def get_string(self, df_head_only=False):
from pymatgen import Structure
lines, scope = [], []
for key,value in self.document.iterate():
if isinstance(value, Table):
lines[-1] = lines[-1].replace('{', '[+').replace('}', ']')
header = any([isinstance(col, str) for col in value])
if isinstance(value.index, MultiIndex):
value.reset_index(inplace=True)
if df_head_only:
value = value.head()
csv_string = value.to_csv(
index=False, header=header, float_format='%g', encoding='utf-8'
)[:-1]
lines += csv_string.split('\n')
if df_head_only:
lines.append('...')
elif isinstance(value, Structure):
from pymatgen.io.cif import CifWriter
cif = CifWriter(value, symprec=symprec).__str__()
lines.append(make_pair(
''.join([replacements.get(c, c) for c in key]), cif+':end'
))
elif Quantity is not None and isinstance(value, Quantity):
lines.append(make_pair(
value.display_symbols[0], value.pretty_string()
))
else:
level, key = key
# truncate scope
level_reduction = bool(level < len(scope))
if level_reduction:
del scope[level:]
# append scope
if value is None:
scope.append(''.join([
replacements.get(c, c) for c in key
]))
# correct scope to omit internal 'general' section
scope_corr = scope
if scope[0] == mp_level01_titles[0]:
scope_corr = scope[1:]
# insert scope line
if (value is None and scope_corr) or \
(value is not None and level_reduction):
lines.append('\n{' + '.'.join(scope_corr) + '}')
# insert key-value line
if value is not None:
val = str(value)
value_lines = [val] if val.startswith('http') \
else textwrap.wrap(val)
if len(value_lines) > 1:
value_lines = [''] + value_lines + [':end']
lines.append(make_pair(
''.join([replacements.get(c, c) for c in key]),
'\n'.join(value_lines)
))
return '\n'.join(lines) + '\n'
def insert_default_plot_options(self, pd_obj, k, update_plot_options=None):
# make default plot (add entry in 'plots') for each
# table, first column as x-column
table_name = ''.join([replacements.get(c, c) for c in k])
key = 'default_{}'.format(table_name)
plots_dict = _OrderedDict([
(mp_level01_titles[2],
_OrderedDict([(key,
_OrderedDict([('x', pd_obj.columns[0]),
('table', table_name)]))]))
])
if update_plot_options is not None:
plots_dict[mp_level01_titles[2]][key].update(update_plot_options)
if mp_level01_titles[2] in self:
self.rec_update(plots_dict)
else:
self[mp_level01_titles[2]] = plots_dict[mp_level01_titles[2]]
def add_data_table(self, identifier, dataframe, name, plot_options=None):
"""add a datatable to the root-level section
Args:
identifier (str): MP category ID (`mp_cat_id`)
dataframe (pandas.DataFrame): tabular data as Pandas DataFrame
name (str): table name, optional if only one table in section
plot_options (dict): options for according plotly graph
"""
# TODO: optional table name, required if multiple tables per root-level section
name = ''.join([replacements.get(c, c) for c in name])
self.document.rec_update(nest_dict(
Table(dataframe).to_dict(), [identifier, name]
))
self.document[identifier].insert_default_plot_options(
dataframe, name, update_plot_options=plot_options
)
def rec_update(self, other=None, overwrite=False, replace_newlines=True):
"""https://gist.github.com/Xjs/114831"""
# overwrite=False: don't overwrite existing unnested key
if other is None: # mode to force RecursiveDicts to be used
other = self
overwrite = True
for key, value in other.items():
if isinstance(key, six.string_types):
key = ''.join([replacements.get(c, c) for c in key])
if key in self and \
isinstance(self[key], dict) and \
isinstance(value, dict):
# ensure RecursiveDict and update key (w/o underscores)
self[key] = RecursiveDict(self[key])
replace_newlines = bool(key != mp_level01_titles[3])
self[key].rec_update(other=value,
overwrite=overwrite,
replace_newlines=replace_newlines)
elif (key in self and overwrite) or key not in self:
if isinstance(value, six.string_types) and replace_newlines:
self[key] = value.replace('\n', ' ')
else:
self[key] = value
def get_string(self):
from pymatgen import Structure
lines, scope = [], []
table_start = mp_level01_titles[1] + '_'
