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"""
File input and output.
This module contains classes implementing file input and output.
"""
__author__ = 'Florian Krause <florian@expyriment.org>, \
Oliver Lindemann <oliver@expyriment.org>'
__version__ = '0.7.0'
__revision__ = '55a4e7e'
__date__ = 'Wed Mar 26 14:33:37 2014 +0100'
import atexit
import os
try:
import locale
except ImportError:
locale = None # Does not exist on Android
import codecs
import re
import types
import sys
import uuid
import time
from time import strftime
from platform import uname
import defaults
import expyriment
from expyriment.misc._timer import get_time
from expyriment.misc import unicode2str, str2unicode
from _input_output import Input, Output
class InputFile(Input):
"""A class implementing an input file."""
def __init__(self, filename, encoding=None):
"""Create an input file.
All lines in the specified text file will be read into a list of
strings.
Parameters
----------
filename : str, optional
name of the input file
encoding : str, optional
the encoding used to read the content of the file
"""
self._filename = filename
self._current_line = 1
self._lines = []
if not(os.path.isfile(self._filename)):
raise IOError("The input file '{0}' does not exist.".format(
unicode2str(self._filename)))
if encoding is None:
with open(filename, 'r') as fl:
first_line = fl.readline()
encoding = re.findall("coding[:=]\s*([-\w.]+)", first_line)
if encoding == []:
second_line = fl.readline()
encoding = re.findall("coding[:=]\s*([-\w.]+)",
second_line)
if encoding == []:
encoding = [None]
else:
encoding = [encoding]
with codecs.open(self._filename, 'rb', encoding[0],
errors='replace') as f:
for line in f:
self._lines.append(str2unicode(line.rstrip('\r\n')))
@property
def filename(self):
"""Getter for filename."""
return self._filename
@property
def current_line(self):
"""Getter for current_line."""
return self._current_line
@property
def n_lines(self):
"""Getter for n_lines."""
return len(self._lines)
@property
def lines(self):
"""Getter for lines."""
return self._lines
def get_line(self, line=None):
"""Get a specific line.
If no line is given, the current line will be returned and the value
of current_line will be increased by one. First line is line 1.
Parameters
----------
line : int, optional
number of the line to get
Returns
-------
line : str
line as string or None if line does not exist
"""
if line is not None and line < 1 or line > len(self._lines):
return None
if line is not None:
return self._lines[line - 1]
else:
current_line = self._current_line
if current_line != len(self._lines):
self._current_line += 1
return self._lines[current_line - 1]
class OutputFile(Output):
"""A class implementing an output file."""
def __init__(self, suffix, directory, comment_char=None,
time_stamp=None):
"""Create an output file.
Filename: {MAINFILE_NAME}_{SUBJECT_ID}_{TIME_STAMP}{suffix}
Parameters
----------
suffix : str
file suffix/extension (str)
directory : str
create file in given directory
comment_char : str, optional
comment character
time_stamp : bool, optional
using time stamps, based on the experiment start time,
not the current time
"""
Output.__init__(self)
self._suffix = suffix
self._directory = directory
if comment_char is not None:
self._comment_char = comment_char
else:
self._comment_char = defaults.outputfile_comment_char
if time_stamp is not None:
self._time_stamp = time_stamp
else:
self._time_stamp = defaults.outputfile_time_stamp
self._buffer = []
if not os.path.isdir(directory):
os.mkdir(directory)
self._filename = self.standard_file_name
self._fullpath = directory + "/{0}".format(self._filename)
atexit.register(self.save)
# Create new file
fl = open(self._fullpath, 'w+')
fl.close()
try:
locale_enc = locale.getdefaultlocale()[1]
except:
locale_enc = "UTF-8"
self.write_comment("Expyriment {0}, {1}-file, coding: {2}".format(
expyriment.get_version(), self._suffix,
locale_enc))
if expyriment._active_exp.is_initialized:
self.write_comment("date: {0}".format(time.strftime(
"%a %b %d %Y %H:%M:%S",
expyriment._active_exp.clock.init_localtime)))
@property
def fullpath(self):
"""Getter for fullpath"""
return self._fullpath
@property
def filename(self):
"""Getter for filename"""
return self._filename
@property
def directory(self):
"""Getter for directory"""
return self._directory
@property
def suffix(self):
"""Getter for directory"""
return self._suffix
@property
def comment_char(self):
"""Getter for comment_char"""
return self._comment_char
@property
def standard_file_name(self):
"""Getter for the standard expyriment outputfile name.
