def save_dialog(gui):
dialog = gtk.FileChooserDialog(_('Save ...'),
None,
gtk.FILE_CHOOSER_ACTION_SAVE,
(gtk.STOCK_SAVE, gtk.RESPONSE_OK,
gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL))
dialog.set_current_name('')
dialog.set_current_folder(os.getcwd())
text = _('Append name with "@n" in order to write image number "n" '
'instead of the current image.\n'
'Append "@start:stop" or "@start:stop:step" if you want to write '
'a range of images.\n'
'You can leave out "start" and "stop" so that "name@:" will '
'give you all images.\n'
'Negative numbers count from the last image '
'("name@-1": last image, "name@-2:": last two).')
dialog.set_extra_widget(gtk.Label(text))
response = dialog.run()
if response == gtk.RESPONSE_OK:
filename = dialog.get_filename()
dialog.destroy()
else:
dialog.destroy()
return
filename, index = parse_filename(filename)
if index is None:
index = slice(gui.frame, gui.frame + 1)
if isinstance(index, str):
index = string2index(index)
format = filetype(filename, read=False)
io = get_ioformat(format)
extra = {}
remove_hidden = False
if format in ['png', 'eps', 'pov']:
bbox = np.empty(4)
size = np.array([gui.width, gui.height]) / gui.scale
bbox[0:2] = np.dot(gui.center, gui.axes[:, :2]) - size / 2
bbox[2:] = bbox[:2] + size
extra['rotation'] = gui.axes
extra['show_unit_cell'] = gui.ui.get_widget(
'/MenuBar/ViewMenu/ShowUnitCell').get_active()
extra['bbox'] = bbox
extra['colors'] = gui.get_colors(rgb=True)[gui.images.visible]
remove_hidden = True
images = [gui.images.get_atoms(i, remove_hidden=remove_hidden)
for i in range(*index.indices(gui.images.nimages))]
if len(images) > 1 and io.single:
# 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.
j = filename.rfind('.')
filename = filename[:j] + '{0:05d}' + filename[j:]
for i, atoms in enumerate(images):
write(filename.format(i), atoms, **extra)
else:
write(filename, images, **extra)
def check(path, query, verbose):
"""Check a path.
Returns a (filetype, AtomsRow object) tuple.
"""
try:
format = filetype(path, guess=False)
except (OSError, UnknownFileTypeError):
return '', None
if format in ['db', 'json']:
db = connect(path)
else:
try:
atoms = read(path, format=format)
except Exception as x:
if verbose:
print(path + ':', x, file=sys.stderr)
return '', None
db = FakeDB(atoms)
try:
for row in db._select(*query):
return format, row
except Exception as x:
if verbose:
print(path + ':', x, file=sys.stderr)
return '', None
def run(args):
if not args.filename:
print_info()
if args.formats:
print()
print_formats()
return
n = max(len(filename) for filename in args.filename) + 2
for filename in args.filename:
try:
format = filetype(filename)
except FileNotFoundError:
format = '?'
description = 'No such file'
except UnknownFileTypeError:
format = '?'
description = '?'
else:
description, code = all_formats.get(format, ('?', '?'))
print('{:{}}{} ({})'.format(filename + ':', n,
description, format))
if args.verbose:
if format == 'traj':
print_ulm_info(filename)
elif format == 'bundletrajectory':
print_bundletrajectory_info(filename)
def run(args):
if not args.filenames:
print_info()
return
n = max(len(filename) for filename in args.filenames) + 2
for filename in args.filenames:
try:
format = filetype(filename)
except FileNotFoundError:
format = '?'
description = 'No such file'
else:
if format and format in all_formats:
description, code = all_formats[format]
else:
format = '?'
description = '?'
print('{:{}}{} ({})'.format(filename + ':', n, description,
format))
if args.verbose:
if format == 'traj':
print_ulm_info(filename)
elif format == 'bundletrajectory':
print_bundletrajectory_info(filename)
def run(args):
if not args.filenames:
print_info()
return
n = max(len(filename) for filename in args.filenames) + 2
for filename in args.filenames:
try:
format = filetype(filename)
except FileNotFoundError:
format = '?'
description = 'No such file'
else:
if format and format in all_formats:
description, code = all_formats[format]
else:
format = '?'
description = '?'
print('{:{}}{} ({})'.format(filename + ':', n,
description, format))
if args.verbose:
if format == 'traj':
print_ulm_info(filename)
elif format == 'bundletrajectory':
print_bundletrajectory_info(filename)
def save_dialog(gui, filename=None):
dialog = ui.SaveFileDialog(gui.window.win, _('Save ...'))
