default_index=':', filetype=None):
from ase.utils import basestring
if isinstance(default_index, basestring):
default_index = string2index(default_index)
images = []
names = []
for filename in filenames:
from ase.io.formats import parse_filename
if '@' in filename and 'postgres' not in filename or \
'postgres' in filename and filename.count('@') == 2:
actual_filename, index = parse_filename(filename, None)
else:
actual_filename, index = parse_filename(
filename, default_index)
# Read from stdin:
if filename == '-':
import sys
from io import BytesIO
buf = BytesIO(sys.stdin.buffer.read())
buf.seek(0)
filename = buf
filetype = 'traj'
imgs = read(filename, index, filetype)
if hasattr(imgs, 'iterimages'):
imgs = list(imgs.iterimages())
images.extend(imgs)
# Name each file as filename@index:
if isinstance(index, slice):
start = index.start or 0
step = index.step or 1
else:
start = index
step = 1
for i, img in enumerate(imgs):
if isinstance(start, int):
names.append('{}@{}'.format(actual_filename,
start + i * step))
else:
names.append('{}@{}'.format(actual_filename, start))
self.initialize(images, names)
def parse(self, opts, args):
if opts.tag:
self.tag = opts.tag
if opts.magnetic_moment:
self.magmoms = np.array([float(m) for m in opts.magnetic_moment.split(",")])
self.gui = opts.gui
self.write_summary = opts.write_summary
self.write_to_file = opts.write_to_file
self.use_lock_files = opts.use_lock_files
self.interactive_python_session = opts.interactive_python_session
self.contains = opts.contains
self.modify = opts.modify
if opts.slice:
self.slice = string2index(opts.slice)
def run(opt, args):
images = Images()
if opt.aneb:
opt.image_number = '-1'
if len(args) > 0:
from ase.io import string2index
images.read(args, string2index(opt.image_number))
else:
images.initialize([Atoms()])
if opt.interpolate:
images.interpolate(opt.interpolate)
if opt.aneb:
images.aneb()
if opt.repeat != '1':
r = opt.repeat.split(',')
if len(r) == 1:
r = 3 * r
images.repeat_images([int(c) for c in r])
if opt.radii_scale:
images.set_radii(opt.radii_scale)
if opt.output is not None:
images.write(opt.output, rotations=opt.rotations,
show_unit_cell=opt.show_unit_cell)
opt.terminal = True
if opt.terminal:
if opt.graph is not None:
data = images.graph(opt.graph)
for line in data.T:
for x in line:
print(x, end=' ')
print()
else:
from ase.gui.gui import GUI
import ase.gui.gtkexcepthook
ase
gui = GUI(images, opt.rotations, opt.show_unit_cell, opt.bonds)
gui.run(opt.graph)
def write(self, filename, rotations='', show_unit_cell=False, bbox=None):
indices = range(self.nimages)
p = filename.rfind('@')
if p != -1:
try:
slice = string2index(filename[p + 1:])
except ValueError:
pass
else:
indices = indices[slice]
filename = filename[:p]
if isinstance(indices, int):
indices = [indices]
images = [self.get_atoms(i) for i in indices]
write(filename, images,
rotation=rotations, show_unit_cell=show_unit_cell,
bbox=bbox)
def parse(self, opts, args):
if opts.tag:
self.tag = opts.tag
if opts.magnetic_moment:
self.magmoms = np.array(
[float(m) for m in opts.magnetic_moment.split(',')])
self.gui = opts.gui
self.write_summary = opts.write_summary
self.write_to_file = opts.write_to_file
self.use_lock_files = opts.use_lock_files
self.interactive_python_session = opts.interactive_python_session
self.contains = opts.contains
self.modify = opts.modify
if opts.slice:
self.slice = string2index(opts.slice)
def run(opt, args):
images = Images()
if opt.aneb:
opt.image_number = '-1'
if len(args) > 0:
from ase.io import string2index
images.read(args, string2index(opt.image_number))
else:
images.initialize([Atoms()])
if opt.interpolate:
images.interpolate(opt.interpolate)
if opt.aneb:
images.aneb()
if opt.repeat != '1':
r = opt.repeat.split(',')
if len(r) == 1:
r = 3 * r
images.repeat_images([int(c) for c in r])
if opt.output is not None:
images.write(opt.output,
rotations=opt.rotations,
show_unit_cell=opt.show_unit_cell)
opt.terminal = True
if opt.terminal:
if opt.graph is not None:
data = images.graph(opt.graph)
for line in data.T:
for x in line:
print x,
print
else:
from ase.gui.gui import GUI
import ase.gui.gtkexcepthook
gui = GUI(images, opt.rotations, opt.show_unit_cell, opt.bonds)
gui.run(opt.graph)
def write(self, filename, rotations='', bbox=None, **kwargs):
# XXX We should show the unit cell whenever there is one
indices = range(len(self))
