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 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 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 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 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 populate(filename,mode):
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()
# 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()
# 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):
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()
# 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()
# 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
