def testCheckParameters(self):
xsDataInput = XSDataInputAlignStack()
xsDataInput.setHDF5File(XSDataFile())
xsDataInput.setInternalHDF5Path(XSDataString())
edPluginExecAlignStack = self.createPlugin()
edPluginExecAlignStack.setDataInput(xsDataInput)
edPluginExecAlignStack.checkParameters()
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlFullFieldXASv1_0.preProcess")
sdi = self.dataInput
self.index = sdi.index.value
self.HDF5filename = sdi.HDF5File
self.internalHDF5Path = sdi.internalHDF5Path
self.xsdMeasureOffset = sdi.measureOffset
if sdi.energy is not None:
self.energy = sdi.energy.value
if sdi.reference is not None:
self.reference = sdi.reference.value
self.xsdNormalizedFilename = sdi.saveNormalized
self.xsdAlignStack = XSDataInputAlignStack()
if sdi.dontAlign is not None:
self.xsdAlignStack.dontAlign = sdi.dontAlign
def testCheckParameters(self):
xsDataInput = XSDataInputAlignStack()
xsDataInput.setHDF5File(XSDataFile())
xsDataInput.setInternalHDF5Path(XSDataString())
edPluginExecAlignStack = self.createPlugin()
edPluginExecAlignStack.setDataInput(xsDataInput)
edPluginExecAlignStack.checkParameters()
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlFullFieldXASv1_0.preProcess")
sdi = self.dataInput
self.index = sdi.index.value
self.HDF5filename = sdi.HDF5File
self.internalHDF5Path = sdi.internalHDF5Path
self.xsdMeasureOffset = sdi.measureOffset
if sdi.energy is not None:
self.energy = sdi.energy.value
if sdi.reference is not None:
self.reference = sdi.reference.value
self.xsdNormalizedFilename = sdi.saveNormalized
self.xsdAlignStack = XSDataInputAlignStack()
if sdi.dontAlign is not None:
self.xsdAlignStack.dontAlign = sdi.dontAlign
class EDPluginControlFullFieldXASv1_0(EDPluginControl):
"""
Plugin to control Full Field XRay Absorption Spectroscopy Experiment, ID21 ESRF
"""
_semaphore = Semaphore()
TITLE = "FullField XANES mapping"
start_time = time.time()
DSenergy = "energy"
DSstack = "data"
energyAttr = {"unit":"keV",
"long_name": "Energy of the monochromated beam",
"interpretation": "scalar",
"axis" : "1"
}
maxIntAttr = {"long_name": "Mean of the last percentil on the frame",
"interpretation": "scalar",
"monitor": "1"
}
dataAttr = {"axes":DSenergy,
"long_name":TITLE,
"interpretation":"image",
"signal":1}
NXdataAttr = {"NX_class":"NXdata"}
NXdata = "NXdata"
NXentryAttr = {"NX_class":"NXentry",
"index":"1"}
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputFullFieldXAS)
self.__strControlledNormalize = "EDPluginExecNormalizeImagev1_2"
self.__strControlledAlign = "EDPluginControlAlignStackv1_0"
self.index = None
self.energy = None
self.reference = 0
self.HDF5filename = None
self.internalHDF5Path = None
self.xsdMeasureOffset = None
self.xsdNormalizedFilename = None
self.xsdAlignStack = None
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginControlFullFieldXASv1_0.checkParameters")
self.checkMandatoryParameters(self.dataInput, "Data Input is None")
self.checkMandatoryParameters(self.dataInput.index, "No index given for data input ")
self.checkMandatoryParameters(self.dataInput.HDF5File, "No HDF5 file given for data input")
self.checkMandatoryParameters(self.dataInput.internalHDF5Path, "No HDF5 internal path given for data input")