p = filename.rfind('@')
if p != -1:
try:
slice = string2index(filename[p + 1:])
except ValueError:
pass
else:
indices = indices[slice]
filename = filename[:p]
if isinstance(indices, int):
indices = [indices]
images = [self.get_atoms(i) for i in indices]
if len(filename) > 4 and filename[-4:] in ['.eps', '.png', '.pov']:
write(filename, images, rotation=rotations, bbox=bbox, **kwargs)
else:
write(filename, images, **kwargs)
def run(args):
from ase.gui.images import Images
from ase.atoms import Atoms
images = Images()
if args.filenames:
from ase.io import string2index
images.read(args.filenames, string2index(args.image_number))
else:
images.initialize([Atoms()])
if args.interpolate:
images.interpolate(args.interpolate)
if args.repeat != '1':
r = args.repeat.split(',')
if len(r) == 1:
r = 3 * r
images.repeat_images([int(c) for c in r])
if args.radii_scale:
images.set_radii(args.radii_scale)
if args.output is not None:
images.write(args.output,
rotations=args.rotations,
show_unit_cell=args.show_unit_cell)
args.terminal = True
if args.terminal:
if args.graph is not None:
data = images.graph(args.graph)
for line in data.T:
for x in line:
print(x, end=' ')
print()
else:
from ase.gui.gui import GUI
gui = GUI(images, args.rotations, args.show_unit_cell, args.bonds)
gui.run(args.graph)
def write(self, filename, rotations='', show_unit_cell=False, bbox=None, **kwargs):
indices = range(self.nimages)
p = filename.rfind('@')
if p != -1:
try:
slice = string2index(filename[p + 1:])
except ValueError:
pass
else:
indices = indices[slice]
filename = filename[:p]
if isinstance(indices, int):
indices = [indices]
images = [self.get_atoms(i) for i in indices]
if len(filename) > 4 and filename[-4:] in ['.eps', '.png', '.pov']:
write(filename, images,
rotation=rotations, show_unit_cell=show_unit_cell,
bbox=bbox, **kwargs)
else:
write(filename, images, **kwargs)
def run(args):
from ase.gui.images import Images
from ase.atoms import Atoms
images = Images()
if args.filenames:
from ase.io import string2index
images.read(args.filenames, string2index(args.image_number))
else:
images.initialize([Atoms()])
if args.interpolate:
images.interpolate(args.interpolate)
if args.repeat != '1':
r = args.repeat.split(',')
if len(r) == 1:
r = 3 * r
images.repeat_images([int(c) for c in r])
if args.radii_scale:
images.set_radii(args.radii_scale)
if args.output is not None:
images.write(args.output, rotations=args.rotations,
show_unit_cell=args.show_unit_cell)
args.terminal = True
if args.terminal:
if args.graph is not None:
data = images.graph(args.graph)
for line in data.T:
for x in line:
print(x, end=' ')
print()
else:
from ase.gui.gui import GUI
gui = GUI(images, args.rotations, args.show_unit_cell, args.bonds)
gui.run(args.graph)
def save(self, dummy):
"The user has pressed the SAVE button."
filename = self.chooser.get_filename()
if not filename or filename == "<<filename>>":
oops("Please specify a file name")
return
# Check file type
suffix = os.path.splitext(filename)[1][1:]
if 'POSCAR' in filename or 'CONTCAR' in filename:
suffix = 'POSCAR'
if suffix == '':
# No suffix chosen
filt = self.chooser.get_filter().get_name()
suffix = self.name_to_suffix[filt]
if suffix is None:
oops(
"Specify file type by giving a suffix or selecting a file type."
)
return
else:
filename = filename + '.' + suffix
else:
# Suffix given - check that it is not in conflict with selected file type.
filt = self.chooser.get_filter().get_name()
suffix2 = self.name_to_suffix[filt]
if suffix2 is not None and suffix != suffix2:
oops(
"Your filename suffix conflicts with the file type you have selected."
)
return
if suffix not in self.name_to_suffix.values():
oops("Unknown file suffix " + suffix)
return
# We now have a consistent file name with an allowed suffix.
# Find out which images we want to save.
if self.radio_thisconf.get_active():
indices = [self.gui.frame]
elif self.radio_allconf.get_active():
indices = range(self.gui.images.nimages)
elif self.radio_someconf.get_active():
txt = self.whichconf.get_text()
if not txt:
oops("Please specify which images to save.")
return
try:
slice = string2index(txt)
except ValueError:
oops("ERROR: Failed to parse image specification '%s'" %
(txt, ))
return
indices = range(self.gui.images.nimages)[slice]
if isinstance(indices, int):
indices = [indices]
else:
raise RuntimeError(
"No radio button selected - should not be possible!")