Filename: {MAINFILE_NAME}_{SUBJECT_ID}_{TIME_STAMP}{suffix}
"""
rtn = os.path.split(sys.argv[0])[1].replace(".py", "")
if expyriment._active_exp.is_started:
rtn = rtn + '_' + repr(expyriment._active_exp.subject).zfill(2)
if self._time_stamp:
rtn = rtn + '_' + strftime(
"%Y%m%d%H%M", expyriment._active_exp.clock.init_localtime)
return rtn + self.suffix
def save(self):
"""Save file to disk."""
start = get_time()
if self._buffer != []:
with open(self._fullpath, 'a') as f:
f.write("".join(self._buffer))
self._buffer = []
return int((get_time() - start) * 1000)
def write(self, content):
"""Write to file.
Parameters
----------
content : str
content to be written (anything, will be casted to str)
"""
if type(content) is unicode:
self._buffer.append(unicode2str(content))
else:
self._buffer.append(str(content))
def write_line(self, content):
"""Write a text line to files.
Parameters
----------
content : str
content to be written (anything, will be casted to str)
"""
self.write(content)
self.write(unicode2str(defaults.outputfile_eol))
def write_list(self, list_):
"""Write a list in a row. Data are separated by a delimiter.
Parameters
----------
list_ : list
list to be written
"""
for elem in list:
self.write(elem)
self.write(',')
self.write(unicode2str(defaults.outputfile_eol))
# self.write_line(repr(list_)[1:-1].replace(" ", ""))
def write_comment(self, comment):
"""Write a comment line to files.
(i.e., text is proceeded by comment char).
Parameters
----------
comment : str
comment to be written (anything, will be casted to str)
"""
self.write(unicode2str(self.comment_char))
self.write_line(comment)
def rename(self, new_filename):
"""Renames the output file."""
self.save()
new_fullpath = self.directory + "/{0}".format(new_filename)
os.rename(self._fullpath, new_fullpath)
self._filename = new_filename
self._fullpath = new_fullpath
class DataFile(OutputFile):
"""A class implementing a data file."""
_file_suffix = ".xpd"
def __init__(self, additional_suffix, directory=None, delimiter=None,
time_stamp=None):
"""Create a data file.
Filename: {MAINFILE_NAME}_{SUBJECT_ID}_{TIME_STAMP}{ADD_SUFFIX}.xpd
Parameters
----------
additional_suffix : str
additional suffix
directory : str, optional
directory of the file
delimiter : str, optional
symbol between variables
time_stamp : bool, optional
using time stamps, based on the experiment start time,
not the current time
"""
if expyriment._active_exp.is_initialized:
self._subject = expyriment._active_exp.subject
else:
self._subject = None
if directory is None:
directory = defaults.datafile_directory
if additional_suffix is None:
additional_suffix = ''
if len(additional_suffix) > 0:
suffix = ".{0}{1}".format(additional_suffix, self._file_suffix)
else:
suffix = self._file_suffix
OutputFile.__init__(self, suffix, directory, time_stamp=time_stamp)
if delimiter is not None:
self._delimiter = delimiter
else:
self._delimiter = defaults.datafile_delimiter
self._subject_info = []
self._experiment_info = []
self._variable_names = []
self.write_comment("--EXPERIMENT INFO")
self.write_comment("e mainfile: {0}".format(os.path.split(
sys.argv[0])[1]))
self.write_comment("e sha1: {0}".format(
expyriment.get_experiment_secure_hash()))
self.write_comment("--SUBJECT INFO")
self.write_comment("s id: {0}".format(self._subject))
self.write_line(self.variable_names)
self._variable_names_changed = False
self.save()
@property
def delimiter(self):
"""Getter for delimiter"""
return self._delimiter
@staticmethod
def _typecheck_and_cast2str(data):
"""Check if data are string or numeric and cast to string"""
if data is None:
data = "None"
if isinstance(data, types.UnicodeType):
return unicode2str(data)
elif type(data) in [types.StringType, types.IntType,
types.LongType, types.FloatType,
types.BooleanType]:
return str(data)
else:
message = "Data to be added must to be " + \
"booleans, strings, numerics (i.e. floats or integers) " + \
"or None.\n {0} is not allowed.".format(type(data))
raise TypeError(message)
def add(self, data):
"""Add data.
