def testWriter(self):
'''test the writer.Writer class'''
spec_data = spec.SpecDataFile(self.fname)
out = writer.Writer(spec_data)
scan_list = [1, 5, 7]
out.save(self.hname, scan_list)
dd = out.root_attributes()
self.assertTrue(isinstance(dd, dict))
# TODO: test writer's various functions and methods
# test file written by Writer
with h5py.File(self.hname, "r") as hp:
root = hp["/"]
default = root.attrs.get("default")
self.assertNotEqual(default, None)
self.assertTrue(default in root)
nxentry = root[default]
default = nxentry.attrs.get("default")
self.assertNotEqual(default, None)
self.assertTrue(default in nxentry)
nxdata = nxentry[default]
signal = nxdata.attrs.get("signal")
self.assertNotEqual(signal, None)
self.assertTrue(signal in nxdata)
def test_geometry_plugin(self):
fname = os.path.join(_path, "spec2nexus", 'data', '33bm_spec.dat')
scan_number = 17
sdf = spec.SpecDataFile(fname)
scan = sdf.getScan(scan_number)
self.assertEqual(scan.diffractometer.geometry_name_full,
"fourc.default")
self.assertEqual(scan.diffractometer.mode, "Omega equals zero")
self.assertEqual(scan.diffractometer.sector, 0)
self.assertIsNotNone(scan.diffractometer.lattice)
self.assertEqual(len(scan.diffractometer.reflections), 2)
out = writer.Writer(sdf)
out.save(self.hname, [scan_number])
with h5py.File(self.hname, "r") as hp:
nxentry = hp["/S17"]
group = nxentry["instrument/geometry_parameters"]
self.assertIn("instrument/name", nxentry)
self.assertEqual(nxentry["instrument/name"][0],
scan.diffractometer.geometry_name_full.encode())
self.assertIn("diffractometer_simple", group)
self.assertEqual(group["diffractometer_simple"][0], b"fourc")
self.assertIn("diffractometer_full", group)
self.assertEqual(group["diffractometer_full"][0], b"fourc.default")
self.assertIn("diffractometer_variant", group)
self.assertEqual(group["diffractometer_variant"][0], b"default")
for k in "g_aa g_bb g_cc g_al g_be g_ga LAMBDA".split():
self.assertIn(k, group)
v = group[k][()][0]
self.assertGreater(v, 0)
self.assertIn("sample/unit_cell_abc", nxentry)
self.assertIn("sample/unit_cell_alphabetagamma", nxentry)
self.assertIn("sample/unit_cell", nxentry)
self.assertIn("sample/ub_matrix", nxentry)
ds = nxentry["sample/ub_matrix"]
self.assertTupleEqual(ds.shape, (3, 3))
self.assertIn("sample/or0", nxentry)
self.assertIn("sample/or0/h", nxentry)
self.assertIn("sample/or0/k", nxentry)
self.assertIn("sample/or0/l", nxentry)
self.assertIn("sample/or1", nxentry)
self.assertIn("sample/or1/h", nxentry)
self.assertIn("sample/or1/k", nxentry)
self.assertIn("sample/or1/l", nxentry)
self.assertIn("instrument/monochromator/wavelength", nxentry)
self.assertIn("sample/beam/incident_wavelength", nxentry)
self.assertEqual(
nxentry["instrument/monochromator/wavelength"],
nxentry["sample/beam/incident_wavelength"],
)
def test_contents(self):
spec_data = SpecDataFile(self.fname)
self.assertTrue(isinstance(spec_data, SpecDataFile))
out = writer.Writer(spec_data)
scan_list = [
1,
]
out.save(self.hname, scan_list)
# text that UXML group defined as expected
self.assertTrue(os.path.exists(self.hname))
with h5py.File(self.hname) as h5_file:
self.assertTrue("S1" in h5_file)
nxentry = h5_file["/S1"]
self.assertTrue("UXML" in nxentry)
uxml = nxentry["UXML"]
self.assertTrue("NX_class" in uxml.attrs)
self.assertEqual(uxml.attrs["NX_class"], "NXnote")
