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# This class provides access to selected data from a trajectory
# via an interface that can be accessed remotely by Pyro. It
# can be used by programs that wish to inspect a trajectory that
# resides on a different machine.
#
# Written by Konrad Hinsen
#
from Scientific.IO.NetCDF import NetCDFFile
from Scientific import N as Numeric
class TrajectoryInspector:
def __init__(self, filename):
self.filename = filename
self.file = NetCDFFile(self.filename, 'r')
try:
self.block_size = self.file.dimensions['minor_step_number']
except KeyError:
self.block_size = 1
self._countSteps()
def close(self):
self.file.close()
def reopen(self):
self.file.close()
self.file = NetCDFFile(self.filename, 'r')
self._countSteps()
def _countSteps(self):
if self.block_size == 1:
self.nsteps = self.file.variables['step'].shape[0]
else:
blocks = self.file.variables['step'].shape[0]
last_block = self.file.variables['step'][blocks-1]
unused = Numeric.sum(Numeric.equal(last_block, -2147483647))
self.nsteps = blocks*self.block_size-unused
def comment(self):
try:
return self.file.comment
except AttributeError:
return ''
def history(self):
try:
return self.file.history
except AttributeError:
return ''
def description(self):
return self.file.variables['description'][:].tostring()
def numberOfAtoms(self):
return self.file.dimensions['atom_number']
def numberOfSteps(self):
return self.nsteps
def variableNames(self):
return self.file.variables.keys()
def readScalarVariable(self, name, first=0, last=None, step=1):
if last is None:
last = self.nsteps
variable = self.file.variables[name]
if self.block_size > 1:
variable = Numeric.ravel(variable[:, :])
return variable[first:last:step]
def readConfiguration(self, index):
if self.block_size == 1:
try:
cell = self.file.variables['box_size'][index]
except KeyError:
cell = None
return cell, self.file.variables['configuration'][index]
else:
i1 = index / self.block_size
i2 = index % self.block_size
try:
cell = self.file.variables['box_size'][i1, :, i2]
except KeyError:
cell = None
return cell, self.file.variables['configuration'][i1, :, :, i2]
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