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-# coding: utf-8
-# /*##########################################################################
-# Copyright (C) 2016-2019 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ############################################################################*/
-"""Tests for specfile wrapper"""
-
-__authors__ = ["P. Knobel", "V.A. Sole"]
-__license__ = "MIT"
-__date__ = "17/01/2018"
-
-
-import locale
-import logging
-import numpy
-import os
-import sys
-import tempfile
-import unittest
-
-from silx.utils import testutils
-
-from ..specfile import SpecFile, Scan
-from .. import specfile
-
-
-logger1 = logging.getLogger(__name__)
-
-sftext = """#F /tmp/sf.dat
-#E 1455180875
-#D Thu Feb 11 09:54:35 2016
-#C imaging User = opid17
-#U00 user comment first line
-#U01 This is a dummy file to test SpecFile parsing
-#U02
-#U03 last line
-
-#O0 Pslit HGap MRTSlit UP MRTSlit DOWN
-#O1 Sslit1 VOff Sslit1 HOff Sslit1 VGap
-#o0 pshg mrtu mrtd
-#o2 ss1vo ss1ho ss1vg
-
-#J0 Seconds IA ion.mono Current
-#J1 xbpmc2 idgap1 Inorm
-
-#S 1 ascan ss1vo -4.55687 -0.556875 40 0.2
-#D Thu Feb 11 09:55:20 2016
-#T 0.2 (Seconds)
-#G0 0
-#G1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-#G3 0 0 0 0 0 0 0 0 0
-#G4 0
-#Q
-#P0 180.005 -0.66875 0.87125
-#P1 14.74255 16.197579 12.238283
-#UMI0 Current AutoM Shutter
-#UMI1 192.51 OFF FE open
-#UMI2 Refill in 39883 sec, Fill Mode: uniform multibunch / Message: Feb 11 08:00 Delivery:Next Refill at 21:00;
-#N 4
-#L first column second column 3rd_col
--1.23 5.89 8
-8.478100E+01 5 1.56
-3.14 2.73 -3.14
-1.2 2.3 3.4
-
-#S 25 ascan c3th 1.33245 1.52245 40 0.15
-#D Thu Feb 11 10:00:31 2016
-#P0 80.005 -1.66875 1.87125
-#P1 4.74255 6.197579 2.238283
-#N 5
-#L column0 column1 col2 col3
-0.0 0.1 0.2 0.3
-1.0 1.1 1.2 1.3
-2.0 2.1 2.2 2.3
-3.0 3.1 3.2 3.3
-
-#S 26 yyyyyy
-#D Thu Feb 11 09:55:20 2016
-#P0 80.005 -1.66875 1.87125
-#P1 4.74255 6.197579 2.238283
-#N 4
-#L first column second column 3rd_col
-#C Sat Oct 31 15:51:47 1998. Scan aborted after 0 points.
