def test_iso8601(self):
expected = "2010-11-03T13:39:34"
spec = utils.iso8601("Wed Nov 03 13:39:34 2010")
self.assertEqual(spec, expected)
expected = "2017-09-15T04:39:10"
spock = utils.iso8601("09/15/17 04:39:10")
self.assertEqual(spock, expected)
def toTree(self, scan_list=[]):
'''
convert scans from chosen SPEC file into NXroot object and structure
called from nexpy.readers.readspec.ImportDialog.get_data__prjPySpec() after clicking <Ok> in dialog
Each scan in the range from self.scanmin to self.scanmax (inclusive)
will be converted to a NXentry. Scan data will go in a NXdata where
the signal=1 is the last column and the corresponding axes= is the first column.
:param [int] scanlist
:raises: ValueError is Min or Max scan number are not given properly
'''
import spec2nexus
from spec2nexus import utils
# check that scan_list is valid
if len(scan_list) == 0:
return None
if self.SPECfile is None:
return None
complete_scan_list = list(self.SPECfile.scans)
for key in [str(s) for s in scan_list]:
if key not in complete_scan_list:
msg = 'scan ' + str(key) + ' was not found'
raise ValueError(msg)
root = NXroot()
root.attrs['spec2nexus'] = str(spec2nexus.__version__)
header0 = self.SPECfile.headers[0]
root.attrs['SPEC_file'] = self.SPECfile.fileName
root.attrs['SPEC_epoch'] = header0.epoch
root.attrs['SPEC_date'] = utils.iso8601(header0.date)
root.attrs['SPEC_comments'] = '\n'.join(header0.comments)
try:
c = header0.comments[0]
user = c[c.find('User = '******'=')[1].strip()
root.attrs['SPEC_user'] = user
except:
pass
root.attrs['SPEC_num_headers'] = len(self.SPECfile.headers)
self.progress_bar.setVisible(True)
self.progress_bar.setRange(scan_list[0], scan_list[-1])
for key in [str(s) for s in scan_list]:
scan = self.SPECfile.getScan(key)
scan.interpret()
entry = NXentry()
entry.title = str(scan)
entry.date = utils.iso8601(scan.date)
entry.command = scan.scanCmd
entry.scan_number = NXfield(scan.scanNum)
entry.comments = '\n'.join(scan.comments)
entry.data = self.scan_NXdata(scan) # store the scan data
entry.positioners = self.metadata_NXlog(
scan.positioner, 'SPEC positioners (#P & #O lines)')
if hasattr(scan, 'metadata') and len(scan.metadata) > 0:
entry.metadata = self.metadata_NXlog(
scan.metadata,
'SPEC metadata (UNICAT-style #H & #V lines)')
if len(scan.G) > 0:
entry.G = NXlog()
desc = "SPEC geometry arrays, meanings defined by SPEC diffractometer support"
# e.g.: SPECD/four.mac
# http://certif.com/spec_manual/fourc_4_9.html
entry.G.attrs['description'] = desc
for item, value in scan.G.items():
entry.G[item] = NXfield(list(map(float, value.split())))
if scan.T != '':
entry['counting_basis'] = NXfield(
'SPEC scan with constant counting time')
entry['T'] = NXfield(float(scan.T))
entry['T'].units = 'seconds'
entry[
'T'].description = 'SPEC scan with constant counting time'
elif scan.M != '':
entry['counting_basis'] = NXfield(
'SPEC scan with constant monitor count')
entry['M'] = NXfield(float(scan.M))
entry['M'].units = 'counts'
entry[
'M'].description = 'SPEC scan with constant monitor count'
if scan.Q != '':
entry['Q'] = NXfield(list(map(float, scan.Q)))
entry['Q'].description = 'hkl at start of scan'
root['scan_' + str(key)] = entry
self.progress_bar.setValue(int(key))
self.update_progress()
return root
def toTree(self, scan_list=[]):
"""
convert scans from chosen SPEC file into NXroot object and structure
called from nexpy.readers.readspec.ImportDialog.get_data__prjPySpec() after clicking <Ok> in dialog
Each scan in the range from self.scanmin to self.scanmax (inclusive)
will be converted to a NXentry. Scan data will go in a NXdata where
the signal=1 is the last column and the corresponding axes= is the first column.
:param [int] scanlist
:raises: ValueError is Min or Max scan number are not given properly
"""
import spec2nexus
from spec2nexus import utils
# check that scan_list is valid
if len(scan_list) == 0:
return None
if self.SPECfile is None:
return None
complete_scan_list = self.SPECfile.scans.keys()
for key in scan_list:
if key not in complete_scan_list:
msg = "scan " + str(key) + " was not found"
raise ValueError, msg
root = NXroot()
root.attrs["spec2nexus"] = str(spec2nexus.__version__)
header0 = self.SPECfile.headers[0]
root.attrs["SPEC_file"] = self.SPECfile.fileName
root.attrs["SPEC_epoch"] = header0.epoch
root.attrs["SPEC_date"] = utils.iso8601(header0.date)
root.attrs["SPEC_comments"] = "\n".join(header0.comments)
try:
c = header0.comments[0]
user = c[c.find("User = "******"=")[1].strip()
root.attrs["SPEC_user"] = user
except:
pass
root.attrs["SPEC_num_headers"] = len(self.SPECfile.headers)
self.progress_bar.setVisible(True)
self.progress_bar.setRange(scan_list[0], scan_list[-1])
for key in scan_list:
scan = self.SPECfile.getScan(key)
scan.interpret()
entry = NXentry()
entry.title = str(scan)
entry.date = utils.iso8601(scan.date)
entry.command = scan.scanCmd
entry.scan_number = NXfield(scan.scanNum)
entry.comments = "\n".join(scan.comments)
entry.data = self.scan_NXdata(scan) # store the scan data
entry.positioners = self.metadata_NXlog(scan.positioner, "SPEC positioners (#P & #O lines)")
if hasattr(scan, "metadata") and len(scan.metadata) > 0:
entry.metadata = self.metadata_NXlog(scan.metadata, "SPEC metadata (UNICAT-style #H & #V lines)")
if len(scan.G) > 0:
entry.G = NXlog()
desc = "SPEC geometry arrays, meanings defined by SPEC diffractometer support"
# e.g.: SPECD/four.mac
# http://certif.com/spec_manual/fourc_4_9.html
entry.G.attrs["description"] = desc
for item, value in scan.G.items():
entry.G[item] = NXfield(map(float, value.split()))
if scan.T != "":
entry["counting_basis"] = NXfield("SPEC scan with constant counting time")
entry["T"] = NXfield(float(scan.T))
entry["T"].units = "seconds"
entry["T"].description = "SPEC scan with constant counting time"
elif scan.M != "":
entry["counting_basis"] = NXfield("SPEC scan with constant monitor count")
entry["M"] = NXfield(float(scan.M))
entry["M"].units = "counts"
entry["M"].description = "SPEC scan with constant monitor count"
if scan.Q != "":
entry["Q"] = NXfield(map(float, scan.Q))
entry["Q"].description = "hkl at start of scan"
root["scan_" + str(key)] = entry
self.progress_bar.setValue(key)
self.update_progress()
return root
def writer(self, h5parent, writer, scan, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
write_dataset(h5parent, "date", iso8601(scan.date) )
def writer(self, h5parent, writer, scan, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
write_dataset(h5parent, "date", iso8601(scan.date))
