def loadFOCUS(source) :
f = nxs.open(source,'r')
f.openpath("entry1/FOCUS/merged/counts")
dim,datatype= f.getinfo()
size = np.prod(dim)
data = f.getdata()
f.close()
f = nxs.open(source,'r')
f.openpath("entry1/FOCUS/merged/time_binning")
tof = f.getdata()
f.close()
nEvents = np.sum(data)
signal = np.empty(nEvents,dtype=neventarray.event_t)
nEv = 0
detID = 0
for row in range(dim[0]):
for it in range(dim[1]):
events = data[row][it]
if events > 0:
signal[nEv:nEv+events]["x"] = row
signal[nEv:nEv+events]["y"] = it
nEv = nEv+events
if not signal.shape[0] == nEv:
raise Exception("Error in reading NeXus data: wrong number of events",nEv)
return signal
def loadAMOR(source) :
f = nxs.open(source,'r')
f.openpath("entry1/AMOR/area_detector/data")
dim,datatype= f.getinfo()
size = np.prod(dim)
data = f.getdata()
f.close()
f = nxs.open(source,'r')
f.openpath("entry1/AMOR/area_detector/time_binning")
tof = f.getdata()
f.close()
nEvents = np.sum(data)
signal = np.empty(nEvents,dtype=neventarray.event_t)
nEv = 0
detID = 0
for row in range(dim[0]):
for col in range(dim[1]):
for it in range(dim[2]):
events = data[row][col][it]
if events > 0:
signal[nEv:nEv+events]["ts"] = round(tof[it]/10.)
signal[nEv:nEv+events]["x"] = row
signal[nEv:nEv+events]["y"] = col
nEv = nEv+events
if not signal.shape[0] == nEv:
raise Exception("Error in reading NeXus data: wrong number of events",nEv)
return signal
def loadFOCUS(source):
f = nxs.open(source, 'r')
f.openpath("entry1/FOCUS/merged/counts")
dim, datatype = f.getinfo()
size = np.prod(dim)
data = f.getdata()
f.close()
f = nxs.open(source, 'r')
f.openpath("entry1/FOCUS/merged/time_binning")
tof = f.getdata()
f.close()
nEvents = np.sum(data)
signal = np.empty(nEvents, dtype=neventarray.event_t)
nEv = 0
detID = 0
for row in range(dim[0]):
for it in range(dim[1]):
events = data[row][it]
if events > 0:
signal[nEv:nEv + events]["x"] = row
signal[nEv:nEv + events]["y"] = it
nEv = nEv + events
if not signal.shape[0] == nEv:
raise Exception("Error in reading NeXus data: wrong number of events",
nEv)
return signal
def loadAMOR(source):
f = nxs.open(source, 'r')
f.openpath("entry1/AMOR/area_detector/data")
dim, datatype = f.getinfo()
size = np.prod(dim)
data = f.getdata()
f.close()
f = nxs.open(source, 'r')
f.openpath("entry1/AMOR/area_detector/time_binning")
tof = f.getdata()
f.close()
nEvents = np.sum(data)
signal = np.empty(nEvents, dtype=neventarray.event_t)
nEv = 0
detID = 0
for row in range(dim[0]):
for col in range(dim[1]):
for it in range(dim[2]):
events = data[row][col][it]
if events > 0:
signal[nEv:nEv + events]["ts"] = round(tof[it] / 10.)
signal[nEv:nEv + events]["x"] = row
signal[nEv:nEv + events]["y"] = col
nEv = nEv + events
if not signal.shape[0] == nEv:
raise Exception("Error in reading NeXus data: wrong number of events",
nEv)
return signal
def open(self, **kwds):
if not self.isopen():
if self._mode == 'rw':
self._file = nxs.open(self._filename, 'w5')
else:
self._file = nxs.open(self._filename, 'w5')
self.nxpath = '/'
return self
def isValid(self):
try :
fp = nxs.open(self.filepath,'r')
fp.close()
except Exception:
return False
return True
def check_external(filename,mode):
ext = dict(w5='.h5',w4='.hdf',wx='.xml')[mode]
file = nxs.open(filename,'rw')
file.openpath('/entry1/start_time')
time = file.getdata()
get = file.inquirefile()
expected = 'nxfile://data/dmc01'+ext
if expected != get: fail("first external file returned %s"%(get))
file.openpath('/entry2/sample/sample_name')
sample = file.getdata()
get = file.inquirefile()
expected = 'nxfile://data/dmc02'+ext
if expected != get: fail("second external file returned %s"%(get))
file.openpath('/')
remote = file.isexternalgroup('entry1','NXentry')
if remote is None:
fail("failed to identify /entry1 as external")
remote = file.isexternalgroup('entry3','NXentry')
if remote is not None:
fail('incorrectly identified /entry3 as external')
file.close()
def __init__(self, nexusname):
self.logger = logging
self.detdict = {}
self.det2fileno = {"SAXS": 1, "CALIB": 2, "WAXS": 3, "TIMES": 4}
self.logger.info("looking at " + nexusname + " " +
datetime.datetime.now().__str__())
self.nexusname = nexusname
self.nexusfile = nxs.open(self.nexusname)
self.instrumentname = "DLS"
self.inspectfile()
self.iscommissioningvisit = False
self.isindlsdata = False
components = self.nexusname.split("/")
if len(components) > 6:
if "dls" == components[1]:
if "data" == components[3]:
try:
int(components[4])
# is int
self.isindlsdata = True
self.logger.debug("is in dls data")
if components[5].startswith("cm"):
self.iscommissioningvisit = True
self.logger.debug("is commissioning")
except:
#not in year dir
self.logger.debug("no int year")
pass
def isValid(self):
try:
fp = nxs.open(self.filepath, 'r')
fp.close()
except Exception:
return False
return True
def loadRITA2(source):
f = nxs.open(source, 'r')
f.openpath("entry1/RITA-2/detector/counts")
dim, datatype = f.getinfo()
size = np.prod(dim)
data = f.getdata()
f.close()
np.random.seed(1234)
timestamp = np.sort(np.random.randint(2**32 - 1, size=dim[0]))
nEvents = np.sum(data)
signal = np.empty(nEvents, dtype=neventarray.event_t)
nEv = 0
detID = 0
row = np.uint16
col = np.uint16
for row in range(dim[1]):
for col in range(dim[2]):
for it in range(dim[0]):
events = data[it][row][col]
if events > 0:
signal[nEv:nEv + events]["ts"] = timestamp[it]
signal[nEv:nEv + events]["sync"] = 0
signal[nEv:nEv + events]["x"] = row
signal[nEv:nEv + events]["y"] = col
nEv = nEv + events
return signal
def check_external(filename,mode):
ext = dict(w5='.h5',w4='.hdf',wx='.xml')[mode]
file = nxs.open(filename,'rw')