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlFullFieldXASv1_0.preProcess")
sdi = self.dataInput
self.index = sdi.index.value
self.HDF5filename = sdi.HDF5File
self.internalHDF5Path = sdi.internalHDF5Path
self.xsdMeasureOffset = sdi.measureOffset
if sdi.energy is not None:
self.energy = sdi.energy.value
if sdi.reference is not None:
self.reference = sdi.reference.value
self.xsdNormalizedFilename = sdi.saveNormalized
self.xsdAlignStack = XSDataInputAlignStack()
if sdi.dontAlign is not None:
self.xsdAlignStack.dontAlign = sdi.dontAlign
def process(self, _edObject=None):
EDPluginControl.process(self)
h5Grp = EDPluginHDF5.createStructure(self.HDF5filename.path.value, self.internalHDF5Path.value)
self.DEBUG("EDPluginControlFullFieldXASv1_0.process")
self.makeHDF5OffsetStructure()
if self.energy is not None:
self.makeHDF5EnergyStructure()
edPluginExecNormalize = self.loadPlugin(self.__strControlledNormalize)
edPluginExecNormalize.connectSUCCESS(self.doSuccessExecNormalize)
edPluginExecNormalize.connectFAILURE(self.doFailureExecNormalize)
sdi = self.dataInput
xsdInNorm = XSDataInputNormalize(data=sdi.data,
flat=sdi.flat,
dark=sdi.dark,
dataScaleFactor=sdi.dataScaleFactor,
darkScaleFactor=sdi.darkScaleFactor,
flatScaleFactor=sdi.flatScaleFactor)
if self.xsdNormalizedFilename is not None:
xsdInNorm.output = XSDataImageExt(path=self.xsdNormalizedFilename.path)
else:
xsdInNorm.output = XSDataImageExt(shared=XSDataString("Normalized-%06i" % sdi.index.value))
edPluginExecNormalize.dataInput = xsdInNorm
edPluginExecNormalize.executeSynchronous()
if self.xsdAlignStack is not None:
edPluginAlign = self.loadPlugin(self.__strControlledAlign)
edPluginAlign.dataInput = self.xsdAlignStack
edPluginAlign.connectSUCCESS(self.doSuccessExecAlign)
edPluginAlign.connectFAILURE(self.doFailureExecAlign)
edPluginAlign.executeSynchronous()
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginControlFullFieldXASv1_0.postProcess")
# Create some output data
self.synchronizePlugins()
self.makeHDF5NeXus()
xsDataResult = XSDataResultFullFieldXAS()
xsDataResult.setHDF5File(self.dataInput.getHDF5File())
xsDataResult.setInternalHDF5Path(self.dataInput.getInternalHDF5Path())
self.setDataOutput(xsDataResult)
self.emptyListOfLoadedPlugin()
self.xsdMeasureOffset = None
self.xsdNormalizedFilename = None
self.xsdAlignStack = None
def doSuccessExecNormalize(self, _edPlugin=None):
with self.locked():
self.DEBUG("EDPluginControlFullFieldXASv1_0.doSuccessExecNormalize")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlFullFieldXASv1_0.doSuccessExecNormalize")
self.xsdAlignStack.setMeasureOffset(self.xsdMeasureOffset)
output = _edPlugin.dataOutput.output
self.xsdAlignStack.images = [output]
data = EDUtilsArray.getArray(output)
data.shape = -1
self.xsdAlignStack.index = [XSDataInteger(self.index)]
self.xsdAlignStack.frameReference = XSDataInteger(self.reference)
self.xsdAlignStack.HDF5File = self.dataInput.getHDF5File()
self.xsdAlignStack.internalHDF5Path = self.internalHDF5Path
internalHDF5Path = self.internalHDF5Path.value
if not internalHDF5Path.startswith("/"):
internalHDF5Path = "/" + internalHDF5Path
