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_xmlAttrSpectrum(self):
fun = sys._getframe().f_code.co_name
print("Run: %s.%s() " % (self.__class__.__name__, fun))
fname = '%s/%s%s.h5' % (os.getcwd(), self.__class__.__name__, fun)
xml = """<definition>
<group type="NXentry" name="entry1">
<group type="NXinstrument" name="instrument">
<group type="NXdetector" name="detector">
<attribute type="NX_FLOAT" name="spectrum_float">
<dimensions rank="1">
<dim value="4" index="1"/>
</dimensions>
<strategy mode="STEP"/>
2.344e-4 234.34 -34.4e+3 -0.34
</attribute>
<attribute type="NX_INT32" name="init_spectrum_int32">
<dimensions rank="1" />
<strategy mode="INIT"/>
1 2 3 4 5
</attribute>
<attribute type="NX_BOOLEAN" name="spectrum_bool">
<dimensions rank="1">
<dim value="4" index="1"/>
</dimensions>
<strategy mode="STEP"/>
True False 1 0
</attribute>
</group>
<field type="NX_FLOAT" name="counter">
<attribute type="NX_FLOAT32" name="spectrum_float32">
<dimensions rank="1" />
<strategy mode="STEP"/>
2.344e-4 234.34 -34.4e+3 -0.34
</attribute>
<attribute type="NX_UINT64" name="final_spectrum_uint64">
<dimensions rank="1">
<dim value="5" index="1"/>
</dimensions>
<strategy mode="FINAL"/>
1 2 3 4 5
</attribute>
<attribute type="NX_BOOLEAN" name="final_spectrum_bool">
<dimensions rank="1" />
<strategy mode="FINAL"/>
True False 1 0
</attribute>
1.2
</field>
</group>
</group>
</definition>
"""
# <attribute type="NX_CHAR" name="flag_spectrum_string">
# <dimensions rank="1">
# <dim value="8" index="1"/>
# </dimensions>
# </attribute>
spec = [2.344e-4, 234.34, -34.4e+3, -0.34]
ins = [1, 2, 3, 4, 5]
ls = [True, False, True, False]
tdw = self.openWriter(fname, xml)
for i in range(3):
self.record(tdw, '{ }')
self.closeWriter(tdw)
# check the created file
FileWriter.writer = H5PYWriter
f = FileWriter.open_file(fname, readonly=True)
det, field = self._sc.checkAttributeTree(f, fname, 3, 3)
self._sc.checkSpectrumAttribute(det,
"spectrum_float",
"float64",
spec,
error=1.e-14)
self._sc.checkSpectrumAttribute(det, "init_spectrum_int32", "int32",
ins)
self._sc.checkSpectrumAttribute(det, "spectrum_bool", "bool", ls)
self._sc.checkSpectrumAttribute(field,
"spectrum_float32",
"float32",
spec,
error=1.e-5)
self._sc.checkSpectrumAttribute(field, "final_spectrum_uint64",
"uint64", ins)
self._sc.checkSpectrumAttribute(field, "final_spectrum_bool", "bool",
ls)
# NOT SUPPORTED BY PNINX
# self._sc.checkSpectrumAttribute(field, "flag_spectrum_string", "string",
# logical)
f.close()
os.remove(fname)
def test_xmlImage(self):
fun = sys._getframe().f_code.co_name
print("Run: %s.%s() " % (self.__class__.__name__, fun))
fname = '%s/%s%s.h5' % (os.getcwd(), self.__class__.__name__, fun)
xml = """<definition>
<group type="NXentry" name="entry1">
<group type="NXinstrument" name="instrument">
<group type="NXdetector" name="detector">
<field units="" type="NX_INT" name="pco_int">
<dimensions rank="2">
<dim value="3" index="1"/>
<dim value="2" index="2"/>
</dimensions>
<strategy mode="STEP"/>
11 12
21 22
31 32
</field>
<field units="" type="NX_INT8" name="pco_int8">
<dimensions rank="2">
<dim value="3" index="1"/>
<dim value="2" index="2"/>
</dimensions>
<strategy mode="STEP" grows="2"/>
11 12
21 22
31 32
</field>
<field units="" type="NX_INT16" name="pco_int16">
<dimensions rank="2" />
<strategy mode="STEP" compression="true" grows="3"/>
11 12
21 22
31 32
</field>
<field units="" type="NX_INT32" name="pco_int32">
<dimensions rank="2">
<dim value="3" index="1"/>
<dim value="2" index="2"/>
</dimensions>
<strategy mode="STEP" compression="true" grows="2"
shuffle="false" />
11 12
21 22
31 32
</field>
<field units="" type="NX_INT64" name="pco_int64">
<dimensions rank="2">
<dim value="3" index="1"/>
<dim value="2" index="2"/>
</dimensions>
<strategy mode="STEP" compression="true" rate="3"/>
11 12
21 22
31 32
</field>
<field units="" type="NX_UINT" name="pco_uint">
<dimensions rank="2">
<dim value="3" index="1"/>
