def save_scan(self, nxentry, scan):
'''*internal*: save the data from each SPEC scan to its own NXentry group'''
scan.interpret() # ensure interpretation is complete
eznx.addAttributes(nxentry, default="data")
eznx.write_dataset(nxentry, "title", str(scan))
eznx.write_dataset(nxentry, "scan_number", scan.scanNum)
eznx.write_dataset(nxentry, "command", scan.scanCmd)
for func in scan.header.h5writers.values():
# ask the header plugins to save their part
func(nxentry, self, scan.header, nxclass=CONTAINER_CLASS)
for func in scan.h5writers.values():
# ask the scan plugins to save their part
func(nxentry, self, scan, nxclass=CONTAINER_CLASS)
def save_scan(self, nxentry, scan):
'''*internal*: save the data from each SPEC scan to its own NXentry group'''
scan.interpret() # ensure interpretation is complete
eznx.addAttributes(nxentry, default="data")
eznx.write_dataset(nxentry, "title", str(scan))
eznx.write_dataset(nxentry, "scan_number", scan.scanNum)
eznx.write_dataset(nxentry, "command", scan.scanCmd)
for func in scan.header.h5writers.values():
# ask the header plugins to save their part
func(nxentry, self, scan.header, nxclass=CONTAINER_CLASS)
for func in scan.h5writers.values():
# ask the scan plugins to save their part
func(nxentry, self, scan, nxclass=CONTAINER_CLASS)
def save_data(self, nxdata, scan):
'''*internal*: store the scan data'''
scan_type = scan.scanCmd.split()[0]
signal, axes = '', [
'',
]
if scan_type in ('mesh', 'hklmesh'):
# hklmesh H 1.9 2.1 100 K 1.9 2.1 100 -800000
signal, axes = self.mesh(nxdata, scan)
elif scan_type in ('hscan', 'kscan', 'lscan', 'hklscan'):
# hklscan 1.00133 1.00133 1.00133 1.00133 2.85 3.05 200 -400000
h_0, h_N, k_0, k_N, l_0, l_N = scan.scanCmd.split()[1:7]
if h_0 != h_N: axes = [
'H',
]
elif k_0 != k_N: axes = [
'K',
]
elif l_0 != l_N: axes = [
'L',
]
signal, axes = self.oneD(nxdata, scan)
else:
signal, axes = self.oneD(nxdata, scan)
# these locations suggested to NIAC, easier to parse than attached to dataset!
if len(signal) == 0:
pass
# Syntax of axes attribute (http://wiki.nexusformat.org/2014_axes_and_uncertainties):
# @axes="H:K" INCOREECT
# @axes="H", "K" CORRECT
if axes.find(':') >= 0:
axes = axes.split(':')
eznx.addAttributes(nxdata, signal=signal, axes=axes)
#eznx.addAttributes(nxdata[signal], signal=1, axes=axes) # deprecated now
# assume here that "axis_name" has rank=1
# TODO: test that scan.data[axis_name] has rank=1
indices = [
0,
] # 0-based reference
if isinstance(axes, str):
eznx.addAttributes(nxdata, **{axes + '_indices': indices})
else:
for axis_name in axes:
eznx.addAttributes(nxdata, **{axis_name + '_indices': indices})
def save_data(self, nxdata, scan):
'''*internal*: store the scan data'''
scan_type = scan.scanCmd.split()[0]
signal, axes = '', ['',]
if scan_type in ('mesh', 'hklmesh'):
# hklmesh H 1.9 2.1 100 K 1.9 2.1 100 -800000
signal, axes = self.mesh(nxdata, scan)
elif scan_type in ('hscan', 'kscan', 'lscan', 'hklscan'):
# hklscan 1.00133 1.00133 1.00133 1.00133 2.85 3.05 200 -400000
h_0, h_N, k_0, k_N, l_0, l_N = scan.scanCmd.split()[1:7]
if h_0 != h_N: axes = ['H',]
elif k_0 != k_N: axes = ['K',]
elif l_0 != l_N: axes = ['L',]
signal, axes = self.oneD(nxdata, scan)
else:
signal, axes = self.oneD(nxdata, scan)
# these locations suggested to NIAC, easier to parse than attached to dataset!
if len(signal) == 0:
pass
# Syntax of axes attribute (http://wiki.nexusformat.org/2014_axes_and_uncertainties):
# @axes="H:K" INCOREECT
# @axes="H", "K" CORRECT
if axes.find(':') >= 0:
axes = axes.split(':')
eznx.addAttributes(nxdata, signal=signal, axes=axes)
#eznx.addAttributes(nxdata[signal], signal=1, axes=axes) # deprecated now
# assume here that "axis_name" has rank=1
# TODO: test that scan.data[axis_name] has rank=1
indices = [0,] # 0-based reference
if isinstance(axes, str):
eznx.addAttributes(nxdata, **{axes+'_indices': indices})
else:
for axis_name in axes:
eznx.addAttributes(nxdata, **{axis_name+'_indices': indices})
def save(self, hdf_file, scan_list=[]):
'''
save the information in this SPEC data file to a NeXus HDF5 file
Each scan in scan_list will be converted to a **NXentry** group.