# Now we are ready to write the file!
extra = {}
remove_hidden = False
if self.is_graphics[suffix]:
bbox = np.empty(4)
size = np.array([self.gui.width, self.gui.height]) / self.gui.scale
bbox[0:2] = np.dot(self.gui.center,
self.gui.axes[:, :2]) - size / 2
bbox[2:] = bbox[:2] + size
extra['rotation'] = self.gui.axes
extra['show_unit_cell'] = self.gui.ui.get_widget(
'/MenuBar/ViewMenu/ShowUnitCell').get_active()
extra['bbox'] = bbox
extra['colors'] = self.gui.get_colors(
rgb=True)[self.gui.images.visible]
remove_hidden = True
if len(indices) == 1:
# Saving a single configuration is always possible.
write(
filename,
self.gui.images.get_atoms(indices[0],
remove_hidden=remove_hidden),
**extra)
elif self.support_multi[suffix]:
images = [
self.gui.images.get_atoms(i, remove_hidden=remove_hidden)
for i in indices
]
write(filename, images, **extra)
else:
# We want to write multiple images, but the file format does not support it.
# The solution is to write multiple files, inserting a number in the file name
# before the suffix.
filename = filename.replace('%', '%%') # Preserve % in filenames.
suffixpos = filename.rfind('.')
filename = filename[:suffixpos] + '%05d' + filename[suffixpos:]
for i, idx in enumerate(indices):
write(
filename % (i, ),
self.gui.images.get_atoms(idx,
remove_hidden=remove_hidden),
**extra)
oops("Wrote %d files" % (len(indices), ), (filename % (0, )) +
' .. ' + (filename % (len(indices) - 1, )))
self.destroy()
for field in self.fields])
sorting_array = field_data * self.scent[:, np.newaxis]
sorting_array = sorting_array[self.hier]
sorting_array = prec_round(sorting_array, self.tableformat.precision)
field_data = field_data[:, np.lexsort(sorting_array)].transpose()
if csv:
rowformat = ','.join(
['{:h}' if field == 'el' else '{}' for field in self.fields])
else:
rowformat = ''.join([self.tableformat.fmt[field]
for field in self.fields])
body = [
self.tableformat.formatter(
rowformat,
*row) for row in field_data]
return '\n'.join(body)
default_index = string2index(':')
def slice_split(filename):
if '@' in filename:
filename, index = parse_filename(filename, None)
else:
filename, index = parse_filename(filename, default_index)
return filename, index
def save(self, dummy):
"The user has pressed the SAVE button."
filename = self.chooser.get_filename()
if not filename or filename == "<<filename>>":
oops("Please specify a file name")
return
# Check file type
suffix = os.path.splitext(filename)[1][1:]
if 'POSCAR' in filename or 'CONTCAR' in filename:
suffix = 'POSCAR'
if suffix == '':
# No suffix chosen
filt = self.chooser.get_filter().get_name()
suffix = self.name_to_suffix[filt]
if suffix is None:
oops("Specify file type by giving a suffix or selecting a file type.")
return
else:
filename = filename + '.' + suffix
else:
# Suffix given - check that it is not in conflict with selected file type.
filt = self.chooser.get_filter().get_name()
suffix2 = self.name_to_suffix[filt]
if suffix2 is not None and suffix != suffix2:
oops("Your filename suffix conflicts with the file type you have selected.")
return
if suffix not in self.name_to_suffix.values():
oops("Unknown file suffix "+suffix)
return
# We now have a consistent file name with an allowed suffix.
# Find out which images we want to save.
if self.radio_thisconf.get_active():
indices = [self.gui.frame]
elif self.radio_allconf.get_active():
indices = range(self.gui.images.nimages)
elif self.radio_someconf.get_active():
txt = self.whichconf.get_text()
if not txt:
oops("Please specify which images to save.")
return
try:
slice = string2index(txt)
except ValueError:
oops("ERROR: Failed to parse image specification '%s'" % (txt,))
return
indices = range(self.gui.images.nimages)[slice]
if isinstance(indices, int):
indices = [indices]
else:
raise RuntimeError("No radio button selected - should not be possible!")
# Now we are ready to write the file!
extra = {}
remove_hidden = False
if self.is_graphics[suffix]:
bbox = np.empty(4)
size = np.array([self.gui.width, self.gui.height]) / self.gui.scale
bbox[0:2] = np.dot(self.gui.center, self.gui.axes[:, :2]) - size / 2
bbox[2:] = bbox[:2] + size
extra['rotation'] = self.gui.axes
extra['show_unit_cell'] = self.gui.ui.get_widget('/MenuBar/ViewMenu/ShowUnitCell').get_active()
extra['bbox'] = bbox
extra['colors'] = self.gui.get_colors(rgb=True)[self.gui.images.visible]
remove_hidden = True
if len(indices) == 1:
# Saving a single configuration is always possible.
write(filename, self.gui.images.get_atoms(indices[0],
remove_hidden=remove_hidden),
**extra)
elif self.support_multi[suffix]:
images = [self.gui.images.get_atoms(i, remove_hidden=remove_hidden)
for i in indices]
write(filename, images, **extra)
else:
# We want to write multiple images, but the file format does not support it.
# The solution is to write multiple files, inserting a number in the file name
# before the suffix.
filename = filename.replace('%', '%%') # Preserve % in filenames.
suffixpos = filename.rfind('.')
filename = filename[:suffixpos] + '%05d' + filename[suffixpos:]
for i, idx in enumerate(indices):
write(filename % (i,),
self.gui.images.get_atoms(idx, remove_hidden=remove_hidden),
**extra)
oops("Wrote %d files" % (len(indices),),
(filename % (0,)) + ' .. ' + (filename % (len(indices)-1,)))
self.destroy()