def __init__(self, filename, mode, timestamp=None, creator=None, compression=zipfile.ZIP_DEFLATED, rootpath=None, attrs={}, **kw):
fn = tempfile.mkdtemp()
# os.close(fd) # to be opened by name
self.fn = fn
self.filename = filename
self.mode = mode
self.compression = compression
if rootpath is None:
rootpath = filename.split('.')[0]
self.path = rootpath
preexisting = os.path.exists(os.path.join(self.fn, self.path))
if (mode == "a" and not preexisting) or mode == "w":
os.mkdir(os.path.join(self.fn, self.path))
if timestamp is None:
timestr = iso8601.now()
else:
# If given a time string, check that it is valid
try:
timestamp = iso8601.parse_date(timestamp)
except TypeError:
pass
timestr = iso8601.format_date(timestamp)
attrs['NX_class'] = 'NXroot'
attrs['file_name'] = filename
attrs['file_time'] = timestr
attrs['NeXus_version'] = __version__
if creator is not None:
attrs['creator'] = creator
self.attrs = attrs
def __init__(self, filename, mode="r", timestamp=None, creator=None, compression=zipfile.ZIP_DEFLATED, attrs={}, **kw):
fn = tempfile.mkdtemp()
self.os_path = fn
self.root_node = self
self.filename = filename
self.mode = mode
self.compression = compression
file_exists = os.path.exists(filename)
if file_exists and (mode == "a" or mode == "r"):
zipfile.ZipFile(filename).extractall(self.os_path)
Node.__init__(self, parent_node=self, path="/")
if mode == "a" or mode == "w":
#os.mkdir(os.path.join(self.os_path, self.path.lstrip("/")))
if timestamp is None:
timestr = iso8601.now()
else:
# If given a time string, check that it is valid
try:
timestamp = iso8601.parse_date(timestamp)
except TypeError:
pass
timestr = iso8601.format_date(timestamp)
attrs['NX_class'] = 'NXroot'
attrs['file_name'] = filename
attrs['file_time'] = timestr
attrs['NeXus_version'] = __version__
if creator is not None:
attrs['creator'] = creator
self.attrs.update(attrs)
self.attrs._write()
def bt7_ice_to_nice(icedata):
"""
Convert BT-7 ice data to NeXus.
The instrument description is stored in bt7.xml.
"""
# Pull together header and columns
data = icedata.metadata.copy()
data.update(icedata.data)
# Expand lattice parameters
data.update((k.capitalize(),v) for k,v in data['Lattice'].items())
# Fix up monochromator selection
if abs(data["MonoSpacing"] - 1.278) < 1e-4:
data["MonoMaterial"] = "Cu220"
data["MonoFocus"] = data["FocusCu"]
else:
data["MonoMaterial"] = "PG002"
data["MonoFocus"] = data["FocusPG"]
# Gang monochromator and analyzer blades
data['MonoBlades'] = numpy.array([data[f] for f in iceformat.BT7_MONOCHROMATOR_BLADES])
data['AnaBlades'] = numpy.array([data[f] for f in iceformat.BT7_ANALYZER_BLADES])
# Gather detector data columns
data['SDC'] = numpy.array([icedata.data['SDC%d'%d] for d in range(3)])
data['DDC'] = numpy.array([icedata.data['DDC%d'%d] for d in range(3)])
data['TDC'] = numpy.array([icedata.data['TDC%02d'%d] for d in range(9)])
if 'PSDC0' in icedata.data:
data['PSDC'] = numpy.array([icedata.data['PSDC%02d'%d] for d in range(48)])
# get counts on the detector
data['Counts'] = icedata.counts()
# Only include base E for FixedE. Fixed value is already reported
if 'FixedE' in icedata.metadata:
data['FixedE'] = icedata.metadata['FixedE'][0]
lattice = data['Lattice']
data['Lattice'] = [lattice[k] for k in 'a', 'b', 'c', 'alpha', 'beta', 'gamma']
orient = data['Orient1']
data['Orient1'] = [orient[k] for k in 'h','k','l']
orient = data['Orient2']
data['Orient2'] = [orient[k] for k in 'h','k','l']
data['FilTran'] = data['FilTran'][0]
data['ScanVarying'] = ", ".join(data['ScanVarying'])
data['Date'] = iso8601.format_date(data['Date'])
data['Flip'] = data['Flip'][0]
#data['Flip'] = [{'A':0,'B':1,'C':2,'D':3}.get(c,0)
# for c in data['Flip']]
nicedata = dict((nicekey, {'value': data[icekey],
'units': icedata.units(icekey),
#'shortname': rename_field(nicekey),
})
for icekey,nicekey in _ICE_TO_NICE.items()
if icekey in data and nicekey)
return nicedata
def list(self, response):
"""
Returns { experiments: [[id, title, date], ...] }.
Experiment id, title and date are strings, with date formatted
like 2007-01-25T07:00:00-05:00. The experiments are sorted by
experiment id.
"""
items = ((exp['id'], exp['title'], iso8601.format_date(exp['creationTimeStamp']*0.001))
for exp in self.experiments.values())
return { 'experiments': list(sorted(items)) }
def list(self, response):
"""
Returns { experiments: [[id, title, date], ...] }.