Scan data will be placed in a **NXdata** group where the attribute **signal=1** is the
last column and the corresponding attribute **axes=<name of the first column>**.
There are variations on this for 2-D and higher dimensionality data, such as mesh scans.
In general, the tree structure of the NeXus HDF5 file is::
hdf5_file: NXroot
@default="S1"
definition="NXspecdata"
# attributes
S1:NXentry
@default="data"
# attributes and metadata fields
data:NXdata
@signal=<name of signal field>
@axes=<name(s) of axes of signal>
@<axis>_indices=<list of indices in "axis1">
<signal_is_the_last_column>:NX_NUMBER[number of points] = ... data ...
@signal=1
@axes='<axis_is_name_of_first_column>'
@<axis>_indices=<list of indices in "axis1" used as dimension scales of the "signal">
<axis_is_name_of_first_column>:NX_NUMBER[number of points] = ... data ...
# other columns from the scan
:param str hdf_file: name of NeXus/HDF5 file to be written
:param [int] scanlist: list of scan numbers to be read
'''
root = eznx.makeFile(hdf_file, **self.root_attributes())
pick_first_entry = True
for key in scan_list:
nxentry = eznx.makeGroup(root, 'S'+str(key), 'NXentry')
eznx.makeDataset(nxentry,
'definition',
'NXspecdata',
description='NeXus application definition (status pending)')
self.save_scan(nxentry, self.spec.getScan(key))
if pick_first_entry:
pick_first_entry = False
eznx.addAttributes(root, default='S'+str(key))
if 'data' not in nxentry:
# NXentry MUST have a NXdata group with data for default plot
nxdata = eznx.makeGroup(nxentry,
'data',
'NXdata',
signal='no_y_data',
axes='no_x_data',
no_x_data_indices=[0,],
)
eznx.makeDataset(nxdata,
"no_x_data",
(0, 1),
units='none',
long_name='no data points in this scan')
eznx.makeDataset(nxdata,
"no_y_data",
(0, 1),
units='none',
long_name='no data points in this scan')
root.close() # be CERTAIN to close the file
def save(self, hdf_file, scan_list=[]):
'''
save the information in this SPEC data file to a NeXus HDF5 file
Each scan in scan_list will be converted to a **NXentry** group.
Scan data will be placed in a **NXdata** group where the attribute **signal=1** is the
last column and the corresponding attribute **axes=<name of the first column>**.
There are variations on this for 2-D and higher dimensionality data, such as mesh scans.
In general, the tree structure of the NeXus HDF5 file is::
hdf5_file: NXroot
@default="S1"
definition="NXspecdata"
# attributes
S1:NXentry
@default="data"
# attributes and metadata fields
data:NXdata
@signal=<name of signal field>
@axes=<name(s) of axes of signal>
@<axis>_indices=<list of indices in "axis1">
<signal_is_the_last_column>:NX_NUMBER[number of points] = ... data ...
@signal=1
@axes='<axis_is_name_of_first_column>'
@<axis>_indices=<list of indices in "axis1" used as dimension scales of the "signal">
<axis_is_name_of_first_column>:NX_NUMBER[number of points] = ... data ...
# other columns from the scan
:param str hdf_file: name of NeXus/HDF5 file to be written
:param [int] scanlist: list of scan numbers to be read
'''
root = eznx.makeFile(hdf_file, **self.root_attributes())
pick_first_entry = True
for key in scan_list:
nxentry = eznx.makeGroup(root, 'S' + str(key), 'NXentry')
eznx.makeDataset(
nxentry,
'definition',
'NXspecdata',
description='NeXus application definition (status pending)')
self.save_scan(nxentry, self.spec.getScan(key))
if pick_first_entry:
pick_first_entry = False
eznx.addAttributes(root, default='S' + str(key))
if 'data' not in nxentry:
# NXentry MUST have a NXdata group with data for default plot
nxdata = eznx.makeGroup(
nxentry,
'data',
'NXdata',
signal='no_y_data',
axes='no_x_data',
no_x_data_indices=[
0,
],
)
eznx.makeDataset(nxdata,
"no_x_data", (0, 1),
units='none',
long_name='no data points in this scan')
eznx.makeDataset(nxdata,
"no_y_data", (0, 1),
units='none',
long_name='no data points in this scan')
root.close() # be CERTAIN to close the file