file.openpath('/entry1/start_time')
time = file.getdata()
get = file.inquirefile()
expected = 'nxfile://data/dmc01'+ext
if expected != get: fail("first external file returned %s"%(get))
file.openpath('/entry2/sample/sample_name')
sample = file.getdata()
get = file.inquirefile()
expected = 'nxfile://data/dmc02'+ext
if expected != get: fail("second external file returned %s"%(get))
file.openpath('/')
remote = file.isexternalgroup('entry1','NXentry')
if remote is None:
fail("failed to identify /entry1 as external")
remote = file.isexternalgroup('entry3','NXentry')
if remote is not None:
fail('incorrectly identified /entry3 as external')
file.close()
def __init__(self, filename, verbosity, elements_list):
self.filename = filename
self.verbosity = verbosity
self.elements_list = elements_list
self.warnings_set = set()
self.basename = os.path.basename(filename)
self.nexusfile = nxs.open(self.filename)
self.metadata = {}
root_entries = self.nexusfile.getentries()
if len(root_entries) != 1:
warning = "unexpected extra root entries, reading first one only:" \
"\n %r" % root_entries
print >>sys.stderr, "%s: Warning, %s" % (self.filename, warning)
self.warnings_set.add(warning)
root_group = root_entries.keys()[0]
if root_group != "entry1":
warning = "first root entry is not entry1, using: %s" % root_group
print >>sys.stderr, "%s: Warning, %s" % (self.filename, warning)
self.warnings_set.add(warning)
self.nexusfile.opengroup(root_group)
self.init_root()
def populate_external(filename,mode):
ext = dict(w5='.h5',w4='.hdf',wx='.xml')[mode]
file = nxs.open(filename,mode)
file.makegroup('entry1','NXentry')
file.linkexternal('entry1','NXentry','nxfile://data/dmc01'+ext)
file.makegroup('entry2','NXentry')
file.linkexternal('entry2','NXentry','nxfile://data/dmc02'+ext)
file.makegroup('entry3','NXentry')
file.close()
def populate_external(filename,mode):
ext = dict(w5='.h5',w4='.hdf',wx='.xml')[mode]
file = nxs.open(filename,mode)
file.makegroup('entry1','NXentry')
file.linkexternal('entry1','NXentry','nxfile://data/dmc01'+ext)
file.makegroup('entry2','NXentry')
file.linkexternal('entry2','NXentry','nxfile://data/dmc02'+ext)
file.makegroup('entry3','NXentry')
file.close()
def openFile(self):
logger.debug("Opening nexus file...")
if self.file is None:
try:
self.file = nxs.open(self.tempFile.name,'r')
except Exception:
logger.info("Problems opening the nexus file...It was either deleted or is not valid!")
raise
else:
logger.warning("Nexus file appears to be open already.")
def __init__(self, resource, *args, **kwargs):
"""
Object constructor
@param resource: The handle to the input NeXus geometry file
@type resource: C{file}
@param args: Argument objects that the class accepts (UNUSED)
@param kwargs: A list of keyword arguments that the class accepts:
"""
self.__file = nxs.open(resource, nxs.napi.ACC_CREATE5)
def readData(self):
f = nxs.open(self.filepath)
f.opengroup('MDHistoWorkspace')
f.opendata('signal')
self.data = f.getdata()
f.closedata()
self.qs = self.read_axes(f)
f.closegroup()
f.close()
def __init__(self, nexusname):
self.logger = logging
self.detdict = {}
self.det2fileno = {"SAXS": 1, "CALIB": 2, "WAXS": 3, "TIMES": 4}
self.logger.info("looking at " + nexusname + " " + datetime.datetime.now().__str__())
self.nexusname = nexusname
self.nexusfile = nxs.open(self.nexusname)
self.instrumentname = "DLS"
self.inspectfile()
def __init__(self, name, mode='r', **kwds):
"""Create a Nexus File object for reading and writing."""
self._file = None
name = os.path.abspath(name)
self.name = name
if mode == 'w4' or mode == 'wx':
raise NeXusError('Only HDF5 files supported')
elif mode == 'w' or mode == 'w-' or mode == 'w5':
if mode == 'w5':
mode = 'w'
self._mode = 'rw'
self._file = nxs.open(name, 'w5')
else:
if mode == 'rw' or mode == 'r+':
self._mode = 'rw'
mode = 'r+'
else:
self._mode = 'r'
self._file = nxs.open(name, 'w5')
self._filename = self._file.filename
self._path = '/'
def readData(self):
f = nxs.open(self.filepath)
f.opengroup('MDHistoWorkspace')
f.opendata('signal')
self.data = f.getdata()
f.closedata()
self.qs = self.read_axes(f)
f.closegroup()
f.close()
def __init__(self, resource, *args, **kwargs):
"""
Object constructor
@param resource: The handle to the input NeXus geometry file
@type resource: C{file}
@param args: Argument objects that the class accepts (UNUSED)
@param kwargs: A list of keyword arguments that the class accepts:
"""
self.__file = nxs.open(resource, nxs.napi.ACC_CREATE5)
def readData(filePath='/home/leal/Documents/Mantid/IN5/094460.nxs'):
f = nxs.open(filePath)
f.opengroup('entry0')
f.opengroup('data')
f.opendata('data')
a = f.getdata()
f.closedata()
f.closegroup()
f.closegroup()
f.close()
# a.shape
# Out[15]: (384, 256, 512)
return a
def readData(filePath='/home/leal/Documents/Mantid/D33/Didier TOF/001030.nxs'):
f = nxs.open(filePath)
f.opengroup('entry0')
f.opengroup('data1')
f.opendata('data1')
a = f.getdata()
f.closedata()
f.closegroup()
f.closegroup()
f.close()
# a.shape
# Out[15]: (384, 256, 512)
return a
def readData(filePath):
f = nxs.open(filePath)
f.opengroup('entry0')
f.opengroup('data')
f.opendata('multiSD1_data')
a = f.getdata()
f.closedata()
f.closegroup()
f.closegroup()
f.close()
# a.shape
# Out[15]: (384, 256, 512)
return a
def _addCustomData(self, value, name, nxpath=None, dtype=None, **kwargs):
'''
apart from value and name, this recorder can use the following optional parameters:
:param nxpath: (str) a nexus path (optionally using name:nxclass notation for
the group names). See the rules for automatic nxclass
resolution used by
:meth:`NXscan_FileRecorder._createBranch`.
