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Diffstat (limited to 'src/silx/io/test/test_spectoh5.py')
| -rw-r--r-- | src/silx/io/test/test_spectoh5.py | 183 |
1 files changed, 183 insertions, 0 deletions
diff --git a/src/silx/io/test/test_spectoh5.py b/src/silx/io/test/test_spectoh5.py new file mode 100644 index 0000000..66bf8d6 --- /dev/null +++ b/src/silx/io/test/test_spectoh5.py @@ -0,0 +1,183 @@ +# 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 to HDF5 converter""" + +from numpy import array_equal +import os +import sys +import tempfile +import unittest + +import h5py + +from ..spech5 import SpecH5, SpecH5Group +from ..convert import convert, write_to_h5 +from ..utils import h5py_read_dataset + +__authors__ = ["P. Knobel"] +__license__ = "MIT" +__date__ = "12/02/2018" + + +sfdata = b"""#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 1 aaaaaa +#D Thu Feb 11 10:00:32 2016 +#@MCADEV 1 +#@MCA %16C +#@CHANN 3 0 2 1 +#@CALIB 1 2 3 +#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 TestConvertSpecHDF5(unittest.TestCase): + @classmethod + def setUpClass(cls): + fd, cls.spec_fname = tempfile.mkstemp(prefix="TestConvertSpecHDF5") + os.write(fd, sfdata) + os.close(fd) + + fd, cls.h5_fname = tempfile.mkstemp(prefix="TestConvertSpecHDF5") + # Close and delete (we just need the name) + os.close(fd) + os.unlink(cls.h5_fname) + + @classmethod + def tearDownClass(cls): + os.unlink(cls.spec_fname) + + def setUp(self): + convert(self.spec_fname, self.h5_fname) + + self.sfh5 = SpecH5(self.spec_fname) + self.h5f = h5py.File(self.h5_fname, "a") + + def tearDown(self): + self.h5f.close() + self.sfh5.close() + os.unlink(self.h5_fname) + + def testAppendToHDF5(self): + write_to_h5(self.sfh5, self.h5f, h5path="/foo/bar/spam") + self.assertTrue( + array_equal(self.h5f["/1.2/measurement/mca_1/data"], + self.h5f["/foo/bar/spam/1.2/measurement/mca_1/data"]) + ) + + def testWriteSpecH5Group(self): + """Test passing a SpecH5Group as parameter, instead of a Spec filename + or a SpecH5.""" + g = self.sfh5["1.1/instrument"] + self.assertIsInstance(g, SpecH5Group) # let's be paranoid + write_to_h5(g, self.h5f, h5path="my instruments") + + self.assertAlmostEqual(self.h5f["my instruments/positioners/Sslit1 HOff"][tuple()], + 16.197579, places=4) + + def testTitle(self): + """Test the value of a dataset""" + title12 = h5py_read_dataset(self.h5f["/1.2/title"]) + self.assertEqual(title12, + u"aaaaaa") + + def testAttrs(self): + # Test root group (file) attributes + self.assertEqual(self.h5f.attrs["NX_class"], + u"NXroot") + # Test dataset attributes + ds = self.h5f["/1.2/instrument/mca_1/data"] + self.assertTrue("interpretation" in ds.attrs) + self.assertEqual(list(ds.attrs.values()), + [u"spectrum"]) + # Test group attributes + grp = self.h5f["1.1"] + self.assertEqual(grp.attrs["NX_class"], + u"NXentry") + self.assertEqual(len(list(grp.attrs.keys())), + 1) + + def testHdf5HasSameMembers(self): + spec_member_list = [] + + def append_spec_members(name): + spec_member_list.append(name) + self.sfh5.visit(append_spec_members) + + hdf5_member_list = [] + + def append_hdf5_members(name): + hdf5_member_list.append(name) + self.h5f.visit(append_hdf5_members) + + # 1. For some reason, h5py visit method doesn't include the leading + # "/" character when it passes the member name to the function, + # even though an explicit the .name attribute of a member will + # have a leading "/" + spec_member_list = [m.lstrip("/") for m in spec_member_list] + + self.assertEqual(set(hdf5_member_list), + set(spec_member_list)) + + def testLinks(self): + self.assertTrue( + array_equal(self.sfh5["/1.2/measurement/mca_0/data"], + self.h5f["/1.2/measurement/mca_0/data"]) + ) + self.assertTrue( + array_equal(self.h5f["/1.2/instrument/mca_1/channels"], + self.h5f["/1.2/measurement/mca_1/info/channels"]) + ) |