# spot-check a couple items
# group: attenuator_set
self.assertTrue("attenuator_set" in uxml)
group = uxml["attenuator_set"]
prefix = group.attrs.get("prefix")
description = group.attrs.get("description")
unique_id = group.attrs.get("unique_id")
self.assertEqual(prefix, "33idd:filter:")
self.assertEqual(description, "33-ID-D Filters")
self.assertEqual(unique_id, None)
# <dataset name="corrdet_counter">corrdet</dataset>
self.assertTrue("corrdet_counter" in group)
ds = group["corrdet_counter"]
# http://docs.h5py.org/en/stable/whatsnew/2.1.html?highlight=dataset#dataset-value-property-is-now-deprecated
value = ds[()] # ds.value deprecated in h5py
self.assertEqual(value, [b"corrdet"])
# <dataset name="wait_time" type="float" units="s">0.500</dataset>
self.assertTrue("wait_time" in group)
ds = group["wait_time"]
attrs = dict(ds.attrs)
self.assertEqual(ds.attrs.get("units"), "s")
value = ds[()] # ds.value deprecated in h5py
self.assertEqual(value, numpy.array([.5]))
# <hardlink name="attenuator1" target_id="33idd:filter:Fi1:"/>
self.assertTrue("attenuator1" in group)
attenuator1 = group["attenuator1"]
target = attenuator1.attrs.get("target")
self.assertNotEqual(target, attenuator1.name)
self.assertEqual(target, uxml["attenuator1"].name)
addr = "/S1/UXML/ad_file_info/file_format"
self.assertTrue(addr in h5_file)
ds = h5_file[addr]
value = ds[()] # ds.value deprecated in h5py
self.assertEqual(value, [b"TIFF"])
def testWriter(self):
'''test the writer.Writer class'''
spec_data = spec.SpecDataFile(self.fname)
out = writer.Writer(spec_data)
scan_list = [1, 5, 7]
out.save(self.hname, scan_list)
# TODO: make tests of other things in the Writer
dd = out.root_attributes()
self.assertTrue(isinstance(dd, dict))
def test_the_data_file(self):
'''
write all as HDF5: 1-D scans, USAXS scans, Fly scans, #O+#o and #J+#j control lines
'''
prefix = os.path.abspath(
os.path.join(_path, 'spec2nexus', 'data', '03_06_JanTest'))
file1 = prefix + '.dat'
hfile = tests.common.create_test_file()
# writer interface has changed, must use new spec module to proceed
specfile = spec.SpecDataFile(file1)
self.assertTrue(isinstance(specfile, spec2nexus.spec.SpecDataFile),
file1)
specwriter = writer.Writer(specfile)
self.assertTrue(isinstance(specwriter, spec2nexus.writer.Writer),
file1)
specwriter.save(hfile, sorted(specfile.getScanNumbers()))
self.assertTrue(os.path.exists(hfile))
def subgroup_list(parent, nxclass):
children = []
for item in sorted(parent):
obj = parent[item]
if isinstance(obj, h5py.Group):
if obj.attrs.get('NX_class', '') == nxclass:
children.append(obj)
return children
fp = h5py.File(hfile, 'r')
self.assertTrue(isinstance(fp, h5py.File), hfile)
nxentry_groups = subgroup_list(fp, 'NXentry')
self.assertGreater(len(nxentry_groups), 0)
for nxentry in nxentry_groups:
nxdata_groups = subgroup_list(nxentry, 'NXdata')
self.assertGreater(len(nxdata_groups), 0)
for nxdata in nxdata_groups:
signal = nxdata.attrs.get('signal')
self.assertTrue(signal in nxdata)
default = fp.attrs.get('default')
self.assertTrue(default in fp)
nxentry = fp[default]
default = nxentry.attrs.get('default')
self.assertTrue(default in nxentry)
nxdata = nxentry[default]
signal = nxdata.attrs.get('signal')
self.assertTrue(signal in nxdata)
fp.close()
os.remove(hfile)
self.assertFalse(os.path.exists(hfile))
def test_the_data_file(self):
'''
look for the metadata
'''
prefix = os.path.abspath(