for key, value in self.document.iterate():
if isinstance(value, Table):
header = any([
bool(isinstance(col, unicode) or isinstance(col, str))
for col in value
])
if isinstance(value.index, MultiIndex):
value.reset_index(inplace=True)
csv_string = value.to_csv(index=False,
header=header,
float_format='%g',
encoding='utf-8')[:-1]
lines += csv_string.decode('utf-8').split('\n')
elif isinstance(value, Structure):
from pymatgen.io.cif import CifWriter
cif = CifWriter(value, symprec=symprec).__str__()
lines.append(
make_pair(''.join([replacements.get(c, c) for c in key]),
cif + ':end'))
else:
level, key = key
key = key if isinstance(key, unicode) else key.decode('utf-8')
# truncate scope
level_reduction = bool(level < len(scope))
if level_reduction: del scope[level:]
# append scope and set delimiters
if value is None:
is_table = key.startswith(table_start)
if is_table:
# account for 'data_' prefix
key = key[len(table_start):]
start, end = '\n[+', ']'
else:
start, end = '\n{', '}'
scope.append(''.join([replacements.get(c, c)
for c in key]))
# correct scope to omit internal 'general' section
scope_corr = scope
if scope[0] == mp_level01_titles[0]:
scope_corr = scope[1:]
# insert scope line
if (value is None and scope_corr)or \
(value is not None and level_reduction):
lines.append(start + '.'.join(scope_corr) + end)
# insert key-value line
if value is not None:
val = unicode(value) if not isinstance(value,
str) else value
value_lines = [val] if val.startswith('http') \
else textwrap.wrap(val)
if len(value_lines) > 1:
value_lines = [''] + value_lines + [':end']
lines.append(
make_pair(
''.join([replacements.get(c, c) for c in key]),
'\n'.join(value_lines)))
return '\n'.join(lines) + '\n'
def from_string(data):
# use archieml-python parse to import data
rdct = RecursiveDict(archieml.loads(data))
rdct.rec_update()
# post-process internal representation of file contents
for key in list(rdct.keys()):
is_general, root_key = normalize_root_level(key)
if is_general:
# make part of shared (meta-)data, i.e. nest under `general` at
# the beginning of the MPFile
if mp_level01_titles[0] not in rdct:
rdct[mp_level01_titles[0]] = RecursiveDict()
rdct.move_to_end(mp_level01_titles[0], last=False)
# normalize identifier key (pop & insert)
# using rec_update since we're looping over all entries
# also: support data in bare tables (marked-up only by
# root-level identifier) by nesting under 'data'
value = rdct.pop(key)
keys = [mp_level01_titles[0]] if is_general else []
keys.append(root_key)
if isinstance(value, list):
keys.append('table')
rdct.rec_update(nest_dict(value, keys))
# reference to section to iterate or parse as CIF
section = rdct[mp_level01_titles[0]][root_key] \
if is_general else rdct[root_key]
# iterate to find CSV sections to parse
# also parse propnet quantities
if isinstance(section, dict):
scope = []
for k, v in section.iterate():
level, key = k
key = ''.join([replacements.get(c, c) for c in key])
level_reduction = bool(level < len(scope))
if level_reduction:
del scope[level:]
if v is None:
scope.append(key)
elif isinstance(v, list) and isinstance(v[0], dict):
table = ''
for row_dct in v:
table = '\n'.join([table, row_dct['value']])
pd_obj = read_csv(table)
d = nest_dict(pd_obj.to_dict(), scope + [key])
section.rec_update(d, overwrite=True)
if not is_general and level == 0:
section.insert_default_plot_options(pd_obj, key)
elif Quantity is not None and isinstance(v, six.string_types) and ' ' in v:
quantity = Quantity.from_key_value(key, v)
d = nest_dict(quantity.as_dict(), scope + [key]) # TODO quantity.symbol.name
section.rec_update(d, overwrite=True)
# convert CIF strings into pymatgen structures
if mp_level01_titles[3] in section:
from pymatgen.io.cif import CifParser
for name in section[mp_level01_titles[3]].keys():
cif = section[mp_level01_titles[3]].pop(name)
parser = CifParser.from_string(cif)
structure = parser.get_structures(primitive=False)[0]
section[mp_level01_titles[3]].rec_update(nest_dict(
structure.as_dict(), [name]
))
return MPFile.from_dict(rdct)