"""
A collection of utilities for file wrapping.
Note: This is a work in progress.
"""
import re
try:
import pyparsing
from pyparsing import CaselessLiteral, Combine, OneOrMore, Optional, \
TokenConverter, Word, nums, oneOf, printables, ParserElement, alphanums
except ImportError:
pyparsing = None
TokenConverter = object
import numpy as np
def _getformat(val):
"""
Get the output format for a floating point number.
The general format is used with 16 places of accuracy, except for when
the floating point value is an integer, in which case a decimal point
followed by a single zero is used.
Parameters
----------
val : float or int
the number which needs formatted.
Returns
-------
string
the format string.
"""
if int(val) == val:
return "%.1f"
else:
return "%.16g"
class _SubHelper(object):
"""
Replaces file text at the correct word location in a line.
This class contains the Helper Function that is passed to re.sub.
Attributes
----------
_newtext : str
text to insert.
_replace_location : int
location in the file where replacement is to occur.
_current_location : int
current location in the file.
_counter : int
counter
_start_location : int
initial location where replacement is to occur.
_end_location : int
final location where replacement is to occur.
"""
def __init__(self):
"""
Initialize attributes.
"""
self._newtext = ""
self._replace_location = 0
self._current_location = 0
self._counter = 0
self._start_location = 0
self._end_location = 0
def set(self, newtext, location):
"""
Set a new word location and value for replacement.
Parameters
----------
newtext : str
text to insert.
location : int
location in the file where replacement is to occur.
"""
self._newtext = newtext
self._replace_location = location
self._current_location = 0
def set_array(self, newtext, start_location, end_location):
"""
Set a new starting location, ending location, and value for replacement.
Parameters
----------
newtext : str
text to insert.
start_location : int
location
end_location : int
location
"""
self._newtext = newtext
self._start_location = start_location
self._end_location = end_location
self._current_location = 0
def replace(self, text):
"""
Replace text in file.
This function should be passed to re.sub.
Parameters
----------
text : str
text to insert.
Returns
-------
string
newtext if current location is replace location else the input text.
"""
self._current_location += 1
if self._current_location == self._replace_location:
if isinstance(self._newtext, float):
return _getformat(self._newtext) % self._newtext
else:
return str(self._newtext)
else:
return text.group()
def replace_array(self, text):
"""
Replace array of text values in file.
This function should be passed to re.sub.
Parameters
----------
text : str
text to insert.
Returns
-------
string
newtext if current location is replace location else the input text.
"""
self._current_location += 1
end = len(self._newtext)
if self._current_location >= self._start_location and \
self._current_location <= self._end_location and \
self._counter < end:
if isinstance(self._newtext[self._counter], float):
val = self._newtext[self._counter]
newval = _getformat(val) % val
else:
newval = str(self._newtext[self._counter])
self._counter += 1
return newval
else:
return text.group()
class _ToInteger(TokenConverter):
"""
Converter for PyParsing that is used to turn a token into an int.
"""
def postParse(self, instring, loc, tokenlist):
"""
Convert token into an integer.
Parameters
----------
instring : str
the input string
loc : int
the location of the matching string
tokenlist : list
list of matched tokens
Returns
-------
int
integer value for token.
"""
return int(tokenlist[0])
class _ToFloat(TokenConverter):
"""
Converter for PyParsing that is used to turn a token into a float.
"""
def postParse(self, instring, loc, tokenlist):
"""
Convert token into a float.
Parameters
----------
instring : str
the input string
loc : int
the location of the matching string
tokenlist : list
list of matched tokens
Returns
-------
float
float value for token.
"""
return float(tokenlist[0].replace('D', 'E'))
class _ToNan(TokenConverter):
"""
Converter for PyParsing that is used to turn a token into Python nan.
"""
def postParse(self, instring, loc, tokenlist):
"""
Convert token into Python nan.
Parameters
----------
instring : str
the input string
loc : int
the location of the matching string
tokenlist : list
list of matched tokens
Returns
-------
float
the float value for NaN.
"""
return float('nan')
class _ToInf(TokenConverter):
"""
Converter for PyParsing that is used to turn a token into Python inf.
"""
def postParse(self, instring, loc, tokenlist):
"""
Convert token into Python inf.
Parameters
----------
instring : str
the input string
loc : int
the location of the matching string
tokenlist : list
list of matched tokens
Returns
-------
float
the float value for infinity.