-
-#F /tmp/sf.dat
-#E 1455180876
-#D Thu Feb 11 09:54:36 2016
-
-#S 1 aaaaaa
-#U first duplicate line
-#U second duplicate line
-#@MCADEV 1
-#@MCA %16C
-#@CHANN 3 0 2 1
-#@CALIB 1 2 3
-#N 3
-#L uno duo
-1 2
-@A 0 1 2
-3 4
-@A 3.1 4 5
-5 6
-@A 6 7.7 8
-"""
-
-
-loc = locale.getlocale(locale.LC_NUMERIC)
-try:
- locale.setlocale(locale.LC_NUMERIC, 'de_DE.utf8')
-except locale.Error:
- try_DE = False
-else:
- try_DE = True
- locale.setlocale(locale.LC_NUMERIC, loc)
-
-
-class TestSpecFile(unittest.TestCase):
- @classmethod
- def setUpClass(cls):
- fd, cls.fname1 = tempfile.mkstemp(text=False)
- if sys.version_info < (3, ):
- os.write(fd, sftext)
- else:
- os.write(fd, bytes(sftext, 'ascii'))
- os.close(fd)
-
- fd2, cls.fname2 = tempfile.mkstemp(text=False)
- if sys.version_info < (3, ):
- os.write(fd2, sftext[370:923])
- else:
- os.write(fd2, bytes(sftext[370:923], 'ascii'))
- os.close(fd2)
-
- fd3, cls.fname3 = tempfile.mkstemp(text=False)
- txt = sftext[371:923]
- if sys.version_info < (3, ):
- os.write(fd3, txt)
- else:
- os.write(fd3, bytes(txt, 'ascii'))
- os.close(fd3)
-
- @classmethod
- def tearDownClass(cls):
- os.unlink(cls.fname1)
- os.unlink(cls.fname2)
- os.unlink(cls.fname3)
-
- def setUp(self):
- self.sf = SpecFile(self.fname1)
- self.scan1 = self.sf[0]
- self.scan1_2 = self.sf["1.2"]
- self.scan25 = self.sf["25.1"]
- self.empty_scan = self.sf["26.1"]
-
- self.sf_no_fhdr = SpecFile(self.fname2)
- self.scan1_no_fhdr = self.sf_no_fhdr[0]
-
- self.sf_no_fhdr_crash = SpecFile(self.fname3)
- self.scan1_no_fhdr_crash = self.sf_no_fhdr_crash[0]
-
- def tearDown(self):
- self.sf.close()
- self.sf_no_fhdr.close()
- self.sf_no_fhdr_crash.close()
-
- def test_open(self):
- self.assertIsInstance(self.sf, SpecFile)
- with self.assertRaises(specfile.SfErrFileOpen):
- SpecFile("doesnt_exist.dat")
-
- # test filename types unicode and bytes
- if sys.version_info[0] < 3:
- try:
- SpecFile(self.fname1)
- except TypeError:
- self.fail("failed to handle filename as python2 str")
- try:
- SpecFile(unicode(self.fname1))
- except TypeError:
- self.fail("failed to handle filename as python2 unicode")
- else:
- try:
- SpecFile(self.fname1)
- except TypeError:
- self.fail("failed to handle filename as python3 str")
- try:
- SpecFile(bytes(self.fname1, 'utf-8'))
- except TypeError:
- self.fail("failed to handle filename as python3 bytes")
-
- def test_number_of_scans(self):
- self.assertEqual(4, len(self.sf))
-
- def test_list_of_scan_indices(self):
- self.assertEqual(self.sf.list(),
- [1, 25, 26, 1])
- self.assertEqual(self.sf.keys(),
- ["1.1", "25.1", "26.1", "1.2"])
-
- def test_index_number_order(self):
- self.assertEqual(self.sf.index(1, 2), 3) # sf["1.2"]==sf[3]
- self.assertEqual(self.sf.number(1), 25) # sf[1]==sf["25"]
- self.assertEqual(self.sf.order(3), 2) # sf[3]==sf["1.2"]
- with self.assertRaises(specfile.SfErrScanNotFound):
- self.sf.index(3, 2)
- with self.assertRaises(specfile.SfErrScanNotFound):
- self.sf.index(99)
-
- def assertRaisesRegex(self, *args, **kwargs):
- # Python 2 compatibility
- if sys.version_info.major >= 3:
- return super(TestSpecFile, self).assertRaisesRegex(*args, **kwargs)
- else:
- return self.assertRaisesRegexp(*args, **kwargs)
-
- def test_getitem(self):
- self.assertIsInstance(self.sf[2], Scan)
- self.assertIsInstance(self.sf["1.2"], Scan)
- # int out of range
- with self.assertRaisesRegex(IndexError, 'Scan index must be in ran'):
- self.sf[107]
- # float indexing not allowed
- with self.assertRaisesRegex(TypeError, 'The scan identification k'):
- self.sf[1.2]
- # non existant scan with "N.M" indexing
- with self.assertRaises(KeyError):
- self.sf["3.2"]
-
- def test_specfile_iterator(self):
- i = 0
- for scan in self.sf:
- if i == 1:
- self.assertEqual(scan.motor_positions,
- self.sf[1].motor_positions)
- i += 1
- # number of returned scans
- self.assertEqual(i, len(self.sf))
-
- def test_scan_index(self):
- self.assertEqual(self.scan1.index, 0)
- self.assertEqual(self.scan1_2.index, 3)
- self.assertEqual(self.scan25.index, 1)
-
- def test_scan_headers(self):
- self.assertEqual(self.scan25.scan_header_dict['S'],
- "25 ascan c3th 1.33245 1.52245 40 0.15")
- self.assertEqual(self.scan1.header[17], '#G0 0')
- self.assertEqual(len(self.scan1.header), 29)
- # parsing headers with long keys
- self.assertEqual(self.scan1.scan_header_dict['UMI0'],
- 'Current AutoM Shutter')
- # parsing empty headers
- self.assertEqual(self.scan1.scan_header_dict['Q'], '')
- # duplicate headers: concatenated (with newline)
- self.assertEqual(self.scan1_2.scan_header_dict["U"],
- "first duplicate line\nsecond duplicate line")
-
- def test_file_headers(self):
- self.assertEqual(self.scan1.header[1],
- '#E 1455180875')
- self.assertEqual(self.scan1.file_header_dict['F'],
- '/tmp/sf.dat')
-
- def test_multiple_file_headers(self):
- """Scan 1.2 is after the second file header, with a different
- Epoch"""
- self.assertEqual(self.scan1_2.header[1],
- '#E 1455180876')
-
- def test_scan_labels(self):
- self.assertEqual(self.scan1.labels,
- ['first column', 'second column', '3rd_col'])
-
- def test_data(self):
- # data_line() and data_col() take 1-based indices as arg
- self.assertAlmostEqual(self.scan1.data_line(1)[2],
- 1.56)
- # tests for data transposition between original file and .data attr
- self.assertAlmostEqual(self.scan1.data[2, 0],
- 8)
- self.assertEqual(self.scan1.data.shape, (3, 4))
- self.assertAlmostEqual(numpy.sum(self.scan1.data), 113.631)
-
- def test_data_column_by_name(self):
- self.assertAlmostEqual(self.scan25.data_column_by_name("col2")[1],
- 1.2)
- # Scan.data is transposed after readinq, so column is the first index
- self.assertAlmostEqual(numpy.sum(self.scan25.data_column_by_name("col2")),
- numpy.sum(self.scan25.data[2, :]))
- with self.assertRaises(specfile.SfErrColNotFound):
- self.scan25.data_column_by_name("ygfxgfyxg")
-
- def test_motors(self):
- self.assertEqual(len(self.scan1.motor_names), 6)
- self.assertEqual(len(self.scan1.motor_positions), 6)
- self.assertAlmostEqual(sum(self.scan1.motor_positions),
- 223.385912)
- self.assertEqual(self.scan1.motor_names[1], 'MRTSlit UP')
- self.assertAlmostEqual(
- self.scan25.motor_position_by_name('MRTSlit UP'),
- -1.66875)
-
- def test_absence_of_file_header(self):
- """We expect Scan.file_header to be an empty list in the absence
- of a file header.