os.path.join(_path, 'spec2nexus', 'data',
'usaxs-bluesky-specwritercallback'))
file1 = prefix + '.dat'
hfile = tests.common.create_test_file()
# writer interface has changed, must use new spec module to proceed
specfile = spec.SpecDataFile(file1)
self.assertTrue(isinstance(specfile, spec2nexus.spec.SpecDataFile),
file1)
for scan_num, scan in specfile.scans.items():
msg = "Scan %s MD test" % scan_num
scan.interpret() # force lazy-loader to parse this scan
self.assertTrue(hasattr(scan, "MD"), msg)
self.assertTrue(isinstance(scan.MD, OrderedDict), msg)
self.assertGreater(len(scan.MD), 0, msg)
# test the metadata in a NeXus file
specwriter = writer.Writer(specfile)
self.assertTrue(isinstance(specwriter, spec2nexus.writer.Writer),
file1)
specwriter.save(hfile, sorted(specfile.getScanNumbers()))
self.assertTrue(os.path.exists(hfile))
def subgroup_list(parent, nxclass):
children = []
for item in sorted(parent):
obj = parent[item]
if isinstance(obj, h5py.Group):
if obj.attrs.get('NX_class', '') == nxclass:
children.append(obj)
return children
fp = h5py.File(hfile, 'r')
for nxentry in subgroup_list(fp, 'NXentry'):
# nxinstrument_groups = subgroup_list(nxentry, 'NXinstrument')
# self.assertEqual(len(nxinstrument_groups), 1)
# nxinstrument = nxinstrument_groups[0]
nxcollection_groups = subgroup_list(nxentry, 'NXcollection')
self.assertGreater(len(nxcollection_groups), 0)
md_group = nxentry.get("bluesky_metadata")
self.assertIsNotNone(md_group, "bluesky_metadata in NeXus file")
fp.close()
os.remove(hfile)
self.assertFalse(os.path.exists(hfile))
def testName(self):
spec_data = SpecDataFile(self.fname)
self.assertTrue(isinstance(spec_data, SpecDataFile))
out = writer.Writer(spec_data)
scan_list = [
1,
]
out.save(self.hname, scan_list)
# TODO: make tests of other things in the Writer
dd = out.root_attributes()
self.assertTrue(isinstance(dd, dict))
def test_data_file(self):
self.assertTrue(os.path.exists(self.testfile))
specfile = spec2nexus.spec.SpecDataFile(self.testfile)
scanNum = 1
scan = specfile.getScan(scanNum)
# issue #137 & #140
try:
u = scan.__getattribute__("U")
except AttributeError:
u = None
self.assertNotEqual(u, None, "U attribute lazy loaded")
# not needed: scan.interpret()
self.assertTrue(hasattr(scan, "U"), "#U in scan #1")
self.assertEqual(len(scan.U), 1, "only one #U in scan #1")
self.assertTrue(hasattr(scan.header, "U"), "#U in scan header")
self.assertEqual(len(scan.header.U), 1, "only one #U in header")
# test for UserReserved in a NeXus file
specwriter = writer.Writer(specfile)
specwriter.save(self.hfile, "1 2 3 4 5".split())
self.assertTrue(os.path.exists(self.hfile))
fp = h5py.File(self.hfile, 'r')
entry = fp.get("/S1")
self.assertIsNot(entry, None, "group /S1")
u = entry.get("UserReserved")
self.assertNotEqual(u, None, "group /S1/UserReserved")
self.assertNotEqual(u.get("header_1"), None,
"dataset /S1/UserReserved/header_1")
self.assertEqual(u.get("header_2"), None,
"dataset /S1/UserReserved/header_2")
self.assertNotEqual(u.get("item_1"), None,
"dataset /S1/UserReserved/item_1")
self.assertEqual(u.get("item_2"), None,
"dataset /S1/UserReserved/item_2")
entry = fp.get("/S2")
self.assertIsNot(entry, None, "group /S2")
u = entry.get("UserReserved")
self.assertNotEqual(u, None, "group /S2/UserReserved")
self.assertNotEqual(u.get("header_1"), None,
"dataset /S1/UserReserved/header_1")