If None given, it defaults to
nxpath='custom_data:NXcollection'
:param dtype: name of data type (it is inferred from value if not given)
'''
if nxpath is None:
nxpath = 'custom_data:NXcollection'
if dtype is None:
if numpy.isscalar(value):
dtype = numpy.dtype(type(value)).name
if numpy.issubdtype(dtype, str):
dtype = 'char'
if dtype == 'bool':
value, dtype = int(value), 'int8'
else:
value = numpy.array(value)
dtype = value.dtype.name
if dtype not in self.supported_dtypes and dtype != 'char':
self.warning("cannot write '%s'. Reason: unsupported data type",
name)
return
# open the file if necessary
fileWasClosed = self.fd is None or not self.fd.isopen
if fileWasClosed:
if not self.overwrite and os.path.exists(self.filename):
nxfilemode = 'rw'
import nxs
self.fd = nxs.open(self.filename, nxfilemode)
# write the data
self._createBranch(nxpath)
try:
self._writeData(name, value, dtype)
except ValueError as e:
msg = "Error writing %s. Reason: %s" % (name, str(e))
self.warning(msg)
self.macro.warning(msg)
# leave the file as it was
if fileWasClosed:
self.fd.close()
def fillRunData(self):
#open nexus file
file = nxs.open(self._infilename, 'r')
for node in self._nodes:
try:
file.openpath(node)
value = file.getdata()
if isinstance(value, numpy.ndarray):
value = sum(value)
except Exception as e:
print e
value = 'N/A'
self._values.append(str(value))
file.close()
def __init__(self, normalizedfile, alignfile):
self.normalized_nexusfile = nxs.open(normalizedfile, 'r')
self.aligned_nexusfile = nxs.nxload(alignfile, 'rw')
self.util_obj = Utils()
try:
vectors = self.aligned_nexusfile['FastAligned']['move_vectors']
self.move_vectors = vectors
except Exception:
print("\nMove vectors could NOT be found.\n")
raise
self.nFrames = 0
self.numrows = 0
self.numcols = 0
def _addCustomData(self, value, name, nxpath=None, dtype=None, **kwargs):
'''
apart from value and name, this recorder can use the following optional parameters:
:param nxpath: (str) a nexus path (optionally using name:nxclass notation for
the group names). See the rules for automatic nxclass
resolution used by
:meth:`NXscan_FileRecorder._createBranch`.
If None given, it defaults to
nxpath='custom_data:NXcollection'
:param dtype: name of data type (it is inferred from value if not given)
'''
if nxpath is None:
nxpath = 'custom_data:NXcollection'
if dtype is None:
if numpy.isscalar(value):
dtype = numpy.dtype(type(value)).name
if numpy.issubdtype(dtype, str):
dtype = 'char'
if dtype == 'bool':
value, dtype = int(value), 'int8'
else:
value = numpy.array(value)
dtype = value.dtype.name
if dtype not in self.supported_dtypes and dtype != 'char':
self.warning(
"cannot write '%s'. Reason: unsupported data type", name)
return
# open the file if necessary
fileWasClosed = self.fd is None or not self.fd.isopen
if fileWasClosed:
if not self.overwrite and os.path.exists(self.filename):
nxfilemode = 'rw'
import nxs
self.fd = nxs.open(self.filename, nxfilemode)
# write the data
self._createBranch(nxpath)
try:
self._writeData(name, value, dtype)
except ValueError, e:
msg = "Error writing %s. Reason: %s" % (name, str(e))
self.warning(msg)
self.macro.warning(msg)
def show(filename):
print filename,
f = nxs.open(filename)
# /entry0
f.opengroup('entry0')
# /entry0/start_time
f.opendata('start_time')
print ';', f.getdata(),
# /entry0
f.closedata()
# /entry0/title
f.opendata('title')
print ';', f.getdata(),
# /entry0
f.closedata()
# /entry0/sample
f.opengroup('sample')
# /entry0/sample/chemical_formula
f.opendata('chemical_formula')
print '; Chem:', f.getdata(),
# /entry0/sample
f.closedata()
# /entry0
f.closegroup()
# /entry0/walength
f.opendata('wavelength')
print ';', f.getdata(), 'A',
# /entry0
f.closedata()
# /entry0/experiment_identifier
f.opendata('experiment_identifier')
print '; Id:', f.getdata(),
# /entry0
f.closedata()
# /
f.closegroup()
f.close()
print
def export_nxspe2phx(filename):
file = nxs.open(filename, 'r')
entries = file.getentries()
if len(entries) == 0:
raise IOError(
" Can not find nexus entries in the file: {0}".format(filename))
nxspe_data = entries.keys()
if len(nxspe_data) > 1:
raise IOError(
" Currently do not support more then one nexus enrty in the file : {0}"
.format(filename))
file.opengroup(nxspe_data[0])
file.opengroup('data')
phx_par = {
"polar": [],
"polar_width": [],
"azimuthal": [],
"azimuthal_width": []
}
for key in phx_par:
file.opendata(key)
phx_par[key] = file.getdata()
file.closedata()
file.closegroup()
file.closegroup()
file.close()
out_file = os.path.splitext(filename)[0] + '.phx'
if os.path.exists(out_file):
os.unlink(out_file)
ft = open(out_file, 'w')
numdet = len(phx_par["polar"])
ft.write("{0}\n".format(numdet))
for i in xrange(0, numdet):
ft.write(
"1\t0\t{0: 5.2f}\t{1: 5.2f}\t{2: 5.2f}\t{3: 5.2f}\t0\n".format(
phx_par['polar'][i], phx_par['azimuthal'][i],
phx_par['polar_width'][i], phx_par['azimuthal_width'][i]))
ft.close()
pass
def leak_test1(n = 1000, mode='w5'):
# import gc
# gc.enable()
# gc.set_debug(gc.DEBUG_LEAK)
filename = "leak_test1.nxs"
try: os.unlink(filename)
except OSError: pass
file = nxs.open(filename,mode)
file.close()
print "File should exist now"
for i in range(n):
if i%100 == 0:
print "loop count %d"%i
memfootprint()
file.open()
file.close()
# gc.collect()
os.unlink(filename)
def show(filename):
print filename,
f = nxs.open(filename)
# /entry0
f.opengroup('entry0')
# /entry0/title
f.opendata('title')
print ' : ', f.getdata(),
# /entry0
f.closedata()
# /
f.closegroup()
f.close()
print
def leak_test1(n = 1000, mode='w5'):
# import gc
# gc.enable()
# gc.set_debug(gc.DEBUG_LEAK)
filename = "leak_test1.nxs"
try: os.unlink(filename)
except OSError: pass
file = nxs.open(filename,mode)
file.close()
print("File should exist now")
for i in range(n):
if i%100 == 0:
print("loop count %d"%i)
memfootprint()
file.open()
file.close()
# gc.collect()
os.unlink(filename)
def show(filename):
print filename,
f = nxs.open(filename)
# /entry0
f.opengroup('entry0')
# /entry0/start_time
f.opendata('start_time')
print ';', f.getdata(),
# /entry0
f.closedata()
# /entry0/mode
f.opendata('mode')
print '; Mode=', f.getdata(),
# /entry0
f.closedata()
# /entry0/D33
f.opengroup('D22')
# /entry0/D33/selector
f.opengroup('selector')
# /entry0/D33/selector/wavelength
f.opendata('wavelength')
print '; wavelength=', f.getdata(),
f.closedata()
f.closegroup()
f.closegroup()
# /entry0/sample_description
f.opendata('sample_description')
print ':', f.getdata(),
# /entry0
f.closedata()
# /
f.closegroup()
f.close()
print
def showSnapShot(self,filename):
"""
It prints the snapshot in the Lamp nexus file
There's no really use for these...
