def metadata_NXlog(self, spec_metadata, description):
"""Return the specific metadata in an NXlog object."""
from spec2nexus import utils
nxlog = NXlog()
nxlog.attrs['description'] = description
for subkey, value in spec_metadata.items():
clean_name = utils.sanitize_name(nxlog, subkey)
nxlog[clean_name] = NXfield(value)
nxlog[clean_name].original_name = subkey
return nxlog
def metadata_NXlog(self, spec_metadata, description):
'''
return the specific metadata in an NXlog object
'''
from spec2nexus import utils
nxlog = NXlog()
nxlog.attrs['description'] = description
for subkey, value in spec_metadata.items():
clean_name = utils.sanitize_name(nxlog, subkey)
nxlog[clean_name] = NXfield(value)
nxlog[clean_name].original_name = subkey
return nxlog
def parser_mca_spectra(self, nxdata, scan, primary_axis_label):
'''parse for optional MCA spectra'''
if '_mca_' in scan.data: # check for it
for mca_key, mca_data in scan.data['_mca_'].items():
key = "__" + mca_key
nxdata[key] = NXfield(mca_data)
nxdata[key].units = "counts"
ch_key = key + "_channel"
nxdata[ch_key] = NXfield(range(1, len(mca_data[0])+1))
nxdata[ch_key].units = 'channel'
axes = (primary_axis_label, ch_key)
nxdata[key].axes = ':'.join( axes )
def parser_1D_columns(self, nxdata, scan):
'''generic data parser for 1-D column data'''
from spec2nexus import utils
for column in scan.L:
if column in scan.data:
clean_name = utils.sanitize_name(nxdata, column)
nxdata[clean_name] = NXfield(scan.data[column])
nxdata[clean_name].original_name = column
signal = utils.sanitize_name(nxdata, scan.column_last) # primary Y axis
axis = utils.sanitize_name(nxdata, scan.column_first) # primary X axis
nxdata.nxsignal = nxdata[signal]
nxdata.nxaxes = nxdata[axis]
self.parser_mca_spectra(nxdata, scan, axis)
def parser_1D_columns(self, nxdata, scan):
'''generic data parser for 1-D column data'''
from spec2nexus import utils
for column in scan.L:
if column in scan.data:
clean_name = utils.sanitize_name(nxdata, column)
nxdata[clean_name] = NXfield(scan.data[column])
nxdata[clean_name].original_name = column
signal = utils.sanitize_name(nxdata,
scan.column_last) # primary Y axis
axis = utils.sanitize_name(nxdata, scan.column_first) # primary X axis
nxdata.nxsignal = nxdata[signal]
nxdata.nxaxes = nxdata[axis]
self.parser_mca_spectra(nxdata, scan, axis)
def scan_NXdata(self, scan):
'''
return the scan data in an NXdata object
'''
nxdata = NXdata()
if len(scan.data) == 0: # what if no data?
# since no data available, provide trivial, fake data
# this keeps the NXdata base class compliant with the NeXus standard
nxdata.attrs['description'] = 'SPEC scan has no data'
nxdata['noSpecData_y'] = NXfield([0, 0]) # primary Y axis
nxdata['noSpecData_x'] = NXfield([0, 0]) # primary X axis
nxdata.nxsignal = nxdata['noSpecData_y']
nxdata.nxaxes = [
nxdata['noSpecData_x'],
]
return nxdata
nxdata.attrs['description'] = 'SPEC scan data'
scan_type = scan.scanCmd.split()[0]
if scan_type in ('mesh', 'hklmesh'):
# hklmesh H 1.9 2.1 100 K 1.9 2.1 100 -800000
self.parser_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: axis = 'H'
elif k_0 != k_N: axis = 'K'
elif l_0 != l_N: axis = 'L'
else: axis = 'H'
self.parser_1D_columns(nxdata, scan)
nxdata.nxaxes = nxdata[axis]
else:
self.parser_1D_columns(nxdata, scan)
# these locations suggested to NIAC, easier to parse than attached to dataset!
# but these are already set by the `nxsignal` and `nxaxes` assignments
#nxdata.attrs['signal'] = nxdata.nxsignal.nxname
#nxdata.attrs['axes'] = ':'.join([obj.nxname for obj in nxdata.nxaxes])
return nxdata
def parser_mca_spectra(self, nxdata, scan, primary_axis_label):
'''parse for optional MCA spectra'''
if '_mca_' in scan.data: # check for it
for mca_key, mca_data in scan.data['_mca_'].items():
key = "__" + mca_key
nxdata[key] = NXfield(mca_data)
nxdata[key].units = "counts"
ch_key = key + "_channel"
nxdata[ch_key] = NXfield(range(1, len(mca_data[0]) + 1))
nxdata[ch_key].units = 'channel'
axes = (primary_axis_label, ch_key)
nxdata[key].axes = ':'.join(axes)
def scan_NXdata(self, scan):
"""Return the scan data in an NXdata object."""
nxdata = NXdata()
if len(scan.data) == 0: # what if no data?
