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lvm_read.py
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lvm_read.py
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"""
This module is used for the reading LabView Measurement File
Author: Janko Slavič et al. (janko.slavic@fs.uni-lj.si)
"""
from os import path
import pickle
import numpy as np
import io
__version__ = '1.23'
def _lvm_pickle(filename):
""" Reads pickle file (for local use)
:param filename: filename of lvm file
:return lvm_data: dict with lvm data
"""
p_file = '{}.pkl'.format(filename)
pickle_file_exist = path.exists(p_file)
original_file_exist = path.exists(filename)
if pickle_file_exist and original_file_exist:
read_pickle = path.getctime(p_file) > path.getctime(filename)
if not original_file_exist:
read_pickle = True
lvm_data = False
if pickle_file_exist and read_pickle:
f = open(p_file, 'rb')
lvm_data = pickle.load(f)
f.close()
return lvm_data
def _lvm_dump(lvm_data, filename, protocol=-1):
""" Dump lvm_data dict to disc
:param lvm_data: lvm data dict
:param filename: filename of the lvm file
:param protocol: pickle protocol
"""
p_file = '{}.pkl'.format(filename)
output = open(p_file, 'wb')
pickle.dump(lvm_data, output, protocol=protocol)
output.close()
def _get_separator(file):
separator = '\t'
i = 0
for line in file:
if line.startswith('Separator'):
separator = line.strip()[9]
break
if i>20:
break
i+=1
if isinstance(file, io.IOBase):
file.seek(0)
return separator
def _read_lvm_base(filename):
""" Base lvm reader. Should be called from ``read``, only
:param filename: filename of the lvm file
:return lvm_data: lvm dict
"""
with open(filename, 'r', encoding="utf8", errors='ignore') as f:
separator = _get_separator(f)
lvm_data = read_lines(f, separator=separator)
return lvm_data
def read_lines(lines, separator='\t'):
""" Read lines of strings.
:param lines: lines of the lvm file
:return lvm_data: lvm dict
"""
lvm_data = dict()
lvm_data['Decimal_Separator'] = '.'
data_channels_comment_reading = False
data_reading = False
segment = None
seg_data = []
first_column = 0
nr_of_columns = 0
segment_nr = 0
def to_float(a):
try:
return float(a.replace(lvm_data['Decimal_Separator'], '.'))
except:
return np.nan
for line in lines:
line = line.replace('\r', '')
line_sp = line.replace('\n', '').split(separator)
if line_sp[0] in ['***End_of_Header***', 'LabVIEW Measurement']:
continue
elif line in ['\n', separator+'\n']:
# segment finished, new segment follows
segment = dict()
lvm_data[segment_nr] = segment
data_reading = False
segment_nr += 1
continue
elif data_reading: # this was moved up, to speed up the reading
seg_data.append([to_float(a) for a in
line_sp[first_column:(nr_of_columns + 1)]])
elif segment == None:
if len(line_sp) == 2:
key, value = line_sp
lvm_data[key] = value
elif segment != None:
if line_sp[0] == 'Channels':
key, value = line_sp[:2]
nr_of_columns = len(line_sp) - 1
segment[key] = eval(value)
if nr_of_columns < segment['Channels']:
nr_of_columns = segment['Channels']
data_channels_comment_reading = True
elif line_sp[0] == 'X_Value':
seg_data = []
segment['data'] = seg_data
if lvm_data['X_Columns'] == 'No':
first_column = 1
segment['Channel names'] = line_sp[first_column:(nr_of_columns + 1)]
data_channels_comment_reading = False
data_reading = True
elif data_channels_comment_reading:
key, values = line_sp[0], line_sp[1:(nr_of_columns + 1)]
if key in ['Delta_X', 'X0', 'Samples']:
segment[key] = [eval(val.replace(lvm_data['Decimal_Separator'], '.')) if val else np.nan for val in
values]
else:
segment[key] = values
elif len(line_sp) == 2:
key, value = line_sp
segment[key] = value
if not lvm_data[segment_nr - 1]:
del lvm_data[segment_nr - 1]
segment_nr -= 1
lvm_data['Segments'] = segment_nr
for s in range(segment_nr):
lvm_data[s]['data'] = np.asarray(lvm_data[s]['data'])
return lvm_data
def read_str(str):
"""
Parse the string as the content of lvm file.
:param str: input string
:return: dictionary with lvm data
Examples
--------
>>> import numpy as np
>>> import urllib
>>> filename = 'short.lvm' #download a sample file from github
>>> sample_file = urllib.request.urlopen('https://github.com/ladisk/lvm_read/blob/master/data/'+filename).read()
>>> str = sample_file.decode('utf-8') # convert to string
>>> lvm = lvm_read.read_str(str) #read the string as lvm file content
>>> lvm.keys() #explore the dictionary
dict_keys(['', 'Date', 'X_Columns', 'Time_Pref', 'Time', 'Writer_Version',...
"""
return read_lines(str.splitlines(keepends=True))
def read(filename, read_from_pickle=True, dump_file=True):
"""Read from .lvm file and by default for faster reading save to pickle.
See also specifications: http://www.ni.com/tutorial/4139/en/
:param filename: file which should be read
:param read_from_pickle: if True, it tries to read from pickle
:param dump_file: dump file to pickle (significantly increases performance)
:return: dictionary with lvm data
Examples
--------
>>> import numpy as np
>>> import urllib
>>> filename = 'short.lvm' #download a sample file from github
>>> sample_file = urllib.request.urlopen('https://github.com/ladisk/lvm_read/blob/master/data/'+filename).read()
>>> with open(filename, 'wb') as f: # save the file locally
f.write(sample_file)
>>> lvm = lvm_read.read('short.lvm') #read the file
>>> lvm.keys() #explore the dictionary
dict_keys(['', 'Date', 'X_Columns', 'Time_Pref', 'Time', 'Writer_Version',...
"""
lvm_data = _lvm_pickle(filename)
if read_from_pickle and lvm_data:
return lvm_data
else:
lvm_data = _read_lvm_base(filename)
if dump_file:
_lvm_dump(lvm_data, filename)
return lvm_data
if __name__ == '__main__':
import matplotlib.pyplot as plt
da = read('data/with_comments.lvm',read_from_pickle=False)
#da = read('data\with_empty_fields.lvm',read_from_pickle=False)
print(da.keys())
print('Number of segments:', da['Segments'])
plt.plot(da[0]['data'])
plt.show()