@param filename:
"""
f = nxs.open(filename)
f.opengroup('entry1')
f.opengroup('data1')
f.opendata('SNAPSHOT')
a = f.getdata()
f.closedata()
f.closegroup()
f.closegroup()
f.close()
import matplotlib.pyplot as plt
plt.imshow(a)
plt.show()
def show(filename):
print filename,
f = nxs.open(filename)
# /entry0
f.opengroup('entry0')
# /entry0/title
f.opendata('title')
print ' : ', f.getdata(),
# /entry0
f.closedata()
# /
f.closegroup()
f.close()
print
def __init__(self, inputfile, avgtomnorm):
self.avgtomnorm = avgtomnorm
self.filename_nexus = inputfile
self.input_nexusfile=nxs.open(self.filename_nexus, 'r')
self.tomonorm = nxs.NXentry(name= "TomoNormalized")
self.nxdata = nxs.NXdata(name = 'ratios')
self.tomonorm.insert(self.nxdata)
self.outputfilehdf5 = inputfile.split('.')[0]+'_norm'+'.hdf5'
self.tomonorm.save(self.outputfilehdf5, 'w5')
# Ratios for the exposure times
self.ratios_exptimes = list()
# Ratios for the currents.
self.ratios_currents_tomo = list()
self.ratios_currents_brightfield = list()
# Note: brightfield= FlatField= FF
self.exposuretimes_brightfield = 0
self.averagebrightfield_exptimes = 0
self.currents_brightfield = 0
self.data_brightfield = 0
self.nFramesFF = 0
self.numrowsFF = 0
self.numcolsFF = 0
self.exposuretimes_tomo = 0
self.currents_tomo = 0
self.data_tomo = 0
self.nFramesSample = 0
self.numrows = 0
self.numcols = 0
self.averagebright = 0
self.normalizedtomo_singleimage = 0
self.normalizedTomoStack = 0
self.boolean_current_exists = 0
return
def show(filename):
print filename,
f = nxs.open(filename)
# /entry0
f.opengroup('entry0')
# /entry0/start_time
f.opendata('start_time')
print ';', f.getdata(),
# /entry0
f.closedata()
# /entry0/mode
f.opendata('mode')
print '; Mode=', f.getdata(),
# /entry0
f.closedata()
# /entry0/D33
f.opengroup('D33')
# /entry0/D33/selector
f.opengroup('selector')
# /entry0/D33/selector/wavelength
f.opendata('wavelength')
print '; wavelength=', f.getdata(),
f.closedata()
f.closegroup()
f.closegroup()
# /entry0/sample_description
f.opendata('sample_description')
print ':', f.getdata(),
# /entry0
f.closedata()
# /
f.closegroup()
f.close()
print
def __init__(self,filename) :
print "Initialising Extractor"
self.filename = filename
self.nexusfile = nxs.open(self.filename)
# initialy open the file
# ok navigate to the correct place in the structure
entries = self.nexusfile.getentries()
if len(entries) != 1:
self.logger.warning("unexpected number of root entries, reading first one only")
# open entry1
self.nexusfile.opengroup(entries.keys()[0])
entries = self.nexusfile.getentries()
if not "instrument" in entries:
raise RuntimeError("No instrument definition missing")
# open the instrument data
self.nexusfile.opengroup("instrument")
def loadRITA2(source):
f = nxs.open(source, 'r')
f.openpath("entry1/RITA-2/detector/counts")
dim, datatype = f.getinfo()
size = np.prod(dim)
data = f.getdata()
f.close()
np.random.seed(1234)
timestamp = np.sort(np.random.randint(2**32 - 1, size=dim[0]))
nEvents = np.sum(data)
signal = np.empty(nEvents, dtype=neventarray.event_t)
nEv = 0
detID = 0
row = np.uint16
col = np.uint16
m = np.sum(data, 0)
np.savetxt('orig.out', m, delimiter=' ')
for row in range(dim[1]):
for col in range(dim[2]):
for it in range(dim[0]):
events = data[it][row][col]
if events > 0:
signal[nEv:nEv + events]["ts"] = timestamp[it]
signal[nEv:nEv +
events]["data"] = (1 << 31 | 1 << 30 | 1 << 29
| 1 << 28 | 4 << 24 | col << 12
| row)
nEv = nEv + events
print signal[0:9]
return signal
def loadRITA2(source) :
f = nxs.open(source,'r')
f.openpath("entry1/RITA-2/detector/counts")
dim,datatype= f.getinfo()
size = np.prod(dim)
data = f.getdata()
f.close()
np.random.seed(1234)
timestamp = np.sort(np.random.randint(2**32-1,size=dim[0]))
nEvents = np.sum(data)
signal = np.empty(nEvents,dtype=neventarray.event_t)
nEv = 0
detID = 0
row = np.uint16
col = np.uint16
m = np.sum(data,0)
np.savetxt('orig.out',m,delimiter=' ')
for row in range(dim[1]):
for col in range(dim[2]):
for it in range(dim[0]):
events = data[it][row][col]
if events > 0:
signal[nEv:nEv+events]["ts"] = timestamp[it]
signal[nEv:nEv+events]["data"] = (1 << 31 | 1 << 30 | 1 << 29 | 1 << 28 | 4 << 24 | col << 12 | row )
nEv = nEv+events
print signal[0:9]
return signal
def export_nxspe2phx(filename):
file = nxs.open(filename,'r');
entries = file.getentries()
if len(entries) == 0:
raise IOError(" Can not find nexus entries in the file: {0}".format(filename));
nxspe_data = entries.keys();
if len(nxspe_data)> 1:
raise IOError(" Currently do not support more then one nexus enrty in the file : {0}".format(filename));
file.opengroup(nxspe_data[0])
file.opengroup('data')
phx_par = {"polar":[],"polar_width":[],"azimuthal":[],"azimuthal_width":[]};
for key in phx_par:
file.opendata(key)
phx_par[key]=file.getdata();
file.closedata();
file.closegroup();
file.closegroup();
file.close();
out_file = os.path.splitext(filename)[0]+'.phx'
if os.path.exists(out_file) :
os.unlink(out_file);
ft = open(out_file,'w');
numdet = len(phx_par["polar"]);
ft.write("{0}\n".format(numdet))
for i in xrange(0,numdet):
ft.write("1\t0\t{0: 5.2f}\t{1: 5.2f}\t{2: 5.2f}\t{3: 5.2f}\t0\n".format(phx_par['polar'][i],phx_par['azimuthal'][i],phx_par['polar_width'][i],phx_par['azimuthal_width'][i]));
ft.close()
pass
def plot_data_as_images(self, normalise=True):
f = nxs.open(self.filepath)
f.opengroup('entry')
if normalise:
sum = self.get_monitor_counts(f)
else:
sum = 1
entries = f.getentries()
banks = [key for key, value in entries.items() if value == 'NXdata']
for bank in banks:
f.opengroup(bank)
f.opendata('data_x_y')
data = f.getdata()
data = data / np.float32(sum) * sum
self.save_as_plot(data, bank)
f.closedata()
f.closegroup()
f.closegroup()
f.close()
def plot_data_as_images(self, normalise=True):
f = nxs.open(self.filepath)
f.opengroup('entry')
if normalise:
sum = self.get_monitor_counts(f)
else:
sum = 1
