def test_last_novalue(self):
fun = sys._getframe().f_code.co_name
print("Run: %s.%s() " % (self.__class__.__name__, fun))
fname = "test.h5"
nxFile = None
eFile = None
# gname = "testGroup"
# gtype = "NXentry"
# fdname = "testField"
# fdtype = "int64"
# file handle
nxFile = FileWriter.create_file(fname, overwrite=True).root()
# element file objects
eFile = EFile([], None, nxFile)
el = Element(self._tfname, self._fattrs2, eFile)
fi = EField(self._fattrs2, el)
el2 = EDimensions(self._fattrs4, fi)
el3 = EDim(self._attrs3, el2)
self.assertEqual(fi.tagName, "field")
self.assertEqual(fi.content, [])
self.assertEqual(fi._tagAttrs, self._fattrs2)
self.assertEqual(fi.doc, "")
self.assertEqual(fi._lastObject(), None)
self.assertEqual(type(el2.last), EField)
self.assertEqual(el2.last.rank, "1")
self.assertEqual(el3._beforeLast().lengths, {})
self.assertEqual(fi.lengths, {})
self.assertEqual(fi.rank, "1")
nxFile.close()
os.remove(fname)
def test_store_default(self):
fun = sys._getframe().f_code.co_name
print("Run: %s.%s() " % (self.__class__.__name__, fun))
self._fname = '%s/%s%s.h5' % (os.getcwd(), self.__class__.__name__,
fun)
FileWriter.writer = H5CppWriter
self._nxFile = FileWriter.create_file(self._fname,
overwrite=True).root()
eFile = EFile({}, None, self._nxFile)
el = EGroup(self._gattrs, eFile)
self.assertTrue(isinstance(el, Element))
self.assertTrue(isinstance(el, FElement))
self.assertTrue(isinstance(el, FElementWithAttr))
self.assertEqual(el.tagName, "group")
self.assertEqual(el.content, [])
el.store()
self.assertEqual(el.h5Object.name, self._gattrs["name"])
self.assertEqual(len(el.h5Object.attributes), 1)
self.assertEqual(el.h5Object.attributes["NX_class"][...],
self._gattrs["type"])
# self.myAssertRaise(ValueError, el.store)
self._nxFile.close()
os.remove(self._fname)
def test_fetchName_notype(self):
fun = sys._getframe().f_code.co_name
print("Run: %s.%s() " % (self.__class__.__name__, fun))
self._fname = '%s/%s%s.h5' % (os.getcwd(), self.__class__.__name__,
fun)
FileWriter.writer = H5CppWriter
self._nxFile = FileWriter.create_file(self._fname,
overwrite=True).root()
eFile = EFile({}, None, self._nxFile)
gattrs = {"type": "NXentry"}
el = EGroup(gattrs, eFile)
self.assertTrue(isinstance(el, Element))
self.assertTrue(isinstance(el, FElement))
self.assertTrue(isinstance(el, FElementWithAttr))
self.assertEqual(el.tagName, "group")
self.assertEqual(el.content, [])
self.assertEqual(type(el.h5Object), H5CppWriter.H5CppGroup)
self.assertEqual(el.h5Object.name, gattrs["type"][2:])
self.assertEqual(len(el.h5Object.attributes), 1)
self.assertEqual(el.h5Object.attributes["NX_class"][...],
gattrs["type"])
self.assertEqual(el.h5Object.attributes["NX_class"].dtype, "string")
self.assertEqual(el.h5Object.attributes["NX_class"].shape, ())
# gNames = {}
el._tagAttrs.pop("type")
self._nxFile.close()
