def open(self, button=None, filename=None):
from ase.io.formats import all_formats, get_ioformat
labels = [_('Automatic')]
values = ['']
def key(item):
return item[1][0]
for format, (description, code) in sorted(list(all_formats.items()),
key=key):
io = get_ioformat(format)
if io.read and description != '?':
labels.append(_(description))
values.append(format)
format = [None]
def callback(value):
format[0] = value
chooser = ui.LoadFileDialog(self.window.win, _('Open ...'))
ui.Label(_('Choose parser:')).pack(chooser.top)
formats = ui.ComboBox(labels, values, callback)
formats.pack(chooser.top)
filename = filename or chooser.go()
if filename:
self.images.read([filename], slice(None), format[0])
self.set_colors()
self.set_coordinates(self.images.nimages - 1, focus=True)
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 open(self, button=None, filename=None):
from ase.io.formats import all_formats, get_ioformat
labels = [_('Automatic')]
values = ['']
def key(item):
return item[1][0]
for format, (description, code) in sorted(all_formats.items(),
key=key):
io = get_ioformat(format)
if io.read and description != '?':
labels.append(_(description))
values.append(format)
format = [None]
def callback(value):
format[0] = value
chooser = ui.LoadFileDialog(self.window.win, _('Open ...'))
ui.Label(_('Choose parser:')).pack(chooser.top)
formats = ui.ComboBox(labels, values, callback)
formats.pack(chooser.top)
filename = filename or chooser.go()
if filename:
self.images.read([filename], slice(None), format[0])
self.set_frame(len(self.images) - 1, focus=True)
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 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 open(self, button=None):
from ase.io.formats import all_formats, get_ioformat
formats = [(_('Automatic'), None)]
def key(item):
return item[1][0]
for format, (description, code) in sorted(all_formats.items(),
key=key):
io = get_ioformat(format)
if io.read and description != '?':
formats.append((_(description), format))
chooser = gtk.FileChooserDialog(
_('Open ...'), None, gtk.FILE_CHOOSER_ACTION_OPEN,
(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, gtk.STOCK_OPEN,
gtk.RESPONSE_OK))
chooser.set_filename(_("<<filename>>"))
# Add a file type filter
name_to_format = {}
types = gtk.combo_box_new_text()
for name, format in formats:
types.append_text(name)
name_to_format[name] = format
types.set_active(0)
img_vbox = gtk.VBox()
pack(img_vbox, [gtk.Label(_('File type:')), types])
img_vbox.show()
chooser.set_extra_widget(img_vbox)
ok = chooser.run() == gtk.RESPONSE_OK
if ok:
filenames = [chooser.get_filename()]
filetype = types.get_active_text()
chooser.destroy()
if not ok:
return
self.reset_tools_modes()
self.images.read(filenames, slice(None), name_to_format[filetype])
self.set_colors()
self.set_coordinates(self.images.nimages - 1, focus=True)
def __init__(self, win, formatcallback=lambda event: None):
from ase.io.formats import all_formats, get_ioformat
LoadFileDialog.__init__(self, win, _('Open ...'))
labels = [_('Automatic')]
values = ['']
def key(item):
return item[1][0]
for format, (description, code) in sorted(all_formats.items(),
key=key):
io = get_ioformat(format)
if io.read and description != '?':
labels.append(_(description))
values.append(format)
self.format = None
def callback(value):
self.format = value
Label(_('Choose parser:')).pack(self.top)
formats = ComboBox(labels, values, callback)
formats.pack(self.top)
continue
if not matplotlib and format in ['eps', 'png']:
continue
if not etree and format == 'exciting':
continue
if not Scientific and format == 'etsf':
continue
atoms = get_atoms()
images = [atoms, atoms]
io = get_ioformat(format)
print('{0:20}{1}{2}{3}{4}'.format(format,
' R'[bool(io.read)],
' W'[bool(io.write)],
'+1'[io.single],
'SF'[io.acceptsfd]))
fname1 = '{}/io-test.1.{}'.format(testdir, format)
fname2 = '{}/io-test.2.{}'.format(testdir, format)
if io.write:
write(fname1, atoms, format=format)
if not io.single:
write(fname2, images, format=format)
if io.read:
for a in [read(fname1, format=format), read(fname1)]:
check(a, atoms, format)
def test(format):
if format in ['abinit', 'castep-cell', 'dftb', 'eon', 'gaussian']:
# Someone should do something ...
return
if format in ['v-sim', 'mustem']:
# Standalone test used as not compatible with 1D periodicity
return
if format in ['mustem']:
# Standalone test used as specific arguments are required
return
if format in ['dmol-arc', 'dmol-car', 'dmol-incoor']:
# We have a standalone dmol test
return
if format in ['gif', 'mp4']:
# Complex dependencies; see animate.py test
return
if format in ['postgresql', 'trj', 'vti', 'vtu']:
# Let's not worry about these.
return
if not matplotlib and format in ['eps', 'png']:
return
if not etree and format == 'exciting':
return
if not Scientific and format == 'etsf':
return
if not netCDF4 and format == 'netcdftrajectory':
return
atoms = get_atoms()
if format == 'dlp4':
atoms.pbc = (1, 1, 0)
images = [atoms, atoms]
io = get_ioformat(format)
print('{0:20}{1}{2}{3}{4}'.format(format, ' R'[bool(io.read)],
' W'[bool(io.write)], '+1'[io.single],
'SF'[io.acceptsfd]))
fname1 = '{}/io-test.1.{}'.format(testdir, format)
fname2 = '{}/io-test.2.{}'.format(testdir, format)
if io.write:
write(fname1, atoms, format=format)
if not io.single:
write(fname2, images, format=format)
if io.read:
for a in [read(fname1, format=format), read(fname1)]:
check(a, atoms, format)
if not io.single:
if format in ['json', 'db']:
aa = read(fname2 + '@id=1') + read(fname2 + '@id=2')
else:
aa = [read(fname2), read(fname2, 0)]
aa += read(fname2, ':')
for a in iread(fname2, format=format):
aa.append(a)
assert len(aa) == 6, aa
for a in aa:
check(a, atoms, format)
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)
continue
if format in ['postgresql', 'trj', 'vti', 'vtu']:
# Let's not worry about these.
continue
if not matplotlib and format in ['eps', 'png']:
continue
if not etree and format == 'exciting':
continue
if not Scientific and format == 'etsf':
continue
io = get_ioformat(format)
print('{0:20}{1}{2}{3}{4}'.format(format, ' R'[bool(io.read)],
' W'[bool(io.write)], '+1'[io.single],
'SF'[io.acceptsfd]))
fname1 = 'io-test.1.' + format
fname2 = 'io-test.2.' + format
if io.write:
write(fname1, atoms, format=format)
if not io.single:
write(fname2, images, format=format)
if io.read:
for a in [read(fname1, format=format), read(fname1)]:
check(a, format)
if not io.single:
