class image_data_cache(object):
def __init__(self, imageset, size=10):
self.imageset = imageset
self.size = size
self._image_data = OrderedDict()
def __getitem__(self, i):
image_data = self._image_data.get(i)
if image_data is None:
image_data = self.imageset.get_raw_data(i)
if len(self._image_data) >= self.size:
# remove the oldest entry in the cache
del self._image_data[self._image_data.keys()[0]]
self._image_data[i] = image_data
return image_data
class image_data_cache(object):
def __init__(self, imageset, size=10):
self.imageset = imageset
self.size = size
self._image_data = OrderedDict()
def __getitem__(self, i):
image_data = self._image_data.get(i)
if image_data is None:
image_data = self.imageset.get_raw_data(i)
if len(self._image_data) >= self.size:
# remove the oldest entry in the cache
del self._image_data[self._image_data.keys()[0]]
self._image_data[i] = image_data
return image_data
class cif(DictMixin):
def __init__(self, blocks=None):
if blocks is not None:
self.blocks = OrderedDict(blocks)
else:
self.blocks = OrderedDict()
self.keys_lower = dict([(key.lower(), key)
for key in self.blocks.keys()])
def __setitem__(self, key, value):
assert isinstance(value, block)
if not re.match(tag_re, '_' + key):
raise Sorry("%s is not a valid data block name" % key)
self.blocks[key] = value
self.keys_lower[key.lower()] = key
def get(self, key, default=None):
key_lower = self.keys_lower.get(key.lower())
if (key_lower is None):
return default
return self.blocks.get(key_lower, default)
def __getitem__(self, key):
result = self.get(key)
if (result is None):
raise KeyError('Unknown CIF data block name: "%s"' % key)
return result
def __delitem__(self, key):
del self.blocks[self.keys_lower[key.lower()]]
del self.keys_lower[key.lower()]
def keys(self):
return self.blocks.keys()
def __repr__(self):
return repr(OrderedDict(self.iteritems()))
def __copy__(self):
return cif(self.blocks.copy())
copy = __copy__
def __deepcopy__(self, memo):
return cif(copy.deepcopy(self.blocks, memo))
def deepcopy(self):
return copy.deepcopy(self)
def show(self,
out=None,
indent=" ",
indent_row=None,
data_name_field_width=34,
loop_format_strings=None,
align_columns=True):
if out is None:
out = sys.stdout
for name, block in self.items():
print >> out, "data_%s" % name
block.show(out=out,
indent=indent,
indent_row=indent_row,
data_name_field_width=data_name_field_width,
loop_format_strings=loop_format_strings,
align_columns=align_columns)
def __str__(self):
s = StringIO()
self.show(out=s)
return s.getvalue()
def validate(self,
dictionary,
show_warnings=True,
error_handler=None,
out=None):
if out is None: out = sys.stdout
from iotbx.cif import validation
errors = {}
if error_handler is None:
error_handler = validation.ErrorHandler()
for key, block in self.blocks.iteritems():
error_handler = error_handler.__class__()
dictionary.set_error_handler(error_handler)
block.validate(dictionary)
errors.setdefault(key, error_handler)
if error_handler.error_count or error_handler.warning_count:
error_handler.show(show_warnings=show_warnings, out=out)
return error_handler
def sort(self, recursive=False, key=None, reverse=False):
self.blocks = OrderedDict(
sorted(self.blocks.items(), key=key, reverse=reverse))
if recursive:
for b in self.blocks.values():
b.sort(recursive=recursive, reverse=reverse)
class cif(DictMixin):
def __init__(self, blocks=None):
if blocks is not None:
self.blocks = OrderedDict(blocks)
else:
self.blocks = OrderedDict()
self.keys_lower = dict([(key.lower(), key) for key in self.blocks.keys()])
def __setitem__(self, key, value):
assert isinstance(value, block)
if not re.match(tag_re, '_'+key):
raise Sorry("%s is not a valid data block name" %key)
self.blocks[key] = value
self.keys_lower[key.lower()] = key
def get(self, key, default=None):
key_lower = self.keys_lower.get(key.lower())
if (key_lower is None):
return default
return self.blocks.get(key_lower, default)
def __getitem__(self, key):
result = self.get(key)
if (result is None):
raise KeyError('Unknown CIF data block name: "%s"' % key)
return result
def __delitem__(self, key):
del self.blocks[self.keys_lower[key.lower()]]
del self.keys_lower[key.lower()]
def keys(self):
return self.blocks.keys()
def __repr__(self):
return repr(OrderedDict(self.iteritems()))
def __copy__(self):
return cif(self.blocks.copy())
copy = __copy__
def __deepcopy__(self, memo):
return cif(copy.deepcopy(self.blocks, memo))
def deepcopy(self):
return copy.deepcopy(self)
def show(self, out=None, indent=" ", indent_row=None,
data_name_field_width=34,
loop_format_strings=None):
if out is None:
out = sys.stdout
for name, block in self.items():
print >> out, "data_%s" %name
block.show(
out=out, indent=indent, indent_row=indent_row,
data_name_field_width=data_name_field_width,
loop_format_strings=loop_format_strings)
def __str__(self):
s = StringIO()
self.show(out=s)
return s.getvalue()
def validate(self, dictionary, show_warnings=True, error_handler=None, out=None):
if out is None: out = sys.stdout
from iotbx.cif import validation
errors = {}
if error_handler is None:
error_handler = validation.ErrorHandler()
for key, block in self.blocks.iteritems():
error_handler = error_handler.__class__()
dictionary.set_error_handler(error_handler)
block.validate(dictionary)
errors.setdefault(key, error_handler)
if error_handler.error_count or error_handler.warning_count:
error_handler.show(show_warnings=show_warnings, out=out)
return error_handler
def sort(self, recursive=False, key=None, reverse=False):
self.blocks = OrderedDict(sorted(self.blocks.items(), key=key, reverse=reverse))
if recursive:
for b in self.blocks.values():
b.sort(recursive=recursive, reverse=reverse)