<dim value="2" index="2"/>
</dimensions>
<strategy mode="STEP"/>
11 12
21 22
31 32
</field>
<field units="" type="NX_UINT8" name="pco_uint8">
<dimensions rank="2">
<dim value="3" index="1"/>
<dim value="2" index="2"/>
</dimensions>
<strategy mode="STEP" grows="3"/>
11 12
21 22
31 32
</field>
<field units="" type="NX_UINT16" name="pco_uint16">
<dimensions rank="2">
<dim value="3" index="1"/>
<dim value="2" index="2"/>
</dimensions>
<strategy mode="STEP" compression="true"/>
11 12
21 22
31 32
</field>
<field units="" type="NX_UINT32" name="pco_uint32">
<dimensions rank="2">
<dim value="3" index="1"/>
<dim value="2" index="2"/>
</dimensions>
<strategy mode="STEP" compression="true" grows="2"
shuffle="false" />
11 12
21 22
31 32
</field>
<field units="" type="NX_UINT64" name="pco_uint64">
<dimensions rank="2">
<dim value="3" index="1"/>
<dim value="2" index="2"/>
</dimensions>
<strategy mode="STEP" compression="true" rate="3" grows="3"/>
11 12
21 22
31 32
</field>
<field units="" type="NX_FLOAT" name="pco_float">
<dimensions rank="2">
<dim value="2" index="1"/>
<dim value="3" index="2"/>
</dimensions>
<strategy mode="STEP" compression="true" rate="3"/>
-3.43 -3.3e-1 53.1
3.43e+02 3.13e-1 53
</field>
<field units="" type="NX_FLOAT32" name="pco_float32">
<dimensions rank="2">
<dim value="2" index="1"/>
<dim value="3" index="2"/>
</dimensions>
<strategy mode="STEP" compression="true" grows="2" shuffle="true"/>
-3.43 -3.3e-1 53.1
3.43e+02 3.13e-1 53
</field>
<field units="" type="NX_FLOAT64" name="pco_float64">
<dimensions rank="2" />
<strategy mode="STEP" grows="3"/>
-3.43 -3.3e-1 53.1
3.43e+02 3.13e-1 53
</field>
<field units="" type="NX_NUMBER" name="pco_number">
<dimensions rank="2">
<dim value="2" index="1"/>
<dim value="3" index="2"/>
</dimensions>
<strategy mode="STEP" grows = "1" />
-3.43 -3.3e-1 53.1
3.43e+02 3.13e-1 53
</field>
<field units="" type="NX_DATE_TIME" name="time">
<strategy mode="STEP" compression="true" rate="3"/>
<dimensions rank="2">
<dim value="3" index="1"/>
<dim value="4" index="2"/>
</dimensions>
Let's us check it,
and test it here.
, . : ;
</field>
<field units="" type="ISO8601" name="isotime">
<strategy mode="STEP" compression="true" grows="2" shuffle="true"/>
<dimensions rank="2" />
Let's us check it,
and test it here.
, . : ;
</field>
<field units="" type="NX_CHAR" name="string_time">
<strategy mode="STEP" grows="2"/>
<dimensions rank="2"/>
Let's us check it,
and test it here.
, . : ;
</field>
<field units="" type="NX_BOOLEAN" name="flags">
<strategy mode="STEP"/>
<dimensions rank="2">
<dim value="3" index="1"/>
<dim value="4" index="2"/>
</dimensions>
True False 1 0
FALSE TRUE false true
0 1 1 0
</field>
<field units="" type="NX_BOOLEAN" name="flags_dim">
<strategy mode="STEP"/>
<dimensions rank="2" />
True False 1 0
FALSE TRUE false true
0 1 1 0
</field>
</group>
</group>
</group>
</definition>
"""
image = [[11, 12], [21, 22], [31, 32]]
fimage = [[-3.43, -3.3e-1, 53.1], [3.43e+02, 3.13e-1, 53]]
simage = [["Let's", "us", "check", "it,"],
["and", "test", "it", "here."], [",", ".", ":", ";"]]
bimage = [[True, False, True, False], [False, True, False, True],
[False, True, True, False]]
tdw = self.openWriter(fname, xml)
for c in range(3):
self.record(tdw, '{}')
self.closeWriter(tdw)
# check the created file
FileWriter.writer = H5PYWriter
f = FileWriter.open_file(fname, readonly=True)
det = self._sc.checkFieldTree(f, fname, 19)
self._sc.checkXMLImageField(det, "pco_int", "int64", "NX_INT", image)
self._sc.checkXMLImageField(det, "pco_int8", "int8", "NX_INT8", image)
self._sc.checkXMLImageField(det, "pco_int16", "int16", "NX_INT16",
image)
self._sc.checkXMLImageField(det, "pco_int32", "int32", "NX_INT32",
image)
self._sc.checkXMLImageField(det, "pco_int64", "int64", "NX_INT64",
image)
self._sc.checkXMLImageField(det, "pco_uint", "uint64", "NX_UINT",
image)
self._sc.checkXMLImageField(det, "pco_uint8", "uint8", "NX_UINT8",
