# Copyright (c) 2013, System Engineering Software Society
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of the System Engineering Software Society nor the
# names of its contributors may be used to endorse or promote products
# derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED.
# IN NO EVENT SHALL SYSTEM ENGINEERING SOFTWARE SOCIETY BE LIABLE FOR ANY
# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from __future__ import (print_function, division, unicode_literals,
absolute_import)
import re
import time
import os
from sylib.table_sources import ImporterCSV, TableSourceCSV
from sympathy.api import importers
from sympathy.api import table
from sympathy.api.exceptions import SyDataError
from sympathy.api import nodeconfig
CHECK_NO_ROWS = 1
CHECK_FOOT_ROWS = 0
CHECK_OFFSET_ROW = 2
DIVA_TB_COLUMN = u'time'
DIVA_DELIMITER = '\t'
DIVA_ENCODING = 'utf_8'
HEADER_OFFSET_ROW = 7
UNIT_OFFSET_ROW = 8
DATA_NO_ROWS = -1
DATA_FOOT_ROWS = 0
DATA_OFFSET_ROW = 9
def print_timing(func):
def wrapper(*arg):
t1 = time.time()
res = func(*arg)
t2 = time.time()
print('%s took %0.3f ms' % (func.func_name, (t2 - t1) * 1000.0))
return res
return wrapper
def check_file_header(importer):
try:
test_table = table.File()
importer.import_csv(
test_table, CHECK_NO_ROWS, CHECK_FOOT_ROWS, CHECK_OFFSET_ROW)
testname_attr = test_table.get_column_to_array('X0')[0]
if testname_attr != 'TESTNAME':
raise
except Exception:
raise SyDataError('Not a valid DIVA file')
class DataSnifferEE(object):
""" Sniff a file and determine the data format """
ee_format_diva_export = 0
ee_format_unknown = 0xff
def __init__(self, filename):
""" """
self._sample_size = 256
self.filename = filename
self._sample = None
with open(self.filename, 'rb') as f:
self._sample = f.read(self._sample_size)
def evaluate_format(self):
""" Read a sample from file and determine the format """
if self.is_diva_export():
return self.ee_format_diva_export
return self.ee_format_unknown
def is_diva_export(self):
""" Is the sample from a DIVA file """
split_sample = re.split(b'[\\t\n\\r]+', self._sample)
diva_id = b'DIVA ASCII-Export by Textfield Modul Version 2.0'
return split_sample[0] == diva_id
class DataSnifferDIVA(importers.IDataSniffer):
def __init__(self):
super(DataSnifferDIVA, self).__init__()
def sniff(self, path):
ds = DataSnifferEE(path)
return DataSnifferEE.ee_format_diva_export == ds.evaluate_format()
[docs]class DataImportDIVA(importers.ADAFDataImporterBase):
""" Import exported DIVA data into h5 format """
IMPORTER_NAME = "DIVA"
DISPLAY_NAME = 'DIVA (deprecated)'
def __init__(self, fq_infilename, parameters):
super(DataImportDIVA, self).__init__(fq_infilename, parameters)
def valid_for_file(self):
if self._fq_infilename is None or not os.path.isfile(
self._fq_infilename):
return False
return DataSnifferDIVA().sniff(self._fq_infilename)
def import_data(self, out_datafile, parameters=None, progress=None):
""" Import DIVA data from a file """
nodeconfig.deprecated_warn(
'Support for DIVA import',
'1.7.0',
"make a copy of the plugin code and maintain it yourself in your "
"own library")
table_source = TableSourceCSV(self._fq_infilename,
delimiter=DIVA_DELIMITER,
encoding=DIVA_ENCODING)
importer = ImporterCSV(table_source)
check_file_header(importer)
data_table = table.File()
importer.import_csv(
data_table, DATA_NO_ROWS, DATA_FOOT_ROWS, DATA_OFFSET_ROW,
headers_row_offset=HEADER_OFFSET_ROW,
units_row_offset=UNIT_OFFSET_ROW)
if progress:
progress(60)
system = out_datafile.sys.create(self.IMPORTER_NAME)
raster = system.create('Group0')
attributes = data_table.get_column_attributes(DIVA_TB_COLUMN)
attributes.setdefault('unit', 's')
attributes.setdefault('sampling_rate', 0.1)
data_table.set_column_attributes(DIVA_TB_COLUMN, attributes)
raster.from_table(data_table, DIVA_TB_COLUMN)