entries = f.getentries()
banks = [ key for key, value in entries.items() if value == 'NXdata']
for bank in banks:
f.opengroup(bank)
f.opendata('data_x_y')
data = f.getdata()
data = data/np.float32(sum)*sum
self.save_as_plot(data,bank)
f.closedata()
f.closegroup()
f.closegroup()
f.close()
import nxs
filename = 'REF_L_23554.nxs'
file = nxs.open(filename, 'r')
file.opengroup('entry', 'NXentry')
#start_time
file.opendata('start_time')
print 'start_time: ' + file.getdata()
file.closedata()
#duration
file.opendata('duration')
duration = str(file.getdata())
unit = file.getattr('units', 10, 'char')
print 'Duration is: ' + duration + unit
file.closedata()
#proton charge
file.opendata('proton_charge')
proton_charge = str(file.getdata())
unit = file.getattr('units', 15, 'char')
print 'Proton charge is: ' + proton_charge + unit
file.closedata()
#total counts
file.opendata('total_counts')
print 'Total counts: ' + str(file.getdata())
file.closedata()
def retrieve_metadata(self, filename):
QApplication.setOverrideCursor(Qt.WaitCursor)
file = nxs.open(str(filename), 'r')
entry = 'entry'
if (self.instrument == 'REF_M'):
entry = 'entry-Off_Off'
file.opengroup(entry, 'NXentry')
#start time
file.opendata('start_time')
start_time = str(file.getdata())
file.closedata()
self.timestartinfo.setText(start_time)
#duration
file.opendata('duration')
duration = str(file.getdata())
unit = file.getattr('units', 10, 'char')
file.closedata()
self.durationinfo.setText(duration + ' ' + unit)
#proton charge
file.opendata('proton_charge')
proton_charge = str(file.getdata())
unit = file.getattr('units', 10, 'char')
file.closedata()
self.protonchargeinfo.setText(proton_charge + ' ' + unit)
#total counts
file.opendata('total_counts')
total_counts = str(file.getdata())
file.closedata()
self.totalcountsinfo.setText(total_counts)
#slit1 - height
file.opendata('/entry/instrument/aperture1/s1t/value')
s1t = str(file.getdata())
units = file.getattr('units', 10, 'char')
file.closedata()
_s1t = float(s1t)
file.opendata('/entry/instrument/aperture1/s1b/value')
s1b = str(file.getdata())
file.closedata()
_s1b = float(s1b)
_s1h = _s1t - _s1b
self.slit1h.setText(str(_s1h) + ' ' + units)
#slit1 - width
file.opendata('/entry/instrument/aperture1/s1r/value')
s1r = str(file.getdata())
units = file.getattr('units', 10, 'char')
file.closedata()
_s1r = float(s1r)
file.opendata('/entry/instrument/aperture1/s1l/value')
s1l = str(file.getdata())
file.closedata()
_s1l = float(s1l)
_s1w = _s1r - _s1l
self.slit1w.setText(str(_s1w) + ' ' + units)
#slit2 - height
file.opendata('/entry/instrument/aperture2/s2t/value')
s2t = str(file.getdata())
units = file.getattr('units', 10, 'char')
file.closedata()
_s2t = float(s2t)
file.opendata('/entry/instrument/aperture2/s2b/value')
s2b = str(file.getdata())
file.closedata()
_s2b = float(s2b)
_s2h = _s2t - _s2b
self.slit2h.setText(str(_s2h) + ' ' + units)
# width
file.opendata('/entry/instrument/aperture2/s2r/value')
s2r = str(file.getdata())
units = file.getattr('units', 10, 'char')
file.closedata()
_s2r = float(s2r)
file.opendata('/entry/instrument/aperture2/s2l/value')
s2l = str(file.getdata())
file.closedata()
_s2l = float(s2l)
_s2w = _s2r - _s2l
self.slit2w.setText(str(_s2w) + ' ' + units)
#slit3 - height
file.opendata('/entry/instrument/aperture3/s3t/value')
s3t = str(file.getdata())
units = file.getattr('units', 10, 'char')
file.closedata()
_s3t = float(s3t)
file.opendata('/entry/instrument/aperture3/s3b/value')
s3b = str(file.getdata())
file.closedata()
_s3b = float(s3b)
_s3h = _s3t - _s3b
self.slit3h.setText(str(_s3h) + ' ' + units)
# width
file.opendata('/entry/instrument/aperture3/s3r/value')
s3r = str(file.getdata())
units = file.getattr('units', 10, 'char')
file.closedata()
_s3r = float(s3r)
file.opendata('/entry/instrument/aperture3/s3l/value')
s3l = str(file.getdata())
file.closedata()
_s3l = float(s3l)
_s3w = _s3r - _s3l
self.slit3w.setText(str(_s3w) + ' ' + units)
#slit4 - height
file.opendata('/entry/instrument/aperture4/s4t/value')
s4t = str(file.getdata())
units = file.getattr('units', 10, 'char')
file.closedata()
_s4t = float(s4t)
file.opendata('/entry/instrument/aperture4/s4b/value')
s4b = str(file.getdata())
file.closedata()
_s4b = float(s4b)
_s4h = _s4t - _s4b
self.slit4h.setText(str(_s4h) + ' ' + units)
# width
file.opendata('/entry/instrument/aperture4/s4r/value')
s4r = str(file.getdata())
units = file.getattr('units', 10, 'char')
file.closedata()
_s4r = float(s4r)
file.opendata('/entry/instrument/aperture4/s4l/value')
s4l = str(file.getdata())
file.closedata()
_s4l = float(s4l)
_s4w = _s4r - _s4l
self.slit4w.setText(str(_s4w) + ' ' + units)
#ttheta
file.opendata('/entry/instrument/bank1/TwoTheta/readback')
ttheta = str(file.getdata())
units = file.getattr('units', 10, 'char')
file.closedata()
self.tthetainfo.setText(ttheta + ' ' + units)
#tthd
file.opendata('/entry/instrument/bank1/tthd/value')
tthd = str(file.getdata())
units = file.getattr('units', 10, 'char')
file.closedata()
self.tthdinfo.setText(tthd + ' ' + units)
#ths
file.opendata('/entry/sample/ths/value')
ths = str(file.getdata())
units = file.getattr('units', 10, 'char')
file.closedata()
self.thsinfo.setText(ths + ' ' + units)
#thi
file.opendata('/entry/instrument/aperture1/thi/value')
thi = str(file.getdata())
units = file.getattr('units', 10, 'char')
file.closedata()
self.thiinfo.setText(thi + ' ' + units)
file.close()
QApplication.restoreOverrideCursor()
def show_structure(filename):
f = nxs.open(filename)
print "Showing contents for: ", f.inquirefile()
_show(f)
def check(filename):
global failures
failures = 0
file = nxs.open(filename, 'rw')
if filename != file.inquirefile(): fail("Files don't match")
attrs = file.getattrinfo()
if attrs != 4: fail("Expected 4 root attributes but got %d", attrs)
for i in range(attrs):
name, dims, type = file.getnextattr()
if name not in [
'file_time', 'HDF_version', 'HDF5_Version', 'XML_version',