image)
self._sc.checkXMLImageField(det, "pco_uint16", "uint16", "NX_UINT16",
image)
self._sc.checkXMLImageField(det, "pco_uint32", "uint32", "NX_UINT32",
image)
self._sc.checkXMLImageField(det, "pco_uint64", "uint64", "NX_UINT64",
image)
self._sc.checkXMLImageField(det,
"pco_float",
"float64",
"NX_FLOAT",
fimage,
error=1.0e-14)
self._sc.checkXMLImageField(det,
"pco_float32",
"float32",
"NX_FLOAT32",
fimage,
error=1.0e-5)
self._sc.checkXMLImageField(det,
"pco_float64",
"float64",
"NX_FLOAT64",
fimage,
error=1.0e-14)
self._sc.checkXMLImageField(det,
"pco_number",
"float64",
"NX_NUMBER",
fimage,
error=1.0e-14)
self._sc.checkXMLImageField(det, "flags", "bool", "NX_BOOLEAN", bimage)
self._sc.checkXMLImageField(det, "time", "string", "NX_DATE_TIME",
simage)
self._sc.checkXMLImageField(det, "string_time", "string", "NX_CHAR",
simage)
self._sc.checkXMLImageField(det, "isotime", "string", "ISO8601",
simage)
self._sc.checkXMLImageField(det, "flags_dim", "bool", "NX_BOOLEAN",
bimage)
f.close()
os.remove(fname)
def test_xmlSpectrum(self):
fun = sys._getframe().f_code.co_name
print("Run: %s.%s() " % (self.__class__.__name__, fun))
fname = '%s/%s%s.h5' % (os.getcwd(), self.__class__.__name__, fun)
xml = """<definition>
<group type="NXentry" name="entry1">
<group type="NXinstrument" name="instrument">
<group type="NXdetector" name="detector">
<field units="" type="NX_INT" name="mca_int">
<dimensions rank="1">
<dim value="5" index="1"/>
</dimensions>
1 2 3 4 5
</field>
<field units="" type="NX_INT8" name="mca_int8">
<strategy mode="INIT" compression="true"/>
<dimensions rank="1">
<dim value="5" index="1"/>
</dimensions>
1 2 3 4 5
</field>
<field units="" type="NX_INT16" name="mca_int16">
<dimensions rank="1" />
1 2 3 4 5
</field>
<field units="" type="NX_INT32" name="mca_int32">
<dimensions rank="1">
<dim value="5" index="1"/>
</dimensions>
1 2 3 4 5
</field>
<field units="" type="NX_INT64" name="mca_int64">
<dimensions rank="1"/>
1 2 3 4 5
</field>
<field units="" type="NX_UINT" name="mca_uint">
<strategy mode="INIT" compression="true" rate="2"/>
<dimensions rank="1">
<dim value="5" index="1"/>
</dimensions>
1 2 3 4 5
</field>
<field units="" type="NX_UINT8" name="mca_uint8">
<dimensions rank="1"/>
1 2 3 4 5
</field>
<field units="" type="NX_UINT16" name="mca_uint16">
<dimensions rank="1">
<dim value="5" index="1"/>
</dimensions>
1 2 3 4 5
</field>
<field units="" type="NX_UINT32" name="mca_uint32">
<dimensions rank="1">
</dimensions>
1 2 3 4 5
</field>
<field units="" type="NX_UINT64" name="mca_uint64">
<strategy mode="INIT" compression="true" rate="5" shuffle="false"/>
<dimensions rank="1">
<dim value="5" index="1"/>
</dimensions>
1 2 3 4 5
</field>
<field units="" type="NX_INT64" name="mca_int64_dim">
<dimensions rank="1"/>
1 2 3 4 5
</field>
<field units="" type="NX_FLOAT" name="mca_float">
<dimensions rank="1">
<dim value="4" index="1"/>
</dimensions>
<strategy mode="INIT" compression="true" rate="3"/>
2.344e-4 234.34 -34.4e+3 -0.34
</field>
<field units="" type="NX_FLOAT32" name="mca_float32">
<dimensions rank="1">
<dim value="4" index="1"/>
</dimensions>
<strategy mode="INIT" compression="true" grows="2" shuffle="true"/>
2.344e-4 234.34 -34.4e+3 -0.34
</field>
<field units="" type="NX_FLOAT64" name="mca_float64">
<dimensions rank="1">
<dim value="4" index="1"/>
</dimensions>
<strategy mode="INIT" grows="2"/>
2.344e-4 234.34 -34.4e+3 -0.34
</field>
<field units="" type="NX_NUMBER" name="mca_number">
<dimensions rank="1">
<dim value="4" index="1"/>
</dimensions>
<strategy mode="INIT" />
2.344e-4 234.34 -34.4e+3 -0.34
</field>
<field units="" type="NX_FLOAT" name="mca_float_dim">
<dimensions rank="1"/>
<strategy mode="FINAL" />
2.344e-4 234.34 -34.4e+3 -0.34
</field>
<field units="" type="NX_DATE_TIME" name="time">
<strategy mode="INIT" compression="true" rate="3"/>
<dimensions rank="1">
<dim value="4" index="1"/>
</dimensions>
Let's us check it,.
