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# coding: utf-8
#
# Project: X-ray image reader
# https://github.com/silx-kit/fabio
#
# Copyright (C) 2015 European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
"""Cif parser helper functions"""
__author__ = "Jerome Kieffer"
__contact__ = "jerome.kieffer@esrf.eu"
__license__ = "MIT"
__copyright__ = "2014, European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "18/01/2019"
import numpy
import cython
@cython.boundscheck(False)
def split_tokens(bytes_text):
"""
Separate the text representing a CIF file into a list of tokens.
:param bytes_text: the content of the CIF - file
:type bytes_text: 8-bit string (str in python2 or bytes in python3)
:return: list of all the fields of the CIF
:rtype: list
"""
cdef:
unsigned char[:] ary = bytearray(bytes_text)
bint in_comment = False, in_single_quote = False
bint in_double_quote = False, multiline = False, go_on = True
int i = -1, start = -1, end = -1, imax
char prev, next, cur = b"\n"
bytes EOL = b'\r\n'
bytes BLANK = b" \t\r\n"
unsigned char SINGLE_QUOTE = b"'"
unsigned char DOUBLE_QUOTE = b'"'
unsigned char SEMICOLUMN = b';'
unsigned char HASH = b"#"
unsigned char UNDERSCORE = b"_"
unsigned char DASH = b"-"
unsigned char QUESTIONMARK = b"?"
bytes BINARY_MARKER = b"--CIF-BINARY-FORMAT-SECTION--"
int lbms = len(BINARY_MARKER)
next = ary[0]
imax = len(bytes_text) - 1
fields = []
while go_on:
i += 1
prev = cur
cur = next
if i < imax:
next = ary[i + 1]
else:
next = b"\n"
go_on = False
# print(i,chr(prev),chr(cur),chr(next),in_comment,in_single_quote,in_double_quote,multiline, start, cur ==SINGLE_QUOTE)
# Skip comments
if in_comment:
if cur in EOL:
in_comment = False
continue
if prev in EOL:
if cur == HASH:
in_comment = True
continue
if cur == SEMICOLUMN:
if multiline:
fields.append(bytes_text[start:i].strip())
start = -1
multiline = False
else:
multiline = True
start = i + 1
continue
if multiline:
# Handle CBF
if cur == DASH:
if bytes_text[i:i + lbms] == BINARY_MARKER:
end = bytes_text[i + lbms:].find(BINARY_MARKER)
i += end + 2 * lbms
cur = ary[i]
next = ary[i + 1]
continue
# Handle single quote
if cur == SINGLE_QUOTE:
if (not in_single_quote) and (not in_double_quote) and (start < 0) and (prev in BLANK):
start = i + 1
in_single_quote = True
continue
if (in_single_quote) and (not in_double_quote) and (start >= 0) and (next in BLANK):
fields.append(bytes_text[start:i].strip())
start = -1
in_single_quote = False
continue
if in_single_quote:
continue
# Handle double quote
if cur == DOUBLE_QUOTE:
if (not in_single_quote) and (not in_double_quote) and (start < 0) and (prev in BLANK):
start = i + 1
in_double_quote = True
continue
if (not in_single_quote) and (in_double_quote) and (start >= 0) and (next in BLANK):
fields.append(bytes_text[start:i].strip())
start = -1
in_double_quote = False
continue
if in_double_quote:
continue
# Normal fields
if cur in BLANK:
if start >= 0:
fields.append(bytes_text[start:i].strip())
start = -1
else:
if start < 0:
start = i
if start >= 0:
fields.append(bytes_text[start:].strip())
return fields
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