self.assertEqual(u.get("header_2"), None,
"dataset /S1/UserReserved/header_2")
self.assertEqual(u.get("item_1"), None,
"dataset /S1/UserReserved/item_1")
self.assertEqual(u.get("item_2"), None,
"dataset /S1/UserReserved/item_2")
fp.close()
def test_save_data_hklmesh(self):
#S 17 hklmesh H 1.9 2.1 100 K 1.9 2.1 100 -800000
fname = os.path.join(_path, "spec2nexus", 'data', '33bm_spec.dat')
hname = "test.h5"
spec_data = spec.SpecDataFile(fname)
out = writer.Writer(spec_data)
out.save(hname, [17])
with h5py.File(hname, "r") as hp:
root = hp["/"]
nxdata = root["/S17/data"]
signal = nxdata.attrs["signal"]
axes = nxdata.attrs["axes"]
self.assertEqual(axes[0], b"H")
self.assertEqual(axes[1], b"K")
def test_save_data_lscan(self):
# hklscan moving L
test_file = '33bm_spec.dat'
scan_number = 14
fname = os.path.join(_path, "spec2nexus", 'data', test_file)
hname = "test.h5"
spec_data = spec.SpecDataFile(fname)
out = writer.Writer(spec_data)
out.save(hname, [scan_number])
with h5py.File(hname, "r") as hp:
root = hp["/"]
nxdata = root["/S%d/data" % scan_number]
signal = nxdata.attrs["signal"]
axes = nxdata.attrs["axes"]
self.assertEqual(signal, "signal")
self.assertEqual(axes, "L")
def test_save_data_mesh(self):
#S 22 mesh eta 57 57.1 10 chi 90.9 91 10 1
fname = os.path.join(_path, "spec2nexus", 'data', '33id_spec.dat')
hname = "test.h5"
spec_data = spec.SpecDataFile(fname)
out = writer.Writer(spec_data)
out.save(hname, [22])
with h5py.File(hname, "r") as hp:
root = hp["/"]
nxdata = root["/S22/data"]
signal = nxdata.attrs["signal"]
self.assertEqual(nxdata[signal][()].shape, (11, 11))
ds = nxdata["_mca_"]
self.assertEqual(ds[()].shape, (11, 11, 91))
self.assertEqual(ds.attrs["axes"], "eta:chi:_mca_channel_")
self.assertEqual(ds.attrs["spec_name"], "_mca_")
self.assertEqual(ds.attrs["units"], "counts")
def test_contents(self):
spec_data = SpecDataFile(self.fname)
self.assertTrue(isinstance(spec_data, SpecDataFile))
out = writer.Writer(spec_data)
scan_list = [
1,
]
out.save(self.hname, scan_list)
# the ONLY structural difference between test_3.spec
# and test_4.spec is the presence of this hardlink
self.assertTrue(os.path.exists(self.hname))
with h5py.File(self.hname) as h5_file:
source = h5_file["/S1/UXML/ad_detector/beam_center_x"]
link = h5_file["/S1/UXML/beam_center_x"]
target = source.attrs.get("target")
self.assertNotEqual(source.name, link.name)
self.assertNotEqual(target, None)
self.assertEqual(target, source.name)
self.assertEqual(target, link.attrs.get("target"))
"""Process specific data file(s)"""
# TODO: fold into the unit test suite
import os
import sys
sys.path.insert(0, os.path.abspath("../src"))
from spec2nexus import writer
from spec2nexus import spec
if __name__ == '__main__':
pwd = os.path.abspath(os.path.join("..", "src", "spec2nexus"))
prefix = os.path.abspath(os.path.join(pwd, 'data', 'APS_spec_data'))
# file1 = prefix + '.dat'
hfile = prefix + '.hdf5'
# # lmn40.spe has two header sections, 2nd is just before "#S 8"
# prefix = os.path.abspath(os.path.join(pwd, 'data', 'lmn40'))
# file1 = prefix + '.spe'
# CdOsO has four header sections and two #S 1 scans
prefix = os.path.abspath(os.path.join(pwd, 'data', 'CdOsO'))
file1 = prefix
# writer interface has changed, must use new spec module to proceed
specfile = spec.SpecDataFile(file1)
writer = writer.Writer(specfile)
writer.save(hfile, sorted(specfile.getScanNumbers()))