</field>
<field units="" type="ISO8601" name="isotime">
<strategy mode="STEP" compression="true" grows="2" shuffle="true"/>
<dimensions rank="1">
<dim value="4" index="1"/>
</dimensions>
Let's us check it,.
</field>
<field units="" type="NX_CHAR" name="string_time">
<strategy mode="STEP" grows="2"/>
<dimensions rank="1">
<dim value="4" index="1"/>
</dimensions>
Let's us check it,.
</field>
<field units="" type="NX_BOOLEAN" name="flags">
<strategy mode="STEP"/>
<dimensions rank="1">
<dim value="4" index="1"/>
</dimensions>
<strategy mode="STEP" />
True False 1 0
</field>
<field units="" type="NX_BOOLEAN" name="flags_dim">
<dimensions rank="1" />
<strategy mode="STEP" />
True False 1 0
</field>
<field units="" type="NX_CHAR" name="string_time_dim">
<strategy mode="STEP" grows="2"/>
<dimensions rank="1"/>
Let's us check it,.
</field>
</group>
</group>
</group>
</definition>
"""
spec = [2.344e-4, 234.34, -34.4e+3, -0.34]
string = ["Let's", "us", "check", "it,."]
tdw = self.openWriter(fname, xml)
for c in range(3):
self.record(tdw, '{}')
self.closeWriter(tdw)
# check the created file
FileWriter.writer = H5PYWriter
f = FileWriter.open_file(fname, readonly=True)
det = self._sc.checkFieldTree(f, fname, 22)
self._sc.checkXMLSpectrumField(det,
"mca_int",
"int64",
"NX_INT", [1, 2, 3, 4, 5],
attrs={
"type": "NX_INT",
"units": ""
})
self._sc.checkXMLSpectrumField(det, "mca_int8", "int8", "NX_INT8",
[1, 2, 3, 4, 5])
self._sc.checkXMLSpectrumField(det,
"mca_int16",
"int16",
"NX_INT16", [1, 2, 3, 4, 5],
attrs={
"type": "NX_INT16",
"units": ""
})
self._sc.checkXMLSpectrumField(det,
"mca_int32",
"int32",
"NX_INT32", [1, 2, 3, 4, 5],
attrs={
"type": "NX_INT32",
"units": ""
})
self._sc.checkXMLSpectrumField(det,
"mca_int64",
"int64",
"NX_INT64", [1, 2, 3, 4, 5],
attrs={
"type": "NX_INT64",
"units": ""
})
self._sc.checkXMLSpectrumField(det, "mca_uint", "uint64", "NX_UINT",
[1, 2, 3, 4, 5])
self._sc.checkXMLSpectrumField(det,
"mca_uint8",
"uint8",
"NX_UINT8", [1, 2, 3, 4, 5],
attrs={
"type": "NX_UINT8",
"units": ""
})
self._sc.checkXMLSpectrumField(det,
"mca_uint16",
"uint16",
"NX_UINT16", [1, 2, 3, 4, 5],
attrs={
"type": "NX_UINT16",
"units": ""
})
self._sc.checkXMLSpectrumField(det,
"mca_uint32",
"uint32",
"NX_UINT32", [1, 2, 3, 4, 5],
attrs={
"type": "NX_UINT32",
"units": ""
})
self._sc.checkXMLSpectrumField(det, "mca_uint64", "uint64",
"NX_UINT64", [1, 2, 3, 4, 5])
self._sc.checkXMLSpectrumField(det,
"mca_int64_dim",
"int64",
"NX_INT64", [1, 2, 3, 4, 5],
attrs={
"type": "NX_INT64",
"units": ""
})
self._sc.checkXMLSpectrumField(det,
"mca_float",
"float64",
"NX_FLOAT",
spec,
error=1.0e-14)
self._sc.checkXMLSpectrumField(det,
"mca_float_dim",
"float64",
"NX_FLOAT",
spec,
error=1.0e-14)
self._sc.checkXMLSpectrumField(det,
"mca_float32",
"float32",
"NX_FLOAT32",
spec,
error=1.0e-5)
self._sc.checkXMLSpectrumField(det,
"mca_float64",
"float64",
"NX_FLOAT64",
spec,
error=1.0e-14)
self._sc.checkXMLSpectrumField(det,
"mca_number",
"float64",
"NX_NUMBER",
spec,
error=1.0e-14)
self._sc.checkXMLSpectrumField(det, "flags", "bool", "NX_BOOLEAN",
[True, False, True, False])
self._sc.checkXMLSpectrumField(det, "time", "string", "NX_DATE_TIME",
string)
self._sc.checkXMLSpectrumField(det, "string_time", "string", "NX_CHAR",
string)
self._sc.checkXMLSpectrumField(det, "isotime", "string", "ISO8601",
string)
self._sc.checkXMLSpectrumField(det, "string_time_dim", "string",
"NX_CHAR", string)
f.close()
os.remove(fname)
def test_xmlAttrScalar(self):
fun = sys._getframe().f_code.co_name
print("Run: %s.%s() " % (self.__class__.__name__, fun))
fname = '%s/%s%s.h5' % (os.getcwd(), self.__class__.__name__, fun)
xml = """<definition>
<group type="NXentry" name="entry1">
<group type="NXinstrument" name="instrument">
<group type="NXdetector" name="detector">
<attribute type="NX_FLOAT" name="scalar_float">
-1.3e-1
</attribute>
<attribute type="NX_CHAR" name="scalar_string">
Let's go.