"""
return float('inf')
[docs]
class FileParser(object):
"""
Utility to locate and read data from a file.
Parameters
----------
end_of_line_comment_char : str, optional
End-of-line comment character to be ignored
(e.g., Python supports in-line comments with "#").
full_line_comment_char : str, optional
Comment character that signifies a line should be skipped.
Attributes
----------
_filename : str
the name of the file.
_data : list of string
the contents of the file, by line
_delimiter : str
the name of the file.
_end_of_line_comment_char : str
end-of-line comment character to be ignored.
_full_line_comment_char : str
comment character that signifies a line should be skipped.
_current_row : int
the current row of the file.
_anchored : bool
indicator that position is relative to a landmark location.
"""
[docs]
def __init__(self, end_of_line_comment_char=None, full_line_comment_char=None):
"""
Initialize attributes.
"""
if pyparsing is None:
raise RuntimeError("The 'pyparsing' package is required to use the file wrapping "
"utilities but it is not installed. Try 'pip install pyparsing'.")
self._filename = None
self._data = []
self._delimiter = " \t"
self._end_of_line_comment_char = end_of_line_comment_char
self._full_line_comment_char = full_line_comment_char
self._current_row = 0
self._anchored = False
self.set_delimiters(self._delimiter)
[docs]
def set_file(self, filename):
"""
Set the name of the file that will be generated.
Parameters
----------
filename : str
Name of the input file to be generated.
"""
self._filename = filename
inputfile = open(filename, 'r')
if not self._end_of_line_comment_char and not self._full_line_comment_char:
self._data = inputfile.readlines()
else:
self._data = []
for line in inputfile:
if line[0] == self._full_line_comment_char:
continue
self._data.append(line.split(self._end_of_line_comment_char)[0])
inputfile.close()
[docs]
def set_delimiters(self, delimiter):
r"""
Set the delimiters that are used to identify field boundaries.
Parameters
----------
delimiter : str
A string containing characters to be used as delimiters. The
default value is ' \t', which means that spaces and tabs are not
taken as data but instead mark the boundaries. Note that the
parser is smart enough to recognize characters within quotes as
non-delimiters.
"""
self._delimiter = delimiter
if delimiter != "columns":
ParserElement.setDefaultWhitespaceChars(str(delimiter))
self._reset_tokens()
[docs]
def mark_anchor(self, anchor, occurrence=1):
"""
Mark the location of a landmark, which lets you describe data by relative position.
Note that a forward search begins at the old anchor location. If you want to restart
the search for the anchor at the file beginning, then call ``reset_anchor()`` before
``mark_anchor``.
Parameters
----------
anchor : str
The text you want to search for.
occurrence : int
Find nth instance of text; default is 1 (first). Use -1 to
find last occurrence. Reverse searches always start at the end
of the file no matter the state of any previous anchor.
"""
if not isinstance(occurrence, int):
raise ValueError("The value for occurrence must be an integer")
instance = 0
if occurrence > 0:
count = 0
max_lines = len(self._data)
for index in range(self._current_row, max_lines):
line = self._data[index]
# If we are marking a new anchor from an existing anchor, and
# the anchor is mid-line, then we still search the line, but
# only after the anchor.
if count == 0 and self._anchored:
line = line.split(anchor)[-1]
if anchor in line:
instance += 1
if instance == occurrence:
self._current_row += count
self._anchored = True
return
count += 1
elif occurrence < 0:
max_lines = len(self._data) - 1
count = max_lines
for index in range(max_lines, -1, -1):
line = self._data[index]
# If we are marking a new anchor from an existing anchor, and
# the anchor is mid-line, then we still search the line, but
# only before the anchor.
if count == max_lines and self._anchored:
line = line.split(anchor)[0]
if anchor in line:
instance += -1
if instance == occurrence:
self._current_row = count
self._anchored = True
return
count -= 1
else:
raise ValueError("0 is not valid for an anchor occurrence.")
raise RuntimeError("Could not find pattern %s in output file %s" %
(anchor, self._filename))
[docs]
def reset_anchor(self):
"""
Reset anchor to the beginning of the file.
"""
self._current_row = 0
self._anchored = False
[docs]
def transfer_line(self, row):
"""
Return an entire line, relative to current anchor.