ui.Text(text).pack(dialog.top)
filename = filename or dialog.go()
if not filename:
return
filename, index = parse_filename(filename)
if index is None:
index = slice(gui.frame, gui.frame + 1)
elif isinstance(index, basestring):
index = string2index(index)
elif isinstance(index, slice):
pass
else:
if index < 0:
index += len(gui.images)
index = slice(index, index + 1)
format = filetype(filename, read=False)
io = get_ioformat(format)
extra = {}
remove_hidden = False
if format in ['png', 'eps', 'pov']:
bbox = np.empty(4)
size = gui.window.size / gui.scale
bbox[0:2] = np.dot(gui.center, gui.axes[:, :2]) - size / 2
bbox[2:] = bbox[:2] + size
extra['rotation'] = gui.axes
extra['show_unit_cell'] = gui.window['toggle-show-unit-cell']
extra['bbox'] = bbox
colors = gui.get_colors(rgb=True)
extra['colors'] = [
rgb for rgb, visible in zip(colors, gui.images.visible) if visible
]
remove_hidden = True
images = [
gui.images.get_atoms(i, remove_hidden=remove_hidden)
for i in range(*index.indices(len(gui.images)))
]
if len(images) > 1 and io.single:
# 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.
j = filename.rfind('.')
filename = filename[:j] + '{0:05d}' + filename[j:]
for i, atoms in enumerate(images):
write(filename.format(i), atoms, **extra)
else:
try:
write(filename, images, **extra)
except Exception as err:
from ase.gui.ui import showerror
showerror(_('Error'), err)
raise
def check_struct_dir(path, verbose=True):
"""
Checks if the directory is a valid directory with structures inside.
Otherwise, an error will be raised. A valid directory is defined as a
directory that already exists and either:
- Has at least one structure file with a valid file extension
- Has at least one structure that can be read with ASE.io.read
Returns True if either of these conditions are met. Returns False otherwise.
Arguments
---------
path: str
Path to the directory to check.
Returns
-------
bool
"""
if not os.path.exists(path):
raise Exception("Directory {} does not exist.".format(path))
## Create file iterator because we may not wish to generate the entire
## file list
file_iter = os.scandir(path)
for file_name in file_iter:
file_ext = check_ext(file_name, verbose=verbose)
## Directory has at least one valid structure file.
if file_ext in pymove_ext:
return True
## Restart iterator
file_iter = os.scandir(path)
## Now check if ASE can guess file format
for file_name in file_iter:
file_path = os.path.join(path, file_name)
try:
file_format = filetype(file_path)
except:
if verbose:
print("ASE could not find filetype for {}".format(file_path))
continue
## If we get this far, then format
if verbose:
print("ASE identified {} as having file format {}".format(
file_path, file_format))
return True
return False
def save_dialog(gui, filename=None):
dialog = ui.SaveFileDialog(gui.window.win, _('Save ...'))
ui.Text(text).pack(dialog.top)
filename = filename or dialog.go()
if not filename:
return
filename, index = parse_filename(filename)
if index is None:
index = slice(gui.frame, gui.frame + 1)
elif isinstance(index, basestring):
index = string2index(index)
elif isinstance(index, slice):
pass
else:
if index < 0:
index += len(gui.images)
index = slice(index, index + 1)
format = filetype(filename, read=False)
io = get_ioformat(format)
extra = {}
remove_hidden = False
if format in ['png', 'eps', 'pov']:
bbox = np.empty(4)
size = gui.window.size / gui.scale
bbox[0:2] = np.dot(gui.center, gui.axes[:, :2]) - size / 2
bbox[2:] = bbox[:2] + size
extra['rotation'] = gui.axes
extra['show_unit_cell'] = gui.window['toggle-show-unit-cell']
extra['bbox'] = bbox
colors = gui.get_colors(rgb=True)
extra['colors'] = [rgb for rgb, visible
in zip(colors, gui.images.visible)
if visible]
remove_hidden = True
images = [gui.images.get_atoms(i, remove_hidden=remove_hidden)
for i in range(*index.indices(len(gui.images)))]
if len(images) > 1 and io.single:
# 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.
j = filename.rfind('.')
filename = filename[:j] + '{0:05d}' + filename[j:]
for i, atoms in enumerate(images):
write(filename.format(i), atoms, **extra)
else:
write(filename, images, **extra)
def run(args):
if not args.filename:
print_info()
if args.formats:
print()
print_formats()
if args.calculators:
print()
from ase.calculators.autodetect import (detect_calculators,
format_configs)
configs = detect_calculators()
print('Calculators:')
for message in format_configs(configs):
print(' {}'.format(message))
print()
print('Available: {}'.format(','.join(sorted(configs))))
return
n = max(len(filename) for filename in args.filename) + 2
nfiles_not_found = 0
for filename in args.filename:
try:
format = filetype(filename)
except FileNotFoundError:
format = '?'
description = 'No such file'
nfiles_not_found += 1
except UnknownFileTypeError:
format = '?'
description = '?'
else:
if format in ioformats:
description = ioformats[format].description
else:
description = '?'
