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nexpy_modify_nexus_test.py
97 lines (74 loc) · 3.6 KB
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nexpy_modify_nexus_test.py
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#
# changes required
#
# move scan_fields and scan_header up to subentry
# remove fields that are not required by modified defintion (confluece)
# new field in subentry:
# numerical_scale(optional) [n] int # no. of decimal places - to format numerical strings (if required)
# or (better) an optional @scale (int) attribute for each field
# Issues: have to save to new file before modifying (else original read-only)
# Can't move entire entry to a subentry - have entry and subentry for tests
# using link for measurement breaks title
# use sample name only to avoid all the transformations, beam etc
# don't include instrument
# add optional scan_header
# remove non_scan data
# tests: test pdnx with new definition
#test with manual parameters for entry and data
# if entry is the field containing data then update help string
import nexusformat.nexus as nx
inpath = '/dls/i16/data/2020/mm23580-2/'
outpath = '/dls/science/users/spc93/misc_nexus_data/modified/'
filenum = 815893
def getScanOutputNamesFromDatFile(file):
# Extract information from .dat file that is not yet in the NeXus file
# cols: list of scannable output names involved in the scan
# header: list of strings to add to .dat file header
# cmd: scan command (not currently formatted corrected in nexus files)
# decs: decimal places for each field, based on first row
header, cmd, linestr = [], '', ''
with open(file, "r") as f:
for i in range(5): # assume 5 lines for conventional SRS header
header += [f.readline().replace("\n","")]
while not '&END' in linestr:
linestr = f.readline()
if 'cmd' in linestr:
cmd = (linestr.replace("cmd='","")).replace("'\n","")
cols = f.readline().replace('\n','').split('\t')
value_strings = f.readline().replace('\n','').split('\t')
decs = []
for i in range(len(value_strings)):
int_dec = value_strings[i].split('.')
if len(int_dec) == 1:
decs += [0] #must be integer
else:
decs += [len(int_dec[1])] # number of decimal places
return (cols, header, cmd, decs)
(cols, srs_header, cmd, decs) = getScanOutputNamesFromDatFile('%s%i.dat' % (inpath, filenum))
n = nx.nxload('%s%i.nxs' % (inpath, filenum))
n.save('%s%i.nxs' % (outpath, filenum),'w') # seems to be required in order to change read/write mode
with n.nxfile:
n['/entry1'].attrs['default'] ='scan'
n['entry1/scan'] = nx.NXsubentry(definition = 'NXclassic_scan')
n['/entry1/scan'].attrs['default'] = 'measurement'
n['entry1/scan/title'] = cmd #get command string from .dat file
n['entry1/scan/start_time'] = nx.NXlink(n['/entry1/start_time'])
n['entry1/scan/end_time'] = nx.NXlink(n['/entry1/end_time'])
n['entry1/scan/scan_command'] = nx.NXlink(n['/entry1/scan_command'])
n['entry1/scan/measurement'] = n['/entry1/measurement']
n['entry1/scan/scan_header'] = srs_header
n['entry1/scan/scan_fields'] = cols
n['entry1/scan/called_by'] = 'Not yet implemented in GDA'
n['entry1/scan/positioners'] = nx.NXlink(n['/entry1/before_scan'])
ind_str = '%s_indices' % str(n['/entry1/scan/measurement']._attrs['axes'])
n['/entry1/scan/measurement']._attrs[ind_str] = 0
for i in range(len(cols)):
print(cols[i], decs[i])
n['entry1/scan/measurement'][cols[i]].attrs['decimals'] = decs[i]
#del n['/entry1/measurement'] # delete else @default doesn't work
# test new file
new = nx.nxload('%s%i.nxs' % (outpath, filenum))
#print(new.entry1.scan.tree)
#new.entry1.scan.plot()
new.plot()
new['entry1/scan/measurement/eta'].attrs