Parameters
----------
row : int
Number of lines offset from anchor line (0 is anchor line).
This can be negative.
Returns
-------
string
Line at the location requested.
"""
return self._data[self._current_row + row].rstrip()
[docs]
def transfer_var(self, row, field, fieldend=None):
"""
Get a single variable relative to the current anchor.
Parameters
----------
row : int
Number of lines offset from anchor line (0 is anchor line).
This can be negative.
field : int
If the delimiter is a set of chars: which word in line to retrieve.
If the delimiter is 'columns': character position to start.
fieldend : int (optional)
If the delimiter is a set of chars: IGNORED.
If the delimiter is 'columns': position of last character to return, or if
omitted, the end of the line is used.
Returns
-------
string
Data from the requested location in the file.
"""
j = self._current_row + row
line = self._data[j]
if self._delimiter == "columns":
if not fieldend:
line = line[(field - 1):]
else:
line = line[(field - 1):(fieldend)]
# Let pyparsing figure out if this is a number, and return it
# as a float or int as appropriate
data = self._parse_line().parseString(line)
# data might have been split if it contains whitespace. If so,
# just return the whole string
if len(data) > 1:
return line
else:
return data[0]
else:
data = self._parse_line().parseString(line)
return data[field - 1]
[docs]
def transfer_keyvar(self, key, field, occurrence=1, rowoffset=0):
"""
Search for a key relative to the current anchor and get a field from that line.
You can do the same thing with a call to ``mark_anchor`` and ``transfer_var``.
This function just combines them for convenience.
Parameters
----------
key : str
The key to search for.
field : int
Which field to transfer. Field 0 is the key.
occurrence : int
Find nth instance of text; default is 1 (first value
field). Use -1 to find last occurance. Position 0 is the key
field, so it should not be used as a value for occurrence.
rowoffset : int (optional)
Optional row offset from the occurrence of key. This can
also be negative.
Returns
-------
string
Data from the requested location in the file.
"""
if not isinstance(occurrence, int) or occurrence == 0:
msg = "The value for occurrence must be a nonzero integer"
raise ValueError(msg)
instance = 0
if occurrence > 0:
row = 0
for line in self._data[self._current_row:]:
if line.find(key) > -1:
instance += 1
if instance == occurrence:
break
row += 1
elif occurrence < 0:
row = -1
for line in reversed(self._data[self._current_row:]):
if line.find(key) > -1:
instance += -1
if instance == occurrence:
break
row -= 1
j = self._current_row + row + rowoffset
line = self._data[j]
fields = self._parse_line().parseString(line.replace(key, "KeyField"))
return fields[field]
[docs]
def transfer_array(self, rowstart, fieldstart, rowend=None, fieldend=None):
"""
Get an array of variables relative to the current anchor.
Setting the delimiter to 'columns' elicits some special behavior
from this method. Normally, the extraction process wraps around
at the end of a line and continues grabbing each field at the start of
a newline. When the delimiter is set to columns, the parameters
(rowstart, fieldstart, rowend, fieldend) demark a box, and all
values in that box are retrieved. Note that standard whitespace
is the secondary delimiter in this case.
Parameters
----------
rowstart : int
Row number to start, relative to the current anchor.
fieldstart : int
Field number to start.
rowend : int, optional
Row number to end. If not set, then only one row is grabbed.
fieldend : int
Field number to end.
Returns
-------
string
Data from the requested location in the file.
"""
j1 = self._current_row + rowstart
if rowend is None:
j2 = j1 + 1
else:
j2 = self._current_row + rowend + 1
if not fieldend:
raise ValueError("fieldend is missing, currently required")
lines = self._data[j1:j2]
data = np.zeros(shape=(0, 0))
for i, line in enumerate(lines):
if self._delimiter == "columns":
line = line[(fieldstart - 1):fieldend]
# Stripping whitespace may be controversial.
line = line.strip()
# Let pyparsing figure out if this is a number, and return it
# as a float or int as appropriate
parsed = self._parse_line().parseString(line)
newdata = np.array(parsed[:])
# data might have been split if it contains whitespace. If the
# data is string, we probably didn't want this.
if newdata.dtype.type is np.str_:
newdata = np.array(line)
data = np.append(data, newdata)
else:
parsed = self._parse_line().parseString(line)
if i == j2 - j1 - 1:
data = np.append(data, np.array(parsed[(fieldstart - 1):fieldend]))
else:
data = np.append(data, np.array(parsed[(fieldstart - 1):]))
fieldstart = 1
return data
[docs]
def transfer_2Darray(self, rowstart, fieldstart, rowend, fieldend=None):
"""
Get a 2D array of variables relative to the current anchor.