os.remove(self._fname)
def test_store_1d_single(self):
fun = sys._getframe().f_code.co_name
print("Run: %s.%s() " % (self.__class__.__name__, fun))
self._fname = '%s/%s%s.h5' % (os.getcwd(), self.__class__.__name__,
fun)
FileWriter.writer = H5CppWriter
self._nxFile = FileWriter.create_file(self._fname,
overwrite=True).root()
eFile = EFile({}, None, self._nxFile)
el = EGroup(self._gattrs, eFile)
self.assertEqual(el.tagAttributes, {})
attrs = {
# "string":["My string","NX_CHAR", "string" , (1,)],
# "datetime":["12:34:34","NX_DATE_TIME", "string", (1,) ],
# "iso8601":["12:34:34","ISO8601", "string", (1,)],
"int": [-123, "NX_INT", "int64", (1, )],
"int8": [12, "NX_INT8", "int8", (1, )],
"int16": [-123, "NX_INT16", "int16", (1, )],
"int32": [12345, "NX_INT32", "int32", (1, )],
"int64": [-12345, "NX_INT64", "int64", (1, )],
"uint": [123, "NX_UINT", "uint64", (1, )],
"uint8": [12, "NX_UINT8", "uint8", (1, )],
"uint16": [123, "NX_UINT16", "uint16", (1, )],
"uint32": [12345, "NX_UINT32", "uint32", (1, )],
"uint64": [12345, "NX_UINT64", "uint64", (1, )],
"float": [-12.345, "NX_FLOAT", "float64", (1, ), 1.e-14],
"number": [-12.345e+2, "NX_NUMBER", "float64", (1, ), 1.e-14],
"float32": [-12.345e-1, "NX_FLOAT32", "float32", (1, ), 1.e-5],
"float64": [-12.345, "NX_FLOAT64", "float64", (1, ), 1.e-14],
"bool": [True, "NX_BOOLEAN", "bool", (1, )],
"bool2": ["FaLse", "NX_BOOLEAN", "bool", (1, )],
"bool3": ["false", "NX_BOOLEAN", "bool", (1, )],
"bool4": ["true", "NX_BOOLEAN", "bool", (1, )]
}
for nm in attrs.keys():
if attrs[nm][2] == 'string':
"writing multi-dimensional string is not supported by pninx"
continue
el.tagAttributes[nm] = (attrs[nm][1], str(attrs[nm][0]),
attrs[nm][3])
el.store()
at = el.h5Object.attributes[nm]
self.assertEqual(at.dtype, attrs[nm][2])
if attrs[nm][2] == "bool":
self.assertEqual(Converters.toBool(str(attrs[nm][0])), at[...])
elif len(attrs[nm]) > 4:
self.assertTrue(abs(at[...] - attrs[nm][0]) <= attrs[nm][4])
else:
if isinstance(at[...], numpy.ndarray):
self.assertEqual(
at[...], numpy.array(attrs[nm][0], dtype=attrs[nm][2]))
else:
self.assertEqual(at[...], attrs[nm][0])
self._nxFile.close()
os.remove(self._fname)
def test_default_constructor_thesame_name(self):
fun = sys._getframe().f_code.co_name
print("Run: %s.%s() " % (self.__class__.__name__, fun))
self._fname = '%s/%s%s.h5' % (os.getcwd(), self.__class__.__name__,
fun)
FileWriter.writer = H5CppWriter
self._nxFile = FileWriter.create_file(self._fname,
overwrite=True).root()
eFile = EFile({}, None, self._nxFile)
el = EGroup(self._gattrs, eFile)
self.assertTrue(isinstance(el, Element))
self.assertTrue(isinstance(el, FElement))
self.assertTrue(isinstance(el, FElementWithAttr))
self.assertEqual(el.tagName, "group")
self.assertEqual(el.content, [])
self.assertEqual(type(el.h5Object), H5CppWriter.H5CppGroup)