keyValuePair1 = XSDataKeyValuePair(key=XSDataString("axes"), value=XSDataString(self.DSenergy))
keyValuePair2 = XSDataKeyValuePair(key=XSDataString("long_name"), value=XSDataString(self.TITLE))
keyValuePair3 = XSDataKeyValuePair(key=XSDataString("interpretation"), value=XSDataString("image"))
keyValuePair4 = XSDataKeyValuePair(key=XSDataString("signal"), value=XSDataString("1"))
xsAttrDataset = XSDataHDF5Attributes(h5path=XSDataString(posixpath.join(internalHDF5Path, self.DSstack)),
metadata=XSDataDictionary([XSDataKeyValuePair(key=XSDataString(k), value=XSDataString(v)) for k, v in self.dataAttr.items()]))
# NXdata is treated in this file not in HDF5 plugins
# xsAttrNXdata = XSDataHDF5Attributes(h5path=XSDataString(posixpath.join(internalHDF5Path, "NXdata")), \
# metadata=XSDataDictionary([XSDataKeyValuePair(key=XSDataString(k), value=XSDataString(v)) for k, v in self.NXdataAttr.items()]))
xsAttrEntry = XSDataHDF5Attributes(h5path=XSDataString(internalHDF5Path),
metadata=XSDataDictionary([XSDataKeyValuePair(key=XSDataString(k), value=XSDataString(v)) for k, v in self.NXentryAttr.items()]))
self.xsdAlignStack.extraAttributes = [xsAttrDataset, xsAttrEntry]
########################################################################
# Selecte the mean of last centile
########################################################################
data.sort()
fMaxSignal = data[int(0.99 * len(data)):].mean()
self.makeHDF5MaxIntStructure(fMaxSignal)
def doFailureExecNormalize(self, _edPlugin=None):
self.DEBUG("EDPluginControlFullFieldXASv1_0.doFailureExecNormalize")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlFullFieldXASv1_0.doFailureExecNormalize")
self.setFailure()
def doSuccessExecAlign(self, _edPlugin=None):
self.DEBUG("EDPluginControlFullFieldXASv1_0.doSuccessExecAlign")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlFullFieldXASv1_0.doSuccessExecAlign")
def doFailureExecAlign(self, _edPlugin=None):
self.DEBUG("EDPluginControlFullFieldXASv1_0.doFailureExecAlign")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlFullFieldXASv1_0.doFailureExecAlign")
self.setFailure()
def makeHDF5EnergyStructure(self):
self.DEBUG("EDPluginControlFullFieldXASv1_0.makeHDF5EnergyStructure")
h5Grp = EDPluginHDF5.createStructure(self.HDF5filename.path.value, self.internalHDF5Path.value)
with EDPluginHDF5.getFileLock(self.HDF5filename.path.value):
if self.DSenergy in h5Grp:
dataset = h5Grp[self.DSenergy]
else:
dataset = h5Grp.create_dataset(self.DSenergy, shape=(1 + max(self.index, self.reference),), dtype="float32", maxshape=(None,), chunks=(1,))
for key in EDPluginControlFullFieldXASv1_0.energyAttr:
dataset.attrs.create(key, EDPluginControlFullFieldXASv1_0.energyAttr[key])
if self.index >= dataset.shape[0]:
dataset.resize((self.index + 1,))
dataset[self.index] = self.energy
def makeHDF5MaxIntStructure(self, _fMaxIntensity):
self.DEBUG("EDPluginControlFullFieldXASv1_0.makeHDF5MaxIntStructure")
h5Grp = EDPluginHDF5.createStructure(self.HDF5filename.path.value, self.internalHDF5Path.value)
with EDPluginHDF5.getFileLock(self.HDF5filename.path.value):
#Seems strange to redefine h5Grp but if there is a flush in between: h5Grp could be closed
h5Grp = EDPluginHDF5.getHDF5File(self.HDF5filename.path.value)[self.internalHDF5Path.value]
