def createDatasetWithCompoundType(h5file):
# component name -> (offset, size, type)
ht = { 'a_name': (0, 4, H5T_NATIVE_INT),
'b_name': (4, 4, H5T_NATIVE_FLOAT),
'c_name': (8, 8, H5T_NATIVE_DOUBLE) }
sizeof = 0
for k in ht.keys():
sizeof += ht[k][1]
dtype = H5T.create(H5T.CreateClass.COMPOUND, sizeof)
for k in ht.keys():
H5T.insert(dtype, k, ht[k][0], ht[k][2])
npoints = 10
shape = Array[Int64]((npoints,))
dspace = H5S.create_simple(shape.Length, shape)
dset = H5D.create(h5file, 'ArrayOfStructures', dtype, dspace)
# create an array of Byte
# use BitConverter to get Byte representations
shape = Array[Int64]((npoints*sizeof,))
byteArray = Array.CreateInstance(Byte, shape)
for i in range(npoints):
offset = i*sizeof
a = Int32(i)
Array.Copy(BitConverter.GetBytes(a), 0, byteArray,
offset+ht['a_name'][0], ht['a_name'][1])
b = Single(i*i)
Array.Copy(BitConverter.GetBytes(b), 0, byteArray,
offset+ht['b_name'][0], ht['b_name'][1])
c = Double(1.0/(i+1.0))
Array.Copy(BitConverter.GetBytes(c), 0, byteArray,
offset+ht['c_name'][0], ht['c_name'][1])
H5D.write(dset, dtype, H5Array[Byte](byteArray))
H5S.close(dspace)
H5T.close(dtype)
return dset
def writeGroupAndDatasets(h5file):
grp = H5G.create(h5file, 'A')
dtype = H5T.copy(H5T_NATIVE_FLOAT)
shape = Array[Int64]((2, 6))
dspacev = H5S.create_simple(shape.Length, shape)
dsetv = H5D.create(h5file, 'B', dtype, dspacev)
H5T.close(dtype)
dtype = H5T.copy(H5T_STD_REF_OBJ)
shape = Array[Int64]((2, ))
dspacer = H5S.create_simple(shape.Length, shape)
dsetr = H5D.create(h5file, 'R', dtype, dspacer)
oref = Array.CreateInstance(ObjectReference, 2)
oref[0] = H5R.createObjectReference(h5file, 'A')
oref[1] = H5R.createObjectReference(h5file, 'B')
nBytes = ObjectReference.SizeInBytes
data = Array.CreateInstance(Byte, oref.Length * nBytes)
for i in range(oref.Length):
Array.Copy(oref[i].ToByteArray(), 0, data, i * nBytes, nBytes)
H5D.write(dsetr, dtype, H5Array[Byte](data))
H5T.close(dtype)
H5D.close(dsetv)
H5S.close(dspacev)
H5D.close(dsetr)
H5S.close(dspacer)
return None
def writeDatasets(h5file):
dtype = H5T.copy(H5T.H5Type.NATIVE_INT)
shape = Array[Int64]((2, 9))
dspacev = H5S.create_simple(shape.Length, shape)
dsetv = H5D.create(h5file, 'MATRIX', dtype, dspacev)
data = Array.CreateInstance(Int32, shape)
data[0, 0] = data[0, 1] = data[1, 0] = 1
data[0, 2] = data[1, 1] = data[1, 2] = 2
data[0, 3] = data[0, 4] = data[1, 3] = 3
data[0, 5] = data[1, 4] = data[1, 5] = 4
data[0, 6] = data[0, 7] = data[1, 6] = 5
data[0, 8] = data[1, 7] = data[1, 8] = 6
H5D.write(dsetv, dtype, H5Array[Int32](data))
H5T.close(dtype)
dtype = H5T.copy(H5T.H5Type.STD_REF_DSETREG)
shape = Array[Int64]((2, ))
dspacer = H5S.create_simple(shape.Length, shape)
dsetr = H5D.create(h5file, 'REGION_REFERENCES', dtype, dspacer)
start = Array[Int64]((0, 3))
count = Array[Int64]((2, 3))
H5S.selectHyperslab(dspacev, H5S.SelectOperator.SET, start, count)
rr = Array.CreateInstance(RegionReference, 2)
rr[0] = H5R.createRegionReference(h5file, 'MATRIX', dspacev)
coord = Array.CreateInstance(Int64, 6)
coord[0] = coord[1] = coord[4] = 0
coord[2] = 1
coord[3] = 6
coord[5] = 8
H5S.selectNone(dspacev)
H5S.selectElements(dspacev, H5S.SelectOperator.SET, IntPtr(3), coord)
rr[1] = H5R.createRegionReference(h5file, 'MATRIX', dspacev)
nBytes = RegionReference.SizeInBytes
data = Array.CreateInstance(Byte, rr.Length * nBytes)
for i in range(rr.Length):
Array.Copy(rr[i].ToByteArray(), 0, data, i * nBytes, nBytes)
H5D.write(dsetr, dtype, H5Array[Byte](data))
H5T.close(dtype)
H5D.close(dsetv)
H5S.close(dspacev)
H5D.close(dsetr)
H5S.close(dspacer)
return None
def writeVlenData(h5file):
dtype = H5T.vlenCreate(H5T.H5Type.NATIVE_INT)
array = range(16)
npoints = len(array)
shape = Array[Int64]((npoints, ))
dspace = H5S.create_simple(shape.Length, shape)