Parameters
----------
data : string or numeric or list
data to be added
"""
self.write(str(self._subject) + self.delimiter)
if type(data) is list or type(data) is tuple:
line = ""
for counter, elem in enumerate(data):
if counter > 0:
line = line + self.delimiter
line = line + DataFile._typecheck_and_cast2str(elem)
self.write_line(line)
else:
self.write_line(DataFile._typecheck_and_cast2str(data))
def add_subject_info(self, text):
"""Adds a text the subject info header.
Subject information can be extracted afterwards using
misc.data_preprocessing.read_data_file. To defined between subject
variables use a syntax like this: "gender = female" or
"handedness : left"
Parameters
----------
text : str
subject infomation to be add to the file header
Notes
-----
The next data.save() might take longer!
"""
self._subject_info.append("{0}s {1}{2}".format(
unicode2str(self.comment_char), unicode2str(text),
unicode2str(defaults.outputfile_eol)))
def add_experiment_info(self, text):
"""Adds a text the subject info header.
Notes
-----
The next data.save() might take longer!
"""
if isinstance(text, types.UnicodeType):
text = "{0}".format(unicode2str(text))
elif type(text) is not str:
text = "{0}".format(text)
for line in text.splitlines():
self._experiment_info.append("{0}e {1}{2}".format(
unicode2str(self.comment_char), line,
unicode2str(defaults.outputfile_eol)))
@property
def variable_names(self):
"""Getter for variable_names."""
vn = self.delimiter.join(self._variable_names)
return u"subject_id,{0}".format(vn)
def clear_variable_names(self):
"""Remove all variable names from data file.
Notes
-----
The next data.save() might take longer!
"""
self._variable_names = []
self._variable_names_changed = True
def add_variable_names(self, variable_names):
"""Add data variable names to the data file.
Notes
-----
The next data.save() might take longer!
Parameters
----------
variables : str or list of str
variable names
"""
if variable_names is None:
return
if type(variable_names) is not list:
variable_names = [variable_names]
self._variable_names.extend(variable_names)
self._variable_names_changed = True
def save(self):
"""Save the new data to data-file.