'NeXus_version', 'file_name'
]:
fail("attribute %s unexpected" % (name))
file.opengroup('entry', 'NXentry')
expect = dict(hugo='namenlos', cucumber='passion')
#expect['embedded_null'] = "embedded\000null"
get = dict((k, v) for k, v in file.attrs())
same = dicteq(get, expect)
if not same: fail("/entry attributes are %s" % (get))
# Check that the numbers are written correctly
for name,dtype,shape,scale in \
[('i1','int8',(4),1),
('i2','int16',(4),1000),
('i4','int32',(4),1000000),
('i8','int64',(4),1000000000000),
('r4','float32',(5,4),1),
('r8','float64',(5,4),1)
]:
n = numpy.prod(shape)
expected = numpy.arange(n, dtype=dtype).reshape(shape) * scale
file.opendata(name + '_data')
get = file.getdata()
file.closedata()
if not (get == expected).all():
fail("%s retrieved %s" % (dtype, get))
# Check attribute types
file.opendata('r8_data')
get = file.getattr("ch_attribute", 5, 'char')
if not get == "NeXus": fail("ch_attribute retrieved %s" % (get))
get = file.getattr("i4_attribute", 1, 'int32')
if not get == numpy.int32(42): fail("i4_attribute retrieved %s" % (get))
get = file.getattr("r4_attribute", 1, 'float32')
if not get == numpy.float32(3.14159265):
fail("r4_attribute retrieved %s" % (get))
## Oops... NAPI doesn't support array attributes
#expect = numpy.array([3,2],dtype='int32')
#get = file.getattr("i4_array",2,'int32')
#if not (get==expect).all(): fail('i4_array retrieved %s'%(get))
#expect = numpy.array([3.14159265,2.718281828],dtype='float32')
#get = file.getattr("r4_array",2,dtype='float32')
#if not (get==expect).all(): fail("r4_array retrieved %s"%(get))
file.closedata()
# Check reading from compressed datasets
comp_array = numpy.ones((100, 20), dtype='int32')
for i in range(100):
comp_array[i, :] *= i
expected = comp_array
file.opengroup('data', 'NXdata')
file.opendata('comp_data')
get = file.getdata()
file.closedata() #/entry/data/comp_data
file.closegroup() #/entry/data
if not (get == expected).all():
fail("compressed data differs")
print get
file.closegroup() #/entry
# Check read slab (e.g., from extensible)
# Check links
file.opengroup('entry', 'NXentry')
file.opengroup('sample', 'NXsample')
sampleid = file.getgroupID()
file.closegroup() #/entry/sample
file.opengroup('data', 'NXdata') #/entry/data
file.opendata('r8_data') #/entry/data/r8_data
dataid = file.getdataID()
file.closedata() #/entry/data/r8_data
file.closegroup() #/entry/data
file.opendata('r8_data')
data2id = file.getdataID()
file.closedata()
file.closegroup() #/entry
if not (file.sameID(dataid, data2id)):
fail("/entry/data/r8_data not linked to /entry/r8_data")
# Check openpath and getslab
file.openpath('/entry/data/comp_data')
get = file.getslab([4, 4], [5, 3])
expected = comp_array[4:(4 + 5), 4:(4 + 3)]
if not (get == expected).all():
fail("retrieved compressed slabs differ")
print get
file.openpath('/entry/data/comp_data')
get = file.getslab([4, 4], [5, 3])
expected = comp_array[4:(4 + 5), 4:(4 + 3)]
if not (get == expected).all():
fail("after reopen: retrieved compressed slabs differ")
print get
file.openpath('../r8_data')
for k, v in file.attrs():
if k == 'target' and v != '/entry/r8_data':
fail("relative openpath was not successful")
return failures == 0
def read(self, filename=None):
"""
Open and read the data in a file
:param filename: path of the file
"""
try:
import nxs
except:
msg = "Error reading Nexus file: Nexus package is missing.\n"
msg += " Get it from http://http://www.nexusformat.org/"
raise RuntimeError, msg
# Instantiate data object
output = Data2D()
output.filename = os.path.basename(filename)
fd = nxs.open(filename, 'rw')
# Read in the 2D data
fd.opengroup('mantid_workspace_1')
fd.opengroup('workspace')
fd.opendata('values')
output.data = fd.getdata().copy()
fd.closedata()
# Read in the errors
fd.opendata('errors')
output.err_data = fd.getdata().copy()
fd.closedata()
# Read in the values on each axis
fd.opendata('axis1')
output.x_bins = fd.getdata().copy()
fd.closedata()
fd.opendata('axis2')
output.y_bins = fd.getdata().copy()
fd.closedata()
fd.closegroup()
output.xmin = min(output.x_bins)
output.xmax = max(output.x_bins)
output.ymin = min(output.y_bins)
output.ymax = max(output.y_bins)
output.xaxis("\\rm{Q_{x}}", 'A^{-1}')
output.yaxis("\\rm{Q_{y}}", 'A^{-1}')
output.zaxis("\\rm{Intensity}", "cm^{-1}")
# Meta data
fd.opendata('title')
output.title = fd.getdata()
fd.closedata()
fd.opengroup('instrument')
fd.opendata('name')
output.instrument = fd.getdata()
fd.closedata()
fd.closegroup()
fd.opengroup('logs')
fd.opengroup('run_number')
fd.opendata('value')
output.run = fd.getdata()
fd.close()
# Store loading process information
output.meta_data['loader'] = self.type_name
return output
def putArrayData(outf,name, ardata):
outf.makedata(name,ardata.dtype.name,ardata.shape)
outf.opendata(name)
outf.putdata(ardata)
outf.closedata()
def copyData(infile, inpath, outfile, outname):
infile.openpath(inpath)
shape,dtype = infile.getinfo()
outfile.makedata(outname,dtype,shape)
outfile.opendata(outname)
data = infile.getdata()
outfile.putdata(data)
outfile.closedata()
inf = nxs.open(sys.argv[1],'r')
outf = nxs.open(sys.argv[2],'w5')
outf.makegroup('entry','NXentry')
outf.opengroup('entry','NXentry')
#--------- Instrument
outf.makegroup('instrument','NXinstrument')
outf.opengroup('instrument','NXinstrument')
#---------- Detector
outf.makegroup('detector','NXdetector')
outf.opengroup('detector','NXdetector')
copyData(inf,'/entry1/TRICS/area_detector2/data',outf,'data')
copyData(inf,'/entry1/TRICS/area_detector2/distance',outf,'distance')
outf.opendata('data')
#!/usr/bin/python
import sys
import nxs
import numpy
nf = nxs.open("simple3D.h5", "w5")
nf.makegroup("entry", "NXentry")
nf.opengroup("entry", "NXentry")
nf.makegroup("data", "NXdata")
nf.opengroup("data", "NXdata")
a = numpy.zeros((2, 3, 4), dtype=numpy.int)
val = 0
for i in range(2):
for j in range(3):