if "maxInt" in h5Grp:
dataset = h5Grp["maxInt"]
else:
dataset = h5Grp.create_dataset("maxInt", shape=(1 + max(self.index, self.reference),), dtype="float32", maxshape=(None,), chunks=(1,))
for key in EDPluginControlFullFieldXASv1_0.maxIntAttr:
dataset.attrs.create(key, EDPluginControlFullFieldXASv1_0.maxIntAttr[key])
if self.index >= dataset.shape[0]:
dataset.resize((self.index + 1,))
dataset[self.index] = _fMaxIntensity
def makeHDF5NeXus(self):
self.DEBUG("EDPluginControlFullFieldXASv1_0.makeHDF5NeXus")
with EDPluginHDF5.getFileLock(self.HDF5filename.path.value):
#Seems strange to redefine h5Grp but if there is a flush in between: h5Grp could be closed
entry = EDPluginHDF5.getHDF5File(self.HDF5filename.path.value)[self.internalHDF5Path.value]
if not "title" in entry:
entry.create_dataset("title", data=self.TITLE)
if not "program" in entry:
entry.create_dataset("program", data="EDNA EDPluginControlFullFieldXASv1_0")
if not "start_time" in entry:
entry.create_dataset("start_time", data=EDPluginHDF5.getIsoTime(self.start_time))
########################################################################
# Huge hack: for scalar modification: use [()] to refer to the data !!!
########################################################################
if "end_time" in entry:
entry["end_time"][()] = EDPluginHDF5.getIsoTime()
else:
entry.create_dataset("end_time", data=EDPluginHDF5.getIsoTime())
if "duration" in entry:
entry["duration"][()] = time.time() - self.start_time
else:
entry.create_dataset("duration", data=time.time() - self.start_time, dtype="float")
if self.NXdata not in entry:
nxdata = entry.create_group(self.NXdata)
for k, v in self.NXdataAttr.items():
nxdata.attrs[k] = v
else:
nxdata = entry[self.NXdata]
for ds in [self.DSstack, self.DSenergy]:
if (ds in entry) and (ds not in nxdata):
nxdata[ds] = entry[ds]
def makeHDF5OffsetStructure(self):
self.DEBUG("EDPluginControlFullFieldXASv1_0.makeHDF5OffsetStructure")
with EDPluginHDF5.getFileLock(self.HDF5filename.path.value):
h5Grp = EDPluginHDF5.getHDF5File(self.HDF5filename.path.value)[self.internalHDF5Path.value]
if "Offsets" in h5Grp:
dataset = h5Grp["Offsets"]
else:
dataset = h5Grp.create_dataset("Offsets", shape=(1 + max(self.index, self.reference), 2), dtype="float32", maxshape=(None, 2), chunks=(1, 2))
if self.index >= dataset.shape[0]:
dataset.resize((self.index + 1, 2))
class EDPluginControlFullFieldXASv1_0(EDPluginControl):
"""
Plugin to control Full Field XRay Absorption Spectroscopy Experiment, ID21 ESRF
"""
_semaphore = Semaphore()
TITLE = "FullField XANES mapping"
start_time = time.time()
DSenergy = "energy"
DSstack = "data"
energyAttr = {
"unit": "keV",
"long_name": "Energy of the monochromated beam",
"interpretation": "scalar",
"axis": "1"
}
maxIntAttr = {
"long_name": "Mean of the last percentil on the frame",
"interpretation": "scalar",
"monitor": "1"
}
dataAttr = {
"axes": DSenergy,
"long_name": TITLE,
"interpretation": "image",
"signal": 1
}
NXdataAttr = {"NX_class": "NXdata"}
NXdata = "NXdata"
NXentryAttr = {"NX_class": "NXentry", "index": "1"}
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputFullFieldXAS)
