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Diffstat (limited to 'silx/io/test/test_spech5.py')
| -rw-r--r-- | silx/io/test/test_spech5.py | 881 |
1 files changed, 0 insertions, 881 deletions
diff --git a/silx/io/test/test_spech5.py b/silx/io/test/test_spech5.py deleted file mode 100644 index b842243..0000000 --- a/silx/io/test/test_spech5.py +++ /dev/null @@ -1,881 +0,0 @@ -# coding: utf-8 -# /*########################################################################## -# Copyright (C) 2016-2018 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 spech5""" -from numpy import array_equal -import os -import io -import sys -import tempfile -import unittest -import datetime -from functools import partial - -from silx.utils import testutils - -from .. import spech5 -from ..spech5 import (SpecH5, SpecH5Dataset, spec_date_to_iso8601) -from .. import specfile - -try: - import h5py -except ImportError: - h5py = None - -__authors__ = ["P. Knobel"] -__license__ = "MIT" -__date__ = "12/02/2018" - -sftext = """#F /tmp/sf.dat -#E 1455180875 -#D Thu Feb 11 09:54:35 2016 -#C imaging User = opid17 -#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) -#P0 180.005 -0.66875 0.87125 -#P1 14.74255 16.197579 12.238283 -#N 4 -#L MRTSlit UP 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 Sat 2015/03/14 03:53:50 -#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 1 aaaaaa -#D Thu Feb 11 10:00:32 2016 -#@MCADEV 1 -#@MCA %16C -#@CHANN 3 0 2 1 -#@CALIB 1 2 3 -#@CTIME 123.4 234.5 345.6 -#N 3 -#L uno duo -1 2 -@A 0 1 2 -@A 10 9 8 -@A 1 1 1.1 -3 4 -@A 3.1 4 5 -@A 7 6 5 -@A 1 1 1 -5 6 -@A 6 7.7 8 -@A 4 3 2 -@A 1 1 1 - -#S 1000 bbbbb -#G1 3.25 3.25 5.207 90 90 120 2.232368448 2.232368448 1.206680489 90 90 60 1 1 2 -1 2 2 26.132 7.41 -88.96 1.11 1.000012861 15.19 26.06 67.355 -88.96 1.11 1.000012861 15.11 0.723353 0.723353 -#G3 0.0106337923671 0.027529133 1.206191273 -1.43467075 0.7633438883 0.02401568018 -1.709143587 -2.097621783 0.02456954971 -#L a b -1 2 - -#S 1001 ccccc -#G1 0. 0. 0. 0 0 0 2.232368448 2.232368448 1.206680489 90 90 60 1 1 2 -1 2 2 26.132 7.41 -88.96 1.11 1.000012861 15.19 26.06 67.355 -88.96 1.11 1.000012861 15.11 0.723353 0.723353 -#G3 0. 0. 0. 0. 0.0 0. 0. 0. 0. -#L a b -1 2 - -""" - - -class TestSpecDate(unittest.TestCase): - """ - Test of the spec_date_to_iso8601 function. - """ - # TODO : time zone tests - # TODO : error cases - - @classmethod - def setUpClass(cls): - import locale - # FYI : not threadsafe - cls.locale_saved = locale.setlocale(locale.LC_TIME) - locale.setlocale(locale.LC_TIME, 'C') - - @classmethod - def tearDownClass(cls): - import locale - # FYI : not threadsafe - locale.setlocale(locale.LC_TIME, cls.locale_saved) - - def setUp(self): - # covering all week days - self.n_days = range(1, 10) - # covering all months - self.n_months = range(1, 13) - - self.n_years = [1999, 2016, 2020] - self.n_seconds = [0, 5, 26, 59] - self.n_minutes = [0, 9, 42, 59] - self.n_hours = [0, 2, 17, 23] - - self.formats = ['%a %b %d %H:%M:%S %Y', '%a %Y/%m/%d %H:%M:%S'] - - self.check_date_formats = partial(self.