How to use the h5py.h5s function in h5py
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yt-project / yt / yt / frontends / enzo / io.py View on Github 
for g in chunk.objs:
if g.filename is None: continue
if fid is None:
fid = h5py.h5f.open(g.filename.encode('ascii'), h5py.h5f.ACC_RDONLY)
data = np.empty(g.ActiveDimensions[::-1], dtype="float64")
data_view = data.swapaxes(0,2)
nd = 0
for field in fields:
ftype, fname = field
try:
node = "/Grid%08i/%s" % (g.id, fname)
dg = h5py.h5d.open(fid, node.encode('ascii'))
except KeyError:
if fname == "Dark_Matter_Density": continue
raise
dg.read(h5py.h5s.ALL, h5py.h5s.ALL, data)
nd = g.select(selector, data_view, rv[field], ind) # caches
ind += nd
if fid: fid.close()
return rvdef append(self, points):
""" Add the sequence of points to the end of the current selection """
self._perform_selection(points, h5s.SELECT_APPEND)objid = h5py.h5r.dereference(regionRef, self.f.file.file.id)
if objid:
item['id'] = self.getUUIDByAddress(h5py.h5o.get_info(objid).addr)
else:
log.info("region reference unable able to find item with objid: " + objid)
return item
sel = h5py.h5r.get_region(regionRef, objid)
select_type = sel.get_select_type()
if select_type not in selectionEnums:
msg = "Unexpected selection type: " + regionRef.typecode
self.log.error(msg)
raise IOError(errno.EIO, msg)
item['select_type'] = selectionEnums[select_type]
pointlist = None
if select_type == h5py.h5s.SEL_POINTS:
# retrieve a numpy array of selection points
points = sel.get_select_elem_pointlist()
pointlist = points.tolist()
elif select_type == h5py.h5s.SEL_HYPERSLABS:
points = sel.get_select_hyper_blocklist()
if points is not None:
pointlist = points[...].tolist()
# bump up the second coordinate by one to match api spec
for point in pointlist:
coord2 = point[1]
for i in range(len(coord2)):
coord2[i] = coord2[i] + 1
item['selection'] = pointlist
return itemdef __init__(self, shape, spaceid=None):
""" Create a selection. Shape may be None if spaceid is given. """
if spaceid is not None:
self._id = spaceid
self._shape = spaceid.shape
else:
shape = tuple(shape)
self._shape = shape
self._id = h5s.create_simple(shape, (h5s.UNLIMITED,)*len(shape))
self._id.select_all()def createRegionReference(self, item):
selectionEnums = { 'H5S_SEL_NONE': h5py.h5s.SEL_NONE,
'H5S_SEL_ALL': h5py.h5s.SEL_ALL,
'H5S_SEL_POINTS': h5py.h5s.SEL_POINTS,
'H5S_SEL_HYPERSLABS': h5py.h5s.SEL_HYPERSLABS
}
region_ref = None
if 'select_type' not in item:
msg = "select_type not provided for region selection"
self.log.info(msg)
raise IOError(errno.EINVAL, msg)
select_type = item['select_type']
if select_type not in selectionEnums.keys():
msg = "selection type: [" + select_type + "] is not valid"
self.log.info(msg)
raise IOError(errno.EINVAL, msg)
dset = Noneif strLength < len(value):
self.log.warning("makeNullTermStringAttribute: value string longer than length")
#value = value[:strLength] # truncate to length
if six.PY3 and type(attr_name) is str:
try:
attr_name = attr_name.encode('ascii')
except UnicodeDecodeError:
raise TypeError("non-ascii attribute name not allowed")
# create the attribute
tid = h5py.h5t.TypeID.copy(h5py.h5t.C_S1)
tid.set_size(strLength)
tid.set_strpad(h5py.h5t.STR_NULLTERM)
sid = h5py.h5s.create(h5py.h5s.SCALAR)
aid = h5py.h5a.create(obj.id, attr_name, tid, sid)
# write the value
dtype_code = 'S' + str(strLength)
ndarr = np.array(value, dtype=np.dtype(dtype_code))
aid.write(ndarr)dcpl.set_obj_track_times(track_times)
elif track_times is not None:
raise TypeError("track_times must be either True or False")
if track_order == True:
dcpl.set_attr_creation_order(
h5p.CRT_ORDER_TRACKED | h5p.CRT_ORDER_INDEXED)
elif track_order == False:
dcpl.set_attr_creation_order(0)
elif track_order is not None:
raise TypeError("track_order must be either True or False")
if maxshape is not None:
maxshape = tuple(m if m is not None else h5s.UNLIMITED for m in maxshape)
if isinstance(data, Empty):
sid = h5s.create(h5s.NULL)
else:
sid = h5s.create_simple(shape, maxshape)
dset_id = h5d.create(parent.id, None, tid, sid, dcpl=dcpl)
if (data is not None) and (not isinstance(data, Empty)):
dset_id.write(h5s.ALL, h5s.ALL, data)
return dset_idlog.info("region reference unable able to find item with objid: " + objid)
return item
sel = h5py.h5r.get_region(regionRef, objid)
select_type = sel.get_select_type()
if select_type not in selectionEnums:
msg = "Unexpected selection type: " + regionRef.typecode
self.log.error(msg)
raise IOError(errno.EIO, msg)
item['select_type'] = selectionEnums[select_type]
pointlist = None
if select_type == h5py.h5s.SEL_POINTS:
# retrieve a numpy array of selection points
points = sel.get_select_elem_pointlist()
pointlist = points.tolist()
elif select_type == h5py.h5s.SEL_HYPERSLABS:
points = sel.get_select_hyper_blocklist()
if points is not None:
pointlist = points[...].tolist()
# bump up the second coordinate by one to match api spec
for point in pointlist:
coord2 = point[1]
for i in range(len(coord2)):
coord2[i] = coord2[i] + 1
item['selection'] = pointlist
return itemelse:
ret[i, j] = sp.empty(dref.shape, dtype=dref.dtype)
dref.read(h5py.h5s.ALL, h5py.h5s.ALL, ret[i, j])
ret[i, j] = ret[i, j].T
if isinstance(ret[i, j], sp.ndarray):
shp = ret[i, j].shape
if len(shp) == 2 and isinstance(ret[i, j][0, 0], h5py.h5r.Reference):
ret[i, j] = deref_array(ret[i, j], file)
elif len(shp) == 1 and isinstance(ret[i, j][0], h5py.h5r.Reference):
ret[i, j] = deref_array(ret[i, j], file)
else:
for i in xrange(data.shape[0]):
ref = data[i]
dref = h5py.h5r.dereference(ref, file._id)
ret[i] = sp.empty(dref.shape, dtype=dref.dtype)
dref.read(h5py.h5s.ALL, h5py.h5s.ALL, ret[i])
ret[i] = ret[i].T
if isinstance(ret[i], sp.ndarray):
shp = ret[i].shape
if len(shp) == 2 and isinstance(ret[i][0, 0], h5py.h5r.Reference):
ret[i] = deref_array(ret[i], file)
elif len(shp) == 1 and isinstance(ret[i][0], h5py.h5r.Reference):
ret[i] = deref_array(ret[i], file)
return ret