dset = H5D.create(h5file, 'Vlen Dataset', dtype, dspace)
wdata = Array.CreateInstance(hvl_t, npoints)
sizeofInt = 4
for i in range(npoints):
nElems = array[i] + 1
nBytes = nElems * sizeofInt
# the data to be written (array of length i+1 with all elements = i)
data = Array.CreateInstance(Byte, nBytes)
for j in range(nElems):
Array.Copy(System.BitConverter.GetBytes(i), 0, data, j * sizeofInt,
sizeofInt)
# allocate and copy to array in unmanaged memory
mem = Marshal.AllocHGlobal(nBytes)
Marshal.Copy(data, 0, mem, nBytes)
wdata[i] = VLen(IntPtr(nElems), mem).To_hvl_t()
H5D.write(dset, dtype, H5Array[hvl_t](wdata))
# free unmanaged buffer space
for i in range(npoints):
vl = VLen(wdata[i])
Marshal.FreeHGlobal(vl.Pointer)
H5D.close(dset)
H5S.close(dspace)
H5T.close(dtype)
return None
def readAndDereference(h5file):
dsetr = H5D.open(h5file, 'R')
dtyper = H5T.copy(H5T_STD_REF_OBJ)
dspacer = H5D.getSpace(dsetr)
npoints = H5S.getSimpleExtentNPoints(dspacer)
nBytes = ObjectReference.SizeInBytes
datar = Array.CreateInstance(Byte, npoints * nBytes)
H5D.read(dsetr, dtyper, H5Array[Byte](datar))
oref = Array.CreateInstance(ObjectReference, npoints)
a = Array.CreateInstance(Byte, nBytes)
for i in range(oref.Length):
Array.Copy(datar, i * nBytes, a, 0, nBytes)
oref[i] = ObjectReference(a)
otype = H5R.getObjectType(h5file, oref[0])
if (otype == H5O.ObjectType.GROUP):
print 'First dereferenced object is a group.'
otype = H5R.getObjectType(h5file, oref[1])
if (otype == H5O.ObjectType.DATASET):
print 'Second dereferenced object is a dataset.'
dset = H5R.dereference(dsetr, H5R.ReferenceType.OBJECT, oref[1])
dtype = H5D.getType(dset)
dtype1 = H5T.copy(H5T_NATIVE_FLOAT)
if (H5T.equal(dtype, dtype1)):
print 'Datatype of the dataset is H5T_NATIVE_FLOAT.'
H5T.close(dtype)
H5T.close(dtype1)
H5D.close(dset)
H5S.close(dspacer)
H5T.close(dtyper)
H5D.close(dsetr)
return None
def readDatasets(h5file):
dsetr = H5D.open(h5file, 'REGION_REFERENCES')
dtyper = H5T.copy(H5T.H5Type.STD_REF_DSETREG)
dspacer = H5D.getSpace(dsetr)
npoints = H5S.getSimpleExtentNPoints(dspacer)
nBytes = RegionReference.SizeInBytes
datar = Array.CreateInstance(Byte, npoints * nBytes)
H5D.read(dsetr, dtyper, H5Array[Byte](datar))
rr = Array.CreateInstance(RegionReference, npoints)
a = Array.CreateInstance(Byte, nBytes)
for i in range(rr.Length):
Array.Copy(datar, i * nBytes, a, 0, nBytes)
rr[i] = RegionReference(a)
# examine the first region reference
dsetv = H5R.dereference(dsetr, H5R.ReferenceType.DATASET_REGION, rr[0])
name = H5R.getName(dsetr, H5R.ReferenceType.DATASET_REGION, rr[0])
print ' The dataset\'s name (returned by H5Rget_name) the reference points to is \'%s\', name length is %d\n' % (
name, len(name))
name = H5I.getName(dsetv)
print ' The dataset\'s name (returned by H5Iget_name) the reference points to is \'%s\', name length is %d\n' % (
name, len(name))
dspace = H5R.getRegion(dsetr, rr[0])
dtype = H5T.copy(H5T.H5Type.NATIVE_INT)
shape = Array[Int64]((2, 9))
data = Array.CreateInstance(Int32, shape)
H5D.read(dsetv, dtype, H5S_ALL, dspace, H5P_DEFAULT, H5Array[Int32](data))
print 'Selected hyperslab: '
for i in range(data.GetLength(0)):
print ''
for j in range(data.GetLength(1)):
print '%d ' % (data[i, j]),
print '\n'
H5S.close(dspace)
H5D.close(dsetv)
# examine the second region reference
dsetv = H5R.dereference(dsetr, H5R.ReferenceType.DATASET_REGION, rr[1])
dspace = H5R.getRegion(dsetr, rr[1])
H5D.read(dsetv, dtype, H5S_ALL, dspace, H5P_DEFAULT, H5Array[Int32](data))
print 'Selected points: '
for i in range(data.GetLength(0)):
print ''
for j in range(data.GetLength(1)):
print '%d ' % (data[i, j]),
print ''
H5T.close(dtype)
H5S.close(dspace)
H5D.close(dsetv)
H5S.close(dspacer)
H5T.close(dtyper)
H5D.close(dsetr)
return None