__check_date_formats, - year=self.n_years[0], - month=self.n_months[0], - day=self.n_days[0], - hour=self.n_hours[0], - minute=self.n_minutes[0], - second=self.n_seconds[0], - msg=None) - - def __check_date_formats(self, - year, - month, - day, - hour, - minute, - second, - msg=None): - dt = datetime.datetime(year, month, day, hour, minute, second) - expected_date = dt.isoformat() - - for i_fmt, fmt in enumerate(self.formats): - spec_date = dt.strftime(fmt) - iso_date = spec_date_to_iso8601(spec_date) - self.assertEqual(iso_date, - expected_date, - msg='Testing {0}. format={1}. ' - 'Expected "{2}", got "{3} ({4})" (dt={5}).' - ''.format(msg, - i_fmt, - expected_date, - iso_date, - spec_date, - dt)) - - def testYearsNominal(self): - for year in self.n_years: - self.check_date_formats(year=year, msg='year') - - def testMonthsNominal(self): - for month in self.n_months: - self.check_date_formats(month=month, msg='month') - - def testDaysNominal(self): - for day in self.n_days: - self.check_date_formats(day=day, msg='day') - - def testHoursNominal(self): - for hour in self.n_hours: - self.check_date_formats(hour=hour, msg='hour') - - def testMinutesNominal(self): - for minute in self.n_minutes: - self.check_date_formats(minute=minute, msg='minute') - - def testSecondsNominal(self): - for second in self.n_seconds: - self.check_date_formats(second=second, msg='second') - - -class TestSpecH5(unittest.TestCase): - @classmethod - def setUpClass(cls): - fd, cls.fname = tempfile.mkstemp() - 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) - - def setUp(self): - self.sfh5 = SpecH5(self.fname) - - def tearDown(self): - self.sfh5.close() - - def testContainsFile(self): - self.assertIn("/1.2/measurement", self.sfh5) - self.assertIn("/25.1", self.sfh5) - self.assertIn("25.1", self.sfh5) - self.assertNotIn("25.2", self.sfh5) - # measurement is a child of a scan, full path would be required to - # access from root level - self.assertNotIn("measurement", self.sfh5) - # Groups may or may not have a trailing / - self.assertIn("/1.2/measurement/mca_1/", self.sfh5) - self.assertIn("/1.2/measurement/mca_1", self.sfh5) - # Datasets can't have a trailing / - self.assertNotIn("/1.2/measurement/mca_0/info/calibration/ ", self.sfh5) - # No mca_8 - self.assertNotIn("/1.2/measurement/mca_8/info/calibration", self.sfh5) - # Link - self.assertIn("/1.2/measurement/mca_0/info/calibration", self.sfh5) - - def testContainsGroup(self): - self.assertIn("measurement", self.sfh5["/1.2/"]) - self.assertIn("measurement", self.sfh5["/1.2"]) - self.assertIn("25.1", self.sfh5["/"]) - self.assertNotIn("25.2", self.sfh5["/"]) - self.assertIn("instrument/positioners/Sslit1 HOff", self.sfh5["/1.1"]) - # illegal trailing "/" after dataset name - self.assertNotIn("instrument/positioners/Sslit1 HOff/", - self.sfh5["/1.1"]) - # full path to element in group (OK) - self.assertIn("/1.1/instrument/positioners/Sslit1 HOff", - self.sfh5["/1.1/instrument"]) - - def testDataColumn(self): - self.assertAlmostEqual(sum(self.sfh5["/1.2/measurement/duo"]), - 12.0) - self.assertAlmostEqual( - sum(self.sfh5["1.1"]["measurement"]["MRTSlit UP"]), - 87.891, places=4) - - def testDate(self): - # start time is in Iso8601 format - self.assertEqual(self.sfh5["/1.1/start_time"], - u"2016-02-11T09:55:20") - self.assertEqual(self.sfh5["25.1/start_time"], - u"2015-03-14T03:53:50") - - def testDatasetInstanceAttr(self): - """The SpecH5Dataset objects must implement some dummy attributes - to improve compatibility with widgets dealing with h5py datasets.""" - self.assertIsNone(self.sfh5["/1.1/start_time"].compression) - self.assertIsNone(self.sfh5["1.1"]["measurement"]["MRTSlit UP"].chunks) - - # error message must be explicit - with self.assertRaisesRegexp( - AttributeError, - "SpecH5Dataset has no attribute tOTo"): - dummy = self.sfh5["/1.1/start_time"].tOTo - - def testGet(self): - """Test :meth:`SpecH5Group.get`""" - # default value of param *default* is None - self.assertIsNone(self.sfh5.get("toto")) - self.assertEqual(self.sfh5["25.1"].get("toto", default=-3), - -3) - - self.assertEqual(self.sfh5.get("/1.1/start_time", default=-3), - u"2016-02-11T09:55:20") - - def testGetClass(self): - """Test :meth:`SpecH5Group.get`""" - if h5py is None: - self.skipTest("h5py is not available") - self.assertIs(self.sfh5["1.1"].get("start_time", getclass=True), - h5py.Dataset) - self.assertIs(self.sfh5["1.1"].get("instrument", getclass=True), - h5py.Group) - - # spech5 does not define external link, so there is no way - # a group can *get* a SpecH5 class - - @unittest.skipIf(h5py is None, "test requires h5py (not installed)") - def testGetApi(self): - result = self.sfh5.get("1.1", getclass=True, getlink=True) - self.assertIs(result, h5py.HardLink) - result = self.sfh5.get("1.1", getclass=False, getlink=True) - self.assertIsInstance(result, h5py.HardLink) - result = self.sfh5.get("1.1", getclass=True, getlink=False) - self.assertIs(result, h5py.Group) - result = self.sfh5.get("1.1", getclass=False, getlink=False) - self.assertIsInstance(result, spech5.SpecH5Group) - - def testGetItemGroup(self): - group = self.sfh5["25.1"]["instrument"] - self.assertEqual(list(group["positioners"].keys()), - ["Pslit HGap", "MRTSlit UP", "MRTSlit DOWN", - "Sslit1 VOff", "Sslit1 HOff", "Sslit1 VGap"]) - with self.assertRaises(KeyError): - group["Holy Grail"] - - def testGetitemSpecH5(self): - self.assertEqual(self.sfh5["/1.2/instrument/positioners"], - self.sfh5["1.2"]["instrument"]["positioners"]) - - @unittest.skipIf(h5py is None, "test requires h5py (not installed)") - def testH5pyClass(self): - """Test :attr:`h5py_class` returns the corresponding h5py class - (h5py.File, h5py.Group, h5py.Dataset)""" - a_file = self.sfh5 - self.assertIs(a_file.h5py_class, - h5py.File) - - a_group = self.sfh5["/1.2/measurement"] - self.assertIs(a_group.h5py_class, - h5py.Group) - - a_dataset = self.sfh5["/1.1/instrument/positioners/Sslit1 HOff"] - self.assertIs(a_dataset.h5py_class, - h5py.Dataset) - - def testHeader(self): - file_header = self.sfh5["/1.2/instrument/specfile/file_header"] - scan_header = self.sfh5["/1.2/instrument/specfile/scan_header"] - - # File header has 10 lines - self.assertEqual(len(file_header), 10) - # 1.2 has 9 scan & mca header lines - self.assertEqual(len(scan_header), 9) - - # line 4 of file header - self.assertEqual( - file_header[3], - u"#C imaging User = opid17") - # line 4 of scan header - scan_header = self.sfh5["25.1/instrument/specfile/scan_header"] - - self.assertEqual( - scan_header[3], - u"#P1 4.74255 6.197579 2.238283") - - def testLinks(self): - self.assertTrue( - array_equal(self.sfh5["/1.2/measurement/mca_0/data"], - self.sfh5["/1.2/instrument/mca_0/data"]) - ) - self.assertTrue( - array_equal(self.sfh5["/1.2/measurement/mca_0/info/data"], - self.sfh5["/1.2/instrument/mca_0/data"]) - ) - self.assertTrue( - array_equal(self.sfh5["/1.2/measurement/mca_0/info/channels"], - self.sfh5["/1.2/instrument/mca_0/channels"]) - ) - self.assertEqual(self.sfh5["/1.2/measurement/mca_0/info/"].keys(), - self.sfh5["/1.2/instrument/mca_0/"].keys()) - - self.assertEqual(self.sfh5["/1.2/measurement/mca_0/info/preset_time"], - self.sfh5["/1.2/instrument/mca_0/preset_time"]) - self.assertEqual(self.sfh5["/1.2/measurement/mca_0/info/live_time"], - self.sfh5["/1.2/instrument/mca_0/live_time"]) - self.assertEqual(self.sfh5["/1.2/measurement/mca_0/info/elapsed_time"], - self.sfh5["/1.2/instrument/mca_0/elapsed_time"]) - - def testListScanIndices(self): - self.assertEqual(list(self.sfh5.keys()), - ["1.1", "25.1", "1.2", "1000.1", "1001.1"]) - self.assertEqual(self.sfh5["1.2"].attrs, - {"NX_class": "NXentry", }) - - def testMcaAbsent(self): - def access_absent_mca(): - """This must raise a KeyError, because scan 1.1 has no MCA""" - return self.sfh5["/1.1/measurement/mca_0/"] - self.assertRaises(KeyError, access_absent_mca) - - def testMcaCalib(self): - mca0_calib = self.sfh5["/1.2/measurement/mca_0/info/calibration"] - mca1_calib = self.sfh5["/1.2/measurement/mca_1/info/calibration"] - self.assertEqual(mca0_calib.tolist(), - [1, 2, 3]) - # calibration is unique in this scan and applies to all analysers - self.assertEqual(mca0_calib.tolist(), - mca1_calib.tolist()) - - def testMcaChannels(self): - mca0_chann = self.sfh5["/1.2/measurement/mca_0/info/channels"] - mca1_chann = self.sfh5["/1.2/measurement/mca_1/info/channels"] - self.assertEqual(mca0_chann.tolist(), - [0, 1, 2]) - self.assertEqual(mca0_chann.tolist(), - mca1_chann.tolist()) - - def testMcaCtime(self): - """Tests for #@CTIME mca header""" - datasets = ["preset_time", "live_time", "elapsed_time"] - for ds in datasets: - self.assertNotIn("/1.1/instrument/mca_0/" + ds, self.sfh5) - self.assertIn("/1.2/instrument/mca_0/" + ds, self.sfh5) - - mca0_preset_time = self.sfh5["/1.2/instrument/mca_0/preset_time"] - mca1_preset_time = self.sfh5["/1.2/instrument/mca_1/preset_time"] - self.assertLess(mca0_preset_time - 123.4, - 10**-5) - # ctime is unique in a this scan and applies to all analysers - self.assertEqual(mca0_preset_time, - mca1_preset_time) - - mca0_live_time = self.sfh5["/1.2/instrument/mca_0/live_time"] - mca1_live_time = self.sfh5["/1.2/instrument/mca_1/live_time"] - self.assertLess(mca0_live_time - 234.5, - 10**-5) - self.assertEqual(mca0_live_time, - mca1_live_time) - - mca0_elapsed_time = self.sfh5["/1.2/instrument/mca_0/elapsed_time"] - mca1_elapsed_time = self.sfh5["/1.2/instrument/mca_1/elapsed_time"] - self.assertLess(mca0_elapsed_time - 345.6, - 10**-5) - self.assertEqual(mca0_elapsed_time, - mca1_elapsed_time) - - def testMcaData(self): - # sum 1st MCA in scan 1.2 over