self.__strControlledNormalize = "EDPluginExecNormalizeImagev1_2"
self.__strControlledAlign = "EDPluginControlAlignStackv1_0"
self.index = None
self.energy = None
self.reference = 0
self.HDF5filename = None
self.internalHDF5Path = None
self.xsdMeasureOffset = None
self.xsdNormalizedFilename = None
self.xsdAlignStack = None
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginControlFullFieldXASv1_0.checkParameters")
self.checkMandatoryParameters(self.dataInput, "Data Input is None")
self.checkMandatoryParameters(self.dataInput.index,
"No index given for data input ")
self.checkMandatoryParameters(self.dataInput.HDF5File,
"No HDF5 file given for data input")
self.checkMandatoryParameters(
self.dataInput.internalHDF5Path,
"No HDF5 internal path given for data input")
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlFullFieldXASv1_0.preProcess")
sdi = self.dataInput
self.index = sdi.index.value
self.HDF5filename = sdi.HDF5File
self.internalHDF5Path = sdi.internalHDF5Path
self.xsdMeasureOffset = sdi.measureOffset
if sdi.energy is not None:
self.energy = sdi.energy.value
if sdi.reference is not None:
self.reference = sdi.reference.value
self.xsdNormalizedFilename = sdi.saveNormalized
self.xsdAlignStack = XSDataInputAlignStack()
if sdi.dontAlign is not None:
self.xsdAlignStack.dontAlign = sdi.dontAlign
def process(self, _edObject=None):
EDPluginControl.process(self)
h5Grp = EDPluginHDF5.createStructure(self.HDF5filename.path.value,
self.internalHDF5Path.value)
self.DEBUG("EDPluginControlFullFieldXASv1_0.process")
self.makeHDF5OffsetStructure()
if self.energy is not None:
self.makeHDF5EnergyStructure()
edPluginExecNormalize = self.loadPlugin(self.__strControlledNormalize)
edPluginExecNormalize.connectSUCCESS(self.doSuccessExecNormalize)
edPluginExecNormalize.connectFAILURE(self.doFailureExecNormalize)
sdi = self.dataInput
xsdInNorm = XSDataInputNormalize(data=sdi.data,
flat=sdi.flat,
dark=sdi.dark,
dataScaleFactor=sdi.dataScaleFactor,
darkScaleFactor=sdi.darkScaleFactor,
flatScaleFactor=sdi.flatScaleFactor)
if self.xsdNormalizedFilename is not None:
xsdInNorm.output = XSDataImageExt(
path=self.xsdNormalizedFilename.path)
else:
xsdInNorm.output = XSDataImageExt(
shared=XSDataString("Normalized-%06i" % sdi.index.value))
edPluginExecNormalize.dataInput = xsdInNorm
edPluginExecNormalize.executeSynchronous()
if self.xsdAlignStack is not None:
edPluginAlign = self.loadPlugin(self.__strControlledAlign)
edPluginAlign.dataInput = self.xsdAlignStack
edPluginAlign.connectSUCCESS(self.doSuccessExecAlign)
edPluginAlign.connectFAILURE(self.doFailureExecAlign)
edPluginAlign.executeSynchronous()
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginControlFullFieldXASv1_0.postProcess")
# Create some output data
self.synchronizePlugins()
self.makeHDF5NeXus()
xsDataResult = XSDataResultFullFieldXAS()
xsDataResult.setHDF5File(self.dataInput.getHDF5File())
xsDataResult.setInternalHDF5Path(self.dataInput.getInternalHDF5Path())
self.setDataOutput(xsDataResult)
self.emptyListOfLoadedPlugin()
self.xsdMeasureOffset = None
self.xsdNormalizedFilename = None
self.xsdAlignStack = None
def doSuccessExecNormalize(self, _edPlugin=None):
with self.locked():
self.DEBUG(