- """
- self.assertEqual(len(self.scan1_no_fhdr.motor_names), 0)
- # motor positions can still be read in the scan header
- # even in the absence of motor names
- self.assertAlmostEqual(sum(self.scan1_no_fhdr.motor_positions),
- 223.385912)
- self.assertEqual(len(self.scan1_no_fhdr.header), 15)
- self.assertEqual(len(self.scan1_no_fhdr.scan_header), 15)
- self.assertEqual(len(self.scan1_no_fhdr.file_header), 0)
-
- def test_crash_absence_of_file_header(self):
- """Test no crash in absence of file header and no leading newline
- character
- """
- self.assertEqual(len(self.scan1_no_fhdr_crash.motor_names), 0)
- # motor positions can still be read in the scan header
- # even in the absence of motor names
- self.assertAlmostEqual(sum(self.scan1_no_fhdr_crash.motor_positions),
- 223.385912)
- self.assertEqual(len(self.scan1_no_fhdr_crash.scan_header), 15)
- self.assertEqual(len(self.scan1_no_fhdr_crash.file_header), 0)
-
- def test_mca(self):
- self.assertEqual(len(self.scan1.mca), 0)
- self.assertEqual(len(self.scan1_2.mca), 3)
- self.assertEqual(self.scan1_2.mca[1][2], 5)
- self.assertEqual(sum(self.scan1_2.mca[2]), 21.7)
-
- # Negative indexing
- self.assertEqual(sum(self.scan1_2.mca[len(self.scan1_2.mca) - 1]),
- sum(self.scan1_2.mca[-1]))
-
- # Test iterator
- line_count, total_sum = (0, 0)
- for mca_line in self.scan1_2.mca:
- line_count += 1
- total_sum += sum(mca_line)
- self.assertEqual(line_count, 3)
- self.assertAlmostEqual(total_sum, 36.8)
-
- def test_mca_header(self):
- self.assertEqual(self.scan1.mca_header_dict, {})
- self.assertEqual(len(self.scan1_2.mca_header_dict), 4)
- self.assertEqual(self.scan1_2.mca_header_dict["CALIB"], "1 2 3")
- self.assertEqual(self.scan1_2.mca.calibration,
- [[1., 2., 3.]])
- # default calib in the absence of #@CALIB
- self.assertEqual(self.scan25.mca.calibration,
- [[0., 1., 0.]])
- self.assertEqual(self.scan1_2.mca.channels,
- [[0, 1, 2]])
- # absence of #@CHANN and spectra
- self.assertEqual(self.scan25.mca.channels,
- [])
-
- @testutils.test_logging(specfile._logger.name, warning=1)
- def test_empty_scan(self):
- """Test reading a scan with no data points"""
- self.assertEqual(len(self.empty_scan.labels),
- 3)
- col1 = self.empty_scan.data_column_by_name("second column")
- self.assertEqual(col1.shape, (0, ))
-
-
-class TestSFLocale(unittest.TestCase):
- @classmethod
- def setUpClass(cls):
- fd, cls.fname = tempfile.mkstemp(text=False)
- if sys.version_info < (3, ):
- os.write(fd, sftext)
- else:
- os.write(fd, bytes(sftext, 'ascii'))
- os.close(fd)
-
- @classmethod
- def tearDownClass(cls):
- os.unlink(cls.fname)
- locale.setlocale(locale.LC_NUMERIC, loc) # restore saved locale
-
- def crunch_data(self):
- self.sf3 = SpecFile(self.fname)
- self.assertAlmostEqual(self.sf3[0].data_line(1)[2],
- 1.56)
- self.sf3.close()
-
- @unittest.skipIf(not try_DE, "de_DE.utf8 locale not installed")
- def test_locale_de_DE(self):
- locale.setlocale(locale.LC_NUMERIC, 'de_DE.utf8')
- self.crunch_data()
-
- def test_locale_user(self):
- locale.setlocale(locale.LC_NUMERIC, '') # use user's preferred locale
- self.crunch_data()
-
- def test_locale_C(self):
- locale.setlocale(locale.LC_NUMERIC, 'C') # use default (C) locale
- self.crunch_data()
-
-
-def suite():
- test_suite = unittest.TestSuite()
- test_suite.addTest(
- unittest.defaultTestLoader.loadTestsFromTestCase(TestSpecFile))
- test_suite.addTest(
- unittest.defaultTestLoader.loadTestsFromTestCase(TestSFLocale))
- return test_suite
-
-
-if __name__ == '__main__':
- unittest.main(defaultTest="suite")
generated by cgit v1.2.3 (git 2.25.1) at 2024-04-26 07:49:54 +0000