Returns
-------
time : int
the time it took to execute this method
"""
start = get_time()
if len(self._subject_info) > 0 or len(self._experiment_info) > 0 \
or self._variable_names_changed:
# Re-write header and varnames
tmpfile_name = "{0}/{1}".format(self.directory, uuid.uuid4())
os.rename(self._fullpath, tmpfile_name)
fl = open(self._fullpath, 'w+')
tmpfl = open(tmpfile_name, 'r')
section = None
while True:
line = tmpfl.readline()
if not line:
break
if line.startswith(self.comment_char + "e"):
section = "e"
elif line.startswith(self.comment_char + "s"):
section = "s"
else:
if section == "e": # Previous line was last #e
if len(self._experiment_info) > 0:
fl.write("".join(self._experiment_info))
self._experiment_info = []
section = None
elif section == "s": # Previous line was last #s
if len(self._subject_info) > 0:
fl.write("".join(self._subject_info))
self._subject_info = []
section = None
# Re-write variable names after #s-section
fl.write(unicode2str(
self.variable_names + defaults.outputfile_eol))
self._variable_names_changed = False
line = '' # Skip old varnames
fl.write(line)
tmpfl.close()
fl.close()
os.remove(tmpfile_name)
self._subject_info = []
self._experiment_info = []
if self._buffer != []:
OutputFile.save(self)
if self._logging:
expyriment._active_exp._event_file_log("Data,saved")
return int((get_time() - start) * 1000)
@staticmethod
def get_next_subject_number():
"""Return the next subject number based on the existing data files."""
subject_number = 1
if os.path.isdir(defaults.datafile_directory):
mainfile_name = os.path.split(sys.argv[0])[1].replace(".py", "")
for filename in os.listdir(defaults.datafile_directory):
if filename.startswith(mainfile_name) and \
filename.endswith(DataFile._file_suffix):
tmp = filename.replace(mainfile_name, "")
tmp = tmp.replace(DataFile._file_suffix, "")
tmp = tmp.split('_')
try:
num = int(tmp[1])
if num >= subject_number:
subject_number = num + 1
except:
pass
return subject_number
class EventFile(OutputFile):
"""A class implementing an event file."""
_file_suffix = ".xpe"
def __init__(self, additional_suffix, directory=None, delimiter=None,
clock=None, time_stamp=None):
"""Create an event file.
Filename: {MAINFILE_NAME}_{SUBJECT_ID}_{TIME_STAMP}{ADD_SUFFIX}.xpd
Parameters
----------
additional_suffix : str
additional suffix
directory : str, optional
directory of the file
delimiter : str, optional
symbol between timestamp and event
clock : expyriment.Clock, optional
an experimental clock
time_stamp : bool, optional
using time stamps, based on the experiment start time,
not the current time
"""
if directory is None:
directory = defaults.eventfile_directory
if additional_suffix is None:
additional_suffix = ''
if len(additional_suffix) > 0:
suffix = ".{0}{1}".format(additional_suffix, self._file_suffix)
else:
suffix = self._file_suffix
OutputFile.__init__(self, suffix, directory, time_stamp=time_stamp)
if delimiter is not None:
self._delimiter = delimiter
else:
self._delimiter = defaults.eventfile_delimiter
if clock is not None:
self._clock = clock
else:
if not expyriment._active_exp.is_initialized:
raise RuntimeError(
"Cannot find a clock. Initialize Expyriment!")
self._clock = expyriment._active_exp.clock
try:
display = repr(expyriment._active_exp.screen.window_size)
window_mode = repr(expyriment._active_exp.screen.window_mode)
opengl = repr(expyriment._active_exp.screen.open_gl)
except:
display = "unknown"
window_mode = "unknown"
opengl = "unknown"
self.write_comment("sha1: {0}".format(
expyriment.get_experiment_secure_hash()))
self.write_comment("display: size={0}, window_mode={1}, opengl={2}"
.format(display, window_mode, opengl))
self.write_comment("os: {0}".format(uname()))
self.write_line("Time,Type,Event,Value,Detail,Detail2")
self.save()
@property
def clock(self):
"""Getter for clock"""
return self._clock
@property
def delimiter(self):
"""Getter for delimiter"""
return self._delimiter
def log(self, event):
"""Log an event.
Parameters
----------
event : anything
the event to be logged (anything, will be casted to str)
"""
if isinstance(event, types.UnicodeType):
event = unicode2str(event)
line = repr(self._clock.time) + self.delimiter + str(event)
self.write_line(line)
def warn(self, message):
"""Log a warning message.
Parameters
----------
message : str
warning message to log
"""
line = "WARNING: " + message
self.write_line(line)
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