for k in range(4):
a[i, j, k] = val
val = val + 1
nf.makedata("test", 'int32', [2, 3, 4])
nf.opendata("test")
nf.putdata(a)
nf.putattr("signal", 1)
nf.closedata()
nf.closegroup() # NXdata
nf.closegroup() # NXentry
def show_structure(filename):
file = nxs.open(filename)
file.show()
def populate(filename,mode):
c1 = numpy.array(['abcd','efgh','ijkl','mnop','qrst'])
i1 = numpy.arange(4,dtype='uint8')
i2 = numpy.arange(4,dtype='int16')*1000
i4 = numpy.arange(4,dtype='int32')*1000000
i8 = numpy.arange(4,dtype='int64')*1000000000000
r4 = numpy.arange(20,dtype='float32').reshape((5,4))
r8 = numpy.arange(20,dtype='float64').reshape((5,4))
comp_array=numpy.ones((100,20),dtype='int32')
for i in range(100): comp_array[i,:] *= i
file = nxs.open(filename,mode)
file.setnumberformat('float32','%9.3g')
file.makegroup("entry","NXentry")
file.opengroup("entry","NXentry")
file.putattr("hugo","namenlos")
file.putattr("cucumber","passion")
#file.putattr("embedded_null","embedded\000null")
# Write character data
file.makedata("ch_data",'char',[10])
file.opendata("ch_data")
file.putdata("NeXus data")
file.closedata()
file.makedata("c1_data",'char',[5,4])
file.opendata("c1_data")
file.putdata(c1)
file.closedata()
# Write numeric data
for var in ['i1','i2','i4','i8','r4']:
if mode == 'w4' and var == 'i8': continue
name = var+'_data'
val = locals()[var]
file.makedata(name,val.dtype,val.shape)
file.opendata(name)
file.putdata(val)
file.closedata()
# Write r8_data
file.makedata('r8_data','float64',[5,4])
file.opendata('r8_data')
file.putslab(r8[4,:],[4,0],[1,4])
file.putslab(r8[0:4,:],[0,0],[4,4])
file.putattr("ch_attribute","NeXus")
file.putattr("i4_attribute",42,dtype='int32')
file.putattr("r4_attribute",3.14159265,dtype='float32')
## Oops... NAPI doesn't support array attributes
#file.putattr("i4_array",[3,2],dtype='int32')
#file.putattr("r4_array",[3.14159265,2.718281828],dtype='float32')
dataID = file.getdataID()
file.closedata()
# Create the NXdata group
file.makegroup("data","NXdata")
file.opengroup("data","NXdata")
# .. demonstrate linking
file.makelink(dataID)
# .. demonstrate compressed data
file.compmakedata("comp_data",'int32',[100,20],'lzw',[20,20])
file.opendata('comp_data')
file.putdata(comp_array)
file.closedata()
file.flush()
# .. demonstrate extensible data
file.makedata('flush_data','int32',[nxs.UNLIMITED])
file.opendata('flush_data')
for i in range(7):
file.putslab(i,[i],[1])
file.closedata()
file.flush()
file.closegroup()
# Create NXsample group
file.makegroup('sample','NXsample')
file.opengroup('sample','NXsample')
file.makedata('ch_data','char',[20])
file.opendata('ch_data')
file.putdata('NeXus sample')
file.closedata()
sampleID = file.getgroupID()
file.closegroup()
file.closegroup()
# Demonstrate named links
file.makegroup('link','NXentry')
file.opengroup('link','NXentry')
file.makelink(sampleID)
file.makenamedlink('renLinkGroup',sampleID)
file.makenamedlink('renLinkData',dataID)
file.closegroup()
file.close()
return filename
def show_structure(filename):
file = nxs.open(filename)
print("=== File",file.inquirefile())
_show(file)
def check(filename, mode):
global failures
failures = 0
file = nxs.open(filename,'rw')
if filename != file.inquirefile(): fail("Files don't match")
# check headers
num_attrs = file.getattrinfo()
wxattrs = ['xmlns','xmlns:xsi','xsi:schemaLocation', 'XML_version']
w4attrs = ['HDF_version']
w5attrs = ['HDF5_Version']
extras = dict(wx=wxattrs,w4=w4attrs,w5=w5attrs)
expected_attrs = ['NeXus_version','file_name','file_time']+extras[mode]
for i in range(num_attrs):
name,dims,type = file.getnextattr()
if name not in expected_attrs:
fail("attribute %s unexpected"%(name))
if num_attrs != len(expected_attrs):
fail("Expected %d root attributes but got %d"
% (len(expected_attrs),num_attrs))
file.opengroup('entry','NXentry')
expect = dict(hugo='namenlos',cucumber='passion')
#expect['embedded_null'] = "embedded\000null"
get = dict((k,v) for k,v in file.attrs())
same = dicteq(get,expect)
if not same: fail("/entry attributes are %s"%(get))
# Check that the numbers are written correctly
for name,dtype,shape,scale in \
[('i1','int8',(4),1),
('i2','int16',(4),1000),
('i4','int32',(4),1000000),
('i8','int64',(4),1000000000000),
('r4','float32',(5,4),1),
('r8','float64',(5,4),1)
]:
if mode == 'w4' and name == 'i8': continue
n = numpy.prod(shape)
expected = numpy.arange(n,dtype=dtype).reshape(shape)*scale
file.opendata(name+'_data')
get = file.getdata()
file.closedata()
if not (get == expected).all():
fail("%s retrieved %s"%(dtype,get))
# Check attribute types
file.opendata('r8_data')
get = file.getattr("ch_attribute",5,'char')
if not get == "NeXus": fail("ch_attribute retrieved %s"%(get))
get = file.getattr("i4_attribute",1,'int32')
if not get == numpy.int32(42): fail("i4_attribute retrieved %s"%(get))
get = file.getattr("r4_attribute",1,'float32')
if ((mode=='wx' and not abs(get-3.14159265) < 1e-6) or
(mode!='wx' and not get == numpy.float32(3.14159265))):
fail("r4_attribute retrieved %s"%(get))
## Oops... NAPI doesn't support array attributes
#expect = numpy.array([3,2],dtype='int32')
#get = file.getattr("i4_array",2,'int32')
#if not (get==expect).all(): fail('i4_array retrieved %s'%(get))
#expect = numpy.array([3.14159265,2.718281828],dtype='float32')
#get = file.getattr("r4_array",2,dtype='float32')
#if not (get==expect).all(): fail("r4_array retrieved %s"%(get))
file.closedata()
file.opendata('c1_data')
rawshape,rawdtype = file.getrawinfo()
shape,dtype = file.getinfo()
get = file.getdata()
file.closedata()
if not (shape[0]==5 and shape[1]==4 and dtype=='char'):
fail("returned string array info is incorrect")
if not (rawshape[0]==5 and rawshape[1]==4 and rawdtype=='char'):
fail("returned string array storage info is incorrect")
print(rawshape,dtype)
if not (get[0]=="abcd" and get[4]=="qrst"):
fail("returned string is incorrect")
print(shape,dtype)