</attribute>
<attribute type="NX_INT" name="scalar_int">
-12
</attribute>
<attribute type="NX_BOOLEAN" name="flag">
True
</attribute>
</group>
<field type="NX_FLOAT" name="counter">
<attribute type="NX_FLOAT32" name="scalar_float32">
-1.3e-1
</attribute>
<attribute type="NX_CHAR" name="scalar_string">
Let's go.
</attribute>
<attribute type="NX_INT8" name="scalar_int8">
-12
</attribute>
1.2
</field>
</group>
</group>
</definition>
"""
fls = -1.3e-1
ins = -12
sts = "Let's go."
ls = True
tdw = self.openWriter(fname, xml)
for i in range(3):
self.record(tdw, '{}')
self.closeWriter(tdw)
# check the created file
FileWriter.writer = H5PYWriter
f = FileWriter.open_file(fname, readonly=True)
det, field = self._sc.checkAttributeTree(f, fname, 4, 3)
self._sc.checkScalarAttribute(det,
"scalar_float",
"float64",
fls,
error=1.e-14)
self._sc.checkScalarAttribute(det, "scalar_string", "string", sts)
self._sc.checkScalarAttribute(det, "scalar_int", "int64", ins)
self._sc.checkScalarAttribute(det, "flag", "bool", ls)
self._sc.checkScalarAttribute(field,
"scalar_float32",
"float32",
fls,
error=1.e-6)
self._sc.checkScalarAttribute(field, "scalar_string", "string", sts)
self._sc.checkScalarAttribute(field, "scalar_int8", "int8", ins)
f.close()
os.remove(fname)
def test_xmlAttrImage(self):
fun = sys._getframe().f_code.co_name
print("Run: %s.%s() " % (self.__class__.__name__, fun))
fname = '%s/%s%s.h5' % (os.getcwd(), self.__class__.__name__, fun)
xml = """<definition>
<group type="NXentry" name="entry1">
<group type="NXinstrument" name="instrument">
<group type="NXdetector" name="detector">
<attribute type="NX_FLOAT" name="image_float">
<dimensions rank="2">
<dim value="2" index="1"/>
<dim value="3" index="2"/>
</dimensions>
<strategy mode="STEP"/>
-3.43 -3.3e-1 53.1
3.43e+02 3.13e-1 53
</attribute>
<attribute type="NX_INT" name="image_int">
<dimensions rank="2" />
<strategy mode="FINAL"/>
11 12
21 22
31 32
</attribute>
<attribute type="NX_INT32" name="image_int32">
<dimensions rank="2">
<dim value="3" index="1"/>
<dim value="2" index="2"/>
</dimensions>
<strategy mode="STEP"/>
11 12
21 22
31 32
</attribute>
<attribute type="NX_BOOLEAN" name="image_bool">
<dimensions rank="2">
<dim value="3" index="1"/>
<dim value="4" index="2"/>
</dimensions>
<strategy mode="STEP"/>
True False 1 0
FALSE TRUE false true
0 1 1 0
</attribute>
</group>
<field type="NX_FLOAT" name="counter">
<attribute type="NX_FLOAT32" name="image_float32">
<dimensions rank="2" />
<strategy mode="STEP"/>
-3.43 -3.3e-1 53.1
3.43e+02 3.13e-1 53
</attribute>
<attribute type="NX_UINT32" name="image_uint32">
<dimensions rank="2">
<dim value="3" index="1"/>
<dim value="2" index="2"/>
</dimensions>
<strategy mode="STEP"/>
11 12
21 22
31 32
</attribute>
<attribute type="NX_UINT64" name="image_uint64">
<dimensions rank="2"/>
<strategy mode="FINAL"/>
11 12
21 22
31 32
</attribute>
<attribute type="NX_BOOLEAN" name="image_bool">
<dimensions rank="2">
<dim value="3" index="1"/>
<dim value="4" index="2"/>
</dimensions>
<strategy mode="INIT"/>
True False 1 0
FALSE TRUE false true
0 1 1 0
</attribute>
1.2
</field>
</group>
</group>
</definition>
"""
# <attribute type="NX_CHAR" name="flag_spectrum_string">
# <dimensions rank="1">
# <dim value="8" index="1"/>
# </dimensions>
# <strategy mode="STEP"/>
# </attribute>
image = [[11, 12], [21, 22], [31, 32]]
fimage = [[-3.43, -3.3e-1, 53.1], [3.43e+02, 3.13e-1, 53]]
bimage = [[True, False, True, False], [False, True, False, True],
[False, True, True, False]]
tdw = self.openWriter(fname, xml)
for i in range(3):
self.record(tdw, '{ }')
self.closeWriter(tdw)
# check the created file
FileWriter.writer = H5PYWriter
f = FileWriter.open_file(fname, readonly=True)
det, field = self._sc.checkAttributeTree(f, fname, 4, 4)
self._sc.checkImageAttribute(det,
