def read_info(self, framedir, name, split=None):
"""Read information about file contents without reading the data.
Information is a dictionary containing as aminimum the shape and
type.
"""
fn = os.path.join(framedir, name + '.ulm')
if split is None or os.path.exists(fn):
f = ulmopen(fn, 'r')
info = odict()
info['shape'] = f.shape
info['type'] = f.dtype
info['stored_as'] = f.stored_as
info['identical'] = f.all_identical
f.close()
return info
else:
info = odict()
for i in range(split):
fn = os.path.join(framedir, name + '_' + str(i) + '.ulm')
f = ulmopen(fn, 'r')
if i == 0:
info['shape'] = list(f.shape)
info['type'] = f.dtype
info['stored_as'] = f.stored_as
info['identical'] = f.all_identical
else:
info['shape'][0] += f.shape[0]
assert info['type'] == f.dtype
info['identical'] = info['identical'] and f.all_identical
f.close()
info['shape'] = tuple(info['shape'])
return info
def _open(self, filename, mode):
from ase.io.ulm import ulmopen, DummyWriter
if mode not in 'aw':
raise ValueError('mode must be "w" or "a".')
if self.master:
self.backend = ulmopen(filename, mode, tag='ASE-Trajectory')
if len(self.backend) > 0:
r = ulmopen(filename)
self.numbers = r.numbers
self.pbc = r.pbc
else:
self.backend = DummyWriter()
def _open(self, filename):
from ase.io.ulm import ulmopen, InvalidULMFileError
try:
self.backend = ulmopen(filename, 'r')
except InvalidULMFileError:
raise RuntimeError('This is not a valid ASE trajectory file. '
'If this is an old-format (version <3.9) '
'PickleTrajectory file you can convert it '
'with ase.io.trajectory.convert("%s") '
'or:\n\n $ python -m ase.io.trajectory %s'
% (filename, filename))
self._read_header()
def read(self, framedir, name):
"Read data from separate file."
fn = os.path.join(framedir, name + '.ulm')
f = ulmopen(fn, 'r')
if f.all_identical:
# Only a single data value
data = np.zeros(f.shape, dtype=getattr(np, f.dtype)) + f.data
elif f.dtype == f.stored_as:
# Easy, the array can be returned as-is.
data = f.data
else:
# Cast the data back
data = f.data.astype(getattr(np, f.dtype))
f.close()
return data
def write(self, framedir, name, data):
"Write data to separate file."
if self.writelarge:
shape = data.shape
dtype = str(data.dtype)
stored_as = dtype
all_identical = False
# Check if it a type that can be stored with less space
if np.issubdtype(data.dtype, np.integer):
# An integer type, we may want to convert
minval = data.min()
maxval = data.max()
# ulm cannot write np.bool_:
all_identical = bool(minval == maxval)
if all_identical:
data = int(data.flat[0]) # Convert to standard integer
else:
for typ in self.integral_dtypes:
if (minval >= self.int_minval[typ] and
maxval <= self.int_maxval[typ] and
data.itemsize > self.int_itemsize[typ]):
# Convert to smaller type
stored_as = typ
data = data.astype(self.int_dtype[typ])
elif data.dtype == np.float32 or data.dtype == np.float64:
all_identical = bool(data.min() == data.max())
if all_identical:
data = float(data.flat[0]) # Convert to standard float
elif data.dtype == np.float64 and self.singleprecision:
# Downconvert double to single precision
stored_as = 'float32'
data = data.astype(np.float32)
fn = os.path.join(framedir, name + '.ulm')
f = ulmopen(fn, 'w')
f.write(shape=shape,
dtype=dtype,
stored_as=stored_as,
all_identical=all_identical,
data=data)
f.close()
def read_small(self, framedir):
"Read small data."
f = ulmopen(os.path.join(framedir, 'smalldata.ulm'), 'r')
data = f.asdict()
f.close()
return data
def write_small(self, framedir, smalldata):
"Write small data to be written jointly."
if self.writesmall:
f = ulmopen(os.path.join(framedir, 'smalldata.ulm'), 'w')
f.write(**smalldata)
f.close()
def write_small(self, framedir, smalldata):
"Write small data to be written jointly."
if self.writesmall:
f = ulmopen(os.path.join(framedir, 'smalldata.ulm'), 'w')
f.write(**smalldata)
f.close()
def read_gpw(filename):
try:
reader = ulm.ulmopen(filename)
except ulm.InvalidULMFileError:
return read_old_gpw(filename)
return read_atoms(reader.atoms)