# Check reading from compressed datasets
comp_array=numpy.ones((100,20),dtype='int32')
for i in range(100): comp_array[i,:] *= i
expected = comp_array
file.opengroup('data','NXdata') #/entry/data
file.opendata('comp_data') #/entry/data/comp_data
get = file.getdata()
file.closedata() #/entry/data/comp_data
file.closegroup() #/entry/data
if not (get == expected).all():
fail("compressed data differs")
print(get)
# Check strings
file.opengroup('sample','NXsample') #/entry/sample
file.opendata('ch_data') #/entry/sample/ch_data
rawshape,rawdtype = file.getrawinfo()
shape,dtype = file.getinfo()
get = file.getdata()
file.closedata() #/entry/sample/ch_data
file.closegroup() #/entry/sample
if not (shape[0]==12 and dtype=='char'):
fail("returned string info is incorrect")
print(shape,dtype)
if not (rawshape[0]==20 and rawdtype=='char'):
fail("returned string storage info is incorrect")
print(shape,dtype)
if not (get == "NeXus sample"):
fail("returned string is incorrect")
print(shape,dtype)
file.closegroup() #/entry
# Check read slab (e.g., from extensible)
# Check links
file.opengroup('entry','NXentry')
file.opengroup('sample','NXsample')
sampleid = file.getgroupID()
file.closegroup() #/entry/sample
file.opengroup('data','NXdata') #/entry/data
file.opendata('r8_data') #/entry/data/r8_data
dataid = file.getdataID()
file.closedata() #/entry/data/r8_data
file.closegroup() #/entry/data
file.opendata('r8_data')
data2id = file.getdataID()
file.closedata()
file.closegroup() #/entry
if not (file.sameID(dataid,data2id)):
fail("/entry/data/r8_data not linked to /entry/r8_data")
# Check openpath and getslab
file.openpath('/entry/data/comp_data')
get = file.getslab([4,4],[5,3])
expected = comp_array[4:(4+5),4:(4+3)]
if not (get == expected).all():
fail("retrieved compressed slabs differ")
print(get)
file.openpath('/entry/data/comp_data')
get = file.getslab([4,4],[5,3])
expected = comp_array[4:(4+5),4:(4+3)]
if not (get == expected).all():
fail("after reopen: retrieved compressed slabs differ")
print(get)
file.openpath('../r8_data')
for k,v in file.attrs():
if k == 'target' and v != '/entry/r8_data':
fail("relative openpath was not successful")
return failures == 0
def populate(filename,mode):
c1 = numpy.array(['abcd','efgh','ijkl','mnop','qrst'])
i1 = numpy.arange(4,dtype='uint8')
i2 = numpy.arange(4,dtype='int16')*1000
i4 = numpy.arange(4,dtype='int32')*1000000
i8 = numpy.arange(4,dtype='int64')*1000000000000
r4 = numpy.arange(20,dtype='float32').reshape((5,4))
r8 = numpy.arange(20,dtype='float64').reshape((5,4))
comp_array=numpy.ones((100,20),dtype='int32')
for i in range(100): comp_array[i,:] *= i
file = nxs.open(filename,mode)
file.setnumberformat('float32','%9.3g')
file.makegroup("entry","NXentry")
file.opengroup("entry","NXentry")
file.putattr("hugo","namenlos")
file.putattr("cucumber","passion")
#file.putattr("embedded_null","embedded\000null")
# Write character data
file.makedata("ch_data",'char',[10])
file.opendata("ch_data")
file.putdata("NeXus data")
file.closedata()
file.makedata("c1_data",'char',[5,4])
file.opendata("c1_data")
file.putdata(c1)
file.closedata()
# Write numeric data
for var in ['i1','i2','i4','i8','r4']:
if mode == 'w4' and var == 'i8': continue
name = var+'_data'
val = locals()[var]
file.makedata(name,val.dtype,val.shape)
file.opendata(name)
file.putdata(val)
file.closedata()
# Write r8_data
file.makedata('r8_data','float64',[5,4])
file.opendata('r8_data')
file.putslab(r8[4,:],[4,0],[1,4])
file.putslab(r8[0:4,:],[0,0],[4,4])
file.putattr("ch_attribute","NeXus")
file.putattr("i4_attribute",42,dtype='int32')
file.putattr("r4_attribute",3.14159265,dtype='float32')
## Oops... NAPI doesn't support array attributes
#file.putattr("i4_array",[3,2],dtype='int32')
#file.putattr("r4_array",[3.14159265,2.718281828],dtype='float32')
dataID = file.getdataID()
file.closedata()
# Create the NXdata group
file.makegroup("data","NXdata")
file.opengroup("data","NXdata")
# .. demonstrate linking
file.makelink(dataID)
# .. demonstrate compressed data
file.compmakedata("comp_data",'int32',[100,20],'lzw',[20,20])
file.opendata('comp_data')
file.putdata(comp_array)
file.closedata()
file.flush()
# .. demonstrate extensible data
file.makedata('flush_data','int32',[nxs.UNLIMITED])
file.opendata('flush_data')
for i in range(7):
file.putslab(i,[i],[1])
file.closedata()
file.flush()
file.closegroup()
# Create NXsample group
file.makegroup('sample','NXsample')
file.opengroup('sample','NXsample')
file.makedata('ch_data','char',[20])
file.opendata('ch_data')
file.putdata('NeXus sample')
file.closedata()
sampleID = file.getgroupID()
file.closegroup()
file.closegroup()
# Demonstrate named links
file.makegroup('link','NXentry')
file.opengroup('link','NXentry')
file.makelink(sampleID)
file.makenamedlink('renLinkGroup',sampleID)
file.makenamedlink('renLinkData',dataID)
file.closegroup()
file.close()
return filename
#!/usr/bin/python
import sys
import nxs
import numpy
a = numpy.zeros((2,3,4),dtype=numpy.int)
val = 0
for i in range(2):
for j in range(3):
for k in range(4):
a[i,j,k] = val
val = val + 1
nf = nxs.open("simple3D.h5", "w5")
nf.makegroup("entry","NXentry")
nf.opengroup("entry","NXentry")
nf.makegroup("data","NXdata")
nf.opengroup("data","NXdata")
nf.putattr("signal","test")
nf.makedata("test",'int32',[2,3,4])
nf.opendata("test")
nf.putdata(a)
nf.closedata()
nf.closegroup() # NXdata
nf.closegroup() # NXentry
def show_structure(filename):
file = nxs.open(filename)
print "=== File",file.inquirefile()
_show(file)
#!/usr/bin/python
import nxs
nf = nxs.open("hand1.h5", "w5")
nf.makegroup("entry","NXentry")
nf.opengroup("entry","NXentry")
nf.makegroup("data","NXdata")
nf.opengroup("data","NXdata")
nf.closegroup()
nf.makedata("hugo",'int32',[1])
nf.opendata("hugo")
nf.putdata(22.33)
nf.putattr("signal",1)
nxl = nf.getdataID()
nf.closedata()
nf.opengroup("data","NXdata")
nf.makelink(nxl)
nf.close()
exit