"image_float",
"float64",
fimage,
error=1.e-14)
self._sc.checkImageAttribute(det, "image_int", "int64", image)
self._sc.checkImageAttribute(det, "image_bool", "bool", bimage)
self._sc.checkImageAttribute(det, "image_int32", "int32", image)
self._sc.checkImageAttribute(field,
"image_float32",
"float32",
fimage,
error=1.e-5)
self._sc.checkImageAttribute(field, "image_uint32", "uint32", image)
self._sc.checkImageAttribute(field, "image_uint64", "uint64", image)
self._sc.checkImageAttribute(field, "image_bool", "bool", bimage)
# STRING NOT SUPPORTED BY PNINX
f.close()
os.remove(fname)
def test_xmlScalar(self):
fun = sys._getframe().f_code.co_name
print("Run: %s.%s() " % (self.__class__.__name__, fun))
fname = '%s/%s%s.h5' % (os.getcwd(), self.__class__.__name__, fun)
xml = """<definition>
<group type="NXentry" name="entry1">
<group type="NXinstrument" name="instrument">
<group type="NXdetector" name="detector">
<field units="m" type="NX_INT" name="counter">
-12
</field>
<field units="m" type="NX_INT8" name="counter8">
-12
</field>
<field units="m" type="NX_INT16" name="counter16">
-12
</field>
<field units="m" type="NX_INT32" name="counter32">
-12
</field>
<field units="m" type="NX_INT64" name="counter64">
-12
</field>
<field units="m" type="NX_UINT" name="ucounter">
12
</field>
<field units="m" type="NX_POSINT" name="pcounter">
12
</field>
<field units="m" type="NX_UINT8" name="ucounter8">
12
</field>
<field units="m" type="NX_UINT16" name="ucounter16">
12
</field>
<field units="m" type="NX_UINT32" name="ucounter32">
12
</field>
<field units="m" type="NX_UINT64" name="ucounter64">
12
</field>
<field units="m" type="NX_FLOAT" name="float">
-12.3
</field>
<field units="m" type="NX_FLOAT32" name="float32">
-12.3
</field>
<field units="m" type="NX_FLOAT64" name="float64">
-12.3
</field>
<field units="m" type="NX_NUMBER" name="number">
-12.3
</field>
<field units="m" type="NX_DATE_TIME" name="time">
string, string
</field>
<field units="m" type="ISO8601" name="isotime">
string, string
</field>
<field units="m" type="NX_CHAR" name="string_time">
string, string
</field>
<field units="m" type="NX_BOOLEAN" name="flags">
True
</field>
</group>
</group>
</group>
</definition>
"""
uc = 12
mc = -12
fc = -12.3
string = "string, string"
tdw = self.openWriter(fname, xml)
# flip = True
for c in range(4):
self.record(tdw, '{ }')
self.closeWriter(tdw)
# check the created file
FileWriter.writer = H5PYWriter
f = FileWriter.open_file(fname, readonly=True)
det = self._sc.checkFieldTree(f, fname, 19)
self._sc.checkXMLScalarField(det,
"counter",
"int64",
"NX_INT",
mc,
attrs={
"type": "NX_INT",
"units": "m"
})
self._sc.checkXMLScalarField(det,
"counter8",
"int8",
"NX_INT8",
mc,
attrs={
"type": "NX_INT8",
"units": "m"
})
self._sc.checkXMLScalarField(det,
"counter16",
"int16",
"NX_INT16",
mc,
attrs={
"type": "NX_INT16",
"units": "m"
})
self._sc.checkXMLScalarField(det,
"counter32",
"int32",
"NX_INT32",
mc,
attrs={
"type": "NX_INT32",
"units": "m"
})
self._sc.checkXMLScalarField(det,
"counter64",
"int64",
"NX_INT64",
mc,
attrs={
"type": "NX_INT64",
"units": "m"
})
self._sc.checkXMLScalarField(det,
"ucounter",
"uint64",
"NX_UINT",
uc,
attrs={
"type": "NX_UINT",
"units": "m"
})
self._sc.checkXMLScalarField(det,
"ucounter8",
"uint8",
"NX_UINT8",
uc,
attrs={
"type": "NX_UINT8",
"units": "m"
})
self._sc.checkXMLScalarField(det,
"ucounter16",
"uint16",
"NX_UINT16",
uc,
attrs={
"type": "NX_UINT16",
"units": "m"
})
self._sc.checkXMLScalarField(det,
"ucounter32",
"uint32",
"NX_UINT32",
uc,
attrs={
"type": "NX_UINT32",
"units": "m"
})
self._sc.checkXMLScalarField(det,
"ucounter64",
"uint64",
"NX_UINT64",
uc,
attrs={
"type": "NX_UINT64",
"units": "m"
})
self._sc.checkXMLScalarField(det,
"float",
"float64",
"NX_FLOAT",
fc,
1.0e-14,
attrs={
"type": "NX_FLOAT",
"units": "m"