# since no data available, provide trivial, fake data
# keeping the NXdata base class compliant with the NeXus standard
nxdata.attrs['description'] = 'SPEC scan has no data'
nxdata['noSpecData_y'] = NXfield([0, 0]) # primary Y axis
nxdata['noSpecData_x'] = NXfield([0, 0]) # primary X axis
nxdata.nxsignal = nxdata['noSpecData_y']
nxdata.nxaxes = [nxdata['noSpecData_x'], ]
return nxdata
nxdata.attrs['description'] = 'SPEC scan data'
scan_type = scan.scanCmd.split()[0]
if scan_type in ('mesh', 'hklmesh'):
# hklmesh H 1.9 2.1 100 K 1.9 2.1 100 -800000
self.parser_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:
axis = 'H'
elif k_0 != k_N:
axis = 'K'
elif l_0 != l_N:
axis = 'L'
else:
axis = 'H'
self.parser_1D_columns(nxdata, scan)
nxdata.nxaxes = nxdata[axis]
else:
self.parser_1D_columns(nxdata, scan)
return nxdata
def parser_mesh(self, nxdata, scan):
'''data parser for 2-D mesh and hklmesh'''
# 2-D parser: http://www.certif.com/spec_help/mesh.html
# mesh motor1 start1 end1 intervals1 motor2 start2 end2 intervals2 time
# 2-D parser: http://www.certif.com/spec_help/hklmesh.html
# hklmesh Q1 start1 end1 intervals1 Q2 start2 end2 intervals2 time
# mesh: nexpy/examples/33id_spec.dat scan 22 (also has MCA, thus 3-D data)
# hklmesh: nexpy/examples/33bm_spec.dat scan 17 (no MCA data)
from spec2nexus import utils
label1, start1, end1, intervals1, label2, start2, end2, intervals2, time = scan.scanCmd.split(
)[1:]
if label1 not in scan.data:
label1 = scan.L[0] # mnemonic v. name
if label2 not in scan.data:
label2 = scan.L[1] # mnemonic v. name
axis1 = scan.data.get(label1)
axis2 = scan.data.get(label2)
intervals1, intervals2 = int(intervals1), int(intervals2)
start1, end1 = float(start1), float(end1)
start2, end2 = float(start2), float(end2)
time = float(time)
if len(axis1) < intervals1: # stopped scan before second row started
self.parser_1D_columns(nxdata, scan) # fallback support
# TODO: what about the MCA data in this case?
else:
axis1 = axis1[0:intervals1 + 1]
axis2 = [
axis2[row] for row in range(len(axis2))
if row % (intervals1 + 1) == 0
]
column_labels = scan.L
column_labels.remove(label1) # special handling
column_labels.remove(label2) # special handling
if scan.scanCmd.startswith('hkl'):
# find the reciprocal space axis held constant
label3 = [
key for key in ('H', 'K', 'L')
if key not in (label1, label2)
][0]
axis3 = scan.data.get(label3)[0]
nxdata[label3] = NXfield(axis3)
column_labels.remove(label3) # already handled
nxdata[label1] = NXfield(axis1) # 1-D array
nxdata[label2] = NXfield(axis2) # 1-D array
# build 2-D data objects (do not build label1, label2, [or label3] as 2-D objects)
data_shape = [len(axis2), len(axis1)]
for label in column_labels:
axis = np.array(scan.data.get(label))
clean_name = utils.sanitize_name(nxdata, label)
nxdata[clean_name] = NXfield(
utils.reshape_data(axis, data_shape))
nxdata[clean_name].original_name = label
signal_axis_label = utils.sanitize_name(nxdata, scan.column_last)
nxdata.nxsignal = nxdata[signal_axis_label]
nxdata.nxaxes = [nxdata[label2], nxdata[label1]]