print('{:{}}{} ({})'.format(filename + ':', n, description,
format))
if args.verbose:
if format == 'traj':
print_ulm_info(filename)
elif format == 'bundletrajectory':
print_bundletrajectory_info(filename)
raise SystemExit(nfiles_not_found)
def main():
p = OptionParser(usage='%prog file.traj [file2.traj ...]',
description=description)
opts, args = p.parse_args()
if len(args) == 0:
p.error('Incorrect number of arguments')
for f in args:
ft = filetype(f)
print("File type of '{0}' appears to be of type '{1}'".format(f, ft))
if ft == 'traj':
print_aff_info(f)
elif ft == 'trj':
print_trajectory_info(f)
elif ft == 'bundle':
print_bundletrajectory_info(f)
else:
p.error('%s is of type %s; cannot print info about this type of file' % f)
def main():
p = OptionParser(usage='%prog file.traj [file2.traj ...]',
description=description)
opts, args = p.parse_args()
if len(args) == 0:
p.error('Incorrect number of arguments')
for f in args:
ft = filetype(f)
print("File type of '{0}' appears to be of type '{1}'".format(f, ft))
if ft == 'traj':
print_ulm_info(f)
elif ft == 'trj':
print_trajectory_info(f)
elif ft == 'bundletrajectory':
print_bundletrajectory_info(f)
else:
p.error(
'%s is of type %s; cannot print info about this type of file' %
(f, ft))
def check_file_type(file_path, verbose=True):
"""
Returns file type if one is identified by either pymove or ASE.
Returns
-------
str:
Returns either an empty string if no file format was found or the
correctly identified file format for the given file path.
"""
if not os.path.isfile(file_path):
if verbose:
print("{} is not a file".format(file_path))
return ""
ext = check_ext(file_path)
if len(ext) == 0:
try:
file_format = filetype(file_path)
except:
if verbose:
print("ASE could not find filetype for {}".format(file_path))
return ""
if ext not in pymove_ext:
if verbose:
print(
"File extension \".{}\" was not recognized by pymove.".format(
ext))
return ""
else:
file_format = extension2format[ext]
return file_format
'=================================================================================================='
.center(120))
print('')
args = argparse()
## args
alist_files = args.alist_files
## Main
from ase.io import read, write
from ase.io.formats import filetype
for i in range(len(alist_files)):
alist = read(alist_files[i], ':')
new_alist = []
if args.lower_tri:
for atoms in alist:
atoms.set_cell(to_lower_triangular_cell(atoms.get_cell()),
scale_atoms=True)
new_alist.append(atoms)
write('lower-tri_{}'.format(alist_files[i]),
new_alist,
format=filetype(alist_files[i]))
else:
for atoms in alist:
atoms.set_cell(to_upper_triangular_cell(atoms.get_cell()),
scale_atoms=True)
new_alist.append(atoms)
write('upper-tri_{}'.format(alist_files[i]),
new_alist,
format=filetype(alist_files[i]))
def save_dialog(gui):
dialog = gtk.FileChooserDialog(_('Save ...'), None,
gtk.FILE_CHOOSER_ACTION_SAVE,
(gtk.STOCK_SAVE, gtk.RESPONSE_OK,
gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL))
dialog.set_current_name('')
dialog.set_current_folder(os.getcwd())
text = _('Append name with "@n" in order to write image number "n" '
'instead of the current image.\n'
'Append "@start:stop" or "@start:stop:step" if you want to write '
'a range of images.\n'
'You can leave out "start" and "stop" so that "name@:" will '
'give you all images.\n'
'Negative numbers count from the last image '
'("name@-1": last image, "name@-2:": last two).')
dialog.set_extra_widget(gtk.Label(text))
response = dialog.run()
if response == gtk.RESPONSE_OK:
filename = dialog.get_filename()
dialog.destroy()
else:
dialog.destroy()
return
filename, index = parse_filename(filename)
if index is None:
index = slice(gui.frame, gui.frame + 1)
if isinstance(index, str):
index = string2index(index)
format = filetype(filename, read=False)
io = get_ioformat(format)
extra = {}
remove_hidden = False
if format in ['png', 'eps', 'pov']:
bbox = np.empty(4)
size = np.array([gui.width, gui.height]) / gui.scale
bbox[0:2] = np.dot(gui.center, gui.axes[:, :2]) - size / 2
bbox[2:] = bbox[:2] + size
extra['rotation'] = gui.axes
extra['show_unit_cell'] = gui.ui.get_widget(
'/MenuBar/ViewMenu/ShowUnitCell').get_active()
extra['bbox'] = bbox
extra['colors'] = gui.get_colors(rgb=True)[gui.images.visible]
remove_hidden = True
images = [
gui.images.get_atoms(i, remove_hidden=remove_hidden)
for i in range(*index.indices(gui.images.nimages))
]
if len(images) > 1 and io.single:
# 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.
j = filename.rfind('.')
filename = filename[:j] + '{0:05d}' + filename[j:]
for i, atoms in enumerate(images):
write(filename.format(i), atoms, **extra)
else:
write(filename, images, **extra)