})
self._sc.checkXMLScalarField(det,
"float64",
"float64",
"NX_FLOAT64",
fc,
1.0e-14,
attrs={
"type": "NX_FLOAT64",
"units": "m"
})
self._sc.checkXMLScalarField(det,
"float32",
"float32",
"NX_FLOAT32",
fc,
1.0e-06,
attrs={
"type": "NX_FLOAT32",
"units": "m"
})
self._sc.checkXMLScalarField(det,
"number",
"float64",
"NX_NUMBER",
fc,
1.0e-14,
attrs={
"type": "NX_NUMBER",
"units": "m"
})
self._sc.checkXMLStringScalarField(det,
"time",
"string",
"NX_DATE_TIME",
string,
attrs={
"type": "NX_DATE_TIME",
"units": "m"
})
self._sc.checkXMLStringScalarField(det,
"isotime",
"string",
"ISO8601",
string,
attrs={
"type": "ISO8601",
"units": "m"
})
self._sc.checkXMLStringScalarField(det,
"string_time",
"string",
"NX_CHAR",
string,
attrs={
"type": "NX_CHAR",
"units": "m"
})
self._sc.checkXMLScalarField(det,
"flags",
"bool",
"NX_BOOLEAN",
True,
attrs={
"type": "NX_BOOLEAN",
"units": "m"
})
f.close()
os.remove(fname)
def test_scanRecord_nexuspath(self):
fun = sys._getframe().f_code.co_name
print("Run: %s.%s() " % (self.__class__.__name__, fun))
fname = '%s/%s%s.h5' % (os.getcwd(), self.__class__.__name__, fun)
data = '{"exp_c01":' + str(self._counter[0]) + \
', "p09/mca/exp.02":' + str(self._mca1) + ' }'
jdata = '{"data": {"exp_c01":' + str(self._counter[0]) + \
', "p09/mca/exp.02":' + str(self._mca1) + ' } }'
xmlfile = '%s/%s%s.xml' % (os.getcwd(), self.__class__.__name__, fun)
jsonfile = '%s/%s%s.json' % (os.getcwd(), self.__class__.__name__, fun)
nxpath = "/entry1:NXentry"
commands = [
[
'nxsfromxml', '--h5py', '-p',
"%s:/%s" % (fname, nxpath), '--nrecords', '2', '-j', jsonfile,
'--time', '0.5', '-v', self._scanXmlpart
],
[
'nxsfromxml', '--h5py', '--parent',
"%s:/%s" % (fname, nxpath), '--nrecords', '2', '--json-file',
jsonfile, '-x', xmlfile
],
[
'nxsfromxml', '--h5py', '-p',
"%s:/%s" % (fname, nxpath), '-n', '2', '-d', data, '--verbose',
'--xml-file', xmlfile
],
[
'nxsfromxml', '--h5py', '--parent',
"%s:/%s" % (fname, nxpath), '-n', '2', '--data', data, '-t',
'0', self._scanXmlpart
],
]
for ci, cmd in enumerate(commands):
try:
with open(xmlfile, "w") as text_file:
text_file.write(self._scanXmlpart)
with open(jsonfile, "w") as text_file:
text_file.write(jdata)
vl, er = self.runtest(cmd)
if PYTG_BUG_213:
self.assertTrue(er)
else:
print(er)
self.assertEqual('', er)
if ci % 2:
self.assertEqual('', vl)
else:
self.assertTrue(vl)
# check the created file
from nxstools import filewriter as FileWriter
FileWriter.writer = H5PYWriter
f = FileWriter.open_file(fname, readonly=True)
f = f.root()
self.assertEqual(5, len(f.attributes))
self.assertEqual(f.attributes["file_name"][...], fname)
self.assertTrue(f.attributes["NX_class"][...], "NXroot")
self.assertEqual(f.size, 2)
en = f.open("entry1")
self.assertTrue(en.is_valid)
self.assertEqual(en.name, "entry1")
self.assertEqual(len(en.attributes), 1)
self.assertEqual(en.size, 1)
at = en.attributes["NX_class"]
self.assertTrue(at.is_valid)
self.assertTrue(hasattr(at.shape, "__iter__"))
self.assertEqual(len(at.shape), 0)
self.assertEqual(at.shape, ())
self.assertEqual(at.dtype, "string")
self.assertEqual(at.name, "NX_class")
self.assertEqual(at[...], "NXentry")
ins = en.open("instrument")
self.assertTrue(ins.is_valid)
self.assertEqual(ins.name, "instrument")
self.assertEqual(len(ins.attributes), 2)
self.assertEqual(ins.size, 1)
at = ins.attributes["NX_class"]
self.assertTrue(at.is_valid)
self.assertTrue(hasattr(at.shape, "__iter__"))
self.assertEqual(len(at.shape), 0)
self.assertEqual(at.shape, ())
self.assertEqual(at.dtype, "string")
self.assertEqual(at.name, "NX_class")
self.assertEqual(at[...], "NXinstrument")
at = ins.attributes["short_name"]
self.assertTrue(at.is_valid)
self.assertTrue(hasattr(at.shape, "__iter__"))
self.assertEqual(len(at.shape), 0)
self.assertEqual(at.shape, ())