if '_mca_' in scan.data: # 3-D array
# TODO: ?merge with parser_mca_spectra()?
for mca_key, mca_data in scan.data['_mca_'].items():
key = "__" + mca_key
spectra_lengths = list(map(len, mca_data))
num_channels = max(spectra_lengths)
if num_channels != min(spectra_lengths):
msg = 'MCA spectra have different lengths'
msg += ' in scan #' + str(scan.scanNum)
msg += ' in file ' + str(scan.specFile)
raise ValueError(msg)
data_shape += [
num_channels,
]
mca = np.array(mca_data)
nxdata[key] = NXfield(utils.reshape_data(mca, data_shape))
nxdata[key].units = "counts"
try:
# use MCA channel numbers as known at time of scan
chan1 = scan.MCA['first_saved']
chanN = scan.MCA['last_saved']
channel_range = range(chan1, chanN + 1)
except:
# basic indices
channel_range = range(1, num_channels + 1)
ch_key = key + "_channel"
nxdata[ch_key] = NXfield(channel_range)
nxdata[ch_key].units = 'channel'
axes = (label1, label2, ch_key)
nxdata[key].axes = ':'.join(axes)
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 parser_mesh(self, nxdata, scan):
'''data parser for 2-D mesh and hklmesh'''
# 2-D parser: http://www.certif.com/spec_help/mesh.html
# mesh motor1 start1 end1 intervals1 motor2 start2 end2 intervals2 time
# 2-D parser: http://www.certif.com/spec_help/hklmesh.html
# hklmesh Q1 start1 end1 intervals1 Q2 start2 end2 intervals2 time
# mesh: nexpy/examples/33id_spec.dat scan 22 (also has MCA, thus 3-D data)
# hklmesh: nexpy/examples/33bm_spec.dat scan 17 (no MCA data)
from spec2nexus import utils
label1, start1, end1, intervals1, label2, start2, end2, intervals2, time = scan.scanCmd.split()[1:]
if label1 not in scan.data:
label1 = scan.L[0] # mnemonic v. name
if label2 not in scan.data:
label2 = scan.L[1] # mnemonic v. name
axis1 = scan.data.get(label1)
axis2 = scan.data.get(label2)
intervals1, intervals2 = int(intervals1), int(intervals2)
start1, end1 = float(start1), float(end1)
start2, end2 = float(start2), float(end2)
time = float(time)
if len(axis1) < intervals1: # stopped scan before second row started
self.parser_1D_columns(nxdata, scan) # fallback support
# TODO: what about the MCA data in this case?
else:
axis1 = axis1[0:intervals1+1]
axis2 = [axis2[row] for row in range(len(axis2)) if row % (intervals1+1) == 0]
column_labels = scan.L
column_labels.remove(label1) # special handling
column_labels.remove(label2) # special handling
if scan.scanCmd.startswith('hkl'):
# find the reciprocal space axis held constant
label3 = [key for key in ('H', 'K', 'L') if key not in (label1, label2)][0]
axis3 = scan.data.get(label3)[0]
nxdata[label3] = NXfield(axis3)
column_labels.remove(label3) # already handled
nxdata[label1] = NXfield(axis1) # 1-D array
nxdata[label2] = NXfield(axis2) # 1-D array
# build 2-D data objects (do not build label1, label2, [or label3] as 2-D objects)
data_shape = [len(axis2), len(axis1)]
for label in column_labels:
axis = np.array( scan.data.get(label) )
clean_name = utils.sanitize_name(nxdata, label)
nxdata[clean_name] = NXfield(utils.reshape_data(axis, data_shape))
nxdata[clean_name].original_name = label
signal_axis_label = utils.sanitize_name(nxdata, scan.column_last)
nxdata.nxsignal = nxdata[signal_axis_label]
nxdata.nxaxes = [nxdata[label2], nxdata[label1]]
if '_mca_' in scan.data: # 3-D array
# TODO: ?merge with parser_mca_spectra()?
for mca_key, mca_data in scan.data['_mca_'].items():
key = "__" + mca_key
spectra_lengths = list(map(len, mca_data))
num_channels = max(spectra_lengths)
if num_channels != min(spectra_lengths):
msg = 'MCA spectra have different lengths'
msg += ' in scan #' + str(scan.scanNum)
msg += ' in file ' + str(scan.specFile)
raise ValueError(msg)
data_shape += [num_channels, ]
mca = np.array(mca_data)
nxdata[key] = NXfield(utils.reshape_data(mca, data_shape))
nxdata[key].units = "counts"
try:
# use MCA channel numbers as known at time of scan
chan1 = scan.MCA['first_saved']
chanN = scan.MCA['last_saved']
channel_range = range(chan1, chanN+1)
except:
# basic indices
channel_range = range(1, num_channels+1)
ch_key = key + "_channel"
nxdata[ch_key] = NXfield(channel_range)
nxdata[ch_key].units = 'channel'
axes = (label1, label2, ch_key)
nxdata[key].axes = ':'.join( axes )
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
