#!/usr/bin/env python
'''
Writes a simple NeXus HDF5 file using h5py with links
according to the example from Figure 2.1 in the Design chapter
'''
import my_lib
INPUT_FILE = 'input.dat'
HDF5_FILE = 'writer_2_1.hdf5'
#---------------------------
tthData, countsData = my_lib.get2ColumnData(INPUT_FILE)
f = my_lib.makeFile(HDF5_FILE) # create the HDF5 NeXus file
nxentry = my_lib.makeGroup(f, 'entry', 'NXentry')
nxinstrument = my_lib.makeGroup(nxentry, 'instrument', 'NXinstrument')
nxdetector = my_lib.makeGroup(nxinstrument, 'detector', 'NXdetector')
tth = my_lib.makeDataset(nxdetector, "two_theta", tthData, units='degrees')
counts = my_lib.makeDataset(nxdetector,
"counts",
countsData,
units='counts',
signal=1,
axes='two_theta')
nxdata = my_lib.makeGroup(nxentry, 'data', 'NXdata')
my_lib.makeLink(nxdetector, tth, nxdata.name + '/two_theta')
#!/usr/bin/env python
'''
Writes the simplest NeXus HDF5 file using
a simple helper library with h5py and numpy calls
according to the example from Figure 1.3
in the Introduction chapter
'''
import my_lib
INPUT_FILE = 'input.dat'
HDF5_FILE = 'writer_1_3.hdf5'
#---------------------------
tthData, countsData = my_lib.get2ColumnData(INPUT_FILE)
f = my_lib.makeFile(HDF5_FILE)
# since this is a simple example, no attributes are used at this point
nxentry = my_lib.makeGroup(f, 'Scan', 'NXentry')
nxdata = my_lib.makeGroup(nxentry, 'data', 'NXdata')
my_lib.makeDataset(nxdata, "two_theta", tthData, units='degrees')
my_lib.makeDataset(nxdata, "counts", countsData,
units='counts', signal=1, axes='two_theta')
f.close() # be CERTAIN to close the file
'''
import my_lib
FILE_INPUT = 'input.dat'
FILE_HDF5_MASTER = 'external_master.hdf5'
FILE_HDF5_ANGLES = 'external_angles.hdf5'
FILE_HDF5_COUNTS = 'external_counts.hdf5'
#---------------------------
# get some data
tthData, countsData = my_lib.get2ColumnData(FILE_INPUT)
# put the angle data in an external (non-NeXus) HDF5 data file
f = my_lib.makeFile(FILE_HDF5_ANGLES) # create an HDF5 file (non-NeXus)
tth = my_lib.makeDataset(f, "angles", tthData, units='degrees')
f.close() # be CERTAIN to close the file
# put the detector counts in an external NeXus HDF5 data file
f = my_lib.makeFile(FILE_HDF5_COUNTS)
nxentry = my_lib.makeGroup(f, 'entry', 'NXentry')
nxinstrument = my_lib.makeGroup(nxentry, 'instrument', 'NXinstrument')
nxdetector = my_lib.makeGroup(nxinstrument, 'detector', 'NXdetector')
counts = my_lib.makeDataset(nxdetector,
"counts",
countsData,
units='counts',
signal=1,
axes='two_theta')
# make a link since "two_theta" has not been stored here
import my_lib # uses h5py
print "Write a NeXus HDF5 file"
fileName = "prj_test.nexus.hdf5"
timestamp = "2010-10-18T17:17:04-0500"
# load data from two column format
data = numpy.loadtxt('input.dat').T
mr_arr = data[0]
i00_arr = numpy.asarray(data[1], 'int32')
# create the HDF5 NeXus file
f = my_lib.makeFile(fileName,
file_name=fileName,
file_time=timestamp,
instrument="APS USAXS at 32ID-B",
creator="BasicWriter.py",
NeXus_version="4.3.0",
HDF5_Version=h5py.version.hdf5_version,
h5py_version=h5py.version.version)
nxentry = my_lib.makeGroup(f, "entry", "NXentry")
my_lib.makeDataset(nxentry, 'title', data='1-D scan of I00 v. mr')
nxdata = my_lib.makeGroup(nxentry, "mr_scan", "NXdata")
my_lib.makeDataset(nxdata,
"mr",
mr_arr,
units='degrees',
long_name='USAXS mr (degrees)')
#!/usr/bin/env python """ Writes a simple NeXus HDF5 file using h5py with links according to the example from Figure 2.1 in the Design chapter """ import my_lib INPUT_FILE = "input.dat" HDF5_FILE = "writer_2_1.hdf5" # --------------------------- tthData, countsData = my_lib.get2ColumnData(INPUT_FILE) f = my_lib.makeFile(HDF5_FILE) # create the HDF5 NeXus file nxentry = my_lib.makeGroup(f, "entry", "NXentry") nxinstrument = my_lib.makeGroup(nxentry, "instrument", "NXinstrument") nxdetector = my_lib.makeGroup(nxinstrument, "detector", "NXdetector") tth = my_lib.makeDataset(nxdetector, "two_theta", tthData, units="degrees") counts = my_lib.makeDataset(nxdetector, "counts", countsData, units="counts", signal=1, axes="two_theta") nxdata = my_lib.makeGroup(nxentry, "data", "NXdata") my_lib.makeLink(nxdetector, tth, nxdata.name + "/two_theta") my_lib.makeLink(nxdetector, counts, nxdata.name + "/counts") f.close() # be CERTAIN to close the file
import my_lib # uses h5py
print "Write a NeXus HDF5 file"
fileName = "prj_test.nexus.hdf5"
timestamp = "2010-10-18T17:17:04-0500"
# load data from two column format
data = numpy.loadtxt('input.dat').T
mr_arr = data[0]
i00_arr = numpy.asarray(data[1],'int32')
# create the HDF5 NeXus file
f = my_lib.makeFile(fileName, file_name=fileName,
file_time=timestamp,
instrument="APS USAXS at 32ID-B",
creator="BasicWriter.py",
NeXus_version="4.3.0",
HDF5_Version=h5py.version.hdf5_version,
h5py_version=h5py.version.version)
nxentry = my_lib.makeGroup(f, "entry", "NXentry")
my_lib.makeDataset(nxentry, 'title', data='1-D scan of I00 v. mr')
nxdata = my_lib.makeGroup(nxentry, "mr_scan", "NXdata")
my_lib.makeDataset(nxdata, "mr", mr_arr, units='degrees',
long_name='USAXS mr (degrees)')
my_lib.makeDataset(nxdata, "I00", i00_arr, units='counts',
signal=1, # Y axis of default plot
axes='mr', # name "mr" as X axis
Writes the simplest NeXus HDF5 file using
a simple helper library with h5py and numpy calls
according to the example from Figure 1.3
in the Introduction chapter
'''
import my_lib
INPUT_FILE = 'input.dat'
HDF5_FILE = 'writer_1_3.hdf5'
#---------------------------
tthData, countsData = my_lib.get2ColumnData(INPUT_FILE)
f = my_lib.makeFile(HDF5_FILE)
# since this is a simple example, no attributes are used at this point
nxentry = my_lib.makeGroup(f, 'Scan', 'NXentry')
nxdata = my_lib.makeGroup(nxentry, 'data', 'NXdata')
my_lib.makeDataset(nxdata, "two_theta", tthData, units='degrees')
my_lib.makeDataset(nxdata,
"counts",
countsData,
units='counts',
signal=1,
axes='two_theta')
f.close() # be CERTAIN to close the file