Experiment id, title and date are strings, with date formatted
like 2007-01-25T07:00:00-05:00. The experiments are sorted by
experiment id.
"""
items = ((exp['id'], exp['title'],
iso8601.format_date(exp['creationTimeStamp'] * 0.001))
for exp in self.experiments.values())
return {'experiments': list(sorted(items))}
def __init__(self,
filename,
mode="r",
timestamp=None,
creator=None,
compression=zipfile.ZIP_DEFLATED,
attrs={},
os_path=None,
**kw):
self.readonly = (mode == "r")
Node.__init__(self, parent_node=None, path="/")
if self.readonly:
self.zipfile = zipfile.ZipFile(filename)
self.attrs = self.makeAttrs()
self.filename = filename
self.mode = mode
self.compression = compression
file_exists = os.path.exists(filename)
if not self.readonly:
if os_path is None:
fn = tempfile.mkdtemp()
self.os_path = fn
else:
self.os_path = os_path
if file_exists and (mode == "a"):
zipfile.ZipFile(filename).extractall(self.os_path)
if timestamp is None:
timestr = iso8601.now()
else:
# If given a time string, check that it is valid
try:
timestamp = iso8601.parse_date(timestamp)
except TypeError:
pass
timestr = iso8601.format_date(timestamp)
attrs['NX_class'] = 'NXroot'
attrs['file_name'] = filename
attrs['file_time'] = timestr
attrs['NeXus_version'] = __version__
if creator is not None:
attrs['creator'] = creator
self.attrs.update(attrs)
self.attrs._write()
def __init__(self,
filename,
mode,
timestamp=None,
creator=None,
compression=zipfile.ZIP_DEFLATED,
rootpath=None,
attrs={},
**kw):
fn = tempfile.mkdtemp()
# os.close(fd) # to be opened by name
self.fn = fn
self.filename = filename
self.mode = mode
self.compression = compression
if rootpath is None:
rootpath = filename.split('.')[0]
self.path = rootpath
preexisting = os.path.exists(os.path.join(self.fn, self.path))
if (mode == "a" and not preexisting) or mode == "w":
os.mkdir(os.path.join(self.fn, self.path))
if timestamp is None:
timestr = iso8601.now()
else:
# If given a time string, check that it is valid
try:
timestamp = iso8601.parse_date(timestamp)
except TypeError:
pass
timestr = iso8601.format_date(timestamp)
attrs['NX_class'] = 'NXroot'
attrs['file_name'] = filename
attrs['file_time'] = timestr
attrs['NeXus_version'] = __version__
if creator is not None:
attrs['creator'] = creator
self.attrs = attrs
def bt7_ice_to_nice(icedata):
"""
Convert BT-7 ice data to NeXus.
The instrument description is stored in bt7.xml.
"""
# Pull together header and columns
data = icedata.metadata.copy()
data.update(icedata.data)
# Expand lattice parameters
data.update((k.capitalize(), v) for k, v in data['Lattice'].items())
# Fix up monochromator selection
if abs(data["MonoSpacing"] - 1.278) < 1e-4:
data["MonoMaterial"] = "Cu220"
data["MonoFocus"] = data["FocusCu"]
else:
data["MonoMaterial"] = "PG002"
data["MonoFocus"] = data["FocusPG"]
# Gang monochromator and analyzer blades
data['MonoBlades'] = numpy.array(
[data[f] for f in iceformat.BT7_MONOCHROMATOR_BLADES])
data['AnaBlades'] = numpy.array(
[data[f] for f in iceformat.BT7_ANALYZER_BLADES])
# Gather detector data columns
data['SDC'] = numpy.array([icedata.data['SDC%d' % d] for d in range(3)])
data['DDC'] = numpy.array([icedata.data['DDC%d' % d] for d in range(3)])
data['TDC'] = numpy.array([icedata.data['TDC%02d' % d] for d in range(9)])
if 'PSDC0' in icedata.data:
data['PSDC'] = numpy.array(
[icedata.data['PSDC%02d' % d] for d in range(48)])
# get counts on the detector
data['Counts'] = icedata.counts()
# Only include base E for FixedE. Fixed value is already reported
if 'FixedE' in icedata.metadata:
data['FixedE'] = icedata.metadata['FixedE'][0]
lattice = data['Lattice']
data['Lattice'] = [
lattice[k] for k in 'a', 'b', 'c', 'alpha', 'beta', 'gamma'
]
orient = data['Orient1']
data['Orient1'] = [orient[k] for k in 'h', 'k', 'l']
orient = data['Orient2']
data['Orient2'] = [orient[k] for k in 'h', 'k', 'l']
data['FilTran'] = data['FilTran'][0]
data['ScanVarying'] = ", ".join(data['ScanVarying'])
data['Date'] = iso8601.format_date(data['Date'])
data['Flip'] = data['Flip'][0]
#data['Flip'] = [{'A':0,'B':1,'C':2,'D':3}.get(c,0)
# for c in data['Flip']]
nicedata = dict((
nicekey,
{
'value': data[icekey],
'units': icedata.units(icekey),
#'shortname': rename_field(nicekey),
}) for icekey, nicekey in _ICE_TO_NICE.items()
if icekey in data and nicekey)
return nicedata