"EDPluginControlFullFieldXASv1_0.doSuccessExecNormalize")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlFullFieldXASv1_0.doSuccessExecNormalize")
self.xsdAlignStack.setMeasureOffset(self.xsdMeasureOffset)
output = _edPlugin.dataOutput.output
self.xsdAlignStack.images = [output]
data = EDUtilsArray.getArray(output)
data.shape = -1
self.xsdAlignStack.index = [XSDataInteger(self.index)]
self.xsdAlignStack.frameReference = XSDataInteger(self.reference)
self.xsdAlignStack.HDF5File = self.dataInput.getHDF5File()
self.xsdAlignStack.internalHDF5Path = self.internalHDF5Path
internalHDF5Path = self.internalHDF5Path.value
if not internalHDF5Path.startswith("/"):
internalHDF5Path = "/" + internalHDF5Path
keyValuePair1 = XSDataKeyValuePair(key=XSDataString("axes"),
value=XSDataString(
self.DSenergy))
keyValuePair2 = XSDataKeyValuePair(key=XSDataString("long_name"),
value=XSDataString(self.TITLE))
keyValuePair3 = XSDataKeyValuePair(
key=XSDataString("interpretation"),
value=XSDataString("image"))
keyValuePair4 = XSDataKeyValuePair(key=XSDataString("signal"),
value=XSDataString("1"))
xsAttrDataset = XSDataHDF5Attributes(
h5path=XSDataString(
posixpath.join(internalHDF5Path, self.DSstack)),
metadata=XSDataDictionary([
XSDataKeyValuePair(key=XSDataString(k),
value=XSDataString(v))
for k, v in self.dataAttr.items()
]))
# NXdata is treated in this file not in HDF5 plugins
# xsAttrNXdata = XSDataHDF5Attributes(h5path=XSDataString(posixpath.join(internalHDF5Path, "NXdata")), \
# metadata=XSDataDictionary([XSDataKeyValuePair(key=XSDataString(k), value=XSDataString(v)) for k, v in self.NXdataAttr.items()]))
xsAttrEntry = XSDataHDF5Attributes(
h5path=XSDataString(internalHDF5Path),
metadata=XSDataDictionary([
XSDataKeyValuePair(key=XSDataString(k),
value=XSDataString(v))
for k, v in self.NXentryAttr.items()
]))
self.xsdAlignStack.extraAttributes = [xsAttrDataset, xsAttrEntry]
########################################################################
# Selecte the mean of last centile
########################################################################
data.sort()
fMaxSignal = data[int(0.99 * len(data)):].mean()
self.makeHDF5MaxIntStructure(fMaxSignal)
def doFailureExecNormalize(self, _edPlugin=None):
self.DEBUG("EDPluginControlFullFieldXASv1_0.doFailureExecNormalize")
self.retrieveFailureMessages(
_edPlugin,
"EDPluginControlFullFieldXASv1_0.doFailureExecNormalize")
self.setFailure()
def doSuccessExecAlign(self, _edPlugin=None):
self.DEBUG("EDPluginControlFullFieldXASv1_0.doSuccessExecAlign")
self.retrieveSuccessMessages(
_edPlugin, "EDPluginControlFullFieldXASv1_0.doSuccessExecAlign")
def doFailureExecAlign(self, _edPlugin=None):
self.DEBUG("EDPluginControlFullFieldXASv1_0.doFailureExecAlign")
self.retrieveFailureMessages(
_edPlugin, "EDPluginControlFullFieldXASv1_0.doFailureExecAlign")
self.setFailure()
def makeHDF5EnergyStructure(self):
self.DEBUG("EDPluginControlFullFieldXASv1_0.makeHDF5EnergyStructure")
h5Grp = EDPluginHDF5.createStructure(self.HDF5filename.path.value,
self.internalHDF5Path.value)
with EDPluginHDF5.getFileLock(self.HDF5filename.path.value):
if self.DSenergy in h5Grp:
dataset = h5Grp[self.DSenergy]
else:
dataset = h5Grp.create_dataset(