rows - mca_0_data = self.sfh5["/1.2/measurement/mca_0/data"] - for summed_row, expected in zip(mca_0_data.sum(axis=1).tolist(), - [3.0, 12.1, 21.7]): - self.assertAlmostEqual(summed_row, expected, places=4) - - # sum 3rd MCA in scan 1.2 along both axis - mca_2_data = self.sfh5["1.2"]["measurement"]["mca_2"]["data"] - self.assertAlmostEqual(sum(sum(mca_2_data)), 9.1, places=5) - # attrs - self.assertEqual(mca_0_data.attrs, {"interpretation": "spectrum"}) - - def testMotorPosition(self): - positioners_group = self.sfh5["/1.1/instrument/positioners"] - # MRTSlit DOWN position is defined in #P0 san header line - self.assertAlmostEqual(float(positioners_group["MRTSlit DOWN"]), - 0.87125) - # MRTSlit UP position is defined in first data column - for a, b in zip(positioners_group["MRTSlit UP"].tolist(), - [-1.23, 8.478100E+01, 3.14, 1.2]): - self.assertAlmostEqual(float(a), b, places=4) - - def testNumberMcaAnalysers(self): - """Scan 1.2 has 2 data columns + 3 mca spectra per data line.""" - self.assertEqual(len(self.sfh5["1.2"]["measurement"]), 5) - - def testTitle(self): - self.assertEqual(self.sfh5["/25.1/title"], - u"ascan c3th 1.33245 1.52245 40 0.15") - - def testValues(self): - group = self.sfh5["/25.1"] - self.assertTrue(hasattr(group, "values")) - self.assertTrue(callable(group.values)) - self.assertIn(self.sfh5["/25.1/title"], - self.sfh5["/25.1"].values()) - - # visit and visititems ignore links - def testVisit(self): - name_list = [] - self.sfh5.visit(name_list.append) - self.assertIn('1.2/instrument/positioners/Pslit HGap', name_list) - self.assertIn("1.2/instrument/specfile/scan_header", name_list) - self.assertEqual(len(name_list), 117) - - # test also visit of a subgroup, with various group name formats - name_list_leading_and_trailing_slash = [] - self.sfh5['/1.2/instrument/'].visit(name_list_leading_and_trailing_slash.append) - name_list_leading_slash = [] - self.sfh5['/1.2/instrument'].visit(name_list_leading_slash.append) - name_list_trailing_slash = [] - self.sfh5['1.2/instrument/'].visit(name_list_trailing_slash.append) - name_list_no_slash = [] - self.sfh5['1.2/instrument'].visit(name_list_no_slash.append) - - # no differences expected in the output names - self.assertEqual(name_list_leading_and_trailing_slash, - name_list_leading_slash) - self.assertEqual(name_list_leading_slash, - name_list_trailing_slash) - self.assertEqual(name_list_leading_slash, - name_list_no_slash) - self.assertIn("positioners/Pslit HGap", name_list_no_slash) - self.assertIn("positioners", name_list_no_slash) - - def testVisitItems(self): - dataset_name_list = [] - - def func_generator(l): - """return a function appending names to list l""" - def func(name, obj): - if isinstance(obj, SpecH5Dataset): - l.append(name) - return func - - self.sfh5.visititems(func_generator(dataset_name_list)) - self.assertIn('1.2/instrument/positioners/Pslit HGap', dataset_name_list) - self.assertEqual(len(dataset_name_list), 85) - - # test also visit of a subgroup, with various group name formats - name_list_leading_and_trailing_slash = [] - self.sfh5['/1.2/instrument/'].visititems(func_generator(name_list_leading_and_trailing_slash)) - name_list_leading_slash = [] - self.sfh5['/1.2/instrument'].visititems(func_generator(name_list_leading_slash)) - name_list_trailing_slash = [] - self.sfh5['1.2/instrument/'].visititems(func_generator(name_list_trailing_slash)) - name_list_no_slash = [] - self.sfh5['1.2/instrument'].visititems(func_generator(name_list_no_slash)) - - # no differences expected in the output names - self.assertEqual(name_list_leading_and_trailing_slash, - name_list_leading_slash) - self.assertEqual(name_list_leading_slash, - name_list_trailing_slash) - self.assertEqual(name_list_leading_slash, - name_list_no_slash) - self.assertIn("positioners/Pslit HGap", name_list_no_slash) - - def testNotSpecH5(self): - fd, fname = tempfile.mkstemp() - os.write(fd, b"Not a spec file!") - os.close(fd) - self.assertRaises(specfile.SfErrFileOpen, SpecH5, fname) - self.assertRaises(IOError, SpecH5, fname) - os.unlink(fname) - - def testSample(self): - self.assertNotIn("sample", self.sfh5["/1.1"]) - self.assertIn("sample", self.sfh5["/1000.1"]) - self.assertIn("ub_matrix", self.sfh5["/1000.1/sample"]) - self.assertIn("unit_cell", self.sfh5["/1000.1/sample"]) - self.assertIn("unit_cell_abc", self.sfh5["/1000.1/sample"]) - self.assertIn("unit_cell_alphabetagamma", self.sfh5["/1000.1/sample"]) - - # All 0 values - self.assertNotIn("sample", self.sfh5["/1001.1"]) - with self.assertRaises(KeyError): - self.sfh5["/1001.1/sample/unit_cell"] - - @testutils.test_logging(spech5.logger1.name, warning=2) - def testOpenFileDescriptor(self): - """Open a SpecH5 file from a file descriptor""" - with io.open(self.sfh5.filename) as f: - sfh5 = SpecH5(f) - self.assertIsNotNone(sfh5) - name_list = [] - # check if the object is working - self.sfh5.visit(name_list.append) - sfh5.close() - - -sftext_multi_mca_headers = """ -#S 1 aaaaaa -#@MCA %16C -#@CHANN 3 0 2 1 -#@CALIB 1 2 3 -#@CTIME 123.4 234.5 345.6 -#@MCA %16C -#@CHANN 3 1 3 1 -#@CALIB 5.5 6.6 7.7 -#@CTIME 10 11 12 -#N 3 -#L uno duo -1 2 -@A 0 1 2 -@A 10 9 8 -3 4 -@A 3.1 4 5 -@A 7 6 5 -5 6 -@A 6 7.7 8 -@A 4 3 2 - -""" - - -class TestSpecH5MultiMca(unittest.TestCase): - @classmethod - def setUpClass(cls): - fd, cls.fname = tempfile.mkstemp(text=False) - if sys.version_info < (3, ): - os.write(fd, sftext_multi_mca_headers) - else: - os.write(fd, bytes(sftext_multi_mca_headers, 'ascii')) - os.close(fd) - - @classmethod - def tearDownClass(cls): - os.unlink(cls.fname) - - def setUp(self): - self.sfh5 = SpecH5(self.fname) - - def tearDown(self): - self.sfh5.close() - - def testMcaCalib(self): - mca0_calib = self.sfh5["/1.1/measurement/mca_0/info/calibration"] - mca1_calib = self.sfh5["/1.1/measurement/mca_1/info/calibration"] - self.assertEqual(mca0_calib.tolist(), - [1, 2, 3]) - self.assertAlmostEqual(sum(mca1_calib.tolist()), - sum([5.5, 6.6, 7.7]), - places=5) - - def testMcaChannels(self): - mca0_chann = self.sfh5["/1.1/measurement/mca_0/info/channels"] - mca1_chann = self.sfh5["/1.1/measurement/mca_1/info/channels"] - self.assertEqual(mca0_chann.tolist(), - [0., 1., 2.]) - # @CHANN is unique in this scan and applies to all analysers - self.assertEqual(mca1_chann.tolist(), - [1., 2., 3.]) - - def testMcaCtime(self): - """Tests for #@CTIME mca header""" - mca0_preset_time = self.sfh5["/1.1/instrument/mca_0/preset_time"] - mca1_preset_time = self.sfh5["/1.1/instrument/mca_1/preset_time"] - self.assertLess(mca0_preset_time - 123.4, - 10**-5) - self.assertLess(mca1_preset_time - 10, - 10**-5) - - mca0_live_time = self.sfh5["/1.1/instrument/mca_0/live_time"] - mca1_live_time = self.sfh5["/1.1/instrument/mca_1/live_time"] - self.assertLess(mca0_live_time - 234.5, - 10**-5) - self.assertLess(mca1_live_time - 11, - 10**-5) - - mca0_elapsed_time = self.sfh5["/1.1/instrument/mca_0/elapsed_time"] - mca1_elapsed_time = self.sfh5["/1.1/instrument/mca_1/elapsed_time"] - self.assertLess(mca0_elapsed_time - 345.6, - 10**-5) - self.assertLess(mca1_elapsed_time - 12, - 10**-5) - - -sftext_no_cols = r"""#F C:/DATA\test.mca -#D Thu Jul 7 08:40:19 2016 - -#S 1 31oct98.dat 22.1 If4 -#D Thu Jul 7 08:40:19 2016 -#C no data cols, one mca analyser, single spectrum -#@MCA %16C -#@CHANN 151 0 150 1 -#@CALIB 0 2 0 -@A 789 784 788 814 847 862 880 904 925 955 987 1015 1031 1070 1111 1139 \ -1203 1236 1290 1392 1492 1558 1688 1813 1977 2119 2346 2699 3121 3542 4102 4970 \ -6071 7611 10426 16188 28266 40348 50539 55555 56162 54162 47102 35718 24588 17034 12994 11444 \ -11808 13461 15687 18885 23827 31578 41999 49556 58084 59415 59456 55698 44525 28219 17680 12881 \ -9518 7415 6155 5246 4646 3978 3612 3299 3020 2761 2670 2472 2500 2310 2286 2106 \ -1989 1890 1782 1655 1421 1293 1135 990 879 757 672 618 532 488 445 424 \ -414 373 351 325 307 284 270 247 228 213 199 187 183 176 164 156 \ -153 140 142 130 118 118 103 101 97 86 90 86 87 81 75 82 \ -80 76 77 75 76 77 62 69 74 60 65 68 65 58 63 64 \ -63 59 60 56 57 60 55 - -#S 2 31oct98.dat 22.1 If4 -#D Thu Jul 7 08:40:19 2016 -#C no data cols, one mca analyser, multiple spectra -#@MCA %16C -#@CHANN 3 0 2 1 -#@CALIB 1 2 3 -#@CTIME 123.4 234.5 345.6 -@A 0 1 2 -@A 10 9 8 -@A 1 1 1.1 -@A 3.1 4 5 -@A 7 6 5 -@A 1 1 1 -@A 6 7.7 8 -@A 4 3 2 -@A 1 1 1 - -#S 3 31oct98.dat 22.1 If4 -#D Thu Jul 7 08:40:19 2016 -#C no data cols, 3 mca analysers, multiple spectra -#@MCADEV 1 -#@MCA %16C -#@CHANN 3 0 2 1 -#@CALIB 1 2 3 -#@CTIME 123.4 234.5 345.6 -#@MCADEV 2 -#@MCA %16C -#@CHANN 3 0 2 1 -#@CALIB 1 2 3 -#@CTIME 123.4 234.5 345.6 -#@MCADEV 3 -#@MCA %16C -#@CHANN 3 0 2 1 -#@CALIB 1 2 3 -#@CTIME 123.4 234.5 345.6 -@A 0 1 2 -@A 10 9 8 -@A 1 1 1.1 -@A 3.1 4 5 -@A 7 6 5 -@A 1 1 1 -@A 6 7.7 8 -@A 4 3 2 -@A 1 1 1 -""" - - -class TestSpecH5NoDataCols(unittest.TestCase): - """Test reading SPEC files with only MCA data""" - @classmethod - def setUpClass(cls): - fd, cls.fname = tempfile.mkstemp() - if sys.version_info < (3, ): - os.write(fd, sftext_no_cols) - else: - os.write(fd, bytes(sftext_no_cols, 'ascii')) - os.close(fd) - - @classmethod - def tearDownClass(cls): - os.unlink(cls.fname) - - def setUp(self): - self.sfh5 = SpecH5(self.fname) - - def tearDown(self): - self.sfh5.close() - - def testScan1(self): - # 1.1: single analyser, single spectrum, 151 channels - self.assertIn("mca_0", - self.sfh5["1.1/instrument/"]) - self.assertEqual(self.sfh5["1.1/instrument/mca_0/data"].shape, - (1, 151)) - self.assertNotIn("mca_1", - self.sfh5["1.1/instrument/"]) - - def