self.assertEqual(el.h5Object.name, self._gattrs["name"])
self.assertEqual(len(el.h5Object.attributes), 1)
self.assertEqual(el.h5Object.attributes["NX_class"][...],
self._gattrs["type"])
self.assertEqual(el.h5Object.attributes["NX_class"].dtype, "string")
self.assertEqual(el.h5Object.attributes["NX_class"].shape, ())
self.assertEqual(el.h5Object.attributes["NX_class"].shape, ())
self.myAssertRaise(XMLSettingSyntaxError, EGroup, self._gattrs, eFile)
self._nxFile.close()
os.remove(self._fname)
def test_lastObject_hp5y(self):
fun = sys._getframe().f_code.co_name
print("Run: %s.%s() " % (self.__class__.__name__, fun))
self._fname = '%s/%s%s.h5' % (os.getcwd(), self.__class__.__name__,
fun)
FileWriter.writer = H5CppWriter
fname = self._fname
nxFile = None
eFile = None
gname = "testGroup"
gtype = "NXentry"
fdname = "testField"
fdtype = "int64"
# file handle
nxFile = FileWriter.create_file(fname, overwrite=True).root()
# element file objects
eFile = EFile([], None, nxFile)
group = nxFile.create_group(gname, gtype)
group.create_field(fdname, fdtype)
el = Element(self._tfname, self._fattrs, eFile)
el2 = Element(self._tfname, self._fattrs, el)
self.assertEqual(el.tagName, self._tfname)
self.assertEqual(el.content, [])
self.assertEqual(el._tagAttrs, self._fattrs)
self.assertEqual(el.doc, "")
self.assertEqual(el._lastObject(), nxFile)
self.assertEqual(el2._lastObject(), None)
nxFile.close()
os.remove(fname)
def test_last_h5cpp(self):
print("Run: %s.test_last() " % self.__class__.__name__)
fname = "test.h5"
nxFile = None
eFile = None
# gname = "testGroup"
# gtype = "NXentry"
# fdname = "testField"
# fdtype = "int64"
# file handle
FileWriter.writer = H5CppWriter
nxFile = FileWriter.create_file(fname, overwrite=True).root()
# element file objects
eFile = EFile([], None, nxFile)
el = Element(self._tfname, self._fattrs2, eFile)
fi = EField(self._fattrs3, el)
el2 = EDimensions(self._fattrs3, fi)
self.assertEqual(fi.tagName, "field")
self.assertEqual(fi.content, [])
self.assertEqual(fi._tagAttrs, self._fattrs3)
self.assertEqual(fi.doc, "")
self.assertEqual(fi._lastObject(), None)
self.assertEqual(type(el2.last), EField)
self.assertEqual(el2.last.rank, "2")
nxFile.close()
os.remove(fname)
def createTree(self):
# file handle
FileWriter.writer = H5PYWriter
self._nxFile = FileWriter.create_file(self._fname,
overwrite=True).root()
# element file objects
self._group = self._nxFile.create_group(self._gname, self._gtype)
self._field = self._group.create_field(self._fdname, self._fdtype)
def setUp(self):
# file handle
FileWriter.writer = H5CppWriter
self._nxFile = FileWriter.create_file(self._fname, overwrite=True)
self._nxroot = self._nxFile.root()
# element file objects
self._group = self._nxroot.create_group(self._gname, self._gtype)
self._field = self._group.create_field(self._fdname, self._fdtype)
print("\nsetting up...")
