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 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 test_parse_filename_do_not_split():
# check if do_not_split_by_at_sign flag works
from ase.io.formats import parse_filename
filename, index = parse_filename('user@local/file@name',
do_not_split_by_at_sign=True)
assert filename == 'user@local/file@name'
assert index is None
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 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 test_parse_filename_bad_slice():
# parse filename with malformed @-slice
from ase.io.formats import parse_filename
import warnings
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
filename, index = parse_filename('path.to/filename@s:4')
assert filename == 'path.to/filename'
assert len(w) == 1
assert 'Can not parse index' in str(w[-1].message)
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 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_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 test_parse_filename_db_entry():
# parse filename targetting database entry
from ase.io.formats import parse_filename
filename, index = parse_filename('path.to/filename.db@anything')
assert filename == 'path.to/filename.db'
assert index == 'anything'
def test_parse_filename_with_at_no_ext():
# parse filename with no extension but with @-slice
from ase.io.formats import parse_filename
filename, index = parse_filename('path.to/filename@1:4')
assert filename == 'path.to/filename'
assert index == slice(1, 4, None)
def test_parse_filename_no_ext():
# parse filename with no extension
from ase.io.formats import parse_filename
filename, index = parse_filename('path.to/filename')
assert filename == 'path.to/filename'
assert index is None
def test_parse_filename_with_at_in_path():
# parse filename with '@' in path, but not in name
from ase.io.formats import parse_filename
filename, index = parse_filename('user@local/filename.xyz')
assert filename == 'user@local/filename.xyz'
assert index is None
def test_parse_filename_with_at_in_ext():
# parse filename with '@' in extension
from ase.io.formats import parse_filename
filename, index = parse_filename('file_name.traj@1:4:2')
assert filename == 'file_name.traj'
assert index == slice(1, 4, 2)