self.assertEqual(at.dtype, "string")
self.assertEqual(at.name, "short_name")
self.assertEqual(at[...], "scan instrument")
det = ins.open("detector")
self.assertTrue(det.is_valid)
self.assertEqual(det.name, "detector")
self.assertEqual(len(det.attributes), 1)
self.assertEqual(det.size, 2)
at = det.attributes["NX_class"]
self.assertTrue(at.is_valid)
self.assertTrue(hasattr(at.shape, "__iter__"))
self.assertEqual(len(at.shape), 0)
self.assertEqual(at.shape, ())
self.assertEqual(at.dtype, "string")
self.assertEqual(at.name, "NX_class")
self.assertEqual(at[...], "NXdetector")
cnt = det.open("counter1")
self.assertTrue(cnt.is_valid)
self.assertEqual(cnt.name, "counter1")
self.assertTrue(hasattr(cnt.shape, "__iter__"))
self.assertEqual(len(cnt.shape), 1)
self.assertEqual(cnt.shape, (2, ))
self.assertEqual(cnt.dtype, "float64")
self.assertEqual(cnt.size, 2)
value = cnt.read()
# value = cnt[:]
for i in range(len(value)):
self.assertEqual(self._counter[0], value[i])
self.assertEqual(len(cnt.attributes), 4)
at = cnt.attributes["nexdatas_strategy"]
self.assertTrue(at.is_valid)
self.assertTrue(hasattr(at.shape, "__iter__"))
self.assertEqual(len(at.shape), 0)
self.assertEqual(at.shape, ())
self.assertEqual(at.dtype, "string")
self.assertEqual(at.name, "nexdatas_strategy")
self.assertEqual(at[...], "STEP")
at = cnt.attributes["type"]
self.assertTrue(at.is_valid)
self.assertTrue(hasattr(at.shape, "__iter__"))
self.assertEqual(len(at.shape), 0)
self.assertEqual(at.shape, ())
self.assertEqual(at.dtype, "string")
self.assertEqual(at.name, "type")
self.assertEqual(at[...], "NX_FLOAT")
at = cnt.attributes["units"]
self.assertTrue(at.is_valid)
self.assertTrue(hasattr(at.shape, "__iter__"))
self.assertEqual(len(at.shape), 0)
self.assertEqual(at.shape, ())
self.assertEqual(at.dtype, "string")
self.assertEqual(at.name, "units")
self.assertEqual(at[...], "m")
at = cnt.attributes["nexdatas_source"]
self.assertTrue(at.is_valid)
self.assertTrue(hasattr(at.shape, "__iter__"))
self.assertEqual(len(at.shape), 0)
self.assertEqual(at.shape, ())
self.assertEqual(at.dtype, "string")
mca = det.open("mca")
self.assertTrue(mca.is_valid)
self.assertEqual(mca.name, "mca")
self.assertTrue(hasattr(cnt.shape, "__iter__"))
self.assertEqual(len(mca.shape), 2)
self.assertEqual(mca.shape, (2, 2048))
self.assertEqual(mca.dtype, "float64")
self.assertEqual(mca.size, 4096)
value = mca.read()
for i in range(len(value[0])):
self.assertEqual(self._mca1[i], value[0][i])
for i in range(len(value[0])):
self.assertEqual(self._mca1[i], value[1][i])
self.assertEqual(len(mca.attributes), 4)
at = cnt.attributes["nexdatas_strategy"]
self.assertTrue(at.is_valid)
self.assertTrue(hasattr(at.shape, "__iter__"))
self.assertEqual(len(at.shape), 0)
self.assertEqual(at.shape, ())
self.assertEqual(at.dtype, "string")
self.assertEqual(at.name, "nexdatas_strategy")
self.assertEqual(at[...], "STEP")
at = mca.attributes["type"]
self.assertTrue(at.is_valid)
self.assertTrue(hasattr(at.shape, "__iter__"))
self.assertEqual(len(at.shape), 0)
self.assertEqual(at.shape, ())
self.assertEqual(at.dtype, "string")
self.assertEqual(at.name, "type")
self.assertEqual(at[...], "NX_FLOAT")
at = mca.attributes["units"]
self.assertTrue(at.is_valid)
self.assertTrue(hasattr(at.shape, "__iter__"))
self.assertEqual(len(at.shape), 0)
self.assertEqual(at.shape, ())
self.assertEqual(at.dtype, "string")
self.assertEqual(at.name, "units")
self.assertEqual(at[...], "")
at = mca.attributes["nexdatas_source"]
self.assertTrue(at.is_valid)
self.assertTrue(hasattr(at.shape, "__iter__"))
self.assertEqual(len(at.shape), 0)
self.assertEqual(at.shape, ())
self.assertEqual(at.dtype, "string")
f.close()
finally:
if os.path.isfile(fname):
os.remove(fname)
if os.path.isfile(xmlfile):
os.remove(xmlfile)
if os.path.isfile(jsonfile):
os.remove(jsonfile)