def test_store_last_index2(self):
fun = sys._getframe().f_code.co_name
print("Run: %s.%s() " % (self.__class__.__name__, fun))
fname = "test.h5"
nxFile = None
eFile = None
# gname = "testGroup"
# gtype = "NXentry"
# fdname = "testField"
# fdtype = "int64"
# file handle
nxFile = FileWriter.create_file(fname, overwrite=True).root()
# element file objects
eFile = EFile([], None, nxFile)
el = Element(self._tfname, self._fattrs2, eFile)
fi = EField(self._fattrs2, el)
el2 = EDimensions(self._fattrs3, fi)
el3 = EDim(self._attrs5, el2)
ds = TstDataSource()
ds.value0d = self.__rnd.randint(1, 10)
el3.source = ds
el4 = EDim(self._attrs4, el2)
ds2 = TstDataSource()
ds2.value0d = self.__rnd.randint(1, 10)
el4.source = ds2
el3.store()
el4.store()
self.assertEqual(fi.tagName, "field")
self.assertEqual(fi.content, [])
self.assertEqual(fi._tagAttrs, self._fattrs2)
self.assertEqual(fi.doc, "")
self.assertEqual(fi._lastObject(), None)
self.assertEqual(type(el2.last), EField)
self.assertEqual(el2.last.rank, "2")
self.assertEqual(el3._beforeLast().lengths, {
'1': '%s' % ds.value0d,
'2': '%s' % ds2.value0d
})
self.assertEqual(fi.lengths, {
'1': '%s' % ds.value0d,
'2': '%s' % ds2.value0d
})
self.assertEqual(fi.rank, "2")
nxFile.close()
os.remove(fname)
def test_constructor_aTn(self):
fun = sys._getframe().f_code.co_name
print("Run: %s.%s() " % (self.__class__.__name__, fun))
self._fname = '%s/%s%s.h5' % (os.getcwd(), self.__class__.__name__,
fun)
FileWriter.writer = H5CppWriter
self._nxFile = FileWriter.create_file(self._fname,
overwrite=True).root()
eFile = EFile({}, None, self._nxFile)
gattrs = {"type": "NXentry", "name": "shortname"}
# map of tag attribute types
maTn = {
"signal": 1,
"axis": 2,
"primary": 3,
"offset": 4,
"stride": 6,
"file_time": "12:34",
"file_update_time": "12:45",
"restricts": 12,
"ignoreExtraGroups": True,
"ignoreExtraFields": False,
"ignoreExtraAttributes": True,
"minOccus": 1,
"maxOccus": 2
}
gattrs = dict(gattrs, **(maTn))
el = EGroup(gattrs, eFile)
self.assertTrue(isinstance(el, Element))
self.assertTrue(isinstance(el, FElement))
self.assertTrue(isinstance(el, FElementWithAttr))
self.assertEqual(el.tagName, "group")
self.assertEqual(el.content, [])
self.assertEqual(type(el.h5Object), H5CppWriter.H5CppGroup)
self.assertEqual(el.h5Object.name, gattrs["name"])
self.assertEqual(len(el.h5Object.attributes), 14)
self.assertEqual(el.h5Object.attributes["NX_class"][...],
gattrs["type"])
self.assertEqual(el.h5Object.attributes["NX_class"].dtype, "string")
self.assertEqual(el.h5Object.attributes["NX_class"].shape, ())
for k in maTn.keys():
self.assertEqual(el.h5Object.attributes[k][...], gattrs[k])
self.assertEqual(el.h5Object.attributes[k].dtype,
NTP.nTnp[NTP.aTn[k]])
self.assertEqual(el.h5Object.attributes[k].shape, ())
self._nxFile.close()
os.remove(self._fname)
def test_constructor_notype(self):
fun = sys._getframe().f_code.co_name
print("Run: %s.%s() " % (self.__class__.__name__, fun))
self._fname = '%s/%s%s.h5' % (os.getcwd(), self.__class__.__name__,
fun)
FileWriter.writer = H5CppWriter
self._nxFile = FileWriter.create_file(self._fname,
overwrite=True).root()
eFile = EFile({}, None, self._nxFile)
gattrs = {"short_name": "shortname"}
self.myAssertRaise(XMLSettingSyntaxError, EGroup, gattrs, eFile)
self._nxFile.close()
os.remove(self._fname)
def test_constructor_aTnv(self):