self.DSenergy,
shape=(1 + max(self.index, self.reference), ),
dtype="float32",
maxshape=(None, ),
chunks=(1, ))
for key in EDPluginControlFullFieldXASv1_0.energyAttr:
dataset.attrs.create(
key, EDPluginControlFullFieldXASv1_0.energyAttr[key])
if self.index >= dataset.shape[0]:
dataset.resize((self.index + 1, ))
dataset[self.index] = self.energy
def makeHDF5MaxIntStructure(self, _fMaxIntensity):
self.DEBUG("EDPluginControlFullFieldXASv1_0.makeHDF5MaxIntStructure")
h5Grp = EDPluginHDF5.createStructure(self.HDF5filename.path.value,
self.internalHDF5Path.value)
with EDPluginHDF5.getFileLock(self.HDF5filename.path.value):
#Seems strange to redefine h5Grp but if there is a flush in between: h5Grp could be closed
h5Grp = EDPluginHDF5.getHDF5File(
self.HDF5filename.path.value)[self.internalHDF5Path.value]
if "maxInt" in h5Grp:
dataset = h5Grp["maxInt"]
else:
dataset = h5Grp.create_dataset(
"maxInt",
shape=(1 + max(self.index, self.reference), ),
dtype="float32",
maxshape=(None, ),
chunks=(1, ))
for key in EDPluginControlFullFieldXASv1_0.maxIntAttr:
dataset.attrs.create(
key, EDPluginControlFullFieldXASv1_0.maxIntAttr[key])
if self.index >= dataset.shape[0]:
dataset.resize((self.index + 1, ))
dataset[self.index] = _fMaxIntensity
def makeHDF5NeXus(self):
self.DEBUG("EDPluginControlFullFieldXASv1_0.makeHDF5NeXus")
with EDPluginHDF5.getFileLock(self.HDF5filename.path.value):
#Seems strange to redefine h5Grp but if there is a flush in between: h5Grp could be closed
entry = EDPluginHDF5.getHDF5File(
self.HDF5filename.path.value)[self.internalHDF5Path.value]
if not "title" in entry:
entry.create_dataset("title", data=self.TITLE)
if not "program" in entry:
entry.create_dataset(
"program", data="EDNA EDPluginControlFullFieldXASv1_0")
if not "start_time" in entry:
entry.create_dataset("start_time",
data=EDPluginHDF5.getIsoTime(
self.start_time))
########################################################################
# Huge hack: for scalar modification: use [()] to refer to the data !!!
########################################################################
if "end_time" in entry:
entry["end_time"][()] = EDPluginHDF5.getIsoTime()
else:
entry.create_dataset("end_time",
data=EDPluginHDF5.getIsoTime())
if "duration" in entry:
entry["duration"][()] = time.time() - self.start_time
else:
entry.create_dataset("duration",
data=time.time() - self.start_time,
dtype="float")
if self.NXdata not in entry:
nxdata = entry.create_group(self.NXdata)
for k, v in self.NXdataAttr.items():
nxdata.attrs[k] = v
else:
nxdata = entry[self.NXdata]
for ds in [self.DSstack, self.DSenergy]:
if (ds in entry) and (ds not in nxdata):
nxdata[ds] = entry[ds]
def makeHDF5OffsetStructure(self):
self.DEBUG("EDPluginControlFullFieldXASv1_0.makeHDF5OffsetStructure")
with EDPluginHDF5.getFileLock(self.HDF5filename.path.value):
h5Grp = EDPluginHDF5.getHDF5File(
self.HDF5filename.path.value)[self.internalHDF5Path.value]
if "Offsets" in h5Grp:
dataset = h5Grp["Offsets"]
else:
dataset = h5Grp.create_dataset(
"Offsets",
shape=(1 + max(self.index, self.reference), 2),
dtype="float32",
maxshape=(None, 2),
chunks=(1, 2))
if self.index >= dataset.shape[0]:
dataset.resize((self.index + 1, 2))