testScan2(self): - # 2.1: single analyser, 9 spectra, 3 channels - self.assertIn("mca_0", - self.sfh5["2.1/instrument/"]) - self.assertEqual(self.sfh5["2.1/instrument/mca_0/data"].shape, - (9, 3)) - self.assertNotIn("mca_1", - self.sfh5["2.1/instrument/"]) - - def testScan3(self): - # 3.1: 3 analysers, 3 spectra/analyser, 3 channels - for i in range(3): - self.assertIn("mca_%d" % i, - self.sfh5["3.1/instrument/"]) - self.assertEqual( - self.sfh5["3.1/instrument/mca_%d/data" % i].shape, - (3, 3)) - - self.assertNotIn("mca_3", - self.sfh5["3.1/instrument/"]) - - -sf_text_slash = r"""#F /data/id09/archive/logspecfiles/laue/2016/scan_231_laue_16-11-29.dat -#D Sat Dec 10 22:20:59 2016 -#O0 Pslit/HGap MRTSlit%UP - -#S 1 laue_16-11-29.log 231.1 PD3/A -#D Sat Dec 10 22:20:59 2016 -#P0 180.005 -0.66875 -#N 2 -#L GONY/mm PD3%A --2.015 5.250424e-05 --2.01 5.30798e-05 --2.005 5.281903e-05 --2 5.220436e-05 -""" - - -class TestSpecH5SlashInLabels(unittest.TestCase): - """Test reading SPEC files with labels containing a / character - - The / character must be substituted with a % - """ - @classmethod - def setUpClass(cls): - fd, cls.fname = tempfile.mkstemp() - if sys.version_info < (3, ): - os.write(fd, sf_text_slash) - else: - os.write(fd, bytes(sf_text_slash, 'ascii')) - os.close(fd) - - @classmethod - def tearDownClass(cls): - os.unlink(cls.fname) - - def setUp(self): - self.sfh5 = SpecH5(self.fname) - - def tearDown(self): - self.sfh5.close() - - def testLabels(self): - """Ensure `/` is substituted with `%` and - ensure legitimate `%` in names are still working""" - self.assertEqual(list(self.sfh5["1.1/measurement/"].keys()), - ["GONY%mm", "PD3%A"]) - - # substituted "%" - self.assertIn("GONY%mm", - self.sfh5["1.1/measurement/"]) - self.assertNotIn("GONY/mm", - self.sfh5["1.1/measurement/"]) - self.assertAlmostEqual(self.sfh5["1.1/measurement/GONY%mm"][0], - -2.015, places=4) - # legitimate "%" - self.assertIn("PD3%A", - self.sfh5["1.1/measurement/"]) - - def testMotors(self): - """Ensure `/` is substituted with `%` and - ensure legitimate `%` in names are still working""" - self.assertEqual(list(self.sfh5["1.1/instrument/positioners"].keys()), - ["Pslit%HGap", "MRTSlit%UP"]) - # substituted "%" - self.assertIn("Pslit%HGap", - self.sfh5["1.1/instrument/positioners"]) - self.assertNotIn("Pslit/HGap", - self.sfh5["1.1/instrument/positioners"]) - self.assertAlmostEqual( - self.sfh5["1.1/instrument/positioners/Pslit%HGap"], - 180.005, places=4) - # legitimate "%" - self.assertIn("MRTSlit%UP", - self.sfh5["1.1/instrument/positioners"]) - - -def suite(): - test_suite = unittest.TestSuite() - test_suite.addTest( - unittest.defaultTestLoader.loadTestsFromTestCase(TestSpecH5)) - test_suite.addTest( - unittest.defaultTestLoader.loadTestsFromTestCase(TestSpecDate)) - test_suite.addTest( - unittest.defaultTestLoader.loadTestsFromTestCase(TestSpecH5MultiMca)) - test_suite.addTest( - unittest.defaultTestLoader.loadTestsFromTestCase(TestSpecH5NoDataCols)) - test_suite.addTest( - unittest.defaultTestLoader.loadTestsFromTestCase(TestSpecH5SlashInLabels)) - return test_suite - - -if __name__ == '__main__': - unittest.main(defaultTest="suite") |