fun = sys._getframe().f_code.co_name
print("Run: %s.%s() " % (self.__class__.__name__, fun))
self._fname = '%s/%s%s.h5' % (os.getcwd(), self.__class__.__name__,
fun)
FileWriter.writer = H5CppWriter
self._nxFile = FileWriter.create_file(self._fname,
overwrite=True).root()
eFile = EFile({}, None, self._nxFile)
gattrs = {"type": "NXentry", "name": "shortname"}
# map of tag attribute types
maTnv = {"vector": "1 2 3 4 5"}
raTnv = {"vector": [1, 2, 3, 4, 5]}
gattrs = dict(gattrs, **(maTnv))
rattrs = dict(gattrs)
rattrs = dict(rattrs, **(raTnv))
error = 1.e-14
el = EGroup(gattrs, eFile)
self.assertTrue(isinstance(el, Element))
self.assertTrue(isinstance(el, FElement))
self.assertTrue(isinstance(el, FElementWithAttr))
self.assertEqual(el.tagName, "group")
self.assertEqual(el.content, [])
self.assertEqual(type(el.h5Object), H5CppWriter.H5CppGroup)
self.assertEqual(el.h5Object.name, gattrs["name"])
self.assertEqual(len(el.h5Object.attributes), 2)
self.assertEqual(el.h5Object.attributes["NX_class"][...],
gattrs["type"])
self.assertEqual(el.h5Object.attributes["NX_class"].dtype, "string")
self.assertEqual(el.h5Object.attributes["NX_class"].shape, ())
for k in raTnv.keys():
for i in range(len(rattrs[k])):
self.assertTrue(
abs(el.h5Object.attributes[k][i] - rattrs[k][i]) <= error)
self.assertEqual(el.h5Object.attributes[k].dtype,
NTP.nTnp[NTP.aTnv[k]])
self.assertEqual(el.h5Object.attributes[k].shape,
(len(rattrs[k]), ))
self._nxFile.close()
os.remove(self._fname)
def test_constructor_nx(self):
fun = sys._getframe().f_code.co_name
print("Run: %s.%s() " % (self.__class__.__name__, fun))
self._fname = '%s/%s%s.h5' % (os.getcwd(), self.__class__.__name__,
fun)
self._nxFile = FileWriter.create_file(self._fname,
overwrite=True).root()
el = EFile({}, None, self._nxFile)
self.assertTrue(isinstance(el, Element))
self.assertTrue(isinstance(el, FElement))
self.assertEqual(el.tagName, 'file')
self.assertEqual(el.content, [])
self.assertEqual(el.doc, "")
self.assertEqual(el.source, None)
self.assertEqual(el.error, None)
self.assertEqual(el._tagAttrs, {})
self.assertEqual(type(el.h5Object), H5PYWriter.H5PYGroup)
self._nxFile.close()
os.remove(self._fname)
def openFile(self):
""" the H5 file opening
:brief: It opens the H5 file
"""
try:
self.closeFile()
except Exception:
self._streams.warn(
"TangoDataWriter::openFile() - File cannot be closed")
wrmodule = self.__setWriter(self.writer)
self.__nxFile = None
self.__eFile = None
self.__initPool = None
self.__stepPool = None
self.__finalPool = None
self.__triggerPools = {}
self.__currentfileid = 0
self.__pars = self.__getParams(self.writer)
pars = dict(self.__pars)
pars["writer"] = wrmodule
if os.path.isfile(self.__fileName):
self.__nxFile = FileWriter.open_file(self.__fileName, False,
**pars)
else:
self.__nxFile = FileWriter.create_file(self.__fileName, **pars)
self.__fileprefix, self.__fileext = os.path.splitext(
str(self.__fileName))
self.__nxRoot = self.__nxFile.root()
self.__nxRoot.stepsperfile = self.stepsperfile
self.__nxRoot.currentfileid = self.__currentfileid
#: element file objects
self.__eFile = EFile([], None, self.__nxRoot)
last = self.__eFile
for gname, gtype in self.__parents:
last = EGroup({
"name": gname,
"type": gtype
},
last,
reloadmode=True)
self.__nxPath.append(last)
if self.addingLogs:
name = "nexus_logs"
if not self.__nxRoot.exists(name):
