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
17.92508 23819
17.92458 49087
17.92408 66802
17.92358 66206
17.92308 64129
17.92258 56795
17.92208 29315
17.92158 6622
17.92108 1321
'''
#---------------------------
tthData, countsData = zip(*[map(float,_.split()) for _ in I_v_TTH_DATA.strip().splitlines()])
f = eznx.makeFile(HDF5_FILE) # create the HDF5 NeXus file
f.attrs['default'] = 'entry'
nxentry = eznx.makeGroup(f, 'entry', 'NXentry', default='data')
nxinstrument = eznx.makeGroup(nxentry, 'instrument', 'NXinstrument')
nxdetector = eznx.makeGroup(nxinstrument, 'detector', 'NXdetector')
tth = eznx.makeDataset(nxdetector, "two_theta", tthData, units='degrees')
counts = eznx.makeDataset(nxdetector, "counts", countsData, units='counts')
nxdata = eznx.makeGroup(nxentry, 'data', 'NXdata',
signal=1, axes='two_theta', two_theta_indices=0)
eznx.makeLink(nxdetector, tth, nxdata.name+'/two_theta')
eznx.makeLink(nxdetector, counts, nxdata.name+'/counts')
f.close() # be CERTAIN to close the file
