def test_SUFAR4_with_options(self):
input_dir = os.path.join(WD, 'data_files',
'Measurement_Import', 'SUFAR_asc_magic')
infile = 'sufar4-asc_magic_example.txt'
program_ran, outfile = ipmag.SUFAR4_magic(infile, meas_output='my_magic_measurements.txt', aniso_output="my_rmag_anisotropy.txt", specnum=2, locname="Here", instrument="INST", static_15_position_mode=True, input_dir_path=input_dir, sample_naming_con='5')
self.assertTrue(program_ran)
self.assertEqual(outfile, os.path.join('.', 'my_magic_measurements.txt'))
def test_SUFAR4_with_infile(self):
input_dir = os.path.join(WD, 'data_files', 'Measurement_Import',
'SUFAR_asc_magic')
infile = 'sufar4-asc_magic_example.txt'
program_ran, outfile = ipmag.SUFAR4_magic(infile,
input_dir_path=input_dir)
self.assertTrue(program_ran)
self.assertEqual(outfile, os.path.join('.', 'magic_measurements.txt'))
def test_SUFAR4_fail_option4(self):
input_dir = os.path.join(WD, 'data_files',
'Measurement_Import', 'SUFAR_asc_magic')
infile = 'sufar4-asc_magic_example.txt'
program_ran, error_message = ipmag.SUFAR4_magic(infile,
input_dir_path=input_dir,
sample_naming_con='4')
self.assertFalse(program_ran)
self.assertEqual(error_message, "option [4] must be in form 4-Z where Z is an integer")
def test_SUFAR4_with_invalid_file(self):
input_dir = os.path.join(WD, 'data_files', 'Measurement_Import',
'SUFAR_asc_magic')
infile = 'fake_sufar4-asc_magic_example.txt'
program_ran, error_message = ipmag.SUFAR4_magic(
infile, input_dir_path=input_dir)
self.assertFalse(program_ran)
self.assertEqual(
error_message,
'Error opening file: {}'.format(os.path.join(input_dir, infile)))
def test_SUFAR4_with_infile(self):
input_dir = os.path.join(WD, 'data_files', 'Measurement_Import',
'SUFAR_asc_magic')
infile = 'sufar4-asc_magic_example.txt'
program_ran, outfile = ipmag.SUFAR4_magic(infile,
input_dir_path=input_dir,
data_model_num=2)
self.assertTrue(program_ran)
self.assertEqual(outfile, os.path.join('.', 'magic_measurements.txt'))
with open(outfile, 'r') as ofile:
lines = ofile.readlines()
self.assertEqual(292, len(lines))
def test_SUFAR4_succeed_option4(self):
input_dir = os.path.join(WD, 'data_files', 'Measurement_Import',
'SUFAR_asc_magic')
print('WD', WD)
print('input_dir', input_dir)
infile = 'sufar4-asc_magic_example.txt'
ofile = 'my_magic_measurements.txt'
program_ran, outfile = ipmag.SUFAR4_magic(infile,
meas_output=ofile,
input_dir_path=input_dir,
sample_naming_con='4-2')
self.assertTrue(program_ran)
self.assertEqual(outfile, os.path.join('.', ofile))
def test_SUFAR4_succeed_data_model3(self):
input_dir = os.path.join(WD, 'data_files', 'Measurement_Import',
'SUFAR_asc_magic')
infile = 'sufar4-asc_magic_example.txt'
program_ran, outfile = ipmag.SUFAR4_magic(infile,
input_dir_path=input_dir)
self.assertTrue(program_ran)
self.assertEqual(outfile, os.path.join('.', 'measurements.txt'))
with open(outfile, 'r') as ofile:
lines = ofile.readlines()
self.assertEqual(292, len(lines))
self.assertEqual('measurements', lines[0].split('\t')[1].strip())
con = nb.Contribution(WD)
self.assertEqual(
sorted(con.tables),
sorted(['measurements', 'specimens', 'samples', 'sites']))
def test_SUFAR4_with_no_files(self):
with self.assertRaises(TypeError):
ipmag.SUFAR4_magic()
def main():
"""
NAME
sufar4-asc_magic.py
DESCRIPTION
converts ascii files generated by SUFAR ver.4.0 to MagIC formated
files for use with PmagPy plotting software
SYNTAX
sufar4-asc_magic.py -h [command line options]
OPTIONS
-h: prints the help message and quits
-f FILE: specify .asc input file name
-fsi SINFILE: specify er_specimens input file
-F MFILE: specify magic_measurements output file
-Fa AFILE: specify rmag_anisotropy output file
-Fr RFILE: specify rmag_results output file
-Fsi SFILE: specify er_specimens output file with location, sample, site, etc. information
-usr USER: specify who made the measurements
-loc LOC: specify location name for study
-ins INST: specify instrument used
-spc SPEC: specify number of characters to specify specimen from sample
-ncn NCON: specify naming convention: default is #2 below
-k15 : specify static 15 position mode - default is spinning
-new : replace all existing magic files
DEFAULTS
AFILE: rmag_anisotropy.txt
RFILE: rmag_results.txt
SFILE: default is to create new er_specimen.txt file
USER: ""
LOC: "unknown"
INST: ""
SPEC: 0 sample name is same as site (if SPEC is 1, sample is all but last character)
appends to 'er_specimens.txt, er_samples.txt, er_sites.txt' files
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
[8] This is a synthetic
[9] ODP naming convention
"""
args = sys.argv
if '-h' in args:
print main.__doc__
sys.exit()
dataframe = extractor.command_line_dataframe(
[['WD', False, '.'], ['ID', False, '.'], ['usr', False, ''],
['ncn', False, '1'], ['k15', False, False], ['ins', False, ''],
['f', True, ''], ['F', False, 'magic_measurements.txt'],
['Fa', False, 'rmag_anisotropy.txt'],
['Fsi', False, 'er_specimens.txt'], ['loc', False, 'unknown'],
['spc', False, 0], ['fsi', False, None]])
#'WD', 'ID', 'usr', 'ncn', 'k15', 'ins', 'f', 'F', 'Fa', 'Fsi', 'loc', 'spc',
checked_args = extractor.extract_and_check_args(args, dataframe)
output_dir_path, input_dir_path, user, sample_naming_con, static_15_position_mode, instrument, ascfile, meas_output, aniso_output, spec_outfile, locname, specnum, spec_infile = extractor.get_vars(
[
'WD', 'ID', 'usr', 'ncn', 'k15', 'ins', 'f', 'F', 'Fa', 'Fsi',
'loc', 'spc', 'fsi'
], checked_args)
ipmag.SUFAR4_magic(ascfile,
meas_output,
aniso_output,
spec_infile,
spec_outfile,
specnum=specnum,
sample_naming_con=sample_naming_con,
user=user,
locname=locname,
instrument=instrument,
static_15_position_mode=static_15_position_mode,
output_dir_path=output_dir_path,
input_dir_path=input_dir_path)