Each line of data is placed in a separate row.
If the delimiter is set to 'columns', then the values contained in
fieldstart and fieldend should be the column number instead of the
field number.
Parameters
----------
rowstart : int
Row number to start, relative to the current anchor.
fieldstart : int
Field number to start.
rowend : int
Row number to end relative to current anchor.
fieldend : int (optional)
Field number to end. If not specified, grabs all fields up to the
end of the line.
Returns
-------
string
Data from the requested location in the file.
"""
if fieldend and (fieldstart > fieldend):
msg = "fieldend must be greater than fieldstart"
raise ValueError(msg)
if rowstart > rowend:
msg = "rowend must be greater than rowstart"
raise ValueError(msg)
j1 = self._current_row + rowstart
j2 = self._current_row + rowend + 1
lines = list(self._data[j1:j2])
if self._delimiter == "columns":
if fieldend:
line = lines[0][(fieldstart - 1):fieldend]
else:
line = lines[0][(fieldstart - 1):]
parsed = self._parse_line().parseString(line)
row = np.array(parsed[:])
data = np.zeros(shape=(abs(j2 - j1), len(row)))
data[0, :] = row
for i, line in enumerate(list(lines[1:])):
if fieldend:
line = line[(fieldstart - 1):fieldend]
else:
line = line[(fieldstart - 1):]
parsed = self._parse_line().parseString(line)
data[i + 1, :] = np.array(parsed[:])
else:
parsed = self._parse_line().parseString(lines[0])
if fieldend:
row = np.array(parsed[(fieldstart - 1):fieldend])
else:
row = np.array(parsed[(fieldstart - 1):])
data = np.zeros(shape=(abs(j2 - j1), len(row)))
data[0, :] = row
for i, line in enumerate(list(lines[1:])):
parsed = self._parse_line().parseString(line)
if fieldend:
try:
data[i + 1, :] = np.array(parsed[(fieldstart - 1):fieldend])
except Exception:
print(data)
else:
data[i + 1, :] = np.array(parsed[(fieldstart - 1):])
return data
def _parse_line(self):
"""
Parse a single data line that may contain string or numerical data.
Float and Int 'words' are converted to their appropriate type.
Exponentiation is supported, as are NaN and Inf.
Returns
-------
<ParserElement>
the parsed line.
"""
return self.line_parse_token
def _reset_tokens(self):
"""
Set up the tokens for pyparsing.
"""
# Somewhat of a hack, but we can only use printables if the delimiter is
# just whitespace. Otherwise, some seprators (like ',' or '=') potentially
# get parsed into the general string text. So, if we have non whitespace
# delimiters, we need to fall back to just alphanums, and then add in any
# missing but important symbols to parse.
if self._delimiter.isspace():
textchars = printables
else:
textchars = alphanums
symbols = ['.', '/', '+', '*', '^', '(', ')', '[', ']', '=',
':', ';', '?', '%', '&', '!', '#', '|', '<', '>',
'{', '}', '-', '_', '@', '$', '~']
for symbol in symbols:
if symbol not in self._delimiter:
textchars = textchars + symbol
digits = Word(nums)
dot = "."
sign = oneOf("+ -")
ee = CaselessLiteral('E') | CaselessLiteral('D')
num_int = _ToInteger(Combine(Optional(sign) + digits))
num_float = _ToFloat(Combine(
Optional(sign) +
((digits + dot + Optional(digits)) | (dot + digits)) +
Optional(ee + Optional(sign) + digits)
))
# special case for a float written like "3e5"
mixed_exp = _ToFloat(Combine(digits + ee + Optional(sign) + digits))
nan = (_ToInf(oneOf("Inf -Inf")) |
_ToNan(oneOf("NaN nan NaN% NaNQ NaNS qNaN sNaN 1.#SNAN 1.#QNAN -1.#IND")))
string_text = Word(textchars)
self.line_parse_token = (OneOrMore((nan | num_float | mixed_exp | num_int | string_text)))