ngroup = self.__nxRoot.create_group(name, "NXcollection")
else:
ngroup = self.__nxRoot.open(name)
name = "configuration"
error = True
counter = 1
cname = name
while error:
cname = name if counter == 1 else \
("%s_%s" % (name, counter))
if not ngroup.exists(cname):
error = False
else:
counter += 1
self.__logGroup = ngroup.create_group(cname, "NXcollection")
vfield = self.__logGroup.create_field("python_version", "string")
vfield.write(str(sys.version))
vfield.close()
def test_store_2d_single(self):
fun = sys._getframe().f_code.co_name
print("Run: %s.%s() " % (self.__class__.__name__, fun))
self._fname = '%s/%s%s.h5' % (os.getcwd(), self.__class__.__name__,
fun)
FileWriter.writer = H5CppWriter
self._nxFile = FileWriter.create_file(self._fname,
overwrite=True).root()
eFile = EFile({}, None, self._nxFile)
el = EGroup(self._gattrs, eFile)
self.assertEqual(el.tagAttributes, {})
attrs = {
# "string":["My string","NX_CHAR", "string" , (1,)],
# "datetime":["12:34:34","NX_DATE_TIME", "string", (1,) ],
# "iso8601":["12:34:34","ISO8601", "string", (1,)],
"int": [-123, "NX_INT", "int64", (1, )],
"int8": [12, "NX_INT8", "int8", (1, )],
"int16": [-123, "NX_INT16", "int16", (1, )],
"int32": [12345, "NX_INT32", "int32", (1, )],
"int64": [-12345, "NX_INT64", "int64", (1, )],
"uint": [123, "NX_UINT", "uint64", (1, )],
"uint8": [12, "NX_UINT8", "uint8", (1, )],
"uint16": [123, "NX_UINT16", "uint16", (1, )],
"uint32": [12345, "NX_UINT32", "uint32", (1, )],
"uint64": [12345, "NX_UINT64", "uint64", (1, )],
"float": [-12.345, "NX_FLOAT", "float64", (1, ), 1.e-14],
"number": [-12.345e+2, "NX_NUMBER", "float64", (1, ), 1.e-14],
"float32": [-12.345e-1, "NX_FLOAT32", "float32", (1, ), 1.e-5],
"float64": [-12.345, "NX_FLOAT64", "float64", (1, ), 1.e-14],
"bool": [True, "NX_BOOLEAN", "bool", (1, )],
"bool2": ["FaLse", "NX_BOOLEAN", "bool", (1, )],
"bool3": ["false", "NX_BOOLEAN", "bool", (1, )],
"bool4": ["true", "NX_BOOLEAN", "bool", (1, )]
}
for nm in attrs.keys():
if attrs[nm][2] != "bool":
mlen = [
self.__rnd.randint(1, 1),
self.__rnd.randint(1, 1),
(2 << numpy.dtype(attrs[nm][2]).itemsize)
]
# print "SH",nm,mlen[2]
attrs[nm][0] = [[
attrs[nm][0] * self.__rnd.randint(0, 3)
for r in range(mlen[1])
] for c in range(mlen[0])]
else:
mlen = [self.__rnd.randint(1, 1), self.__rnd.randint(1, 1)]
if nm == 'bool':
attrs[nm][0] = [[
bool(self.__rnd.randint(0, 1)) for c in range(mlen[1])
] for r in range(mlen[0])]
else:
attrs[nm][0] = [[
("True" if self.__rnd.randint(0, 1) else "False")
for c in range(mlen[1])
] for r in range(mlen[0])]
attrs[nm][3] = (mlen[0], mlen[1])
for nm in attrs.keys():
el.tagAttributes[nm] = (attrs[nm][1], "".join([
"".join([str(it) + " " for it in sub]) + "\n"
for sub in attrs[nm][0]
]), attrs[nm][3])
el.store()
at = el.h5Object.attributes[nm]
self.assertEqual(at.dtype, attrs[nm][2])
if attrs[nm][2] == "bool":
for i in range(len(attrs[nm][0])):
for j in range(len(attrs[nm][0][i])):
self.assertEqual(
Converters.toBool(str(attrs[nm][0][i][j])),
at[...])
pass
elif len(attrs[nm]) > 4:
for i in range(len(attrs[nm][0])):
for j in range(len(attrs[nm][0][i])):
self.assertTrue(
abs(at[...] - attrs[nm][0][i][j]) <= attrs[nm][4])
else:
for i in range(len(attrs[nm][0])):
for j in range(len(attrs[nm][0][i])):
self.assertEqual(at[...], attrs[nm][0][i][j])
self._nxFile.close()
os.remove(self._fname)